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Rajalingam A, Ganjiwale A. Identification of common genetic factors and immune-related pathways associating more than two autoimmune disorders: implications on risk, diagnosis, and treatment. Genomics Inform 2024; 22:10. [PMID: 38956704 PMCID: PMC11221123 DOI: 10.1186/s44342-024-00004-5] [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: 09/21/2023] [Accepted: 12/22/2023] [Indexed: 07/04/2024] Open
Abstract
Autoimmune disorders (ADs) are chronic conditions resulting from failure or breakdown of immunological tolerance, resulting in the host immune system attacking its cells or tissues. Recent studies report shared effects, mechanisms, and evolutionary origins among ADs; however, the possible factors connecting them are unknown. This study attempts to identify gene signatures commonly shared between different autoimmune disorders and elucidate their molecular pathways linking the pathogenesis of these ADs using an integrated gene expression approach. We employed differential gene expression analysis across 19 datasets of whole blood/peripheral blood cell samples with five different autoimmune disorders (rheumatoid arthritis, multiple sclerosis, systemic lupus erythematosus, Crohn's disease, and type 1 diabetes) to get nine key genes-EGR1, RUNX3, SMAD7, NAMPT, S100A9, S100A8, CYBB, GATA2, and MCEMP1 that were primarily involved in cell and leukocyte activation, leukocyte mediated immunity, IL-17, AGE-RAGE signaling in diabetic complications, prion disease, and NOD-like receptor signaling confirming its role in immune-related pathways. Combined with biological interpretations such as gene ontology (GO), pathway enrichment, and protein-protein interaction (PPI) network, our current study sheds light on the in-depth research on early detection, diagnosis, and prognosis of different ADs.
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Affiliation(s)
- Aruna Rajalingam
- Department of Life Science, Bangalore University, Bangalore, Karnataka, 560056, India
| | - Anjali Ganjiwale
- Department of Life Science, Bangalore University, Bangalore, Karnataka, 560056, India.
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2
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Gosetti di Sturmeck T, Malimpensa L, Ferrazzano G, Belvisi D, Leodori G, Lembo F, Brandi R, Pascale E, Cattaneo A, Salvetti M, Conte A, D’Onofrio M, Arisi I. Exploring miRNAs' Based Modeling Approach for Predicting PIRA in Multiple Sclerosis: A Comprehensive Analysis. Int J Mol Sci 2024; 25:6342. [PMID: 38928049 PMCID: PMC11203572 DOI: 10.3390/ijms25126342] [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: 05/08/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
The current hypothesis on the pathophysiology of multiple sclerosis (MS) suggests the involvement of both inflammatory and neurodegenerative mechanisms. Disease Modifying Therapies (DMTs) effectively decrease relapse rates, thus reducing relapse-associated disability in people with MS. In some patients, disability progression, however, is not solely linked to new lesions and clinical relapses but can manifest independently. Progression Independent of Relapse Activity (PIRA) significantly contributes to long-term disability, stressing the urge to unveil biomarkers to forecast disease progression. Twenty-five adult patients with relapsing-remitting multiple sclerosis (RRMS) were enrolled in a cohort study, according to the latest McDonald criteria, and tested before and after high-efficacy Disease Modifying Therapies (DMTs) (6-24 months). Through Agilent microarrays, we analyzed miRNA profiles from peripheral blood mononuclear cells. Multivariate logistic and linear models with interactions were generated. Robustness was assessed by randomization tests in R. A subset of miRNAs, correlated with PIRA, and the Expanded Disability Status Scale (EDSS), was selected. To refine the patient stratification connected to the disease trajectory, we computed a robust logistic classification model derived from baseline miRNA expression to predict PIRA status (AUC = 0.971). We built an optimal multilinear model by selecting four other miRNA predictors to describe EDSS changes compared to baseline. Multivariate modeling offers a promising avenue to uncover potential biomarkers essential for accurate prediction of disability progression in early MS stages. These models can provide valuable insights into developing personalized and effective treatment strategies.
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Affiliation(s)
- Tommaso Gosetti di Sturmeck
- European Brain Research Institute (EBRI) Rita Levi-Montalcini, 00161 Rome, Italy; (T.G.d.S.); (R.B.); (A.C.)
| | - Leonardo Malimpensa
- IRCCS Istituto Neurologico Mediterraneo Neuromed, 86077 Pozzilli, Italy; (L.M.); (D.B.); (G.L.); (M.S.); (A.C.)
| | - Gina Ferrazzano
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (F.L.)
| | - Daniele Belvisi
- IRCCS Istituto Neurologico Mediterraneo Neuromed, 86077 Pozzilli, Italy; (L.M.); (D.B.); (G.L.); (M.S.); (A.C.)
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (F.L.)
| | - Giorgio Leodori
- IRCCS Istituto Neurologico Mediterraneo Neuromed, 86077 Pozzilli, Italy; (L.M.); (D.B.); (G.L.); (M.S.); (A.C.)
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (F.L.)
| | - Flaminia Lembo
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (F.L.)
| | - Rossella Brandi
- European Brain Research Institute (EBRI) Rita Levi-Montalcini, 00161 Rome, Italy; (T.G.d.S.); (R.B.); (A.C.)
| | - Esterina Pascale
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100 Latina, Italy;
| | - Antonino Cattaneo
- European Brain Research Institute (EBRI) Rita Levi-Montalcini, 00161 Rome, Italy; (T.G.d.S.); (R.B.); (A.C.)
- Bio@SNS Laboratory of Biology, Scuola Normale Superiore (SNS), 56126 Pisa, Italy
| | - Marco Salvetti
- IRCCS Istituto Neurologico Mediterraneo Neuromed, 86077 Pozzilli, Italy; (L.M.); (D.B.); (G.L.); (M.S.); (A.C.)
- Centre for Experimental Neurological Therapies (CENTERS), Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, 00189 Rome, Italy
| | - Antonella Conte
- IRCCS Istituto Neurologico Mediterraneo Neuromed, 86077 Pozzilli, Italy; (L.M.); (D.B.); (G.L.); (M.S.); (A.C.)
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (F.L.)
| | - Mara D’Onofrio
- European Brain Research Institute (EBRI) Rita Levi-Montalcini, 00161 Rome, Italy; (T.G.d.S.); (R.B.); (A.C.)
| | - Ivan Arisi
- European Brain Research Institute (EBRI) Rita Levi-Montalcini, 00161 Rome, Italy; (T.G.d.S.); (R.B.); (A.C.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
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Rau CN, Severin ME, Lee PW, Deffenbaugh JL, Liu Y, Murphy SP, Petersen-Cherubini CL, Lovett-Racke AE. MicroRNAs targeting TGF-β signaling exacerbate central nervous system autoimmunity by disrupting regulatory T cell development and function. Eur J Immunol 2024; 54:e2350548. [PMID: 38634287 PMCID: PMC11156541 DOI: 10.1002/eji.202350548] [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: 04/27/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
Transforming growth factor beta (TGF-β) signaling is essential for a balanced immune response by mediating the development and function of regulatory T cells (Tregs) and suppressing autoreactive T cells. Disruption of this balance can result in autoimmune diseases, including multiple sclerosis (MS). MicroRNAs (miRNAs) targeting TGF-β signaling have been shown to be upregulated in naïve CD4 T cells in MS patients, resulting in a limited in vitro generation of human Tregs. Utilizing the murine model experimental autoimmune encephalomyelitis, we show that perinatal administration of miRNAs, which target the TGF-β signaling pathway, enhanced susceptibility to central nervous system (CNS) autoimmunity. Neonatal mice administered with these miRNAs further exhibited reduced Treg frequencies with a loss in T cell receptor repertoire diversity following the induction of experimental autoimmune encephalomyelitis in adulthood. Exacerbated CNS autoimmunity as a result of miRNA overexpression in CD4 T cells was accompanied by enhanced Th1 and Th17 cell frequencies. These findings demonstrate that increased levels of TGF-β-associated miRNAs impede the development of a diverse Treg population, leading to enhanced effector cell activity, and contributing to an increased susceptibility to CNS autoimmunity. Thus, TGF-β-targeting miRNAs could be a risk factor for MS, and recovering optimal TGF-β signaling may restore immune homeostasis in MS patients.
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Affiliation(s)
- Christina N Rau
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
| | - Mary E Severin
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, USA
| | - Priscilla W Lee
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio, USA
| | - Joshua L Deffenbaugh
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
| | - Yue Liu
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
| | - Shawn P Murphy
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
| | - Cora L Petersen-Cherubini
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
- Neuroscience Graduate Program, The Ohio State University, Columbus, Ohio, USA
| | - Amy E Lovett-Racke
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
- Department of Neuroscience, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
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4
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Emami Nejad A, Mostafavi Zadeh SM, Nickho H, Sadoogh Abbasian A, Forouzan A, Ahmadlou M, Nedaeinia R, Shaverdi S, Manian M. The role of microRNAs involved in the disorder of blood-brain barrier in the pathogenesis of multiple sclerosis. Front Immunol 2023; 14:1281567. [PMID: 38193092 PMCID: PMC10773759 DOI: 10.3389/fimmu.2023.1281567] [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: 08/22/2023] [Accepted: 10/30/2023] [Indexed: 01/10/2024] Open
Abstract
miRNAs are involved in various vital processes, including cell growth, development, apoptosis, cellular differentiation, and pathological cellular activities. Circulating miRNAs can be detected in various body fluids including serum, plasma, saliva, and urine. It is worth mentioning that miRNAs remain stable in the circulation in biological fluids and are released from membrane-bound vesicles called exosomes, which protect them from RNase activity. It has been shown that miRNAs regulate blood-brain barrier integrity by targeting both tight junction and adherens junction molecules and can also influence the expression of inflammatory cytokines. Some recent studies have examined the impact of certain commonly used drugs in Multiple Sclerosis on miRNA levels. In this review, we will focus on the recent findings on the role of miRNAs in multiple sclerosis, including their role in the cause of MS and molecular mechanisms of the disease, utilizing miRNAs as diagnostic and clinical biomarkers, using miRNAs as a therapeutic modality or target for Multiple Sclerosis and drug responses in patients, elucidating their importance as prognosticators of disease progression, and highlighting their potential as a future treatment for MS.
