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Papadimitriou E, Thomaidou D. Post-transcriptional mechanisms controlling neurogenesis and direct neuronal reprogramming. Neural Regen Res 2024; 19:1929-1939. [PMID: 38227517 DOI: 10.4103/1673-5374.390976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/08/2023] [Indexed: 01/17/2024] Open
Abstract
Neurogenesis is a tightly regulated process in time and space both in the developing embryo and in adult neurogenic niches. A drastic change in the transcriptome and proteome of radial glial cells or neural stem cells towards the neuronal state is achieved due to sophisticated mechanisms of epigenetic, transcriptional, and post-transcriptional regulation. Understanding these neurogenic mechanisms is of major importance, not only for shedding light on very complex and crucial developmental processes, but also for the identification of putative reprogramming factors, that harbor hierarchically central regulatory roles in the course of neurogenesis and bare thus the capacity to drive direct reprogramming towards the neuronal fate. The major transcriptional programs that orchestrate the neurogenic process have been the focus of research for many years and key neurogenic transcription factors, as well as repressor complexes, have been identified and employed in direct reprogramming protocols to convert non-neuronal cells, into functional neurons. The post-transcriptional regulation of gene expression during nervous system development has emerged as another important and intricate regulatory layer, strongly contributing to the complexity of the mechanisms controlling neurogenesis and neuronal function. In particular, recent advances are highlighting the importance of specific RNA binding proteins that control major steps of mRNA life cycle during neurogenesis, such as alternative splicing, polyadenylation, stability, and translation. Apart from the RNA binding proteins, microRNAs, a class of small non-coding RNAs that block the translation of their target mRNAs, have also been shown to play crucial roles in all the stages of the neurogenic process, from neural stem/progenitor cell proliferation, neuronal differentiation and migration, to functional maturation. Here, we provide an overview of the most prominent post-transcriptional mechanisms mediated by RNA binding proteins and microRNAs during the neurogenic process, giving particular emphasis on the interplay of specific RNA binding proteins with neurogenic microRNAs. Taking under consideration that the molecular mechanisms of neurogenesis exert high similarity to the ones driving direct neuronal reprogramming, we also discuss the current advances in in vitro and in vivo direct neuronal reprogramming approaches that have employed microRNAs or RNA binding proteins as reprogramming factors, highlighting the so far known mechanisms of their reprogramming action.
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Zhou T, Nguyen S, Wu J, He B, Feng Q. LncRNA LOC730101 Promotes Darolutamide Resistance in Prostate Cancer by Suppressing miR-1-3p. Cancers (Basel) 2024; 16:2594. [PMID: 39061232 PMCID: PMC11274508 DOI: 10.3390/cancers16142594] [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: 06/11/2024] [Revised: 07/14/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Antiandrogen is part of the standard-of-care treatment option for metastatic prostate cancer. However, prostate cancers frequently relapse, and the underlying resistance mechanism remains incompletely understood. This study seeks to investigate whether long non-coding RNAs (lncRNAs) contribute to the resistance against the latest antiandrogen drug, darolutamide. Our RNA sequencing analysis revealed significant overexpression of LOC730101 in darolutamide-resistant cancer cells compared to the parental cells. Elevated LOC730101 levels were also observed in clinical samples of metastatic castration-resistant prostate cancer (CRPC) compared to primary prostate cancer samples. Silencing LOC730101 with siRNA significantly impaired the growth of darolutamide-resistant cells. Additional RNA sequencing analysis identified a set of genes regulated by LOC730101, including key players in the cell cycle regulatory pathway. We further demonstrated that LOC730101 promotes darolutamide resistance by competitively inhibiting microRNA miR-1-3p. Moreover, by Hi-C sequencing, we found that LOC730101 is located in a topologically associating domain (TAD) that undergoes specific gene induction in darolutamide-resistant cells. Collectively, our study demonstrates the crucial role of the lncRNA LOC730101 in darolutamide resistance and its potential as a target for overcoming antiandrogen resistance in CRPC.
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Affiliation(s)
- Tianyi Zhou
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Steven Nguyen
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Jacky Wu
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Bin He
- Immunobiology & Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Medicine-Cancer Biology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Qin Feng
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
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3
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Yoo M, Bunkowski K, Lie A, Junn E. Regulation of MicroRNA-4697-3p by Parkinson's disease-associated SNP rs329648 and its impact on SNCA112 mRNA. Mol Biol Rep 2024; 51:797. [PMID: 39001947 DOI: 10.1007/s11033-024-09725-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/13/2024] [Indexed: 07/15/2024]
Abstract
BACKGROUND Parkinson's disease (PD) is a common neurodegenerative disorder characterized by a multifaceted genetic foundation. Genome-Wide Association Studies (GWAS) have played a crucial role in pinpointing genetic variants linked to PD susceptibility. Current study aims to delve into the mechanistic aspects through which the PD-associated Single Nucleotide Polymorphism (SNP) rs329648, identified in prior GWAS, influences the pathogenesis of PD. METHODS AND RESULTS Employing the CRISPR/Cas9-mediated genome editing mechanism, we demonstrated the association of the disease-associated allele of rs329648 with increased expression of miR-4697-3p in differentiated SH-SY5Y cells. We revealed that miR-4697-3p contributes to the formation of high molecular weight complexes of α-Synuclein (α-Syn), indicative of α-Syn aggregate formation, as evidenced by Western blot analysis. Furthermore, our study unveiled that miR-4697-3p elevates SNCA112 mRNA levels. The resultant protein product, α-Syn 112, a variant of α-Syn with 112 amino acids, is recognized for augmenting α-Syn aggregation. Notably, this regulatory effect minimally impacts the levels of full-length SNCA140 mRNA, as evidenced by qRT-PCR. Additionally, we observed a correlation between the disease-associated allele and miR-4697-3p with increased cell death, substantiated by assessments including cell viability assays, alterations in cell morphology, and TUNEL assays. CONCLUSION Our research reveals that the disease-associated allele of rs329648 is linked to higher levels of miR-4697-3p. This increase in miR-4697-3p leads to elevated SNCA112 mRNA levels, consequently promoting the formation of α-Syn aggregates. Furthermore, miR-4697-3p appears to play a role in increased cell death, potentially contributing to the pathogenesis of PD.
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Affiliation(s)
- Myungsik Yoo
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Klaudia Bunkowski
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Andrew Lie
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Eunsung Junn
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA.
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Zacharjasz J, Sztachera M, Smuszkiewicz M, Piwecka M. Micromanaging the neuroendocrine system - A review on miR-7 and the other physiologically relevant miRNAs in the hypothalamic-pituitary axis. FEBS Lett 2024; 598:1557-1575. [PMID: 38858179 DOI: 10.1002/1873-3468.14948] [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: 03/27/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/12/2024]
Abstract
The hypothalamic-pituitary axis is central to the functioning of the neuroendocrine system and essential for regulating physiological and behavioral homeostasis and coordinating fundamental body functions. The expanding line of evidence shows the indispensable role of the microRNA pathway in regulating the gene expression profile in the developing and adult hypothalamus and pituitary gland. Experiments provoking a depletion of miRNA maturation in the context of the hypothalamic-pituitary axis brought into focus a prominent involvement of miRNAs in neuroendocrine functions. There are also a few individual miRNAs and miRNA families that have been studied in depth revealing their crucial role in mediating the regulation of fundamental processes such as temporal precision of puberty timing, hormone production, fertility and reproduction capacity, and energy balance. Among these miRNAs, miR-7 was shown to be hypothalamus-enriched and the top one highly expressed in the pituitary gland, where it has a profound impact on gene expression regulation. Here, we review miRNA profiles, knockout phenotypes, and miRNA interaction (targets) in the hypothalamic-pituitary axis that advance our understanding of the roles of miRNAs in mammalian neurosecretion and related physiology.
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Affiliation(s)
- Julian Zacharjasz
- Department of Non-coding RNAs, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Marta Sztachera
- Department of Non-coding RNAs, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Michał Smuszkiewicz
- Department of Non-coding RNAs, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Monika Piwecka
- Department of Non-coding RNAs, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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5
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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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Gu J, Li Y, Tian Y, Zhang Y, Cheng Y, Tang Y. Noncanonical functions of microRNAs in the nucleus. Acta Biochim Biophys Sin (Shanghai) 2024; 56:151-161. [PMID: 38167929 PMCID: PMC10984876 DOI: 10.3724/abbs.2023268] [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: 09/02/2023] [Accepted: 11/03/2023] [Indexed: 01/05/2024] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs (ncRNAs) that play their roles in the regulation of physiological and pathological processes. Originally, it was assumed that miRNAs only modulate gene expression posttranscriptionally in the cytoplasm by inducing target mRNA degradation. However, with further research, evidence shows that mature miRNAs also exist in the cell nucleus, where they can impact gene transcription and ncRNA maturation in several ways. This review provides an overview of novel models of nuclear miRNA functions. Some of the models remain to be verified by experimental evidence, and more details of the miRNA regulation network remain to be discovered in the future.
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Affiliation(s)
- Jiayi Gu
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Yuanan Li
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Youtong Tian
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Yehao Zhang
- College of Basic Medical SciencesShanghai Jiao Tong University School of MedicineShanghai200001China
| | - Yongjun Cheng
- Department of Rheumatologythe First People’s Hospital of WenlingWenling317500China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology/Department of RheumatologyRenji HospitalShanghai Jiao Tong University School of MedicineShanghai200001China
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteRenji HospitalShanghai200031China
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7
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Freitas RM, Felipe SMS, Ribeiro JKC, Araújo VR, Martin CPS, Oliveira MAF, Martins SD, Pontes JPA, Alves JO, Soares PM, Ceccatto VM. Evaluation of miRNAs regulation of BDNF and IGF1 genes in T2DM insulin resistance in experimental models: bioinformatics based approach. BRAZ J BIOL 2024; 84:e256691. [DOI: 10.1590/1519-6984.256691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/30/2022] [Indexed: 11/22/2022] Open
Abstract
Abstract microRNAs (miRNAs) are recognized as diabetes mellitus type 2 (T2DM) biomarkers useful for disease metabolism comprehension and have great potential as therapeutics targets. BDNF and IGF1 increased expression are highly involved in the benefits of insulin and glucose paths, however, they are down-regulated in insulin resistance conditions, while their expression increase is correlated to the improvement of glucose and insulin metabolism. Studies suggest the microRNA regulation of these genes in several different contexts, providing a novel investigation approach for comprehending T2DM metabolism and revealing potential therapeutic targets. In the present study, we investigate in different animal models (human, rat, and mouse) miRNAs that target BDNF and IGF1 in skeletal muscle tissue with T2DM physiological conditions. Bioinformatics tools and databases were used to miRNA prediction, molecular homology, experimental validation of interactions, expression in the studied physiological condition, and network interaction. The findings showed three miRNAs candidates for IGF1(miR-29a, miR-29b, and miR-29c) and one for BDNF (miR-206). The experimental evaluations and the search for the expression in skeletal muscle from T2DM subjects confirmed the predicted interaction between miRNA-mRNA for miR-29b and miR-206 through human, rat, and mouse models. This interaction was reaffirmed in multiple network analyses. In conclusion, our results show the regulation relationship between miR-29b and miR-206 with the investigated genes, in several tissues, suggesting an inhibition pattern. Nevertheless, these data show a large number of possible interaction physiological processes, for future biotechnological prospects.
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Koopmans PJ, Ismaeel A, Goljanek-Whysall K, Murach KA. The roles of miRNAs in adult skeletal muscle satellite cells. Free Radic Biol Med 2023; 209:228-238. [PMID: 37879420 PMCID: PMC10911817 DOI: 10.1016/j.freeradbiomed.2023.10.403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/16/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023]
Abstract
Satellite cells are bona fide muscle stem cells that are indispensable for successful post-natal muscle growth and regeneration after severe injury. These cells also participate in adult muscle adaptation in several capacities. MicroRNAs (miRNAs) are post-transcriptional regulators of mRNA that are implicated in several aspects of stem cell function. There is evidence to suggest that miRNAs affect satellite cell behavior in vivo during development and myogenic progenitor behavior in vitro, but the role of miRNAs in adult skeletal muscle satellite cells is less studied. In this review, we provide evidence for how miRNAs control satellite cell function with emphasis on satellite cells of adult skeletal muscle in vivo. We first outline how miRNAs are indispensable for satellite cell viability and control the phases of myogenesis. Next, we discuss the interplay between miRNAs and myogenic cell redox status, senescence, and communication to other muscle-resident cells during muscle adaptation. Results from recent satellite cell miRNA profiling studies are also summarized. In vitro experiments in primary myogenic cells and cell lines have been invaluable for exploring the influence of miRNAs, but we identify a need for novel genetic tools to further interrogate how miRNAs control satellite cell behavior in adult skeletal muscle in vivo.
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Affiliation(s)
- Pieter Jan Koopmans
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, 72701, USA; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Ahmed Ismaeel
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, 40506, USA
| | - Katarzyna Goljanek-Whysall
- School of Medicine, College of Medicine, Nursing, and Health Sciences, University of Galway, Galway, Ireland
| | - Kevin A Murach
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, 72701, USA; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA.
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Martin-Geary AC, Blakes AJM, Dawes R, Findlay SD, Lord J, Walker S, Talbot-Martin J, Wieder N, D’Souza EN, Fernandes M, Hilton S, Lahiri N, Campbell C, Jenkinson S, DeGoede CGEL, Anderson ER, Burge CB, Sanders SJ, Ellingford J, Baralle D, Banka S, Whiffin N. Systematic identification of disease-causing promoter and untranslated region variants in 8,040 undiagnosed individuals with rare disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.12.23295416. [PMID: 37745552 PMCID: PMC10516070 DOI: 10.1101/2023.09.12.23295416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Background Both promoters and untranslated regions (UTRs) have critical regulatory roles, yet variants in these regions are largely excluded from clinical genetic testing due to difficulty in interpreting pathogenicity. The extent to which these regions may harbour diagnoses for individuals with rare disease is currently unknown. Methods We present a framework for the identification and annotation of potentially deleterious proximal promoter and UTR variants in known dominant disease genes. We use this framework to annotate de novo variants (DNVs) in 8,040 undiagnosed individuals in the Genomics England 100,000 genomes project, which were subject to strict region-based filtering, clinical review, and validation studies where possible. In addition, we performed region and variant annotation-based burden testing in 7,862 unrelated probands against matched unaffected controls. Results We prioritised eleven DNVs and identified an additional variant overlapping one of the eleven. Ten of these twelve variants (82%) are in genes that are a strong match to the individual's phenotype and six had not previously been identified. Through burden testing, we did not observe a significant enrichment of potentially deleterious promoter and/or UTR variants in individuals with rare disease collectively across any of our region or variant annotations. Conclusions Overall, we demonstrate the value of screening promoters and UTRs to uncover additional diagnoses for previously undiagnosed individuals with rare disease and provide a framework for doing so without dramatically increasing interpretation burden.
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Affiliation(s)
- Alexandra C Martin-Geary
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Alexander J M Blakes
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Ruebena Dawes
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Scott D Findlay
- Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
| | | | | | | | - Nechama Wieder
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Elston N D’Souza
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Maria Fernandes
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Sarah Hilton
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Nayana Lahiri
- St George’s, University of London & St George’s University Hospitals NHS Foundation Trust, Institute of Molecular and Clinical Sciences, London, SW17 0QT, UK
| | - Christopher Campbell
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Sarah Jenkinson
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Christian G E L DeGoede
- Department of Paediatric Neurology, Clinical research Facility, Lancashire Teaching Hospitals NHS Trust
- Manchester Metropolitan University
| | - Emily R Anderson
- Liverpool Centre for Genomic Medicine, Liverpool Women’s Hospital, Liverpool, UK
| | | | - Stephan J Sanders
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 7TY, UK
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- New York Genome Center, New York, NY, USA
| | - Jamie Ellingford
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Nicola Whiffin
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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10
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Kamal A, Swellam M, M Shalaby N, Darwish MK, M El-Nahrery E. Long non-coding RNAs BACE1-AS and BC200 in multiple sclerosis and their relation to cognitive function: A gene expression analysis. Brain Res 2023; 1814:148424. [PMID: 37245645 DOI: 10.1016/j.brainres.2023.148424] [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: 03/23/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 05/30/2023]
Abstract
Cognitive impairment is a common and debilitating feature of multiple sclerosis (MS), and the dysregulation of synaptic plasticity is one of its direct causes. Long non-coding RNAs (lncRNAs) have been shown to play a role in synaptic plasticity, but their role in cognitive impairment in MS has not been fully explored. In this study, using quantitative real-time PCR, we examined the relative expression of two specific lncRNAs, BACE1-AS and BC200, in the serum of two cohorts of MS patients with and without cognitive impairment. Both lncRNAs were overexpressed in both cognitively impaired and non-cognitively impaired MS patients, with consistently higher levels in the cohort with cognitive impairment. We also found a strong positive correlation between the expression levels of these two lncRNAs. Notably, BACE1-AS was consistently higher in the remitting cases of both relapsing-remitting MS (RRMS) and secondary progressive MS (SPMS) groups than in the respective relapse cases of the same subtype, with the SPMS-Remitting group of cognitively impaired MS patients showing the highest expression of BACE1-AS among all MS groups. Additionally, we observed that the primary progressive MS (PPMS) group had the highest expression of BC200 in both cohorts of MS. Furthermore, we developed a model called Neuro_Lnc-2, which showed better diagnostic performance than either BACE1-AS or BC200 alone in predicting MS. Our findings suggest that these two lncRNAs may have a significant impact on the pathogenesis of the progressive types of MS and on the cognitive function of the patients. Future research is required to confirm these findings.
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Affiliation(s)
- Ahmed Kamal
- Biochemistry Department, Faculty of Science, Suez University, PO Box 43518, Suez 43533, Egypt.
| | - Menha Swellam
- Biochemistry Department, Biotechnology Research Institute, High Throughput Molecular and Genetic Laboratory, Central Laboratories Network and the Centers of Excellence, National Research Centre, Dokki, Giza, Egypt
| | - Nevin M Shalaby
- Neurology Department, Faculty of Medicine, Cairo University, Egypt
| | - Marwa K Darwish
- Biochemistry Department, Faculty of Science, Suez University, PO Box 43518, Suez 43533, Egypt
| | - Eslam M El-Nahrery
- Biochemistry Department, Faculty of Science, Suez University, PO Box 43518, Suez 43533, Egypt
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11
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Singh R, Hussain J, Kaur A, Jamdare BG, Pathak D, Garg K, Kaur R, Shankar S, Sunkaria A. The hidden players: Shedding light on the significance of post-translational modifications and miRNAs in Alzheimer's disease development. Ageing Res Rev 2023; 90:102002. [PMID: 37423542 DOI: 10.1016/j.arr.2023.102002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent, expensive, lethal, and burdening neurodegenerative disease of this century. The initial stages of this disease are characterized by a reduced ability to encode and store new memories. Subsequent cognitive and behavioral deterioration occurs during the later stages. Abnormal cleavage of amyloid precursor protein (APP) resulting in amyloid-beta (Aβ) accumulation along with hyperphosphorylation of tau protein are the two characteristic hallmarks of AD. Recently, several post-translational modifications (PTMs) have been identified on both Aβ as well as tau proteins. However, a complete understanding of how different PTMs influence the structure and function of proteins in both healthy and diseased conditions is still lacking. It has been speculated that these PTMs might play vital roles in the progression of AD. In addition, several short non-coding microRNA (miRNA) sequences have been found to be deregulated in the peripheral blood of Alzheimer patients. The miRNAs are single-stranded RNAs that control gene expression by causing mRNA degradation, deadenylation, or translational repression and have been implicated in the regulation of several neuronal and glial activities. The lack of comprehensive understanding regarding disease mechanisms, biomarkers, and therapeutic targets greatly hampers the development of effective strategies for early diagnosis and the identification of viable therapeutic targets. Moreover, existing treatment options for managing the disease have proven to be ineffective and provide only temporary relief. Therefore, understanding the role of miRNAs and PTMs in AD can provide valuable insights into disease mechanisms, aid in the identification of biomarkers, facilitate the discovery of novel therapeutic targets, and inspire innovative treatments for this challenging condition.
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Affiliation(s)
- Ravinder Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Julfequar Hussain
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Amandeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Balaji Gokul Jamdare
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Deepti Pathak
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Kanchan Garg
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Ramanpreet Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Shivani Shankar
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Aditya Sunkaria
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India.
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12
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Eom S, Peak J, Park J, Ahn SH, Cho YK, Jeong Y, Lee HS, Lee J, Ignatova E, Lee SE, Hong Y, Gu D, Kim GWD, Lee DC, Hahm JY, Jeong J, Choi D, Jang ES, Chi SW. Widespread 8-oxoguanine modifications of miRNA seeds differentially regulate redox-dependent cancer development. Nat Cell Biol 2023; 25:1369-1383. [PMID: 37696949 DOI: 10.1038/s41556-023-01209-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 07/19/2023] [Indexed: 09/13/2023]
Abstract
Oxidative stress contributes to tumourigenesis by altering gene expression. One accompanying modification, 8-oxoguanine (o8G) can change RNA-RNA interactions via o8G•A base pairing, but its regulatory roles remain elusive. Here, on the basis of o8G-induced guanine-to-thymine (o8G > T) variations featured in sequencing, we discovered widespread position-specific o8Gs in tumour microRNAs, preferentially oxidized towards 5' end seed regions (positions 2-8) with clustered sequence patterns and clinically associated with patients in lower-grade gliomas and liver hepatocellular carcinoma. We validated that o8G at position 4 of miR-124 (4o8G-miR-124) and 4o8G-let-7 suppress lower-grade gliomas, whereas 3o8G-miR-122 and 4o8G-let-7 promote malignancy of liver hepatocellular carcinoma by redirecting the target transcriptome to oncogenic regulatory pathways. Stepwise oxidation from tumour-promoting 3o8G-miR-122 to tumour-suppressing 2,3o8G-miR-122 occurs and its specific modulation in mouse liver effectively attenuates diethylnitrosamine-induced hepatocarcinogenesis. These findings provide resources and insights into epitranscriptional o8G regulation of microRNA functions, reprogrammed by redox changes, implicating its control for cancer treatment.
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Affiliation(s)
- Sangkyeong Eom
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Jongjin Peak
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Jongyeun Park
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Seung Hyun Ahn
- Department of Life Sciences, Korea University, Seoul, Korea
| | - You Kyung Cho
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Yeahji Jeong
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Hye-Sook Lee
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Jung Lee
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Korea
| | | | - Sung Eun Lee
- Department of Life Sciences, Korea University, Seoul, Korea
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Yunji Hong
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Dowoon Gu
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Geun-Woo D Kim
- Department of Life Sciences, Korea University, Seoul, Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Korea
| | - Dong Chan Lee
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Ja Young Hahm
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Jaemin Jeong
- Department of Surgery, Hanyang University College of Medicine, Seoul, Korea
| | - Dongho Choi
- Department of Surgery, Hanyang University College of Medicine, Seoul, Korea
| | - Eun-Sook Jang
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Sung Wook Chi
- Department of Life Sciences, Korea University, Seoul, Korea.
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Korea.
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea.
- Medicinal Materials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul, Korea.
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13
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Cohen T, Shomron N. Can RNA Affect Memory Modulation? Implications for PTSD Understanding and Treatment. Int J Mol Sci 2023; 24:12908. [PMID: 37629089 PMCID: PMC10454422 DOI: 10.3390/ijms241612908] [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: 07/19/2023] [Revised: 08/13/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Memories are a central aspect of our lives, but the mechanisms underlying their formation, consolidation, retrieval, and extinction remain poorly understood. In this review, we explore the molecular mechanisms of memory modulation and investigate the effects of RNA on these processes. Specifically, we examine the effects of time and location on gene expression alterations. We then discuss the potential for harnessing these alterations to modulate memories, particularly fear memories, to alleviate post-traumatic stress disorder (PTSD) symptoms. The current state of research suggests that transcriptional changes play a major role in memory modulation and targeting them through microRNAs may hold promise as a novel approach for treating memory-related disorders such as PTSD.
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Affiliation(s)
- Tehila Cohen
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
- Tel Aviv University Innovation Labs (TILabs), Tel Aviv 6997801, Israel
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14
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Liu M, Yu Z, Zhao Z, Yang F, Zhou M, Wang C, Tian X, Zhang B, Liang G, Liu X, Shao J. MiR-24-3p/Dio3 axis is essential for BDE47 to induce local thyroid hormone disorder and neurotoxicity. Toxicology 2023; 491:153527. [PMID: 37116683 DOI: 10.1016/j.tox.2023.153527] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 04/30/2023]
Abstract
BDE47 (2,2,4,4-tetrabromodiphenyl ether) is a member of the most important congeners of polybrominated diphenyl ethers (PBDEs) and has been identified as a developmental, reproductive and nervous system toxicant and endocrine system disruptor due to its frequent detection in human tissue and environmental samples. Our preliminary work suggested that high- and low-level of bromodiphenyl ethers have different effects on neuronal cells with differential targets of actions on neural tissues. In this study, we presented the underlying mechanism of BDE47 neurotoxicity from the perspective of thyroid hormone (TH) metabolism using in vitro model of human SK-N-AS neuronal cells. BDE47 could induce local TH metabolism disorder in neuronal cells by inhibiting the expression of the main enzyme, human type III iodothyronine deiodinase (Dio3). Further elucidation revealed that BDE47 effectively up-regulating miR-24-3p, which binds to the 3'-UTR of Dio3 and inhibits its expression. In addition, BDE47 could also inhibit the deiodinase activity of Dio3. Collectively, our study demonstrates the molecular mechanism of BDE47 regulating Dio3-induced TH metabolism disorder through inducing miR-24-3p, providing new clues for the role of miRNAs in neurodevelopmental toxicity mediated by environmental pollutants.
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Affiliation(s)
- Min Liu
- Department of Environmental Health and Toxicology, School of Public Health, Dalian Medical University, Dalian, 116044, China; Neurology Department, Dalian University Affiliated Xinhua Hospital, Dalian, 116021, China
| | - Zhenlong Yu
- College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Zikuang Zhao
- School of Pharmacy, Hangzhou Normal University, Hangzhou, 116000, China
| | - Fangyu Yang
- General Hospital of Northern Theater Command (General Hospital of Shenyang Military Command), Department of Neurosurgery, Shenyang, China
| | - Meirong Zhou
- College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Chao Wang
- College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Xiangge Tian
- College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Baojing Zhang
- College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Guobiao Liang
- General Hospital of Northern Theater Command (General Hospital of Shenyang Military Command), Department of Neurosurgery, Shenyang, China.
| | - Xiaohui Liu
- Department of Environmental Health and Toxicology, School of Public Health, Dalian Medical University, Dalian, 116044, China
| | - Jing Shao
- Department of Environmental Health and Toxicology, School of Public Health, Dalian Medical University, Dalian, 116044, China; Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine; Liaoning Medical Center for Hematopoietic Stem Cell Transplantation; Dalian Key Laboratory of Hematology; Diamond Bay Institute of Hematology; Second Hospital of Dalian Medical University, Dalian, 116027, China.