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Affiliation(s)
| | - Seyed Mostafa Mostafavi Zadeh
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Nickho
- Department of Immunology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Sadoogh Abbasian
- Department of Internal Medicine, School of Medicine, Amiralmomenin Hospital, Arak University of Medical Sciences, Arak, Iran
| | - Azim Forouzan
- Department of Internal Medicine, School of Medicine, Amiralmomenin Hospital, Arak University of Medical Sciences, Arak, Iran
| | - Mojtaba Ahmadlou
- Department of Biostatistics, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Reza Nedaeinia
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Saham Shaverdi
- Department of Biology, Payame Noor University (PNU), Tehran, Iran
| | - Mostafa Manian
- Department of Medical Laboratory Science, Faculty of Medicine, Islamic Azad University, Kermanshah, Iran
- Neurosciences Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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5
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Khakdan F, Javanmard AS, Shahmoradipour P, Jahromi MJ. The fluctuations of expression profiles of critical genes in the miRNA maturation process and pro-and anti-inflammatory cytokines in the pathogenesis and progression of multiple sclerosis. Mol Biol Rep 2023; 50:9405-9416. [PMID: 37823932 DOI: 10.1007/s11033-023-08812-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Multiple sclerosis (MS) is a central nervous system disease known for immune-mediated demyelination, inflammatory, and neurodegeneration symptoms. Discovering molecular biomarkers to classify RRMS and SPMS patients, monitor the disease activity, and response to particular treatments is one area that has received notable attraction. MicroRNA (miRNA), a single-stranded non-coding RNA molecule, is a significant regulator of gene expression recruited in pathogenic mechanisms in diverse diseases, especially cancer and MS. Also, the relapsing-remitting features of MS exhibit that both inflammatory and anti-inflammatory cytokines are effective in the progression of the disease over time. METHODS AND RESULTS It was assessed the expression patterns of the genes (Drosha, Pasha (DGCR8), and Dicer ) encoding the critical enzymes in the processing steps of miRNA maturation and major pro-inflammatory and anti-inflammatory cytokines (IFN-α, IFN-β, and IL-6) in blood cells of 40 MS patients (two groups of 10 men and women in both clinical courses of RR and SPMS patients) in comparison with 20 healthy control group (10 males and 10 females). The highest transcription activity of Drosha was observed for RRMS patients (4.2 and 3.6-fold, respectively), and the expression ratio was down regulated in male and female patients with SPMS (3.9- and 3.1-fold, respectively). Considering the studied cytokines, the increase in expression ratio of IL-6 in SPMS patients and the decrease in transcript abundance of INF-α, and INF-β cytokines are consistent with the progression of the disease. CONCLUSIONS Our findings showed that the high and low transcriptional levels of the considered genes seem to be effective in the pathogenesis and progression of MS.
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Affiliation(s)
- Fatemeh Khakdan
- Department of Biology, Farzanegan Campus, Semnan University, Semnan, Iran
| | | | - Parisa Shahmoradipour
- Department of Biotechnology, Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
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6
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da Silva EV, Fontes-Dantas FL, Dantas TV, Dutra A, Nascimento OJM, Alves-Leon SV. Shared Molecular Signatures Across Zika Virus Infection and Multiple Sclerosis Highlight AP-1 Transcription Factor as a Potential Player in Post-ZIKV MS-Like Phenotypes. Mol Neurobiol 2023:10.1007/s12035-023-03305-y. [PMID: 37046138 DOI: 10.1007/s12035-023-03305-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 03/08/2023] [Indexed: 04/14/2023]
Abstract
Zika virus (ZIKV) is an arbovirus of the Flaviviridae genus that has rapidly disseminated from across the Pacific to the Americas. Robust evidence has indicated a crucial role of ZIKV in congenital virus syndrome, including neonatal microcephaly. Moreover, emerging evidence suggests an association between ZIKV infection and the development of an extensive spectrum of central nervous system inflammatory demyelinating diseases (CNS IDD), such as multiple sclerosis-like clinical phenotypes. However, the underlying mechanisms of host-pathogen neuro-immune interactions remain to be elucidated. This study aimed to identify common transcriptional signatures between multiple sclerosis (MS) and ZIKV infection to generate molecular interaction networks, thereby leading to the identification of deregulated processes and pathways, which could give an insight of these underlying molecular mechanisms. Our investigation included publicly available transcriptomic data from MS patients in either relapse or remission (RR-MS) and datasets of subjects acutely infected by ZIKV for both immune peripheral cells and central nervous system cells. The protein-protein interaction (PPI) analysis showed upregulated AP-1 transcription factors (JUN and FOS) among the top hub and bottleneck genes in RR-MS and ZIKV data. Gene enrichment analysis retrieved a remarkable presence of ontologies and pathways linked to oxidative stress responses, immune cell function, inflammation, interleukin signaling, cell division, and transcriptional regulation commonly enriched in both scenarios. Considering the recent findings concerning AP-1 function in immunological tolerance breakdown, regulation of inflammation, and its function as an oxidative stress sensor, we postulate that the ZIKV trigger may contribute as a boost for the activation of such AP-1-regulated mechanisms that could favor the development of MS-like phenotypes following ZIKV infection in a genetically susceptible individual.
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Affiliation(s)
- Elielson Veloso da Silva
- Laboratório de Neurociências Translacional, Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de pós-graduação em Medicina (Neurologia/Neurociências), Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Fabrícia Lima Fontes-Dantas
- Laboratório de Neurociências Translacional, Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Farmacologia e Psicobiologia, Instituto de Biologia Roberto Alcântara Gomes, Universidade Estadual do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thiago Viana Dantas
- Programa de Engenharia de Sistemas e Computação-COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amanda Dutra
- Laboratório de Neurociências Translacional, Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Osvaldo J M Nascimento
- Programa de pós-graduação em Medicina (Neurologia/Neurociências), Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Soniza Vieira Alves-Leon
- Laboratório de Neurociências Translacional, Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.
- Hospital Universitário Clementino Fraga Filho, Centro de Referência em Doenças Inflamatórias Desmielinizantes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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7
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Karimi N, Motovali-Bashi M, Ghaderi-Zefrehei M. Gene network reveals LASP1, TUBA1C, and S100A6 are likely playing regulatory roles in multiple sclerosis. Front Neurol 2023; 14:1090631. [PMID: 36970516 PMCID: PMC10035600 DOI: 10.3389/fneur.2023.1090631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/10/2023] [Indexed: 03/11/2023] Open
Abstract
IntroductionMultiple sclerosis (MS), a non-contagious and chronic disease of the central nervous system, is an unpredictable and indirectly inherited disease affecting different people in different ways. Using Omics platforms genomics, transcriptomics, proteomics, epigenomics, interactomics, and metabolomics database, it is now possible to construct sound systems biology models to extract full knowledge of the MS and recognize the pathway to uncover the personalized therapeutic tools.MethodsIn this study, we used several Bayesian Networks in order to find the transcriptional gene regulation networks that drive MS disease. We used a set of BN algorithms using the R add-on package bnlearn. The BN results underwent further downstream analysis and were validated using a wide range of Cytoscape algorithms, web based computational tools and qPCR amplification of blood samples from 56 MS patients and 44 healthy controls. The results were semantically integrated to improve understanding of the complex molecular architecture underlying MS, distinguishing distinct metabolic pathways and providing a valuable foundation for the discovery of involved genes and possibly new treatments.ResultsResults show that the LASP1, TUBA1C, and S100A6 genes were most likely playing a biological role in MS development. Results from qPCR showed a significant increase (P < 0.05) in LASP1 and S100A6 gene expression levels in MS patients compared to that in controls. However, a significant down regulation of TUBA1C gene was observed in the same comparison.ConclusionThis study provides potential diagnostic and therapeutic biomarkers for enhanced understanding of gene regulation underlying MS.
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Affiliation(s)
- Nafiseh Karimi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Majid Motovali-Bashi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
- *Correspondence: Majid Motovali-Bashi
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Paldor I, Madrer N, Vaknine Treidel S, Shulman D, Greenberg DS, Soreq H. Cerebrospinal fluid and blood profiles of transfer RNA fragments show age, sex, and Parkinson's disease-related changes. J Neurochem 2023; 164:671-683. [PMID: 36354307 DOI: 10.1111/jnc.15723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/25/2022] [Indexed: 11/12/2022]
Abstract
Transfer RNA fragments (tRFs) have recently been shown to be an important family of small regulatory RNAs with diverse functions. Recent reports have revealed modified tRF blood levels in a number of nervous system conditions including epilepsy, ischemic stroke, and neurodegenerative diseases, but little is known about tRF levels in the cerebrospinal fluid (CSF). To address this issue, we studied age, sex, and Parkinson's disease (PD) effects on the distributions of tRFs in the CSF and blood data of healthy controls and PD patients from the NIH and the Parkinson's Progression Markers Initiative (PPMI) small RNA-seq datasets. We discovered that long tRFs are expressed in higher levels in the CSF than in the blood. Furthermore, the CSF showed a pronounced age-associated decline in the level of tRFs cleaved from the 3'-end and anti-codon loop of the parental tRNA (3'-tRFs, i-tRFs), and more pronounced profile differences than the blood profiles between the sexes. In comparison, we observed moderate age-related elevation of blood 3'-tRF levels. In addition, distinct sets of tRFs in the CSF and in the blood segregated PD patients from controls. Finally, we found enrichment of tRFs predicted to target cholinergic mRNAs (Cholino-tRFs) among mitochondrial-originated tRFs, raising the possibility that the neurodegeneration-related mitochondrial impairment in PD patients may lead to deregulation of their cholinergic tone. Our findings demonstrate that the CSF and blood tRF profiles are distinct and that the CSF tRF profiles are modified in a sex-, age-, and disease-related manner, suggesting that they reflect the inter-individual cerebral differences and calling for incorporating this important subset of small RNA regulators into future studies.
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Affiliation(s)
- Iddo Paldor
- The Neurosurgery Department, Rambam Health Care Campus, Haifa, Israel
| | - Nimrod Madrer
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shani Vaknine Treidel
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dana Shulman
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David S Greenberg
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hermona Soreq
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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Exosome-Derived microRNAs from Mouthrinse Have the Potential to Be Novel Biomarkers for Sjögren Syndrome. J Pers Med 2022; 12:jpm12091483. [PMID: 36143269 PMCID: PMC9505666 DOI: 10.3390/jpm12091483] [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: 08/10/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Sjögren syndrome (SS) is diagnosed based on invasive tissue biopsies and blood sampling. Therefore, a novel non-invasive and simple inspection diagnostic marker of SS is required. Here, we identified exosome-derived microRNAs (miRNAs) as biomarkers for SS using non-invasive mouthrinse samples collected from patients with SS and healthy volunteers. We compared miRNAs derived from exosomes in mouthrinse samples from the two groups using microarrays and real-time polymerase chain reaction (PCR) and identified 12 miRNAs as biomarker candidates. The expression ratios of four miRNAs were significantly increased in the SS group compared to the control group. Logistic regression analysis revealed a more significant influence of miR-1290 and let-7b-5p in the SS group than that in the control group. We combined these miRNAs to create a diagnostic prediction formula using logistic regression analysis. The combination of miR-1290 and let-7b-5p distinguished SS from the control samples with an AUC, sensitivity, specificity, positive predictive value, and negative predictive value of 0.856, 91.7%, 83.3%, 84.6%, and 90.9%, respectively. These results indicated that an increased ratio of these miRNAs could serve as a novel and non-invasive diagnostic marker for SS. This is the first report of diagnosis and screening of SS by adopting a non-invasive method using mouthrinse.
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10
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Yalman N. LMCD1 antisense RNA 1 is a newly identified long noncoding RNA. Anticancer Drugs 2022; 33:1-5. [PMID: 34232945 DOI: 10.1097/cad.0000000000001124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Long noncoding RNAs (lncRNAs) are one of the interesting fields in cancer researches. LncRNAs are generally dysregulated in many diseases. LMCD1 antisense RNA 1 (LMCD1-AS1) is a newly identified lncRNA with protumorigenic functions on tumor cells. LMCD1-AS1 expression is increased in hepatocellular carcinoma (HCC). LMCD1-AS1 is a sponge of miR-106b-5p activity. LMCD1-AS1 modulates the survival of osteosarcoma via targeting miR-106b-5p. LMCD1-AS1 and Sp1 are highly expressed in osteosarcoma. SP1 can bind to the promoter region of LMCD1-AS1, resulting in its overexpression in osteosarcoma. GLI2 is shown to bind to the LMCD1-AS1 promoter and is transcriptionally activated by LMCD1-AS1. LMCD1 acts as a miR-1287-5p sponge to increase GLI2 expression. LMCD1 is abundantly expressed in kidney tissue. Moreover, it is functionally involved in protein-protein interactions with transcriptional co-repressor activity, including regulation of the calcineurin-NFAT signaling cascade known to play a critical role in recovery from acute kidney injury (AKI). The E2F1/LMCD1-AS1/miR-345-5p/COL6A3 axis is a newly identified regulatory mechanism, which has a function in cholangiocarcinoma (CCA) tumorigenesis and progression and provides potential therapeutic targets for CCA. Also, LMCD1-AS1 functions in thyroid cancer (THCA) development. LMCD1-AS1 is overexpressed in THCA cells, and LMCD1-AS1 knockdown suppresses the malignant phenotypes of THCA cells. In THCA development, LMCD1-AS1 exerts protumorigenic function through sponging miR-1287-5p to increase GLI2 expression, constituting a feedback loop of LMCD1-AS1/miR-1287-5p/GLI2. In this review, the author focuses on the molecular mechanisms of newly identified long noncoding RNA LMCD1 antisense RNA 1 (LMCD1-AS1).
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Affiliation(s)
- Nesil Yalman
- Department of Medical Biology and Genetics, Institute of Health Sciences, Gaziantep University, Gaziantep, Turkey
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11
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Wallach T, Mossmann ZJ, Szczepek M, Wetzel M, Machado R, Raden M, Miladi M, Kleinau G, Krüger C, Dembny P, Adler D, Zhai Y, Kumbol V, Dzaye O, Schüler J, Futschik M, Backofen R, Scheerer P, Lehnardt S. MicroRNA-100-5p and microRNA-298-5p released from apoptotic cortical neurons are endogenous Toll-like receptor 7/8 ligands that contribute to neurodegeneration. Mol Neurodegener 2021; 16:80. [PMID: 34838071 PMCID: PMC8626928 DOI: 10.1186/s13024-021-00498-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/03/2021] [Indexed: 12/30/2022] Open
Abstract
Background MicroRNA (miRNA) expression in the brain is altered in neurodegenerative diseases. Recent studies demonstrated that selected miRNAs conventionally regulating gene expression at the post-transcriptional level can act extracellularly as signaling molecules. The identity of miRNA species serving as membrane receptor ligands involved in neuronal apoptosis in the central nervous system (CNS), as well as the miRNAs’ sequence and structure required for this mode of action remained largely unresolved. Methods Using a microarray-based screening approach we analyzed apoptotic cortical neurons of C56BL/6 mice and their supernatant with respect to alterations in miRNA expression/presence. HEK-Blue Toll-like receptor (TLR) 7/8 reporter cells, primary microglia and macrophages derived from human and mouse were employed to test the potential of the identified miRNAs released from apoptotic neurons to serve as signaling molecules for the RNA-sensing receptors. Biophysical and bioinformatical approaches, as well as immunoassays and sequential microscopy were used to analyze the interaction between candidate miRNA and TLR. Immunocytochemical and -histochemical analyses of murine CNS cultures and adult mice intrathecally injected with miRNAs, respectively, were performed to evaluate the impact of miRNA-induced TLR activation on neuronal survival and microglial activation. Results We identified a specific pattern of miRNAs released from apoptotic cortical neurons that activate TLR7 and/or TLR8, depending on sequence and species. Exposure of microglia and macrophages to certain miRNA classes released from apoptotic neurons resulted in the sequence-specific production of distinct cytokines/chemokines and increased phagocytic activity. Out of those miRNAs miR-100-5p and miR-298-5p, which have consistently been linked to neurodegenerative diseases, entered microglia, located to their endosomes, and directly bound to human TLR8. The miRNA-TLR interaction required novel sequence features, but no specific structure formation of mature miRNA. As a consequence of miR-100-5p- and miR-298-5p-induced TLR activation, cortical neurons underwent cell-autonomous apoptosis. Presence of miR-100-5p and miR-298-5p in cerebrospinal fluid led to neurodegeneration and microglial accumulation in the murine cerebral cortex through TLR7 signaling. Conclusion Our data demonstrate that specific miRNAs are released from apoptotic cortical neurons, serve as endogenous TLR7/8 ligands, and thereby trigger further neuronal apoptosis in the CNS. Our findings underline the recently discovered role of miRNAs as extracellular signaling molecules, particularly in the context of neurodegeneration. Supplementary Information The online version contains supplementary material available at 10.1186/s13024-021-00498-5.
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Affiliation(s)
- Thomas Wallach
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany.
| | - Zoé J Mossmann
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Michal Szczepek
- Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography & Signal Transduction, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Max Wetzel
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Rui Machado
- Department of Biomedical Sciences and Medicine, University of Algarve, 8005-139, Faro, Portugal
| | - Martin Raden
- Bioinformatics, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Milad Miladi
- Bioinformatics, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Gunnar Kleinau
- Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography & Signal Transduction, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Christina Krüger
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Paul Dembny
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Drew Adler
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Yuanyuan Zhai
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Victor Kumbol
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Omar Dzaye
- Department of Radiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Jutta Schüler
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Matthias Futschik
- Department of Biomedical Sciences and Medicine, University of Algarve, 8005-139, Faro, Portugal.,School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, PL6 8BU, UK.,MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Rolf Backofen
- Bioinformatics, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Patrick Scheerer
- Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography & Signal Transduction, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany.,German Centre for Cardiovascular Research, partner site Berlin, Berlin, Germany
| | - Seija Lehnardt
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany. .,Department of Neurology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany.