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15
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Ruffo P, Catalano S, La Bella V, Conforti FL. Deregulation of Plasma microRNA Expression in a TARDBP-ALS Family. Biomolecules 2023; 13:biom13040706. [PMID: 37189452 DOI: 10.3390/biom13040706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/06/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023] Open
Abstract
TDP-43 intracellular aggregates are a pathogenic sign of most amyotrophic lateral sclerosis (ALS) cases. Familial ALS, brought on by TARDBP gene mutations, emphasizes the relevance of this altered protein in pathophysiology. Growing evidence suggests a role for dysregulated microRNA (miRNA) in ALS disease. Furthermore, several studies showed that miRNAs are highly stable in various biological fluids (CSF, blood, plasma, and serum), and they are expressed differentially by comparing ALS patients and controls. In 2011, our research group discovered a rare mutation in a TARDBP gene (G376D) in a large ALS Apulian family with affected members exhibiting a rapidly progressing disease. To identify potential non-invasive biomarkers of preclinical and clinical progression in the TARDBP-ALS family, we assessed the expression levels of plasma microRNAs in affected patients (n = 7) and asymptomatic mutation carriers (n = 7) compared with healthy controls (n = 13). Applying qPCR, we investigate 10 miRNAs that bind TDP-43 in vitro during their biogenesis or in their mature form, and the other nine are known to be deregulated in the disease. We highlight the potential of miR-132-5p, miR-132-3p, miR-124-3p, and miR-133a-3p expression levels in plasma as biomarkers of preclinical progression for G376D-TARDBP-associated ALS. Our research strongly supports the potential of plasma miRNAs as biomarkers for performing predictive diagnostics and identifying new therapeutic targets.
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Affiliation(s)
- Paola Ruffo
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stefania Catalano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Vincenzo La Bella
- ALS Clinical Research Centre and Laboratory of Neurochemistry, Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, 90133 Palermo, Italy
| | - Francesca Luisa Conforti
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
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16
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Li D, Zhao Q, Xie L, Wang C, Tian Z, Tang H, Xia T, Wang A. Fluoride impairs mitochondrial translation by targeting miR-221-3p/c-Fos/RMND1 axis contributing to neurodevelopment defects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161738. [PMID: 36690096 DOI: 10.1016/j.scitotenv.2023.161738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/07/2023] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
Evidence suggests that fluoride-induced neurodevelopment damage is linked to mitochondrial disorder, yet the detailed mechanism remains unclear. A cohort of Sprague-Dawley rats developmentally exposed to sodium fluoride (NaF) was established to simulate actual exposure of human beings. Using high-input proteomics and small RNA sequencing technology in rat hippocampus, we found mitochondrial translation as the most striking enriched biological process after NaF treatment, which involves the differentially expressed Required Meiotic Nuclear Division 1 homolog (RMND1) and neural-specific miR-221-3p. Further experiments in vivo and in vitro neuroendocrine pheochromocytoma (PC12) cells demonstrated that NaF impaired mitochondrial translation and function, as shown by declined mitochondrial membrane potential and inhibited expression of mitochondrial translation factors, mitochondrial translation products, and OXPHOS complexes, which was concomitant with decreased RMND1 and transcription factor c-Fos in mRNA and proteins as well as elevated miR-221-3p. Notably, RMND1 overexpression alleviated the NaF-elicited mitochondrial translation impairment by up-regulating translation factors, but not vice versa. Interestingly, ChIP-qPCR confirmed that c-Fos specifically controls the RMND1 transcription through direct binding with Rmnd1 promotor. Interference of gene expression verified c-Fos as an upstream positive regulator of RMND1, implicating in fluoride-caused mitochondrial translation impairment. Furthermore, dual-luciferase reporter assay evidenced that miR-221-3p targets c-Fos by binding its 3' untranslated region. By modulating the miR-221-3p expression, we identified miR-221-3p as a critical negative regulator of c-Fos. More importantly, we proved that miR-221-3p inhibitor improved mitochondrial translation and mitochondrial function to combat NaF neurotoxicity via activating the c-Fos/RMND1 axis, whereas miR-221-3p mimic tended towards opposite effects. Collectively, our data suggest fluoride impairs mitochondrial translation by dysregulating the miR-221-3p/c-Fos/RMND1 axis to trigger mitochondrial dysfunction, leading to neuronal death and neurodevelopment defects.
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Affiliation(s)
- Dongjie Li
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China; Key Laboratory of Environment and Health, Ministry of Education and Ministry of Environmental Protection, State Key Laboratory of Environmental Health (incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China
| | - Qian Zhao
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China; Key Laboratory of Environment and Health, Ministry of Education and Ministry of Environmental Protection, State Key Laboratory of Environmental Health (incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China
| | - Li Xie
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China; Key Laboratory of Environment and Health, Ministry of Education and Ministry of Environmental Protection, State Key Laboratory of Environmental Health (incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China
| | - Chenxi Wang
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China; Key Laboratory of Environment and Health, Ministry of Education and Ministry of Environmental Protection, State Key Laboratory of Environmental Health (incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China
| | - Zhiyuan Tian
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China; Key Laboratory of Environment and Health, Ministry of Education and Ministry of Environmental Protection, State Key Laboratory of Environmental Health (incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China
| | - Huayang Tang
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China; Key Laboratory of Environment and Health, Ministry of Education and Ministry of Environmental Protection, State Key Laboratory of Environmental Health (incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China
| | - Tao Xia
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China; Key Laboratory of Environment and Health, Ministry of Education and Ministry of Environmental Protection, State Key Laboratory of Environmental Health (incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China
| | - Aiguo Wang
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China; Key Laboratory of Environment and Health, Ministry of Education and Ministry of Environmental Protection, State Key Laboratory of Environmental Health (incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, People's Republic of China.
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17
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Yoo M, Choi DC, Murphy A, Ahsan AM, Junn E. MicroRNA-593-5p contributes to cell death following exposure to 1-methyl-4-phenylpyridinium (MPP +) by targeting PTEN-induced putative kinase 1 (PINK1). J Biol Chem 2023; 299:104709. [PMID: 37060996 DOI: 10.1016/j.jbc.2023.104709] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/03/2023] [Accepted: 04/08/2023] [Indexed: 04/17/2023] Open
Abstract
Neurodegenerative diseases are characterized by a decline in neuronal function and structure, leading to neuronal death. Understanding the molecular mechanisms of neuronal death is crucial for developing therapeutics. MicroRNAs (miRs) are small non-coding RNAs that regulate gene expression by degrading target mRNAs or inhibiting translation. MiR dysregulation has been linked to many neurodegenerative diseases, but the underlying mechanisms are not well understood. As mitochondrial dysfunction is one of the common molecular mechanisms leading to neuronal death in many neurodegenerative diseases, here we studied miRs that modulate neuronal death caused by 1-methyl-4-phenylpyridinium (MPP+), an inhibitor of complex I in mitochondria. We identified miR-593-5p, levels of which were increased in SH-SY5Y human neuronal cells, after exposure to MPP+. We found that intracellular Ca2+, but not of reactive oxygen species (ROS), mediated this miR-593-5p increase. Furthermore, we found the increase in miR-593-5p was due to enhanced stability, not increased transcription or miR processing. Importantly, we show the increase in miR-593-5p contributed to MPP+-induced cell death. Our data revealed that miR-593-5p inhibits a signaling pathway involving PTEN-induced putative kinase 1 (PINK1) and Parkin, two proteins responsible for the removal of damaged mitochondria from cells, by targeting the coding sequence of PINK1 mRNA. Our findings suggest that miR-593-5p contributes to neuronal death resulting from MPP+ toxicity, in part, by impeding the PINK1/Parkin-mediated pathway that facilitates the clearance of damaged mitochondria. Taken together, our observations highlight the potential significance of inhibiting miR-593-5p as a therapeutic approach for neurodegenerative diseases.
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Affiliation(s)
- Myungsik Yoo
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ. 08854, USA
| | - Doo Chul Choi
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ. 08854, USA
| | - Aleta Murphy
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ. 08854, USA
| | - Atiq M Ahsan
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ. 08854, USA
| | - Eunsung Junn
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ. 08854, USA.
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18
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Papadimitriou E, Koutsoudaki PN, Thanou I, Karagkouni D, Karamitros T, Chroni-Tzartou D, Gaitanou M, Gkemisis C, Margariti M, Xingi E, Tzartos SJ, Hatzigeorgiou AG, Thomaidou D. A miR-124-mediated post-transcriptional mechanism controlling the cell fate switch of astrocytes to induced neurons. Stem Cell Reports 2023; 18:915-935. [PMID: 36963393 PMCID: PMC10147664 DOI: 10.1016/j.stemcr.2023.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/26/2023] Open
Abstract
The microRNA (miRNA) miR-124 has been employed supplementary to neurogenic transcription factors (TFs) and other miRNAs to enhance direct neurogenic conversion. The aim of this study was to investigate whether miR-124 is sufficient to drive direct reprogramming of astrocytes to induced neurons (iNs) on its own and elucidate its independent mechanism of reprogramming action. Our data show that miR-124 is a potent driver of the reprogramming switch of astrocytes toward an immature neuronal fate by directly targeting the RNA-binding protein Zfp36L1 implicated in ARE-mediated mRNA decay and subsequently derepressing Zfp36L1 neurogenic interactome. To this end, miR-124 contribution in iNs' production largely recapitulates endogenous neurogenesis pathways, being further enhanced upon addition of the neurogenic compound ISX9, which greatly improves iNs' differentiation and functional maturation. Importantly, miR-124 is potent in guiding direct conversion of reactive astrocytes to immature iNs in vivo following cortical trauma, while ISX9 supplementation confers a survival advantage to newly produced iNs.
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Affiliation(s)
- Elsa Papadimitriou
- Neural Stem Cells and Neuroimaging Group, Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | - Paraskevi N Koutsoudaki
- Neural Stem Cells and Neuroimaging Group, Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | - Irini Thanou
- Neural Stem Cells and Neuroimaging Group, Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | - Dimitra Karagkouni
- DIANA-Lab, Hellenic Pasteur Institute & Department of Computer Science and Biomedical Informatics, University of Thessaly, Larissa, Greece
| | - Timokratis Karamitros
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Dafni Chroni-Tzartou
- Laboratory of Molecular Neurobiology and Immunology, Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | - Maria Gaitanou
- Laboratory of Cellular and Molecular Neurobiology - Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | - Christos Gkemisis
- Neural Stem Cells and Neuroimaging Group, Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | - Maria Margariti
- Neural Stem Cells and Neuroimaging Group, Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | - Evangelia Xingi
- Light Microscopy Unit, Hellenic Pasteur Institute, Athens, Greece
| | - Socrates J Tzartos
- Laboratory of Molecular Neurobiology and Immunology, Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | - Artemis G Hatzigeorgiou
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Dimitra Thomaidou
- Neural Stem Cells and Neuroimaging Group, Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece; Light Microscopy Unit, Hellenic Pasteur Institute, Athens, Greece.
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19
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Carvajal-Moreno J, Hernandez VA, Wang X, Li J, Yalowich JC, Elton TS. Effects of hsa-miR-9-3p and hsa-miR-9-5p on Topoisomerase II β Expression in Human Leukemia K562 Cells with Acquired Resistance to Etoposide. J Pharmacol Exp Ther 2023; 384:265-276. [PMID: 36410793 PMCID: PMC9875313 DOI: 10.1124/jpet.122.001429] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 11/23/2022] Open
Abstract
DNA topoisomerase IIα (TOP2α/170; 170 kDa) and topoisomerase IIβ (TOP2β/180; 180 kDa) are targets for a number of anticancer drugs, whose clinical efficacy is attenuated by chemoresistance. Our laboratory selected for an etoposide-resistant K562 clonal subline designated K/VP.5. These cells exhibited decreased TOP2α/170 and TOP2β/180 expression. We previously demonstrated that a microRNA-9 (miR-9)-mediated posttranscriptional mechanism plays a role in drug resistance via reduced TOP2α/170 protein in K/VP.5 cells. Here, it is hypothesized that a similar miR-9 mechanism is responsible for decreased TOP2β/180 levels in K/VP.5 cells. Both miR-9-3p and miR-9-5p are overexpressed in K/VP.5 compared with K562 cells, demonstrated by microRNA (miRNA) sequencing and quantitative polymerase chain reaction. The 3'-untranslated region (3'-UTR) of TOP2β/180 contains miRNA recognition elements (MRE) for both miRNAs. Cotransfection of K562 cells with a luciferase reporter plasmid harboring TOP2β/180 3'-UTR plus miR-9-3p or miR-9-5p mimics resulted in statistically significant decreased luciferase expression. miR-9-3p and miR-9-5p MRE mutations prevented this decrease, validating direct interaction between these miRNAs and TOP2β/180 mRNA. Transfection of K562 cells with miR-9-3p/5p mimics led to decreased TOP2β protein levels without a change in TOP2β/180 mRNA and resulted in reduced TOP2β-specific XK469-induced DNA damage. Conversely, K/VP.5 cells transfected with miR-9-3p/5p inhibitors led to increased TOP2β/180 protein without a change in TOP2β/180 mRNA and resulted in enhancement of XK469-induced DNA damage. Taken together, these results strongly suggest that TOP2β/180 mRNA is translationally repressed by miR-9-3p/5p, that these miRNAs play a role in acquired resistance to etoposide, and that they are potential targets for circumvention of resistance to TOP2-targeted agents. SIGNIFICANCE STATEMENT: Results presented here indicate that miR-9-3p and miR-9-5p play a role in acquired resistance to etoposide via decreased DNA topoisomerase IIβ 180 kDa protein levels. These findings contribute further information about and potential strategies for circumvention of drug resistance by modulation of microRNA levels. In addition, miR-9-3p and miR-9-5p overexpression in cancer chemoresistance may lead to future validation as biomarkers of responsiveness to DNA topoisomerase II-targeted therapy.