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12
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Hin N, Newman M, Pederson S, Lardelli M. Iron Responsive Element-Mediated Responses to Iron Dyshomeostasis in Alzheimer's Disease. J Alzheimers Dis 2021; 84:1597-1630. [PMID: 34719489 DOI: 10.3233/jad-210200] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Iron trafficking and accumulation is associated with Alzheimer's disease (AD) pathogenesis. However, the role of iron dyshomeostasis in early disease stages is uncertain. Currently, gene expression changes indicative of iron dyshomeostasis are not well characterized, making it difficult to explore these in existing datasets. OBJECTIVE To identify sets of genes predicted to contain iron responsive elements (IREs) and use these to explore possible iron dyshomeostasis-associated gene expression responses in AD. METHODS Comprehensive sets of genes containing predicted IRE or IRE-like motifs in their 3' or 5' untranslated regions (UTRs) were identified in human, mouse, and zebrafish reference transcriptomes. Further analyses focusing on these genes were applied to a range of cultured cell, human, mouse, and zebrafish gene expression datasets. RESULTS IRE gene sets are sufficiently sensitive to distinguish not only between iron overload and deficiency in cultured cells, but also between AD and other pathological brain conditions. Notably, changes in IRE transcript abundance are among the earliest observable changes in zebrafish familial AD (fAD)-like brains, preceding other AD-typical pathologies such as inflammatory changes. Unexpectedly, while some IREs in the 3' untranslated regions of transcripts show significantly increased stability under iron deficiency in line with current assumptions, many such transcripts instead display decreased stability, indicating that this is not a generalizable paradigm. CONCLUSION Our results reveal IRE gene expression changes as early markers of the pathogenic process in fAD and are consistent with iron dyshomeostasis as an important driver of this disease. Our work demonstrates how differences in the stability of IRE-containing transcripts can be used to explore and compare iron dyshomeostasis-associated gene expression responses across different species, tissues, and conditions.
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Affiliation(s)
- Nhi Hin
- South Australian Genomics Centre, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia.,Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Morgan Newman
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Stephen Pederson
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health & Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Michael Lardelli
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA, Australia
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13
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Manian M, Sohrabi E, Eskandari N, Assarehzadegan MA, Ferns GA, Nourbakhsh M, Jazayeri MH, Nedaeinia R. An Integrated Bioinformatics Analysis of the Potential Regulatory Effects of miR-21 on T-cell Related Target Genes in Multiple Sclerosis. Avicenna J Med Biotechnol 2021; 13:149-165. [PMID: 34484645 PMCID: PMC8377402 DOI: 10.18502/ajmb.v13i3.6364] [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: 10/03/2020] [Accepted: 01/16/2021] [Indexed: 11/24/2022] Open
Abstract
Background: Overexpression of miR-21 is a characteristic feature of patients with Multiple Sclerosis (MS) and is involved in gene regulation and the expression enhancement of pro-inflammatory factors including IFNγ and TNF-α following stimulation of T-cells via the T Cell Receptor (TCR). In this study, a novel integrated bioinformatics analysis was used to obtain a better understanding of the involvement of miR-21 in the development of MS, its protein biomarker signatures, RNA levels, and drug interactions through existing microarray and RNA-seq datasets of MS. Methods: In order to obtain data on the Differentially Expressed Genes (DEGs) in patients with MS and normal controls, the GEO2R web tool was used to analyze the Gene Expression Omnibus (GEO) datasets, and then Protein-Protein Interaction (PPI) networks of co-expressed DEGs were designed using STRING. A molecular network of miRNA-genes and drugs based on differentially expressed genes was created for T-cells of MS patients to identify the targets of miR-21, that may act as important regulators and potential biomarkers for early diagnosis, prognosis and, potential therapeutic targets for MS. Results: It found that seven genes (NRIP1, ARNT, KDM7A, S100A10, AK2, TGFβR2, and IL-6R) are regulated by drugs used in MS and miR-21. Finally, three overlapping genes (S100A10, NRIP1, KDM7A) were identified between miRNA-gene-drug network and nineteen genes as hub genes which can reflect the pathophysiology of MS. Conclusion: Our findings suggest that miR-21 and MS-related drugs can act synergistically to regulate several genes in the existing datasets, and miR-21 inhibitors have the potential to be used in MS treatment.
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Affiliation(s)
- Mostafa Manian
- Department of Immunology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ehsan Sohrabi
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Nahid Eskandari
- Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad-Ali Assarehzadegan
- Department of Immunology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Gordon A Ferns
- Brighton and Sussex Medical School, Division of Medical Education, Falmer, Brighton BN1 9PH, Sussex, UK
| | - Mitra Nourbakhsh
- Department of Biochemistry and Nutrition, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mir Hadi Jazayeri
- Department of Immunology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Reza Nedaeinia
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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14
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Wang H. MicroRNAs, Multiple Sclerosis, and Depression. Int J Mol Sci 2021; 22:ijms22157802. [PMID: 34360568 PMCID: PMC8346048 DOI: 10.3390/ijms22157802] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/12/2021] [Accepted: 07/16/2021] [Indexed: 12/16/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic disease of the central nervous system that affects the brain and spinal cord. There are several disease courses in MS including relapsing–remitting MS (RRMS), primary progressive MS (PPMS), and secondary progressive MS (SPMS). Up to 50% of MS patients experience depressive disorders. Major depression (MD) is a serious comorbidity of MS. Many dysfunctions including neuroinflammation, peripheral inflammation, gut dysbiosis, chronic oxidative and nitrosative stress, and neuroendocrine and mitochondrial abnormalities may contribute to the comorbidity between MS and MD. In addition to these actions, medical treatment and microRNA (miRNA) regulation may also be involved in the mechanisms of the comorbidity between MS and MD. In the study, I review many common miRNA biomarkers for both diseases. These common miRNA biomarkers may help further explore the association between MS and MD.
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Affiliation(s)
- Hsiuying Wang
- Institute of Statistics, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
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15
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Ten Bosch GJA, Bolk J, 't Hart BA, Laman JD. Multiple sclerosis is linked to MAPK ERK overactivity in microglia. J Mol Med (Berl) 2021; 99:1033-1042. [PMID: 33948692 PMCID: PMC8313465 DOI: 10.1007/s00109-021-02080-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/31/2021] [Accepted: 04/19/2021] [Indexed: 12/18/2022]
Abstract
Reassessment of published observations in patients with multiple sclerosis (MS) suggests a microglial malfunction due to inappropriate (over)activity of the mitogen-activated protein kinase pathway ERK (MAPKERK). These observations regard biochemistry as well as epigenetics, and all indicate involvement of this pathway. Recent preclinical research on neurodegeneration already pointed towards a role of MAPK pathways, in particular MAPKERK. This is important as microglia with overactive MAPK have been identified to disturb local oligodendrocytes which can lead to locoregional demyelination, hallmark of MS. This constitutes a new concept on pathophysiology of MS, besides the prevailing view, i.e., autoimmunity. Acknowledged risk factors for MS, such as EBV infection, hypovitaminosis D, and smoking, all downregulate MAPKERK negative feedback phosphatases that normally regulate MAPKERK activity. Consequently, these factors may contribute to inappropriate MAPKERK overactivity, and thereby to neurodegeneration. Also, MAPKERK overactivity in microglia, as a factor in the pathophysiology of MS, could explain ongoing neurodegeneration in MS patients despite optimized immunosuppressive or immunomodulatory treatment. Currently, for these patients with progressive disease, no effective treatment exists. In such refractory MS, targeting the cause of overactive MAPKERK in microglia merits further investigation as this phenomenon may imply a novel treatment approach.
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Affiliation(s)
- George J A Ten Bosch
- Department of Medical Oncology, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.
| | - Jolande Bolk
- Department of Anesthesiology, Medisch Spectrum Twente, Enschede, The Netherlands
| | - Bert A 't Hart
- Department Anatomy and Neuroscience, Amsterdam University Medical Center (VUmc), Amsterdam, The Netherlands.,Department Biomedical Sciences of Cells & Systems, University Medical Center Groningen, Groningen, The Netherlands
| | - Jon D Laman
- Department Biomedical Sciences of Cells & Systems, University Medical Center Groningen, Groningen, The Netherlands
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16
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The microRNA let-7b-5p Is Negatively Associated with Inflammation and Disease Severity in Multiple Sclerosis. Cells 2021; 10:cells10020330. [PMID: 33562569 PMCID: PMC7915741 DOI: 10.3390/cells10020330] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022] Open
Abstract
The identification of microRNAs in biological fluids for diagnosis and prognosis is receiving great attention in the field of multiple sclerosis (MS) research but it is still in its infancy. In the present study, we observed in a large sample of MS patients that let-7b-5p levels in the cerebrospinal fluid (CSF) were highly correlated with a number of microRNAs implicated in MS, as well as with a variety of inflammation-related protein factors, showing specific expression patterns coherent with let-7b-5p-mediated regulation. Additionally, we found that the CSF let-7b-5p levels were significantly reduced in patients with the progressive MS compared to patients with relapsing-remitting MS and were negatively correlated with characteristic hallmark processes of the two phases of the disease. Indeed, in the non-progressive phase, let-7b-5p inversely associated with both central and peripheral inflammation; whereas, in progressive MS, the CSF levels of let-7b-5p negatively correlated with clinical disability at disease onset and after a follow-up period. Overall, our results uncovered, by the means of a multidisciplinary approach and multiple statistical analyses, a new possible pleiotropic action of let-7b-5p in MS, with potential utility as a biomarker of MS course.
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17
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Hu R, Lv W, Zhang S, Liu Y, Sun B, Meng Y, Kong Q, Mu L, Wang G, Zhang Y, Li H, Liu X. Combining miR-23b exposure with mesenchymal stem cell transplantation enhances therapeutic effects on EAE. Immunol Lett 2020; 229:18-26. [PMID: 33238163 DOI: 10.1016/j.imlet.2020.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/01/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023]
Abstract
Bone marrow mesenchymal stem cells (BMSCs) have the immuno-modulatory capacity to ameliorate autoimmune diseases, such as multiple schlerosis (MS), systemic lupus erythematosus and rheumatoid arthritis. However, BMSC-mediated immunosuppression can be challenging to achieve. The efficacy of BMSC transplantation may be augmented by an adjuvant therapy. Here, we demonstrated that treatment of mice with experimental autoimmune encephalomyelitis (EAE), a model of MS, with BMSCs over-expressing microRNA (miR)-23b provided better synergistic and longer-term therapeutic effects than treatment with traditional BMSCs. Over-expression of miR-23b enhanced the ability of BMSCs to inhibit differentiation of Th17 cells and reduced IL-17 secretion. Compared to traditional BMSCs, the miR-23b over-expressing BMSCs (miR23b-BMSCs) exhibited enhanced secretion of tumor growth factor beta 1 (TGF-β1), a cytokine that promotes the differentiation of regulatory T (Treg) cells. Pathologically, miR23b-BMSC transplantation delayed EAE progression, apparently by reducing the Th17/Treg cell ratio and inhibiting inflammatory cell infiltration across the blood-brain barrier, and thus slowing spinal cord demyelination. These results may lead to better utility of BMSCs as a treatment for autoimmune diseases.
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Affiliation(s)
- Ruixue Hu
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Weiqi Lv
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Sifan Zhang
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Yumei Liu
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Bo Sun
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Yanting Meng
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Qingfei Kong
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Lili Mu
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Guangyou Wang
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Yao Zhang
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Hulun Li
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Xijun Liu
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang, 150081, China.
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18
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Bouter Y, Kacprowski T, Rößler F, Jensen LR, Kuss AW, Bayer TA. miRNA Alterations Elicit Pathways Involved in Memory Decline and Synaptic Function in the Hippocampus of Aged Tg4-42 Mice. Front Neurosci 2020; 14:580524. [PMID: 33013313 PMCID: PMC7511553 DOI: 10.3389/fnins.2020.580524] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/18/2020] [Indexed: 12/30/2022] Open
Abstract
The transcriptome of non-coding RNA (ncRNA) species is increasingly focused in Alzheimer’s disease (AD) research. NcRNAs comprise, among others, transfer RNAs, long non-coding RNAs and microRNAs (miRs), each with their own specific biological function. We used smallRNASeq to assess miR expression in the hippocampus of young (3 month old) and aged (8 month old) Tg4-42 mice, a model system for sporadic AD, as well as age-matched wildtype controls. Tg4-42 mice express N-truncated Aβ4–42, develop age-related neuron loss, reduced neurogenesis and behavioral deficits. Our results do not only confirm known miR-AD associations in Tg4-42 mice, but more importantly pinpoint 22 additional miRs associated to the disease. Twenty-five miRs were differentially expressed in both aged Tg4-42 and aged wildtype mice while eight miRs were differentially expressed only in aged wildtype mice, and 33 only in aged Tg4-42 mice. No significant alteration in the miRNome was detected in young mice, which indicates that the changes observed in aged mice are down-stream effects of Aβ-induced pathology in the Tg4-42 mouse model for AD. Targets of those miRs were predicted using miRWalk. For miRs that were differentially expressed only in the Tg4-42 model, 128 targets could be identified, whereas 18 genes were targeted by miRs only differentially expressed in wildtype mice and 85 genes were targeted by miRs differentially expressed in both mouse models. Genes targeted by differentially expressed miRs in the Tg4-42 model were enriched for negative regulation of long-term synaptic potentiation, learning or memory, regulation of trans-synaptic signaling and modulation of chemical synaptic transmission obtained. This untargeted miR sequencing approach supports previous reports on the Tg4-42 mice as a valuable model for AD. Furthermore, it revealed miRs involved in AD, which can serve as biomarkers or therapeutic targets.
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Affiliation(s)
- Yvonne Bouter
- Division of Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University Medical Center Göttingen (UMG), Georg-August-University, Göttingen, Germany
| | - Tim Kacprowski
- Research Group Computational Systems Medicine, Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan (WZW), Technical University of Munich (TUM), Weihenstephan, Germany
| | - Fanny Rößler
- Research Group Computational Systems Medicine, Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan (WZW), Technical University of Munich (TUM), Weihenstephan, Germany
| | - Lars R Jensen
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Andreas W Kuss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Thomas A Bayer
- Division of Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University Medical Center Göttingen (UMG), Georg-August-University, Göttingen, Germany
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19
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Chen N, Xiao B, Wang S, Wei B. Bioinformatics analysis of microRNA linked to ubiquitin proteasome system in traumatic osteonecrosis of the femoral head. Medicine (Baltimore) 2020; 99:e21706. [PMID: 32872046 PMCID: PMC7437855 DOI: 10.1097/md.0000000000021706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) have been suggested to act critical roles in the pathophysiology of traumatic osteonecrosis of the femoral head (TONFH). Unfortunately, their roles in the development of TONFH are still ambiguous. The purpose of this study is to identify promising miRNA biomarkers in traumatic osteonecrosis development.We conducted a comprehensive bioinformatics analysis using microarray datasets downloaded from the Gene Expression Omnibus database, and compared the expression of miRNAs in the serum of TONFH patients with controls. Next, we performed target prediction, function enrichment analysis, and protein-protein interaction network analysis based on differentially expressed (DE) miRNAs.We identified 26 DE miRNAs that may contribute to the pathophysiology of TONFH. The miRNAs were linked to ubiquitin proteasome system including conjugating protein ligase activity, ubiquitin-protein ligase activity and ubiquitin mediated proteolysis 5 pathway, and we exposed miR-181a-5p and miR-140-5p as promising biomarkers in TONFH.A predicting model consisting of 5 miRNAs may help discriminating high-risk patients who might develop TONFH after femur neck fracture. Among DE miRNAs, MiR-181a-5p and miR-140-5p may contribute to the development femoral head osteonecrosis after femur neck fracture via ubiquitin proteasome system.
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Affiliation(s)
- Ning Chen
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong
- Department of Femoral Head, Linyi People's Hospital, Linyi, Shandong, China
| | - Bolian Xiao
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong
- Department of Femoral Head, Linyi People's Hospital, Linyi, Shandong, China
| | - Shiying Wang
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong
- Department of Femoral Head, Linyi People's Hospital, Linyi, Shandong, China
| | - Biaofang Wei
- Department of Femoral Head, Linyi People's Hospital, Linyi, Shandong, China
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20
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Serum ROCK2, miR-300 and miR-450b-5p levels in two different clinical phenotypes of multiple sclerosis: Relation to patient disability and disease progression. J Neuroimmunol 2020; 347:577356. [PMID: 32781341 DOI: 10.1016/j.jneuroim.2020.577356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/24/2020] [Accepted: 07/31/2020] [Indexed: 01/03/2023]
Abstract
Relapsing remitting multiple sclerosis (RRMS) is the most prevalent MS subtype. Years after disease onset, most of RRMS patients show transition into secondary progressive form (SPMS). Currently, no biomarkers are available for tracking disease progression. Here, we observed marked elevation of Rho-associated protein kinase 2 (ROCK2) along with significant downregulation of miRNAs 300 and 450b-5p expressions in the serum of 39 RRMS and 35 SPMS Egyptian patients compared to healthy controls. More pronounced alterations were found in SPMS versus RRMS patients. Our findings also suggest relations between elevated ROCK2 and reduced expression of both miRNAs with the degree of disability and disease progression. Notably, these biomarkers effectively discriminated RRMS from SPMS patients with miR-450b-5p showing the highest prognostic power.
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21
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Macchia E, Manoli K, Di Franco C, Picca RA, Österbacka R, Palazzo G, Torricelli F, Scamarcio G, Torsi L. Organic Field-Effect Transistor Platform for Label-Free, Single-Molecule Detection of Genomic Biomarkers. ACS Sens 2020; 5:1822-1830. [PMID: 32495625 DOI: 10.1021/acssensors.0c00694] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The increasing interest in technologies capable of tracking a biomarker down to the physical limit points toward new opportunities in early diagnostics of progressive diseases. Indeed, single-molecule detection technologies are foreseen to enable clinicians to associate the tiniest increase in a biomarker with the progression of a disease, particularly at its early stage. Bioelectronic organic transistors represent an extremely powerful tool to achieve label-free and single-molecule detection of clinically relevant biomarkers. These electronic devices are millimetric in size and in the future could be mass-produced at low cost. The core of the single molecule with a large transistor (SiMoT) platform, based on an electrolyte-gated field-effect transistor, is a gold gate electrode biofunctionalized with a self-assembled monolayer, a densely packed layer of recognition elements. So far, only the SiMoT detection of proteins, using the corresponding antibodies as recognition elements, has been reported. In this study, the SiMoT sensing response toward genomic biomarkers is proposed. Herein, the gate is functionalized with a genomic biomarker for multiple sclerosis (miR-182). This is relevant, not only because a limit of detection of a single molecule is achieved but also because it proves that the SiMoT label-free, single-molecule detection principle is the only one of its kind that can detect, by means of the same platform, both protein and genomic markers.