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Affiliation(s)
- Jessika Carvajal-Moreno
- Division of Pharmaceutics and Pharmacology (J.C.-M., V.A.H., X.W., J.C.Y., T.S.E.) and Division of Outcomes and Translational Science (J.I.), College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Victor A Hernandez
- Division of Pharmaceutics and Pharmacology (J.C.-M., V.A.H., X.W., J.C.Y., T.S.E.) and Division of Outcomes and Translational Science (J.I.), College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Xinyi Wang
- Division of Pharmaceutics and Pharmacology (J.C.-M., V.A.H., X.W., J.C.Y., T.S.E.) and Division of Outcomes and Translational Science (J.I.), College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Junan Li
- Division of Pharmaceutics and Pharmacology (J.C.-M., V.A.H., X.W., J.C.Y., T.S.E.) and Division of Outcomes and Translational Science (J.I.), College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Jack C Yalowich
- Division of Pharmaceutics and Pharmacology (J.C.-M., V.A.H., X.W., J.C.Y., T.S.E.) and Division of Outcomes and Translational Science (J.I.), College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Terry S Elton
- Division of Pharmaceutics and Pharmacology (J.C.-M., V.A.H., X.W., J.C.Y., T.S.E.) and Division of Outcomes and Translational Science (J.I.), College of Pharmacy, The Ohio State University, Columbus, Ohio
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20
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Bonacina G, Carollo A, Esposito G. The Genetic Side of the Mood: A Scientometric Review of the Genetic Basis of Mood Disorders. Genes (Basel) 2023; 14:genes14020352. [PMID: 36833279 PMCID: PMC9956267 DOI: 10.3390/genes14020352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/22/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Mood disorders are highly heritable psychiatric disorders. Over the years, many genetic polymorphisms have been identified to pose a higher risk for the development of mood disorders. To overview the literature on the genetics of mood disorders, a scientometric analysis was performed on a sample of 5342 documents downloaded from Scopus. The most active countries and the most impactful documents in the field were identified. Furthermore, a total of 13 main thematic clusters emerged in the literature. From the qualitative inspection of clusters, it emerged that the research interest moved from a monogenic to a polygenic risk framework. Researchers have moved from the study of single genes in the early 1990s to conducting genome-wide association studies around 2015. In this way, genetic overlaps between mood disorders and other psychiatric conditions emerged too. Furthermore, around the 2010s, the interaction between genes and environmental factors emerged as pivotal in understanding the risk for mood disorders. The inspection of thematic clusters provides a valuable insight into the past and recent trends of research in the genetics of mood disorders and sheds light onto future lines of research.
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21
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Dobricic V, Schilling M, Farkas I, Gveric DO, Ohlei O, Schulz J, Middleton L, Gentleman SM, Parkkinen L, Bertram L, Lill CM. Common signatures of differential microRNA expression in Parkinson's and Alzheimer's disease brains. Brain Commun 2022; 4:fcac274. [PMID: 36382223 PMCID: PMC9645562 DOI: 10.1093/braincomms/fcac274] [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: 04/07/2022] [Revised: 06/22/2022] [Accepted: 10/26/2022] [Indexed: 11/17/2022] Open
Abstract
Dysregulation of microRNA gene expression has been implicated in many neurodegenerative diseases, including Parkinson's disease. However, the individual dysregulated microRNAs remain largely unknown. Previous meta-analyses have highlighted several microRNAs being differentially expressed in post-mortem Parkinson's disease and Alzheimer's disease brains versus controls, but they were based on small sample sizes. In this study, we quantified the expression of the most compelling Parkinson's and Alzheimer's disease microRNAs from these meta-analyses ('candidate miRNAs') in one of the largest Parkinson's/Alzheimer's disease case-control post-mortem brain collections available (n = 451), thereby quadruplicating previously investigated sample sizes. Parkinson's disease candidate microRNA hsa-miR-132-3p was differentially expressed in our Parkinson's (P = 4.89E-06) and Alzheimer's disease samples (P = 3.20E-24) compared with controls. Alzheimer's disease candidate microRNAs hsa-miR-132-5p (P = 4.52E-06) and hsa-miR-129-5p (P = 0.0379) were differentially expressed in our Parkinson's disease samples. Combining these novel data with previously published data substantially improved the statistical support (α = 3.85E-03) of the corresponding meta-analyses, clearly implicating these microRNAs in both Parkinson's and Alzheimer's disease. Furthermore, hsa-miR-132-3p/-5p (but not hsa-miR-129-5p) showed association with α-synuclein neuropathological Braak staging (P = 3.51E-03/P = 0.0117), suggesting that hsa-miR-132-3p/-5p play a role in α-synuclein aggregation beyond the early disease phase. Our study represents the largest independent assessment of recently highlighted candidate microRNAs in Parkinson's and Alzheimer's disease brains, to date. Our results implicate hsa-miR-132-3p/-5p and hsa-miR-129-5p to be differentially expressed in both Parkinson's and Alzheimer's disease, pinpointing shared pathogenic mechanisms across these neurodegenerative diseases. Intriguingly, based on publicly available high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation data, hsa-miR-132 may interact with SNCA messenger RNA in the human brain, possibly pinpointing novel therapeutic approaches in fighting Parkinson's disease.
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Affiliation(s)
- Valerija Dobricic
- Correspondence to: Prof Dr Christina M. Lill, MD, MSc Ageing Epidemiology Unit, School of Public Health Imperial College London, London, UK E-mail: ; Dr. Valerija Dobricic, Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany, E-mail:
| | - Marcel Schilling
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, 23562 Lübeck, Germany
| | - Ildiko Farkas
- Multiple Sclerosis and Parkinson’s Tissue Bank, Imperial College London, London W12 0NN, UK
| | - Djordje O Gveric
- Multiple Sclerosis and Parkinson’s Tissue Bank, Imperial College London, London W12 0NN, UK
| | - Olena Ohlei
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, 23562 Lübeck, Germany
| | - Jessica Schulz
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, 23562 Lübeck, Germany
| | - Lefkos Middleton
- Ageing and Epidemiology Unit (AGE), School of Public Health, Imperial College London, London W6 8RF, UK,Public Health Directorate, Imperial College NHS Healthcare Trust, London W6 8RF, UK
| | - Steve M Gentleman
- Department of Brain Sciences, Hammersmith Hospital campus, Imperial College London, London W12 0HS, UK
| | - Laura Parkkinen
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson’s Disease Centre, University of Oxford, Oxford OX3 9DU, UK
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, 23562 Lübeck, Germany,Department of Psychology, University of Oslo, 0373 Oslo, Norway
| | - Christina M Lill
- Correspondence to: Prof Dr Christina M. Lill, MD, MSc Ageing Epidemiology Unit, School of Public Health Imperial College London, London, UK E-mail: ; Dr. Valerija Dobricic, Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany, E-mail:
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22
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Liu M, Peng Y, Che Y, Zhou M, Bai Y, Tang W, Huang S, Zhang B, Deng S, Wang C, Yu Z. MiR-146b-5p/TRAF6 axis is essential for Ginkgo biloba L. extract GBE to attenuate LPS-induced neuroinflammation. Front Pharmacol 2022; 13:978587. [PMID: 36091773 PMCID: PMC9449131 DOI: 10.3389/fphar.2022.978587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Neuroinflammation plays a crucial role in the pathogenesis and progression of various neurodegenerative diseases, including Alzheimer’s disease. The Ginkgo biloba leaf extract (GBE) has been widely used to treat cerebral and peripheral blood circulation disorders. However, its potential targets and underlying mechanisms regarding neuroinflammation have not yet been characterized. Aims: The purpose of this study was to investigate and validate the anti-neuroinflammatory properties of GBE against lipopolysaccharide (LPS)-mediated inflammation and to determine the underlying molecular mechanisms. Methods: The effect of GBE on LPS-induced release of inflammatory cytokines was examined using ELISA and western blot assay. The effects of GBE on NF-κB binding activity and translocation were determined via luciferase, streptavidin-agarose pulldown, and immunofluorescence assays. The potential targets of GBE were screened from the GEO and microRNA databases and further identified via qPCR, luciferase, gene mutation, and western blot assays. Results: GBE significantly inhibited LPS-induced pro-inflammatory responses in BV-2 and U87 cells, with no obvious cytotoxicity. GBE significantly induced miR-146b-5p expression, which negatively regulated TRAF6 expression by targeting its 3′-UTR. Thus, due to TRAF6 suppression, GBE decreases the transcriptional activity of NF-κB and the expression of pro-inflammatory cytokines, such as interleukin (IL)-1β, IL-6, tumor necrosis factor (TNF)-α, and cyclooxygenase (COX)-2, and finally reverses LPS-induced neuroinflammation. Conclusion: Our study revealed the anti-neuroinflammatory mechanism of GBE through the miR-146b-5p/TRAF6 axis and provided a theoretical basis for its rational clinical application.
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Affiliation(s)
- Min Liu
- Neurology Department, Dalian University Affiliated Xinhua Hospital, Dalian, China
- College of Pharmacy, Dalian Medical University, Dalian, China
| | - Yulin Peng
- College of Pharmacy, Dalian Medical University, Dalian, China
| | - Yilin Che
- The 1st Department of Thoracic Medical Oncology, Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Meirong Zhou
- College of Pharmacy, Dalian Medical University, Dalian, China
| | - Ying Bai
- Neurology Department, Dalian University Affiliated Xinhua Hospital, Dalian, China
| | - Wei Tang
- Neurology Department, Dalian University Affiliated Xinhua Hospital, Dalian, China
| | - Shanshan Huang
- College of Pharmacy, Dalian Medical University, Dalian, China
| | - Baojing Zhang
- College of Pharmacy, Dalian Medical University, Dalian, China
| | - Sa Deng
- College of Pharmacy, Dalian Medical University, Dalian, China
| | - Chao Wang
- College of Pharmacy, Dalian Medical University, Dalian, China
- *Correspondence: Zhenlong Yu, ; Chao Wang,
| | - Zhenlong Yu
- College of Pharmacy, Dalian Medical University, Dalian, China
- *Correspondence: Zhenlong Yu, ; Chao Wang,
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23
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Expression of MicroRNAs in Sepsis-Related Organ Dysfunction: A Systematic Review. Int J Mol Sci 2022; 23:ijms23169354. [PMID: 36012630 PMCID: PMC9409129 DOI: 10.3390/ijms23169354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/10/2022] [Accepted: 08/17/2022] [Indexed: 02/06/2023] Open
Abstract
Sepsis is a critical condition characterized by increased levels of pro-inflammatory cytokines and proliferating cells such as neutrophils and macrophages in response to microbial pathogens. Such processes lead to an abnormal inflammatory response and multi-organ failure. MicroRNAs (miRNA) are single-stranded non-coding RNAs with the function of gene regulation. This means that miRNAs are involved in multiple intracellular pathways and thus contribute to or inhibit inflammation. As a result, their variable expression in different tissues and organs may play a key role in regulating the pathophysiological events of sepsis. Thanks to this property, miRNAs may serve as potential diagnostic and prognostic biomarkers in such life-threatening events. In this narrative review, we collect the results of recent studies on the expression of miRNAs in heart, blood, lung, liver, brain, and kidney during sepsis and the molecular processes in which they are involved. In reviewing the literature, we find at least 122 miRNAs and signaling pathways involved in sepsis-related organ dysfunction. This may help clinicians to detect, prevent, and treat sepsis-related organ failures early, although further studies are needed to deepen the knowledge of their potential contribution.
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24
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Stein CS, McLendon JM, Witmer NH, Boudreau RL. Modulation of miR-181 influences dopaminergic neuronal degeneration in a mouse model of Parkinson's disease. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 28:1-15. [PMID: 35280925 PMCID: PMC8899134 DOI: 10.1016/j.omtn.2022.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/10/2022] [Indexed: 12/30/2022]
Abstract
Parkinson's disease (PD) is caused by the loss of dopaminergic (DA) neurons in the substantia nigra (SN). Although PD pathogenesis is not fully understood, studies implicate perturbations in gene regulation, mitochondrial function, and neuronal activity. MicroRNAs (miRs) are small gene regulatory RNAs that inhibit diverse subsets of target mRNAs, and several studies have noted miR expression alterations in PD brains. For example, miR-181a is abundant in the brain and is increased in PD patient brain samples; however, the disease relevance of this remains unclear. Here, we show that miR-181 target mRNAs are broadly downregulated in aging and PD brains. To address whether the miR-181 family plays a role in PD pathogenesis, we generated adeno-associated viruses (AAVs) to overexpress and inhibit the miR-181 isoforms. After co-injection with AAV overexpressing alpha-synuclein (aSyn) into mouse SN (PD model), we found that moderate miR-181a/b overexpression exacerbated aSyn-induced DA neuronal loss, whereas miR-181 inhibition was neuroprotective relative to controls (GFP alone and/or scrambled RNA). Also, prolonged miR-181 overexpression in SN alone elicited measurable neurotoxicity that is coincident with an increased immune response. mRNA-seq analyses revealed that miR-181a/b inhibits genes involved in synaptic transmission, neurite outgrowth, and mitochondrial respiration, along with several genes having known protective roles and genetic links in PD.
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Affiliation(s)
- Colleen S. Stein
- Department of Internal Medicine, Iowa Neuroscience Institute, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Jared M. McLendon
- Department of Internal Medicine, Iowa Neuroscience Institute, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Nathan H. Witmer
- Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ryan L. Boudreau
- Department of Internal Medicine, Iowa Neuroscience Institute, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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25
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Bianchi N, Doneda L, Elli L, Taccioli C, Vaira V, Scricciolo A, Lombardo V, Terrazzan A, Colapietro P, Terranova L, Bergamini C, Vecchi M, Scaramella L, Nandi N, Roncoroni L. Circulating microRNAs Suggest Networks Associated with Biological Functions in Aggressive Refractory Type 2 Celiac Disease. Biomedicines 2022; 10:biomedicines10061408. [PMID: 35740429 PMCID: PMC9219665 DOI: 10.3390/biomedicines10061408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 02/08/2023] Open
Abstract
Despite following a gluten-free diet, which is currently the only effective therapy for celiac disease, about 5% of patients can develop serious complications, which in the case of refractory type 2 could evolve towards intestinal lymphoma. In this study, we have identified a set of 15 microRNAs in serum discriminating between the two types of refractory disease. Upregulated miR-770-5p, miR-181b-2-3p, miR-1193, and miR-1226-3p could be useful for the better stratification of patients and the monitoring of disease development, while miR-490-3p was found to be dysregulated in patients with refractory type 1. Finally, by using bioinformatic tools applied to the analysis of the targets of dysregulated microRNAs, we have completed a more precise assessment of their functions. These mainly include the pathway of response to Transforming Growth Factor β cell-cell signaling by Wnt; epigenetic regulation, especially novel networks associated with transcriptional and post-transcriptional alterations; and the well-known inflammatory profiles.