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Affiliation(s)
- Eleonora Macchia
- The Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland
| | - Kyriaki Manoli
- Dipartimento di Chimica, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy
| | - Cinzia Di Franco
- Dipartimento di Chimica, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy
- CNR, Istituto di Fotonica e Nanotecnologie, Sede di Bari, 70125 Bari, Italy
| | - Rosaria Anna Picca
- Dipartimento di Chimica, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy
| | - Ronald Österbacka
- The Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland
| | - Gerardo Palazzo
- Dipartimento di Chimica, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy
- CSGI (Centre for Colloid and Surface Science), 70125 Bari, Italy
| | - Fabrizio Torricelli
- Dipartimento Ingegneria dell’Informazione, Università degli Studi di Brescia, 25121 Brescia, Italy
| | - Gaetano Scamarcio
- Dipartimento Interateneo di Fisica “M. Merlin”, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy
- CNR, Istituto di Fotonica e Nanotecnologie, Sede di Bari, 70125 Bari, Italy
| | - Luisa Torsi
- The Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland
- Dipartimento di Chimica, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy
- CSGI (Centre for Colloid and Surface Science), 70125 Bari, Italy
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22
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Early microRNA indicators of PPARα pathway activation in the liver. Toxicol Rep 2020; 7:805-815. [PMID: 32642447 PMCID: PMC7334544 DOI: 10.1016/j.toxrep.2020.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/01/2020] [Accepted: 06/19/2020] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNA species that play key roles in post-transcriptional regulation of gene expression. MiRNAs also serve as a promising source of early biomarkers for different environmental exposures and health effects, although there is limited information linking miRNA changes to specific target pathways. In this study, we measured liver miRNAs in male B6C3F1 mice exposed to a known chemical activator of the peroxisome proliferator-activated receptor alpha (PPARα) pathway, di(2-ethylhexyl) phthalate (DEHP), for 7 and 28 days at concentrations of 0, 750, 1500, 3000, or 6000 ppm in feed. At the highest dose tested, DEHP altered 61 miRNAs after 7 days and 171 miRNAs after 28 days of exposure, with 48 overlapping miRNAs between timepoints. Analysis of these 48 common miRNAs indicated enrichment in PPARα–related targets and other pathways related to liver injury and cancer. Four of the 10 miRNAs exhibiting a clear dose trend were linked to the PPARα pathway: mmu-miRs-125a-5p, -182−5p, -20a−5p, and -378a−3p. mmu-miRs-182−5p and -378a−3p were subsequently measured using digital drop PCR across a dose range for DEHP and two related phthalates with weaker PPARα activity, di-n-octyl phthalate and n-butyl benzyl phthalate, following 7-day exposures. Analysis of mmu-miRs-182−5p and -378a−3p by transcriptional benchmark dose analysis correctly identified DEHP as having the greatest potency. However, benchmark dose estimates for DEHP based on these miRNAs (average 163; range 126−202 mg/kg-day) were higher on average than values for PPARα target genes (average 74; range 29−183 mg/kg-day). These findings identify putative miRNA biomarkers of PPARα pathway activity and suggest that early miRNA changes may be used to stratify chemical potency.
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Key Words
- AIC, Akaike Information Criterion
- ALT, alanine aminotransferase
- AOP, adverse outcome pathway
- AST, aspartate aminotransferase
- Acox1, acyl-Coenzyme A oxidase 1
- Adverse outcome pathway (AOP)
- AhR, aryl hydrocarbon receptor
- BBP, n-butyl benzyl phthalate
- BMD, benchmark dose
- BMDA, apical-based benchmark dose
- BMDL, BMD lower confidence interval
- BMDT, transcriptional-based benchmark dose
- BMR, benchmark response
- BROD, benzyloxyresorufin O-debenzylation
- Benchmark dose (BMD)
- Biomarkers
- CAR, constitutive androstane receptor
- DEGs, differentially expressed genes
- DEHP, di (2-thylhexyl) phthalate
- DEmiRs, differentially expressed miRNAs
- DNOP, di-n-octyl phthalate
- EPA, U.S. Environmental Protection Agency
- EROD, ethoxyresorufin O-dealkylation
- GEO, Gene Expression Omnibus
- HCA, hepatocellular adenoma
- HCC, hepatocellular carcinoma
- Hepatocellular carcinoma
- IPA, Ingenuity Pathway Analysis
- Liver toxicity
- MOA, mode of action
- MicroRNAs
- Mode of action (MOA)
- Nrf2, nuclear receptor erythroid 2-like 2
- POD, point-of-departure
- PPARα, peroxisome proliferator-activated receptor alpha
- PROD, pentoxyresorufin O-depentylation
- PXR, pregnane X receptor
- Peroxisome proliferator-activated receptor alpha (PPARα)
- Phthalate
- SDH, sorbitol dehydrogenase
- TMM, trimmed mean of M-values
- ddPCR, droplet digital polymerase chain reaction
- mRNA, messenger RNA
- miRNAs, microRNAs
- mtDNA, mitochondrial
- rRNA, ribosomal RNA
- smallRNA-seq, small RNA sequencing
- tRNA, transfer RNA
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Nali LH, Olival GS, Sousa FTG, de Oliveira ACS, Montenegro H, da Silva IT, Dias-Neto E, Naya H, Spangenberg L, Penalva-de-Oliveira AC, Romano CM. Whole transcriptome analysis of multiple Sclerosis patients reveals active inflammatory profile in relapsing patients and downregulation of neurological repair pathways in secondary progressive cases. Mult Scler Relat Disord 2020; 44:102243. [PMID: 32559700 DOI: 10.1016/j.msard.2020.102243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/21/2020] [Accepted: 05/25/2020] [Indexed: 01/03/2023]
Abstract
BACKGROUND Multiple sclerosis (MS) is an inflammatory autoimmune neurologic disease that causes progressive destruction of myelin sheath and axons. Affecting more than 2 million people worldwide, MS may presents distinct clinical courses. However, information regarding key gene expression and genic pathways related to each clinical form is still limited. OBJECTIVE To assess the whole transcriptome of blood leukocytes from patients with remittent-recurrent (RRMS) and secondary-progressive (SPMS) forms to explore the gene expression profile of each form. METHODS Total RNA was obtained and sequenced in Illumina HiSeq platform. Reads were aligned to human genome (GRCh38/hg38), BAM files were mapped and differential expression was obtained with DeSeq2. Up or downregulated pathways were obtained through Ingenuity IPA. Pro-inflammatory cytokines levels were also assessed. RESULTS The transcriptome was generated for nine patients (6 SPMS and 3 RRMS) and 5 healthy controls. A total of 731 and 435 differentially expressed genes were identified in SPMS and RRMS, respectively. RERE, IRS2, SIPA1L1, TANC2 and PLAGL1 were upregulated in both forms, whereas PAD2 and PAD4 were upregulated in RRMS and downregulated in SPMS. Inflammatory and neuronal repair pathways were upregulated in RRMS, which was also observed in cytokine analysis. Conversely, SPMS patients presented IL-8, IL-1, Neurothrophin and Neuregulin pathways down regulated. CONCLUSIONS Overall, the transcriptome of RRMS and SPMS clearly indicated distinct inflammatory profiles, where RRMS presented marked pro-inflammatory profile but SPMS did not. SPMS individuals also presented a decrease on expression of neuronal repair pathways.
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Affiliation(s)
- Luiz H Nali
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil.; Post-graduation Program in Health Sciences, Santo Amaro University, Rua Prof. Enéas de Siqueira Neto, 340, São Paulo, 04829-300, Brazil
| | - Guilherme S Olival
- Departamento de Neurologia Santa Casa de Misericórdia de São Paulo, R. Dr. Cesário Mota Júnior, 112, São Paulo, 01221-020 Brazil
| | - Francielle T G Sousa
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil
| | - Ana Carolina S de Oliveira
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil
| | | | - Israel T da Silva
- Laboratory of Medical Genomics, A.C.Camargo Cancer Center, São Paulo, 01525-001, Brazil
| | - Emamnuel Dias-Neto
- Laboratory of Medical Genomics, A.C.Camargo Cancer Center, São Paulo, 01525-001, Brazil; Laboratory of Neurosciences (LIM-27), Institute of Psychiatry, São Paulo Medical School, University of São Paulo, São Paulo, Brazil
| | - Hugo Naya
- Unidad de Bioinformática Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
| | - Lucia Spangenberg
- Unidad de Bioinformática Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
| | - Augusto C Penalva-de-Oliveira
- Departamento de Neurologia Santa Casa de Misericórdia de São Paulo, R. Dr. Cesário Mota Júnior, 112, São Paulo, 01221-020 Brazil; Departamento de Neurologia, Instituto de Infectologia Emilio Ribas, Avenida Doutor Arnaldo, 165, São Paulo, 01246-900, Brazil
| | - Camila M Romano
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil.; Hospital das Clinicas HCFMUSP (LIM52), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.
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24
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Investigation of the miRNA146a and miRNA155 gene expression levels in patients with multiple sclerosis. J Clin Neurosci 2020; 78:189-193. [PMID: 32331943 DOI: 10.1016/j.jocn.2020.04.071] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/12/2020] [Indexed: 12/22/2022]
Abstract
Multiple sclerosis (MS) is a chronic inflammatory disease and the most common neurodegenerative status. MicroRNAs play an important role in macrophage response to inflammatory processes, and alterations in miRNA levels trigger the inactivation of specific T lymphocytes. As a result, these factors can lead to autoimmune diseases such as MS. Therefore, to determine the role of MicroRNA-146a and MicroRNA-155 in MS patients, their expression levels in serum of MS patients were compared with healthy controls. In this study, the expression levels of MicroRNA-146a and MicroRNA-155 in 30 serum samples of MS and healthy patients as a control group. MicroRNA extraction and cDNA synthesis was performed according manufacture protocols. The expression levels of MicroRNAs were evaluated by Real Time-PCR. MicroRNA-146a and MicroRNA-155 levels were increased in patients with MS compared to controls. The results demonstrated that EDSS score are increased with increasing level of MicroRNA-146a and MicroRNA-155. ROC curve analysis showed that the area under curve (AUC) was significant for MicroRNA-146a and MicroRNA-155. Increased expression levels of MicroRNA-146a and MicroRNA-155 may be associated with the pathogenesis of MS disease. If this study is conducted in a larger sample population and the above results can be used to identify patients or control patients who are under medical care.
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25
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Identification of Multiple Sclerosis key genetic factors through multi-staged data mining. Mult Scler Relat Disord 2020; 39:101446. [PMID: 31874362 DOI: 10.1016/j.msard.2019.101446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 10/10/2019] [Accepted: 10/13/2019] [Indexed: 12/14/2022]
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26
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Hu L, Zhang H, Wang B, Ao Q, He Z. MicroRNA-152 attenuates neuroinflammation in intracerebral hemorrhage by inhibiting thioredoxin interacting protein (TXNIP)-mediated NLRP3 inflammasome activation. Int Immunopharmacol 2020; 80:106141. [PMID: 31982825 DOI: 10.1016/j.intimp.2019.106141] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/30/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022]
Abstract
Neuroinflammation significantly contributes to brain injury and neurological deterioration following intracerebral hemorrhage (ICH). MicroRNA-152(miR-152) was reported to be downregulated in ICH patients and to possess anti-inflammatory properties in other diseases. In this study, we aimed to explore the role of miR-152 in ICH, and the underlying mechanisms, using a collagenase-induced rat ICH model and hemin-exposure as a cell model. We first confirmed that miR-152 was consistently downregulated in both models. Overexpression of miR-152 in microglial BV2 cells reduced hemin-induced inflammatory response and reactive oxygen species (ROS) generation, thus protecting co-cultured neuronal HT22 cells. Moreover, overexpression of miR-152 by intracerebroventricular lentivirus injection in ICH rats significantly alleviated neurodecifits, brain edema, and hematoma. These changes were associated with a marked reduction in ICH-induced neuronal death, as detected by co-staining of NeuN and TUNEL, and ICH-induced neuroinflammation, as revealed by inflammatory cytokine levels as well as by the number of Iba1 positive-stained cells in the perihematomal region. Mechanistically, miR-152 significantly inhibited ICH-induced TXNIP expression, and its overexpression blocked the interaction between TXNIP and NOD-like receptor pyrin domain containing 3(NLRP3), thus inhibiting NLRP3-driven inflammasome activation to attenuate neuroinflammation in vivo and in vitro. Moreover, the results of si-TXNIP transfection further confirmed that TXNIP inhibition was involved in the reduction of NLRP3 inflammasome activation by the overexpression of miR-152. Collectively, the present study demonstrates that miR-152 confers protection against ICH-induced neuroinflammation and brain injury by inhibiting TXNIP-mediated NLRP3 inflammasome activation, indicating a potential strategy for ICH treatment.
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Affiliation(s)
- Liuting Hu
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang 110000, People's Republic of China
| | - Heyu Zhang
- Department of Neurology, The First Affiliated Hospital Sun Yat-sen University, Guangzhou 510080, People's Republic of China
| | - Bingyang Wang
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang 110000, People's Republic of China
| | - Qiang Ao
- Department of Tissue Engineering, China Medical University, Shenyang 110122, People's Republic of China
| | - Zhiyi He
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang 110000, People's Republic of China.
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27
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Nuzziello N, Ciaccia L, Liguori M. Precision Medicine in Neurodegenerative Diseases: Some Promising Tips Coming from the microRNAs' World. Cells 2019; 9:E75. [PMID: 31892254 PMCID: PMC7017296 DOI: 10.3390/cells9010075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/22/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
: Novel insights in the development of a precision medicine approach for treating the neurodegenerative diseases (NDDs) are provided by emerging advances in the field of pharmacoepigenomics. In this context, microRNAs (miRNAs) have been extensively studied because of their implication in several disorders related to the central nervous system, as well as for their potential role as biomarkers of diagnosis, prognosis, and response to treatment. Recent studies in the field of neurodegeneration reported evidence that drug response and efficacy can be modulated by miRNA-mediated mechanisms. In fact, miRNAs seem to regulate the expression of pharmacology target genes, while approved (conventional and non-conventional) therapies can restore altered miRNAs observed in NDDs. The knowledge of miRNA pharmacoepigenomics may offers new clues to develop more effective treatments by providing novel insights into interindividual variability in drug disposition and response. Recently, the therapeutic potential of miRNAs is gaining increasing attention, and miRNA-based drugs (for cancer) have been under observation in clinical trials. However, the effective use of miRNAs as therapeutic target still needs to be investigated. Here, we report a brief review of representative studies in which miRNAs related to therapeutic effects have been investigated in NDDs, providing exciting potential prospects of miRNAs in pharmacoepigenomics and translational medicine.
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Affiliation(s)
- Nicoletta Nuzziello
- National Research Council, Institute of Biomedical Technologies, Bari Unit, 70126 Bari, Italy
| | - Loredana Ciaccia
- Department of Biomedical Science and Human Oncology, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Maria Liguori
- National Research Council, Institute of Biomedical Technologies, Bari Unit, 70126 Bari, Italy
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28
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Boxberger N, Hecker M, Zettl UK. Dysregulation of Inflammasome Priming and Activation by MicroRNAs in Human Immune-Mediated Diseases. THE JOURNAL OF IMMUNOLOGY 2019; 202:2177-2187. [PMID: 30962309 DOI: 10.4049/jimmunol.1801416] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/19/2018] [Indexed: 12/13/2022]
Abstract
Inflammasomes are protein complexes that respond to a wide range of pathogens and cellular damage signals. Their activation prompts the caspase-1-mediated cleavage of the proinflammatory cytokines IL-1β and IL-18. Inflammasome dysregulation has been demonstrated to play a role in a range of diseases involving the adaptive immune system like multiple sclerosis, rheumatic diseases, and type 1 diabetes. Priming and activation of inflammasomes can be modulated by microRNAs (miRNAs), small noncoding RNAs that regulate gene expression posttranscriptionally. miRNAs, such as miR-223-3p, have been demonstrated to directly target the inflammasome components NLRP3, caspase-1, and caspase-8. Other miRNAs like miR-155-5p modulate TLR-, IL-1R-, TNFR-, and IFNAR-mediated signaling pathways upstream of the inflammasomes. In this study, we discuss how a more detailed elucidation of miRNA-driven inflammasome regulation helps in understanding the molecular processes underlying immune-mediated human diseases, holds potential for the identification of biomarkers and may offer novel targets for the development of future therapeutics.
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Affiliation(s)
- Nina Boxberger
- Division of Neuroimmunology, Department of Neurology, University of Rostock, 18147 Rostock, Germany; and
| | - Michael Hecker
- Division of Neuroimmunology, Department of Neurology, University of Rostock, 18147 Rostock, Germany; and.,Steinbeis Transfer Center for Proteome Analysis, 18057 Rostock, Germany
| | - Uwe K Zettl
- Division of Neuroimmunology, Department of Neurology, University of Rostock, 18147 Rostock, Germany; and
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29
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Feliciano LM, Sávio ALV, de Castro Marcondes JP, da Silva GN, Salvadori DMF. Genetic Alterations in Patients with Two Clinical Phenotypes of Multiple Sclerosis. J Mol Neurosci 2019; 70:120-130. [PMID: 31686392 DOI: 10.1007/s12031-019-01408-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/26/2019] [Indexed: 11/26/2022]
Abstract
The etiology of multiple sclerosis (MS) is still not known, but the interaction of genetic, immunological, and environmental factors seem to be involved. This study aimed to investigate genetic alterations and the vitamin D status in patients with relapsing-remitting MS (RRMS) and secondary progressive MS (SPMS). A total of 53 patients (29 RRMS; 24 SPMS) and 25 healthy subjects were recruited to evaluate the micronucleated cell (MNC) frequency and nuclear abnormalities in the buccal mucosa, gene expression profiling in mononuclear cells, and plasmatic vitamin D concentration in the blood. Results showed a higher frequency of cells with karyorrhexis (SPMS) and lower frequencies of nuclear pyknosis (RRMS and SPMS) and karyolysis (SPMS) in patients with MS. Significant increase in the frequency of MNC was detected in the buccal mucosa of RRMS and SPMS patients. HIF1A, IL13, IL18, MYC, and TNF were differentially expressed in MS patients, and APP was overexpressed in cells of RRMS compared to SPMS patients. No relationship was observed between vitamin D level and the differentially expressed genes. In conclusion, the cytogenetic alterations in the buccal mucosa can be important indicators of genetic instability and degenerative processes in patients with MS. Furthermore, our data introduced novel biomarkers associated with the molecular pathogenesis of MS.