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Affiliation(s)
- Nicoletta Bianchi
- Department of Translational Medicine, University of Ferrara, Street L. Borsari 46, 44121 Ferrara, Italy; (N.B.); (A.T.)
| | - Luisa Doneda
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Street Pascal 36, 20133 Milan, Italy; (L.D.); (L.R.)
| | - Luca Elli
- Center for Prevention and Diagnosis of Celiac Disease, Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (A.S.); (V.L.); (M.V.); (L.S.); (N.N.)
- Correspondence:
| | - Cristian Taccioli
- Department of Animal Medicine, Production and Health, University of Padova, 35020 Legnaro, Italy;
| | - Valentina Vaira
- Division of Pathology, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Street F. Sforza 35, 20122 Milan, Italy;
- Department of Pathophysiology and Transplantation, University of Milan, Street F. Sforza 35, 20122 Milan, Italy;
| | - Alice Scricciolo
- Center for Prevention and Diagnosis of Celiac Disease, Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (A.S.); (V.L.); (M.V.); (L.S.); (N.N.)
| | - Vincenza Lombardo
- Center for Prevention and Diagnosis of Celiac Disease, Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (A.S.); (V.L.); (M.V.); (L.S.); (N.N.)
| | - Anna Terrazzan
- Department of Translational Medicine, University of Ferrara, Street L. Borsari 46, 44121 Ferrara, Italy; (N.B.); (A.T.)
| | - Patrizia Colapietro
- Department of Pathophysiology and Transplantation, University of Milan, Street F. Sforza 35, 20122 Milan, Italy;
| | - Leonardo Terranova
- Respiratory Unit and Cystic Fibrosis Adult Center, Internal Medicine Department, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Street F. Sforza 35, 20122 Milan, Italy;
| | - Carlo Bergamini
- Department of Neuroscience and Rehabilitation, University of Ferrara, Street L. Borsari 46, 44121 Ferrara, Italy;
| | - Maurizio Vecchi
- Center for Prevention and Diagnosis of Celiac Disease, Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (A.S.); (V.L.); (M.V.); (L.S.); (N.N.)
- Department of Pathophysiology and Transplantation, University of Milan, Street F. Sforza 35, 20122 Milan, Italy;
| | - Lucia Scaramella
- Center for Prevention and Diagnosis of Celiac Disease, Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (A.S.); (V.L.); (M.V.); (L.S.); (N.N.)
| | - Nicoletta Nandi
- Center for Prevention and Diagnosis of Celiac Disease, Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (A.S.); (V.L.); (M.V.); (L.S.); (N.N.)
- Department of Pathophysiology and Transplantation, University of Milan, Street F. Sforza 35, 20122 Milan, Italy;
| | - Leda Roncoroni
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Street Pascal 36, 20133 Milan, Italy; (L.D.); (L.R.)
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26
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Dorostgou Z, Yadegar N, Dorostgou Z, Khorvash F, Vakili O. Novel insights into the role of circular RNAs in Parkinson disease: An emerging renaissance in the management of neurodegenerative diseases. J Neurosci Res 2022; 100:1775-1790. [PMID: 35642104 DOI: 10.1002/jnr.25094] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 05/11/2022] [Accepted: 05/15/2022] [Indexed: 11/06/2022]
Abstract
Parkinson's disease (PD), as a debilitating neurodegenerative disease, particularly affects the elderly population, and is clinically identified by resting tremor, rigidity, and bradykinesia. Pathophysiologically, PD is characterized by an early loss of dopaminergic neurons in the Substantia nigra pars compacta, accompanied by the extensive aggregation of alpha-synuclein (α-Syn) in the form of Lewy bodies. The onset of PD has been reported to be influenced by multiple biological molecules. In this context, circular RNAs (circRNAs), as tissue-specific noncoding RNAs with closed structures, have been recently demonstrated to involve in a set of PD's pathogenic processes. These RNA molecules can either up- or downregulate the expression of α-Syn, as well as moderating its accumulation through different regulatory mechanisms, in which targeting microRNAs (miRNAs) is considered the most common pathway. Since circRNAs have prominent structural and biological characteristics, they could also be considered as promising candidates for PD diagnosis and treatment. Unfortunately, PD has become a global health concern, and a large number of its pathogenic processes are still unclear; thus, it is crucial to elucidate the ambiguous aspects of PD pathophysiology to improve the efficiency of diagnostic and therapeutic strategies. In line with this fact, the current review aims to highlight the interplay between circRNAs and PD pathogenesis, and then discusses the diagnostic and therapeutic potential of circRNAs in PD progression. This study will thus be the first of its kind reviewing the relationship between circRNAs and PD.
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Affiliation(s)
- Zahra Dorostgou
- Department of Biochemistry, Neyshabur Branch, Islamic Azad University, Neyshabur, Iran
| | - Negar Yadegar
- Department of Medical Laboratory Sciences, School of Paramedical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zeynab Dorostgou
- Department of Biology, Kavian Institute of Higher Education, Mashhad, Iran
| | - Fariborz Khorvash
- Department of Neurology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Isfahan Neurosciences Research Center, Al-zahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
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27
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Kim GH, Heo HJ, Kang JW, Kim EK, Baek SE, Kim K, Kim IJ, Suh S, Lee BJ, Kim YH, Pak K. Multi-omics analysis revealed TEK and AXIN2 are potential biomarkers in multifocal papillary thyroid cancer. Cancer Cell Int 2022; 22:185. [PMID: 35550582 PMCID: PMC9097102 DOI: 10.1186/s12935-022-02606-x] [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: 10/16/2021] [Accepted: 05/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Papillary thyroid carcinoma (PTC), the most common endocrine cancer, accounts for 80-85% of all malignant thyroid tumors. This study focused on identifying targets that affect the multifocality of PTC. In a previous study, we determined 158 mRNAs related to multifocality in BRAF-mutated PTC using The Cancer Genome Atlas. METHODS We used multi-omics data (miRNAs and mRNAs) to identify the regulatory mechanisms of the investigated mRNAs. miRNA inhibitors were used to determine the relationship between mRNAs and miRNAs. We analyzed the target protein levels in patient sera using ELISA and immunohistochemical staining of patients' tissues. RESULTS We identified 44 miRNAs that showed a negative correlation with mRNA expression. Using in vitro experiments, we identified four miRNAs that inhibit TEK and/or AXIN2 among the target mRNAs. We also showed that the downregulation of TEK and AXIN2 decreased the proliferation and migration of BRAF ( +) PTC cells. To evaluate the diagnostic ability of multifocal PTC, we examined serum TEK or AXIN2 in unifocal and multifocal PTC patients using ELISA, and showed that the serum TEK in multifocal PTC patients was higher than that in the unifocal PTC patients. The immunohistochemical study showed higher TEK and AXIN2 expression in multifocal PTC than unifocal PTC. CONCLUSIONS Both TEK and AXIN2 play a potential role in the multifocality of PTC, and serum TEK may be a diagnostic marker for multifocal PTC.
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Affiliation(s)
- Ga Hyun Kim
- Interdisciplinary Program of Genomic Data Science, Pusan National University, Yangsan, Republic of Korea
| | - Hye Jin Heo
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Ji Wan Kang
- Interdisciplinary Program of Genomic Data Science, Pusan National University, Yangsan, Republic of Korea
| | - Eun-Kyung Kim
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Seung Eun Baek
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Keunyoung Kim
- Department of Nuclear Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - In Joo Kim
- Department of Nuclear Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Sunghwan Suh
- Department of Internal Medicine, Dong-A University College of Medicine, Busan, Republic of Korea
| | - Byung-Joo Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Pusan National University Hospital, Busan, Republic of Korea
| | - Yun Hak Kim
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea. .,Department of Nuclear Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea. .,Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan, Republic of Korea.
| | - Kyoungjune Pak
- Department of Nuclear Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea.
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28
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Du R, Bai Y, Li L. Biological networks in gestational diabetes mellitus: insights into the mechanism of crosstalk between long non-coding RNA and N 6-methyladenine modification. BMC Pregnancy Childbirth 2022; 22:384. [PMID: 35505296 PMCID: PMC9066898 DOI: 10.1186/s12884-022-04716-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 04/28/2022] [Indexed: 12/24/2022] Open
Abstract
Background Gestational diabetes mellitus (GDM) is one of the most common complications of pregnancy. The mechanism underlying the crosstalk between long non-coding RNAs (lncRNAs) and N6-methyladenine (m6A) modification in GDM remain unclear. Methods We generated a lncRNA-mediated competitive endogenous RNA (ceRNA) network using comprehensive data from the Gene Expression Omnibus database, published data, and our preliminary findings. m6A-related lncRNAs were identified based on Pearson correlation coefficient (PCC) analysis using our previous profiles. An integrated pipeline was established to constructed a m6A-related subnetwork thereby predicting the potential effects of the m6A-related lncRNAs. Results The ceRNA network was composed of 16 lncRNAs, 17 microRNAs, 184 mRNAs, and 338 edges. Analysis with the Kyoto Encyclopedia of Genes and Genomes database demonstrated that genes in the ceRNA network were primarily involved in the development and adverse outcomes of GDM, such as those in the fatty acid-metabolism pathway, the peroxisome proliferator-activated receptor signaling pathway, and thyroid hormone signaling pathway. Four m6A-related lncRNAs were involved in the ceRNA network, including LINC00667, LINC01087, AP000350.6, and CARMN. The m6A-related subnetwork was generated based on these four lncRNAs, their ceRNAs, and their related m6A regulators. Genes in the subnetwork were enriched in certain GDM-associated hormone (thyroid hormone and oxytocin) signaling pathways. LINC00667 was positively correlated with an m6A “reader” (YTHDF3; PCC = 0.95) and exhibited the highest node degree in the ceRNA network. RIP assays showed that YTHDF3 directly bind LINC00667. We further found that MYC possessed the highest node degree in a protein–protein interaction network and competed with LINC00667 for miR-33a-5p. qPCR analysis indicated that LINC00667, YTHDF3 and MYC levels were upregulated in the GDM placentas, while miR-33a-5p was downregulated. In a support-vector machine classifier, an m6A-related module composed of LINC00667, YTHDF3, MYC, and miR-33a-5p showed excellent classifying power for GDM in both the training and the testing dataset, with an accuracy of 76.19 and 71.43%, respectively. Conclusions Our results shed insights into the potential role of m6A-related lncRNAs in GDM and have implications in terms of novel therapeutic targets for GDM. Supplementary Information The online version contains supplementary material available at 10.1186/s12884-022-04716-w.
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Affiliation(s)
- Runyu Du
- Department of Endocrinology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China
| | - Yu Bai
- Department of Endocrinology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China
| | - Ling Li
- Department of Endocrinology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China.
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Context-Dependent Regulation of Gene Expression by Non-Canonical Small RNAs. Noncoding RNA 2022; 8:ncrna8030029. [PMID: 35645336 PMCID: PMC9149963 DOI: 10.3390/ncrna8030029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022] Open
Abstract
In recent functional genomics studies, a large number of non-coding RNAs have been identified. It has become increasingly apparent that noncoding RNAs are crucial players in a wide range of cellular and physiological functions. They have been shown to modulate gene expression on different levels, including transcription, post-transcriptional processing, and translation. This review aims to highlight the diverse mechanisms of the regulation of gene expression by small noncoding RNAs in different conditions and different types of human cells. For this purpose, various cellular functions of microRNAs (miRNAs), circular RNAs (circRNAs), snoRNA-derived small RNAs (sdRNAs) and tRNA-derived fragments (tRFs) will be exemplified, with particular emphasis on the diversity of their occurrence and on the effects on gene expression in different stress conditions and diseased cell types. The synthesis and effect on gene expression of these noncoding RNAs varies in different cell types and may depend on environmental conditions such as different stresses. Moreover, noncoding RNAs play important roles in many diseases, including cancer, neurodegenerative disorders, and viral infections.
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30
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Wang B, Yin Z, Lin Y, Deng X, Liu F, Tao H, Dong R, Lin X, Bi Y. Correlation between microRNA-320 and postoperative delirium in patients undergoing tibial fracture internal fixation surgery. BMC Anesthesiol 2022; 22:75. [PMID: 35317728 PMCID: PMC8939177 DOI: 10.1186/s12871-022-01612-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/07/2022] [Indexed: 11/20/2022] Open
Abstract
Background Although the incidence of postoperative delirium (POD) in the elderly after surgery are rising as individuals are living longer, the pathogenesis of POD remains poorly understood. It has been suggested that miRNA-320 may play a role in POD based on animal study and human study. Methods We first carried out an animal study, and designed and conducted a human study based on the result of animal study. The aged rats were randomly assigned to five groups: the control (C), anesthesia and surgery (AS), saline (NS), agomir-320 (AG), and antagomir-320 (AT) groups. Postoperative spatial learning and memory in rats were analyzed by the Morris water maze and the open field tests. The plasma levels of insulin-like growth factor-1 (IGF-1), amyloid precursor protein (APP) proteins, miRNA320 and IGF-1mRNA were measured by ELISA and qRT-PCR, respectively. A total of 240 Chinese Han patients over 65 years who underwent tibial fracture internal fixation were included in the PNDABLE study. POD cases and non-POD controls (1:1 matched) were selected by an anesthesiologist using Confusion Assessment Method. Results For Group AS, the escape latency was significantly longer and the ratio of time spent in the target quadrant was significantly reduced, APP and miR-320 were upregulated and IGF-1mRNA was downregulated compared with Group C. For Group AG, the escape latency was significantly longer and the ratio of time spent in the target quadrant was significantly reduced, APP and miR-320 were upregulated and IGF-1mRNA was downregulated compared with Group AS. For Group AT, the escape latency was significantly reduced and the ratio of time spent in the target quadrant was significantly longer, APP and miR-320 were downregulated and IGF-1mRNAwas upregulated compared with Group AS. Compared with NPOD patients, the expressions of plasma miR-320 and APP protein were increased and the expression of plasma IGF-1 mRNA was decreased in POD patients after surgery. Conclusions MiRNA-320 might play a role in up-regulating the levels of IGF-1mRNA and APP protein, which offered a new target for POD treatment. Trial registration Correlation of perioperative neurocognitive disorders with lifestyle and biomarkers. ChiCTR2000033439. Registered 1 June 2020. Supplementary Information The online version contains supplementary material available at 10.1186/s12871-022-01612-w.
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Affiliation(s)
- Bin Wang
- Department of Anesthesiology, Qingdao Municipal Hospital Affiliated to Qingdao University, NO. 5 Donghai Middle Road, Qingdao, 266071, Shandong, China
| | - Zeng Yin
- Department of Emergency, Qingdao Municipal Hospital Affiliated to Qingdao University, Qingdao, Shandong province, China
| | - Yanan Lin
- Department of Anesthesiology, Weifang Medical University, Weifang, Shandong province, China
| | - Xiyuan Deng
- Department of Anesthesiology, Dalian Medical University, Dalian, Liaoning province, China
| | - Fanghao Liu
- Department of Anesthesiology, Qingdao Municipal Hospital Affiliated to Qingdao University, NO. 5 Donghai Middle Road, Qingdao, 266071, Shandong, China
| | - He Tao
- Department of Anesthesiology, Dalian Medical University, Dalian, Liaoning province, China
| | - Rui Dong
- Department of Anesthesiology, Drum Tower Hospital Affiliated to Nanjing University Medical School, Nanjing, China
| | - Xu Lin
- Department of Anesthesiology, Qingdao Municipal Hospital Affiliated to Qingdao University, NO. 5 Donghai Middle Road, Qingdao, 266071, Shandong, China
| | - Yanlin Bi
- Department of Anesthesiology, Qingdao Municipal Hospital Affiliated to Qingdao University, NO. 5 Donghai Middle Road, Qingdao, 266071, Shandong, China.
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31
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Banach E, Szczepankiewicz A, Kaczmarek L, Jaworski T, Urban-Ciećko J. Dysregulation of miRNAs levels in GSK3β overexpressing mice and the role of miR-221-5p in synaptic function. Neuroscience 2022; 490:287-295. [PMID: 35331845 DOI: 10.1016/j.neuroscience.2022.03.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 01/01/2023]
Abstract
Glycogen Synthase Kinase-3β (GSK-3β) is a highly expressed kinase in the brain, where it has an important role in synaptic plasticity. Aberrant activity of GSK-3β leads to synaptic dysfunction which results in the development of several neuropsychiatric and neurological diseases. Notably, overexpression of constitutively active form of GSK-3β (GSK-3β[S9A]) in mice recapitulates the cognitive and structural defects characteristic for neurological and psychiatric disorders. However, the mechanisms by which GSK-3β regulates synaptic functions are not clearly known. Here, we investigate the effects of GSK-3β overactivity on neuronal miRNA expression in the mouse hippocampus. We found that GSK-3β overactivity downregulates miRNA network with a potent effect on miR-221-5p (miR-221*). Next, characterization of miR-221* function in primary hippocampal cell culture transfected by miR-221* inhibitor, showed no structural changes in dendritic spine shape and density. Using electrophysiological methods, we found that downregulation of miR-221* increases excitatory synaptic transmission in hippocampal neurons, probably via postsynaptic mechanisms. Thus, our data reveal potential mechanism by which GSK-3β and miRNAs might regulate synaptic function and therefore also synaptic plasticity.
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Affiliation(s)
- Ewa Banach
- Laboratory of Electrophysiology, Nencki Institute of Experimental Biology, PAS, Warsaw, Poland; Laboratory of Animal Models, Nencki Institute of Experimental Biology, PAS, Warsaw, Poland; Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland.
| | | | - Leszek Kaczmarek
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Tomasz Jaworski
- Laboratory of Animal Models, Nencki Institute of Experimental Biology, PAS, Warsaw, Poland; Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; Research and Development Centre, Celon Pharma SA, Kazun Nowy, Poland
| | - Joanna Urban-Ciećko
- Laboratory of Electrophysiology, Nencki Institute of Experimental Biology, PAS, Warsaw, Poland; Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
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32
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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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33
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Shultz SR, Taylor CJ, Aggio-Bruce R, O’Brien WT, Sun M, Cioanca AV, Neocleous G, Symons GF, Brady RD, Hardikar AA, Joglekar MV, Costello DM, O’Brien TJ, Natoli R, McDonald SJ. Decrease in Plasma miR-27a and miR-221 After Concussion in Australian Football Players. Biomark Insights 2022; 17:11772719221081318. [PMID: 35250259 PMCID: PMC8891921 DOI: 10.1177/11772719221081318] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/31/2022] [Indexed: 12/16/2022] Open
Abstract
Introduction: Sports-related concussion (SRC) is a common form of brain injury that lacks reliable methods to guide clinical decisions. MicroRNAs (miRNAs) can influence biological processes involved in SRC, and measurement of miRNAs in biological fluids may provide objective diagnostic and return to play/recovery biomarkers. Therefore, this prospective study investigated the temporal profile of circulating miRNA levels in concussed male and female athletes. Methods: Pre-season baseline blood samples were collected from amateur Australian rules football players (82 males, 45 females). Of these, 20 males and 8 females sustained an SRC during the subsequent season and underwent blood sampling at 2-, 6- and 13-days post-injury. A miRNA discovery Open Array was conducted on plasma to assess the expression of 754 known/validated miRNAs. miRNA target identified were further investigated with quantitative real-time PCR (qRT-PCR) in a validation study. Data pertaining to SRC symptoms, demographics, sporting history, education history and concussion history were also collected. Results: Discovery analysis identified 18 candidate miRNA. The consequent validation study found that plasma miR-221-3p levels were decreased at 6d and 13d, and that miR-27a-3p levels were decreased at 6d, when compared to baseline. Moreover, miR-27a and miR-221-3p levels were inversely correlated with SRC symptom severity. Conclusion: Circulating levels of miR-27a-3p and miR-221-3p were decreased in the sub-acute stages after SRC, and were inversely correlated with SRC symptom severity. Although further studies are required, these analyses have identified miRNA biomarker candidates of SRC severity and recovery that may one day assist in its clinical management.
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Affiliation(s)
- Sandy R Shultz
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, VIC, Australia
| | - Caroline J Taylor
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, VIC, Australia
| | - Riemke Aggio-Bruce
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - William T O’Brien
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
| | - Mujun Sun
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
| | - Adrian V Cioanca
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - George Neocleous
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, VIC, Australia
| | - Georgia F Symons
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
| | - Rhys D Brady
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
| | | | - Mugdha V Joglekar
- School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
| | - Daniel M Costello
- Department of Medicine, The University of Melbourne, Parkville, VIC, Australia
| | - Terence J O’Brien
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Riccardo Natoli
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Stuart J McDonald
- Department of Neuroscience, Monash University, Melbourne, VIC, Australia
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, VIC, Australia
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34
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Yousefi M, Peymani M, Ghaedi K, Irani S, Etemadifar M. Significant modulations of linc001128 and linc0938 with miR-24-3p and miR-30c-5p in Parkinson disease. Sci Rep 2022; 12:2569. [PMID: 35173238 PMCID: PMC8850599 DOI: 10.1038/s41598-022-06539-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/24/2022] [Indexed: 12/22/2022] Open
Abstract
Parkinson disease (PD) is the second most common neurodegenerative disease; the evidence suggests that lncRNAs and miRNAs play an important role in regulating the PD-related genes. The purpose of this research was to introduce two novel lncRNAs as the biomarker of PD diagnosis and treatment. We evaluated the expression profiles of six nodes of two regulatory networks in the PBMCs which had been got from 38 PD patients and 20 healthy individuals by qRT-PCR. Then, we compared the expression of these RNAs in both early and late stages of PD with the controls to determine if their expression could be related to the severity of disease. Further, this study investigated the direct interaction between one of the lncRNAs and target miRNA by using the dual luciferase assay. The results of the expression profiles of six nodes of the two ceRNA networks shown that linc01128, hsa-miR-24-3p and hsa-miR-30c-5p expression were significantly downregulated. While, the Linc00938, LRRK2 and ATP13A2 expression were up-regulated in the PBMC of the PD patients, in comparison to the controls. In addition, this study demonstrated that linc00938 directly sponged hsa-miR-30c-5p. The present study, therefore, for the first time, revealed two candidate lncRNAs as the biomarkers in the PD patients.
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Affiliation(s)
- Maryam Yousefi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Maryam Peymani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. .,Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Masoud Etemadifar
- Department of Neurology and Isfahan Neurosurgery Research Center, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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35
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Ashrafizadeh M, Ahmadi Z, Yaribeygi H, Sathyapalan T, Jamialahmadi T, Sahebkar A. Antitumor and Protective Effects of Melatonin: The Potential Roles of MicroRNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1328:463-471. [PMID: 34981497 DOI: 10.1007/978-3-030-73234-9_31] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are endogenous short noncoding RNAs with approximately 22 nucleotides. The primary function of miRNAs is the negative regulation of target gene expression via mRNA degradation or translation inhibition. During recent years, much attention has been made toward miRNAs' role in different disorders; particularly cancer and compounds with modulatory effects on miRNAs are of interest. Melatonin is one of these compounds which is secreted by the pineal gland. Also, melatonin is present in the leaves, fruits, and seeds of plants. Melatonin has several valuable biological activities such as antioxidant, anti-inflammation, antitumor, and antiaging activities. This important agent is extensively used to treat different disorders such as cancer and neurodegenerative and cardiovascular diseases. This review aims to describe the modulatory effect of melatonin on miRNAs as novel targets.
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Affiliation(s)
- Milad Ashrafizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.,Sabanci University Nanotechnology Research and Application Center (SUNUM), Istanbul, Turkey
| | - Zahra Ahmadi
- Department of Basic Science, Faculty of Veterinary Medicine, Islamic Azad Branch, University of Shushtar, Shushtar, Khuzestan, Iran
| | - Habib Yaribeygi
- Research Center of Physiology, Semnan University of Medical Sciences, Semnan, Iran.
| | - Thozhukat Sathyapalan
- Academic Diabetes, Endocrinology and Metabolism, Hull York Medical School, University of Hull, United Kingdom of Great Britain and Northern Ireland, Hull, UK
| | - Tannaz Jamialahmadi
- Department of Food Science and Technology, Quchan Branch, Islamic Azad University, Quchan, Iran.,Department of Nutrition, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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36
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Zhang Y, Tan YY, Chen PP, Xu H, Xie SJ, Xu SJ, Li B, Li JH, Liu S, Yang JH, Zhou H, Qu LH. Genome-wide identification of microRNA targets reveals positive regulation of the Hippo pathway by miR-122 during liver development. Cell Death Dis 2021; 12:1161. [PMID: 34907157 PMCID: PMC8671590 DOI: 10.1038/s41419-021-04436-7] [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: 05/13/2021] [Revised: 11/16/2021] [Accepted: 11/24/2021] [Indexed: 12/19/2022]
Abstract
Liver development is a highly complex process that is regulated by the orchestrated interplay of epigenetic regulators, transcription factors, and microRNAs (miRNAs). Owing to the lack of global in vivo targets of all miRNAs during liver development, the mechanisms underlying the dynamic control of hepatocyte differentiation by miRNAs remain elusive. Here, using Argonaute (Ago) high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) in the mouse liver at different developmental stages, we characterized massive Ago-binding RNAs and obtained a genome-wide map of liver miRNA-mRNA interactions. The dynamic changes of five clusters of miRNAs and their potential targets were identified to be differentially involved at specific stages, a dozen of high abundant miRNAs and their epigenetic regulation by super-enhancer were found during liver development. Remarkably, miR-122, a liver-specific and most abundant miRNA in newborn and adult livers, was found by its targetome and pathway reporter analyses to regulate the Hippo pathway, which is crucial for liver size control and homeostasis. Mechanistically, we further demonstrated that miR-122 negatively regulates the outcomes of the Hippo pathway transcription factor TEAD by directly targeting a number of hippo pathway regulators, including the coactivator TAZ and a key factor of the phosphatase complex PPP1CC, which contributes to the dephosphorylation of YAP, another coactivator downstream of the Hippo pathway. This study identifies for the first time the genome-wide miRNA targetomes during mouse liver development and demonstrates a novel mechanism of terminal differentiation of hepatocytes regulated by the miR-122/Hippo pathway in a coordinated manner. As the Hippo pathway plays important roles in cell proliferation and liver pathological processes like inflammation, fibrosis, and hepatocellular carcinoma (HCC), our study could also provide a new insight into the function of miR-122 in liver pathology.
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Affiliation(s)
- Yin Zhang
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene function and regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China ,grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120 China
| | - Ye-Ya Tan
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene function and regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Pei-Pei Chen
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene function and regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China ,grid.413402.00000 0004 6068 0570Guangdong Province Hospital of Chinese Medicine, AMI Key Laboratory of Chinese Medicine in Guangzhou, , The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Science, Guangzhou, 510006 China
| | - Hui Xu
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene function and regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Shu-Juan Xie
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene function and regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Shi-Jun Xu
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene function and regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Bin Li
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene function and regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Jun-Hao Li
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene function and regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Shun Liu
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene function and regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Jian-Hua Yang
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene function and regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Hui Zhou
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene function and regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Liang-Hu Qu
- MOE Key Laboratory of Gene function and regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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Kambis TN, Tofilau HMN, Gawargi FI, Chandra S, Mishra PK. Regulating Polyamine Metabolism by miRNAs in Diabetic Cardiomyopathy. Curr Diab Rep 2021; 21:52. [PMID: 34902085 PMCID: PMC8668854 DOI: 10.1007/s11892-021-01429-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/22/2021] [Indexed: 11/08/2022]
Abstract
PURPOSE OF REVIEW Insulin is at the heart of diabetes mellitus (DM). DM alters cardiac metabolism causing cardiomyopathy, ultimately leading to heart failure. Polyamines, organic compounds synthesized by cardiomyocytes, have an insulin-like activity and effect on glucose metabolism, making them metabolites of interest in the DM heart. This review sheds light on the disrupted microRNA network in the DM heart in relation to developing novel therapeutics targeting polyamine biosynthesis to prevent/mitigate diabetic cardiomyopathy. RECENT FINDINGS Polyamines prevent DM-induced upregulation of glucose and ketone body levels similar to insulin. Polyamines also enhance mitochondrial respiration and thereby regulate all major metabolic pathways. Non-coding microRNAs regulate a majority of the biological pathways in our body by modulating gene expression via mRNA degradation or translational repression. However, the role of miRNA in polyamine biosynthesis in the DM heart remains unclear. This review discusses the regulation of polyamine synthesis and metabolism, and its impact on cardiac metabolism and circulating levels of glucose, insulin, and ketone bodies. We provide insights on potential roles of polyamines in diabetic cardiomyopathy and putative miRNAs that could regulate polyamine biosynthesis in the DM heart. Future studies will unravel the regulatory roles these miRNAs play in polyamine biosynthesis and will open new doors in the prevention/treatment of adverse cardiac remodeling in diabetic cardiomyopathy.
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Affiliation(s)
- Tyler N Kambis
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | | | - Flobater I Gawargi
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Surabhi Chandra
- Department of Biology, University of Nebraska-Kearney, Kearney, NE, 68845, USA
| | - Paras K Mishra
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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38
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McClellan S, Pitchaikannu A, Wright R, Bessert D, Iulianelli M, Hazlett LD, Xu S. Prophylactic Knockdown of the miR-183/96/182 Cluster Ameliorates Pseudomonas aeruginosa-Induced Keratitis. Invest Ophthalmol Vis Sci 2021; 62:14. [PMID: 34919120 PMCID: PMC8684302 DOI: 10.1167/iovs.62.15.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Previously, we demonstrated that miR-183/96/182 cluster (miR-183C) knockout mice exhibit decreased severity of Pseudomonas aeruginosa (PA)-induced keratitis. This study tests the hypothesis that prophylactic knockdown of miR-183C ameliorates PA keratitis indicative of a therapeutic potential. Methods Eight-week-old miR-183C wild-type and C57BL/6J inbred mice were used. Locked nucleic acid-modified anti-miR-183C or negative control oligoribonucleotides with scrambled sequences (NC ORNs) were injected subconjunctivally 1 day before and then topically applied once daily for 5 days post-infection (dpi) (strain 19660). Corneal disease was graded at 1, 3, and 5 dpi. Corneas were harvested for RT-PCR, ELISA, immunofluorescence (IF), myeloperoxidase and plate count assays, and flow cytometry. Corneal nerve density was evaluated in flatmounted corneas by IF staining with anti-β-III tubulin antibody. Results Anti-miR-183C downregulated miR-183C in the cornea. It resulted in an increase in IL-1β at 1 dpi, which was decreased at 5 dpi; fewer polymorphonuclear leukocytes (PMNs) at 5 dpi; lower viable bacterial plate count at both 1 and 5 dpi; increased percentages of MHCII+ macrophages (Mϕ) and dendritic cells (DCs), consistent with enhanced activation/maturation; and decreased severity of PA keratitis. Anti-miR-183C treatment in the cornea of naïve mice resulted in a transient reduction of corneal nerve density, which was fully recovered one week after the last anti-miR application. miR-183C targets repulsive axon-guidance receptor molecule Neuropilin 1, which may mediate the effect of anti-miR-183C on corneal nerve regression. Conclusions Prophylactic miR-183C knockdown is protective against PA keratitis through its regulation of innate immunity, corneal innervation, and neuroimmune interactions.
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Affiliation(s)
- Sharon McClellan
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, Michigan, United States
| | - Ahalya Pitchaikannu
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, Michigan, United States
| | - Robert Wright
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, Michigan, United States
| | - Denise Bessert
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, Michigan, United States
| | - Mason Iulianelli
- Departments of Biological Sciences and Public Health, College of Liberal Arts and Sciences, Wayne State University, Detroit, Michigan, United States
| | - Linda D Hazlett
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, Michigan, United States
| | - Shunbin Xu
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, Michigan, United States
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Tayara H, Chong KT. Improved Predicting of The Sequence Specificities of RNA Binding Proteins by Deep Learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2526-2534. [PMID: 32191896 DOI: 10.1109/tcbb.2020.2981335] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA-binding proteins (RBPs) have a significant role in various regulatory tasks. However, the mechanism by which RBPs identify the subsequence target RNAs is still not clear. In recent years, several machine and deep learning-based computational models have been proposed for understanding the binding preferences of RBPs. These methods required integrating multiple features with raw RNA sequences such as secondary structure and their performances can be further improved. In this paper, we propose an efficient and simple convolution neural network, RBPCNN, that relies on the combination of the raw RNA sequence and evolutionary information. We show that conservation scores (evolutionary information) for the RNA sequences can significantly improve the overall performance of the proposed predictor. In addition, the automatic extraction of the binding sequence motifs can enhance our understanding of the binding specificities of RBPs. The experimental results show that RBPCNN outperforms significantly the current state-of-the-art methods. More specifically, the average area under the receiver operator curve was improved by 2.67 percent and the mean average precision was improved by 8.03 percent. The datasets and results can be downloaded from https://home.jbnu.ac.kr/NSCL/RBPCNN.htm.
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Thomas KT, Zakharenko SS. MicroRNAs in the Onset of Schizophrenia. Cells 2021; 10:2679. [PMID: 34685659 PMCID: PMC8534348 DOI: 10.3390/cells10102679] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/30/2021] [Accepted: 10/02/2021] [Indexed: 12/14/2022] Open
Abstract
Mounting evidence implicates microRNAs (miRNAs) in the pathology of schizophrenia. These small noncoding RNAs bind to mRNAs containing complementary sequences and promote their degradation and/or inhibit protein synthesis. A single miRNA may have hundreds of targets, and miRNA targets are overrepresented among schizophrenia-risk genes. Although schizophrenia is a neurodevelopmental disorder, symptoms usually do not appear until adolescence, and most patients do not receive a schizophrenia diagnosis until late adolescence or early adulthood. However, few studies have examined miRNAs during this critical period. First, we examine evidence that the miRNA pathway is dynamic throughout adolescence and adulthood and that miRNAs regulate processes critical to late neurodevelopment that are aberrant in patients with schizophrenia. Next, we examine evidence implicating miRNAs in the conversion to psychosis, including a schizophrenia-associated single nucleotide polymorphism in MIR137HG that is among the strongest known predictors of age of onset in patients with schizophrenia. Finally, we examine how hemizygosity for DGCR8, which encodes an obligate component of the complex that synthesizes miRNA precursors, may contribute to the onset of psychosis in patients with 22q11.2 microdeletions and how animal models of this disorder can help us understand the many roles of miRNAs in the onset of schizophrenia.
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Affiliation(s)
- Kristen T. Thomas
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Stanislav S. Zakharenko
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Rabin A, Zaffagni M, Ashwal-Fluss R, Patop IL, Jajoo A, Shenzis S, Carmel L, Kadener S. SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. Genome Biol 2021; 22:277. [PMID: 34556162 PMCID: PMC8459468 DOI: 10.1186/s13059-021-02497-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Here we describe a new integrative approach for accurate annotation and quantification of circRNAs named Short Read circRNA Pipeline (SRCP). Our strategy involves two steps: annotation of validated circRNAs followed by a quantification step. We show that SRCP is more sensitive than other individual pipelines and allows for more comprehensive quantification of a larger number of differentially expressed circRNAs. To facilitate the use of SRCP, we generate a comprehensive collection of validated circRNAs in five different organisms, including humans. We then utilize our approach and identify a subset of circRNAs bound to the miRNA-effector protein AGO2 in human brain samples.
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Affiliation(s)
- Avigayel Rabin
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Michela Zaffagni
- Biology Department, Brandeis University, Waltham, MA, 02454, USA
| | - Reut Ashwal-Fluss
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Ines Lucia Patop
- Biology Department, Brandeis University, Waltham, MA, 02454, USA
| | - Aarti Jajoo
- Biology Department, Brandeis University, Waltham, MA, 02454, USA
| | - Shlomo Shenzis
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Liran Carmel
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Sebastian Kadener
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
- Biology Department, Brandeis University, Waltham, MA, 02454, USA.
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
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Osgood C, Ahmed Z, Di Pietro V. Co-Expression Network Analysis of MicroRNAs and Proteins in Severe Traumatic Brain Injury: A Systematic Review. Cells 2021; 10:cells10092425. [PMID: 34572074 PMCID: PMC8465595 DOI: 10.3390/cells10092425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/06/2021] [Accepted: 09/13/2021] [Indexed: 01/14/2023] Open
Abstract
Traumatic brain injury (TBI) represents one of the leading causes of mortality and morbidity worldwide, placing an enormous socioeconomic burden on healthcare services and communities around the world. Survivors of TBI can experience complications ranging from temporary neurological and psychosocial problems to long-term, severe disability and neurodegenerative disease. The current lack of therapeutic agents able to mitigate the effects of secondary brain injury highlights the urgent need for novel target discovery. This study comprises two independent systematic reviews, investigating both microRNA (miRNA) and proteomic expression in rat models of severe TBI (sTBI). The results were combined to perform integrated miRNA-protein co-expression analyses with the aim of uncovering the potential roles of miRNAs in sTBI and to ultimately identify new targets for therapy. Thirty-four studies were included in total. Bioinformatic analysis was performed to identify any miRNA–protein associations. Endocytosis and TNF signalling pathways were highlighted as common pathways involving both miRNAs and proteins found to be differentially expressed in rat brain tissue following sTBI, suggesting efforts to find novel therapeutic targets that should be focused here. Further high-quality investigations are required to ascertain the involvement of these pathways and their miRNAs in the pathogenesis of TBI and other CNS diseases and to therefore uncover those targets with the greatest therapeutic potential.
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Affiliation(s)
- Claire Osgood
- Neuroscience and Ophthalmology Group, Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - Zubair Ahmed
- Neuroscience and Ophthalmology Group, Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
- Centre for Trauma Sciences Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Surgical Reconstruction and Microbiology Research Centre, National Institute for Health Research, Queen Elizabeth Hospital, Birmingham B15 2TH, UK
- Correspondence: (Z.A.); (V.D.P.)
| | - Valentina Di Pietro
- Neuroscience and Ophthalmology Group, Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
- Centre for Trauma Sciences Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Surgical Reconstruction and Microbiology Research Centre, National Institute for Health Research, Queen Elizabeth Hospital, Birmingham B15 2TH, UK
- Correspondence: (Z.A.); (V.D.P.)
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Chu Y, Yokota S, Liu J, Kilikevicius A, Johnson KC, Corey DR. Argonaute binding within human nuclear RNA and its impact on alternative splicing. RNA (NEW YORK, N.Y.) 2021; 27:991-1003. [PMID: 34108230 PMCID: PMC8370746 DOI: 10.1261/rna.078707.121] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/04/2021] [Indexed: 05/03/2023]
Abstract
Mammalian RNA interference (RNAi) is often linked to the regulation of gene expression in the cytoplasm. Synthetic RNAs, however, can also act through the RNAi pathway to regulate transcription and splicing. While nuclear regulation by synthetic RNAs can be robust, a critical unanswered question is whether endogenous functions for nuclear RNAi exist in mammalian cells. Using enhanced crosslinking immunoprecipitation (eCLIP) in combination with RNA sequencing (RNA-seq) and multiple AGO knockout cell lines, we mapped AGO2 protein binding sites within nuclear RNA. The strongest AGO2 binding sites were mapped to micro RNAs (miRNAs). The most abundant miRNAs were distributed similarly between the cytoplasm and nucleus, providing no evidence for mechanisms that facilitate localization of miRNAs in one compartment versus the other. Beyond miRNAs, most statistically significant AGO2 binding was within introns. Splicing changes were confirmed by RT-PCR and recapitulated by synthetic miRNA mimics complementary to the sites of AGO2 binding. These data support the hypothesis that miRNAs can control gene splicing. While nuclear RNAi proteins have the potential to be natural regulatory mechanisms, careful study will be necessary to identify critical RNA drivers of normal physiology and disease.
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Affiliation(s)
- Yongjun Chu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - Shinnichi Yokota
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - Jing Liu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - Audrius Kilikevicius
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - Krystal C Johnson
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - David R Corey
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
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Chu-Tan JA, Cioanca AV, Feng ZP, Wooff Y, Schumann U, Aggio-Bruce R, Patel H, Rutar M, Hannan K, Panov K, Provis J, Natoli R. Functional microRNA targetome undergoes degeneration-induced shift in the retina. Mol Neurodegener 2021; 16:60. [PMID: 34465369 PMCID: PMC8406976 DOI: 10.1186/s13024-021-00478-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/03/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND MicroRNA (miRNA) play a significant role in the pathogenesis of complex neurodegenerative diseases including age-related macular degeneration (AMD), acting as post-transcriptional gene suppressors through their association with argonaute 2 (AGO2) - a key member of the RNA Induced Silencing Complex (RISC). Identifying the retinal miRNA/mRNA interactions in health and disease will provide important insight into the key pathways miRNA regulate in disease pathogenesis and may lead to potential therapeutic targets to mediate retinal degeneration. METHODS To identify the active miRnome targetome interactions in the healthy and degenerating retina, AGO2 HITS-CLIP was performed using a rodent model of photoreceptor degeneration. Analysis of publicly available single-cell RNA sequencing (scRNAseq) data was performed to identify the cellular location of AGO2 and key members of the microRNA targetome in the retina. AGO2 findings were verified by in situ hybridization (RNA) and immunohistochemistry (protein). RESULTS Analysis revealed a similar miRnome between healthy and damaged retinas, however, a shift in the active targetome was observed with an enrichment of miRNA involvement in inflammatory pathways. This shift was further demonstrated by a change in the seed binding regions of miR-124-3p, the most abundant retinal AGO2-bound miRNA, and has known roles in regulating retinal inflammation. Additionally, photoreceptor cluster miR-183/96/182 were all among the most highly abundant miRNA bound to AGO2. Following damage, AGO2 expression was localized to the inner retinal layers and more in the OLM than in healthy retinas, indicating a locational miRNA response to retinal damage. CONCLUSIONS This study provides important insight into the alteration of miRNA regulatory activity that occurs as a response to retinal degeneration and explores the miRNA-mRNA targetome as a consequence of retinal degenerations. Further characterisation of these miRNA/mRNA interactions in the context of the degenerating retina may provide an important insight into the active role these miRNA may play in diseases such as AMD.
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Affiliation(s)
- Joshua A. Chu-Tan
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
- The Australian National University Medical School, College of Health and Medicine, Canberra, ACT 2601 Australia
| | - Adrian V. Cioanca
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
| | - Zhi-Ping Feng
- The ANU Bioinformatics Consultancy, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
| | - Yvette Wooff
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
- The Australian National University Medical School, College of Health and Medicine, Canberra, ACT 2601 Australia
| | - Ulrike Schumann
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
| | - Riemke Aggio-Bruce
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
- The Australian National University Medical School, College of Health and Medicine, Canberra, ACT 2601 Australia
| | - Hardip Patel
- The ANU Bioinformatics Consultancy, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
| | - Matt Rutar
- School of Biomedical Sciences, The University of Melbourne, Parkville, Victoria 3010 Australia
- Faculty of Science and Technology, University of Canberra, Bruce, ACT 2617 Australia
| | - Katherine Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
| | - Konstantin Panov
- School of Biological Sciences Queen’s University Belfast, Belfast, BT9 5DL Northern Ireland
| | - Jan Provis
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
- The Australian National University Medical School, College of Health and Medicine, Canberra, ACT 2601 Australia
| | - Riccardo Natoli
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
- The Australian National University Medical School, College of Health and Medicine, Canberra, ACT 2601 Australia
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Aberrant expression profile of miR-32, miR-98 and miR-374 in chronic lymphocytic leukemia. Leuk Res 2021; 111:106691. [PMID: 34455196 DOI: 10.1016/j.leukres.2021.106691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/12/2021] [Accepted: 08/19/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Leukemia is a malignant and progressive disease of hematopoiesis. The disease arises due to abnormal proliferation and development of white blood cells and their precursors in the blood and bone marrow. Chronic lymphoblastic leukemia (CLL) is a subtype of blood cancers, with the origin of B lymphocytes and the involvement of bone marrow, blood and lymph nodes. MicroRNAs (miRNAs) are small non-coding RNAs with pivotal roles in cellular and molecular processes related to different malignancies, including CLL. In this way, we aimed to evaluate the expression of miR-32-5p, miR-98-5p, and miR-374b-5p in CLL patients. We also investigated the signaling pathways regulated by the studied miRs and also frequently disturbed miRs in CLL. METHODS Blood samples were collected from 32 CLL patients from Kermanshah province, Iran and 34 age and sex-matched healthy individuals. RNA was extracted from PBMCs and then was subjected to cDNA synthesis. Using specifically designed primers and Real-Time PCR method the expression of miRNAs was detected and was statistically analyzed. Using mirPath v.3, systematic pathway enrichment analysis was performed for the three studied miRNAs here along with the frequently disturbed miRNAs in CLL. RESULTS The experiments indicated a significant reduction in the expression of all three miRs (p-value<0.0001) in CLL patients compared with healthy individuals. ROC analysis suggested that the three studied miRs can serve as potential biomarkers for early diagnosis of CLL. The in silico analysis suggested proteoglycans in cancer as a pathway regulated by the studied miRs and frequently dysregulated miRs in CLL. CONCLUSION The observed reduction in expression of miR-32-5p, miR-98-5p, and miR-374b-5p in treatment naïve CLL patients here might be suggestive of their modulatory protective role in CLL progression. Moreover, the candidate peripheral miRNAs could potentially serve as diagnostic biomarkers which warrant further investigation in a larger sample size.
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Świderska E, Strycharz J, Wróblewski A, Czarny P, Szemraj J, Drzewoski J, Śliwińska A. Chronic and Intermittent Hyperglycemia Modulates Expression of Key Molecules of PI3K/AKT Pathway in Differentiating Human Visceral Adipocytes. Int J Mol Sci 2021; 22:ijms22147712. [PMID: 34299331 PMCID: PMC8304829 DOI: 10.3390/ijms22147712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Due to its prominence in the regulation of metabolism and inflammation, adipose tissue is a major target to investigate alterations in insulin action. This hormone activates PI3K/AKT pathway which is essential for glucose homeostasis, cell differentiation, and proliferation in insulin-sensitive tissues, like adipose tissue. The aim of this work was to evaluate the impact of chronic and intermittent high glucose on the expression of biomolecules of insulin signaling pathway during the differentiation and maturation of human visceral preadipocytes. Methods: Human visceral preadipocytes (HPA-V) cells were treated with high glucose (30 mM)during the proliferation and/or differentiation and/or maturation stage. The level of mRNA (by Real-Time PCR) and protein (by Elisa tests) expression of IRS1, PI3K, PTEN, AKT2, and GLUT4 was examined after each culture stage. Furthermore, we investigated whether miR-29a-3p, miR-143-3p, miR-152-3p, miR-186-5p, miR-370-3p, and miR-374b-5p may affect the expression of biomolecules of the insulin signaling pathway. Results: Both chronic and intermittent hyperglycemia affects insulin signaling in visceral pre/adipocytes by upregulation of analyzed PI3K/AKT pathway molecules. Both mRNA and protein expression level is more dependent on stage-specific events than the length of the period of high glucose exposure. What is more, miRs expression changes seem to be involved in PI3K/AKT expression regulation in response to hyperglycemic stimulation.
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Affiliation(s)
- Ewa Świderska
- Department of Medical Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland; (J.S.); (A.W.); (P.C.); (J.S.)
- Correspondence: ; Tel.: +48-693-843-960
| | - Justyna Strycharz
- Department of Medical Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland; (J.S.); (A.W.); (P.C.); (J.S.)
| | - Adam Wróblewski
- Department of Medical Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland; (J.S.); (A.W.); (P.C.); (J.S.)
| | - Piotr Czarny
- Department of Medical Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland; (J.S.); (A.W.); (P.C.); (J.S.)
| | - Janusz Szemraj
- Department of Medical Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland; (J.S.); (A.W.); (P.C.); (J.S.)
| | - Józef Drzewoski
- Central Hospital of Medical University, 92-213 Lodz, Poland;
| | - Agnieszka Śliwińska
- Department of Nucleic Acids Biochemistry, Medical University of Lodz, 92-213 Lodz, Poland;
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Serra F, Bottini S, Pratella D, Stathopoulou MG, Sebille W, El-Hami L, Repetto E, Mauduit C, Benahmed M, Grandjean V, Trabucchi M. Systemic CLIP-seq analysis and game theory approach to model microRNA mode of binding. Nucleic Acids Res 2021; 49:e66. [PMID: 33823551 PMCID: PMC8216473 DOI: 10.1093/nar/gkab198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/19/2021] [Accepted: 03/10/2021] [Indexed: 12/18/2022] Open
Abstract
microRNAs (miRNAs) associate with Ago proteins to post-transcriptionally silence gene expression by targeting mRNAs. To characterize the modes of miRNA-binding, we developed a novel computational framework, called optiCLIP, which considers the reproducibility of the identified peaks among replicates based on the peak overlap. We identified 98 999 binding sites for mouse and human miRNAs, from eleven Ago2 CLIP-seq datasets. Clustering the binding preferences, we found heterogeneity of the mode of binding for different miRNAs. Finally, we set up a quantitative model, named miRgame, based on an adaptation of the game theory. We have developed a new algorithm to translate the miRgame into a score that corresponds to a miRNA degree of occupancy for each Ago2 peak. The degree of occupancy summarizes the number of miRNA-binding sites and miRNAs targeting each binding site, and binding energy of each miRNA::RNA heteroduplex in each peak. Ago peaks were stratified accordingly to the degree of occupancy. Target repression correlates with higher score of degree of occupancy and number of miRNA-binding sites within each Ago peak. We validated the biological performance of our new method on miR-155-5p. In conclusion, our data demonstrate that miRNA-binding sites within each Ago2 CLIP-seq peak synergistically interplay to enhance target repression.
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Affiliation(s)
- Fabrizio Serra
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Silvia Bottini
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - David Pratella
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Maria G Stathopoulou
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Wanda Sebille
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Loubna El-Hami
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Emanuela Repetto
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Claire Mauduit
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Mohamed Benahmed
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Valerie Grandjean
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Michele Trabucchi
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
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Muluhngwi P, Klinge CM. Identification and Roles of miR-29b-1-3p and miR29a-3p-Regulated and Non-Regulated lncRNAs in Endocrine-Sensitive and Resistant Breast Cancer Cells. Cancers (Basel) 2021; 13:3530. [PMID: 34298743 PMCID: PMC8307416 DOI: 10.3390/cancers13143530] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 01/05/2023] Open
Abstract
Despite improvements in the treatment of endocrine-resistant metastatic disease using combination therapies in patients with estrogen receptor α (ERα) primary tumors, the mechanisms underlying endocrine resistance remain to be elucidated. Non-coding RNAs (ncRNAs), including microRNAs (miRNA) and long non-coding RNAs (lncRNA), are targets and regulators of cell signaling pathways and their exosomal transport may contribute to metastasis. Previous studies have shown that a low expression of miR-29a-3p and miR-29b-3p is associated with lower overall breast cancer survival before 150 mos. Transient, modest overexpression of miR-29b1-3p or miR-29a-3p inhibited MCF-7 tamoxifen-sensitive and LCC9 tamoxifen-resistant cell proliferation. Here, we identify miR-29b-1/a-regulated and non-regulated differentially expressed lncRNAs in MCF-7 and LCC9 cells using next-generation RNA seq. More lncRNAs were miR-29b-1/a-regulated in LCC9 cells than in MCF-7 cells, including DANCR, GAS5, DSCAM-AS1, SNHG5, and CRND. We examined the roles of miR-29-regulated and differentially expressed lncRNAs in endocrine-resistant breast cancer, including putative and proven targets and expression patterns in survival analysis using the KM Plotter and TCGA databases. This study provides new insights into lncRNAs in endocrine-resistant breast cancer.
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Affiliation(s)
- Penn Muluhngwi
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
| | - Carolyn M. Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
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Osca-Verdegal R, Beltrán-García J, Pallardó FV, García-Giménez JL. Role of microRNAs As Biomarkers in Sepsis-Associated Encephalopathy. Mol Neurobiol 2021; 58:4682-4693. [PMID: 34160774 PMCID: PMC8220114 DOI: 10.1007/s12035-021-02445-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/06/2021] [Indexed: 12/29/2022]
Abstract
Sepsis-associated encephalopathy (SAE) is a neurological complication of sepsis, characterized by brain dysfunction without any direct central nervous system infection. The diagnosis of SAE is currently a challenge. In fact, problems in making a diagnosis of SAE cause a great variability of incidence that can reach up to 70% of all septic patients. Even more, despite SAE is the most frequent type of encephalopathy occurring in critically ill patients, the molecular mechanisms that guide its progression have not been completely elucidated. On the other hand, miRNAs have proven to be excellent biomarkers for both diagnosis and prognosis, especially in brain pathologies because of their small size they can cross the blood–brain barrier easier than other biomolecules. The identification of new miRNAs as biomarkers may help to improve SAE diagnosis and prognosis and also to design new therapies for this clinical manifestation that produces diffuse cerebral dysfunction. This review is focused on SAE physiopathology and the need to have clear criteria for its diagnosis; thus, this work postulates some miRNA candidates to be used for SAE biomarkers because of their role in both, neurological damage and sepsis.
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Affiliation(s)
- Rebeca Osca-Verdegal
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Valencia, Spain
- Departamento de Fisiología, Facultad de Medicina Y Odontología, Universitat de València, València, Spain
| | - Jesús Beltrán-García
- Departamento de Fisiología, Facultad de Medicina Y Odontología, Universitat de València, València, Spain
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
| | - Federico V. Pallardó
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Valencia, Spain
- Departamento de Fisiología, Facultad de Medicina Y Odontología, Universitat de València, València, Spain
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
| | - José Luis García-Giménez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Valencia, Spain
- Departamento de Fisiología, Facultad de Medicina Y Odontología, Universitat de València, València, Spain
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
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50
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Xu M, Chen Y, Lu W, Kong L, Fang J, Li Z, Zhang L, Pian C. SPMLMI: predicting lncRNA-miRNA interactions in humans using a structural perturbation method. PeerJ 2021; 9:e11426. [PMID: 34055486 PMCID: PMC8140594 DOI: 10.7717/peerj.11426] [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: 01/26/2021] [Accepted: 04/18/2021] [Indexed: 01/06/2023] Open
Abstract
Long non-coding RNA (lncRNA)-microRNA (miRNA) interactions are quickly emerging as important mechanisms underlying the functions of non-coding RNAs. Accordingly, predicting lncRNA-miRNA interactions provides an important basis for understanding the mechanisms of action of ncRNAs. However, the accuracy of the established prediction methods is still limited. In this study, we used structural consistency to measure the predictability of interactive links based on a bilayer network by integrating information for known lncRNA-miRNA interactions, an lncRNA similarity network, and an miRNA similarity network. In particular, by using the structural perturbation method, we proposed a framework called SPMLMI to predict potential lncRNA-miRNA interactions based on the bilayer network. We found that the structural consistency of the bilayer network was higher than that of any single network, supporting the utility of bilayer network construction for the prediction of lncRNA-miRNA interactions. Applying SPMLMI to three real datasets, we obtained areas under the curves of 0.9512 ± 0.0034, 0.8767 ± 0.0033, and 0.8653 ± 0.0021 based on 5-fold cross-validation, suggesting good model performance. In addition, the generalizability of SPMLMI was better than that of the previously established methods. Case studies of two lncRNAs (i.e., SNHG14 and MALAT1) further demonstrated the feasibility and effectiveness of the method. Therefore, SPMLMI is a feasible approach to identify novel lncRNA-miRNA interactions underlying complex biological processes.
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Affiliation(s)
- Mingmin Xu
- College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yuanyuan Chen
- College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Wei Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Lingpeng Kong
- College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jingya Fang
- College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zutan Li
- College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Liangyun Zhang
- College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Cong Pian
- College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
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