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30
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Zajdel M, Rymkiewicz G, Sromek M, Cieslikowska M, Swoboda P, Kulinczak M, Goryca K, Bystydzienski Z, Blachnio K, Ostrowska B, Borysiuk A, Druzd-Sitek A, Walewski J, Chechlinska M, Siwicki JK. Tumor and Cerebrospinal Fluid microRNAs in Primary Central Nervous System Lymphomas. Cancers (Basel) 2019; 11:E1647. [PMID: 31731456 PMCID: PMC6895823 DOI: 10.3390/cancers11111647] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 10/20/2019] [Accepted: 10/22/2019] [Indexed: 11/16/2022] Open
Abstract
Primary central nervous system lymphoma (PCNSL) is a rare, highly aggressive, extranodal form of non-Hodgkin lymphoma, predominantly diagnosed as primary diffuse large B-cell lymphoma of the central nervous system (CNS DLBCL). Fast and precise diagnosis of PCNSL is critical yet challenging. microRNAs, important regulators in physiology and pathology are potential biomarkers. In 131 patients with CNS DLBCL and with non-malignant brain lesions (n-ML), miR-21, miR-19b and miR-92a, miR-155, miR-196b, miR-let-7b, miR-125b, and miR-9 were examined by RT-qPCR in brain biopsy samples (formalin-fixed paraffin-embedded tissues, FFPET; CNS DLBCL, n = 52; n-ML, n = 42) and cerebrospinal fluid samples (CSF; CNS DLBCL, n = 30; n-ML, n = 23) taken for routine diagnosis. FFPET samples were split into study and validation sets. Significantly higher CSF levels of miR-21, miR-19b, and miR-92a were identified in PCNSL but not in n-ML, and differentiated PCNSL from n-ML with 63.33% sensitivity and 80.77% specificity. In FFPETs, miR-155 and miR-196b were significantly overexpressed and miR-let-7b, miR-125b, and miR-9 were downregulated in PCNSL as compared to n-ML. Combined miR-155 and miR-let-7b expression levels in FFPETs discriminated PCNSL and n-ML with a 97% accuracy. In conclusion, tissue miR-155, miR-196b, miR-9, miR-125b, and miR-let-7b expression profiles differentiate PCNSL from n-ML. PCNSL CSFs and the relevant biopsy samples are characterized by specific, different microRNA profiles. A logistic regression model is proposed to discriminate between PCNSL and non-malignant brain lesions. None of the examined microRNAs influenced overall survival of PCNSL patients. Further ongoing developments involve next generation sequencing-based profiling of biopsy and CSF samples.
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Affiliation(s)
- Michalina Zajdel
- Department of Immunology, Maria Sklodowska-Curie Institute—Oncology Center, 02-781 Warsaw, Poland; (M.Z.)
| | - Grzegorz Rymkiewicz
- Flow Cytometry Laboratory, Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Institute—Oncology Center, 02-781 Warsaw, Poland; (G.R.)
| | - Maria Sromek
- Department of Immunology, Maria Sklodowska-Curie Institute—Oncology Center, 02-781 Warsaw, Poland; (M.Z.)
| | - Maria Cieslikowska
- Department of Immunology, Maria Sklodowska-Curie Institute—Oncology Center, 02-781 Warsaw, Poland; (M.Z.)
| | - Pawel Swoboda
- Department of Immunology, Maria Sklodowska-Curie Institute—Oncology Center, 02-781 Warsaw, Poland; (M.Z.)
| | - Mariusz Kulinczak
- Department of Immunology, Maria Sklodowska-Curie Institute—Oncology Center, 02-781 Warsaw, Poland; (M.Z.)
| | - Krzysztof Goryca
- Department of Medical Genetics, Maria Sklodowska-Curie Institute—Oncology Center, 02-781 Warsaw, Poland
- Core Facilities CeNT, University of Warsaw, 02-097 Warsaw, Poland
| | - Zbigniew Bystydzienski
- Flow Cytometry Laboratory, Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Institute—Oncology Center, 02-781 Warsaw, Poland; (G.R.)
| | - Katarzyna Blachnio
- Flow Cytometry Laboratory, Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Institute—Oncology Center, 02-781 Warsaw, Poland; (G.R.)
| | - Beata Ostrowska
- Department of Lymphoid Malignancies, Maria Sklodowska-Curie Institute—Oncology Center, 02-781 Warsaw, Poland
| | - Anita Borysiuk
- Flow Cytometry Laboratory, Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Institute—Oncology Center, 02-781 Warsaw, Poland; (G.R.)
| | - Agnieszka Druzd-Sitek
- Department of Lymphoid Malignancies, Maria Sklodowska-Curie Institute—Oncology Center, 02-781 Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoid Malignancies, Maria Sklodowska-Curie Institute—Oncology Center, 02-781 Warsaw, Poland
| | - Magdalena Chechlinska
- Department of Immunology, Maria Sklodowska-Curie Institute—Oncology Center, 02-781 Warsaw, Poland; (M.Z.)
| | - Jan Konrad Siwicki
- Department of Immunology, Maria Sklodowska-Curie Institute—Oncology Center, 02-781 Warsaw, Poland; (M.Z.)
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31
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Li G, Liu Y, Meng F, Xia Z, Wu X, Fang Y, Zhang C, Zhang Y, Liu D. LncRNA MEG3 inhibits rheumatoid arthritis through miR-141 and inactivation of AKT/mTOR signalling pathway. J Cell Mol Med 2019; 23:7116-7120. [PMID: 31411001 PMCID: PMC6787440 DOI: 10.1111/jcmm.14591] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 07/21/2019] [Accepted: 07/24/2019] [Indexed: 12/19/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic inflammation mediated by autoimmune responses. MEG3, a kind of long noncoding RNA (lncRNA), participates in cell proliferation in cancer tissues. However, the correlation between MEG3 and RA is yet unclear. Therefore, to clarify how MEG3 works in RA, we performed a series of experiments using RA samples. We found that MEG3 was downregulated in the fibroblast-like synoviocytes of RA patients (RA-FLS), in comparison with healthy subjects. MEG3 was also down-regulated evidently in lipopolysaccharide (LPS)-treated chondrocyte. As part of our experiments, MEG3 was overexpressed in chondrocyte by transfection with lentivirus containing sequences encoding MEG3. In addition, in presence of LPS, reductions were identified not only in the cell proliferation, but also in the generation of interleukin-23 (IL-23), which, however were reversed in the lentivirus (containing MEG3-encoding sequences)-transfected chondrocytes. Up-regulated MEG3 resulted in an increase the level of Ki67. Moreover, MEG3 was negatively correlated with miR-141, and miR-141 was up-regulated in LPS-treated chondrocyte. Inhibitory effects of MEG3 overexpression, mentioned above, were partially abolished by overexpressed miR-141. Further, animal experiment also showed the inhibitory effect of MEG3 in overexpression on the AKT/mTOR signaling pathway. In-vivoexperiments also showed that cell proliferation was facilitated by MEG3 overexpression with inhibited inflammation. In summary, the protective role of MEG3 in RA was proved to be exerted by the increase in the rate of proliferation, which might correlate to the regulatory role of miR-141 and AKT/mTOR signal pathway, suggesting that MEG3 holds great promise as a therapeutic strategy for RA.
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Affiliation(s)
- Guoqing Li
- Department of Rheumatology, Affiliated Hospital of Yangzhou UniversityYangzhou UniversityYangzhouChina
| | - Ying Liu
- Department of Rheumatology, Affiliated Hospital of Yangzhou UniversityYangzhou UniversityYangzhouChina
- Clinical Medical CollegeDalian Medical UniversityDalianChina
| | - Fanru Meng
- Department of Rheumatology, Affiliated Hospital of Yangzhou UniversityYangzhou UniversityYangzhouChina
- Clinical Medical CollegeDalian Medical UniversityDalianChina
| | - Zhongbin Xia
- Department of Rheumatology, Affiliated Hospital of Yangzhou UniversityYangzhou UniversityYangzhouChina
| | - Xia Wu
- Department of Rheumatology, Affiliated Hospital of Yangzhou UniversityYangzhou UniversityYangzhouChina
- Clinical Medical CollegeDalian Medical UniversityDalianChina
| | - Yuxuan Fang
- Department of Rheumatology, Affiliated Hospital of Yangzhou UniversityYangzhou UniversityYangzhouChina
- Clinical Medical CollegeDalian Medical UniversityDalianChina
| | - Chunwang Zhang
- Department of Rheumatology, Affiliated Hospital of Yangzhou UniversityYangzhou UniversityYangzhouChina
- Clinical Medical CollegeDalian Medical UniversityDalianChina
| | - Yu Zhang
- Department of Rheumatology, Affiliated Hospital of Yangzhou UniversityYangzhou UniversityYangzhouChina
| | - Dan Liu
- Department of Pathology, Clinical Medical CollegeYangzhou UniversityYangzhouChina
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Gnanakkumaar P, Murugesan R, Ahmed SSSJ. Gene Regulatory Networks in Peripheral Mononuclear Cells Reveals Critical Regulatory Modules and Regulators of Multiple Sclerosis. Sci Rep 2019; 9:12732. [PMID: 31484947 PMCID: PMC6726613 DOI: 10.1038/s41598-019-49124-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 08/20/2019] [Indexed: 01/08/2023] Open
Abstract
Multiple sclerosis (MS) is a complex, demyelinating disease with the involvement of autoimmunity and neurodegeneration. Increasing efforts have been made towards identifying the diagnostic markers to differentiate the classes of MS from other similar neurological conditions. Using a systems biology approach, we constructed four types of gene regulatory networks (GRNs) involved in peripheral blood mononuclear cells (PBMCs). The regulatory strength of each GRN across primary progressive MS (PPMS), relapsing-remitting MS (RRMS), secondary progressive MS (SPMS), and control were evaluated by an integrity algorithm. Among the constructed GRNs (referred as TF_gene_miRNA), POU3F2_CDK6_hsa-miR-590-3p, MEIS1_CASC3_hsa-miR-1261, STAT3_OGG1_hsa-miR-298, and TCF4_FMR1_hsa-miR-301b were top-ranked and differentially regulated in all classes of MS compared to control. These GRNs showed potential involvement in regulating various molecular pathways such as interleukin, integrin, glypican, sphingosine phosphate, androgen, and Wnt signaling pathways. For validation, the qPCR analysis of the GRN components (TFs, gene, and miRNAs) in PBMCs of healthy controls (n = 30), RRMS (n = 14), PPMS (n = 13) and SPMS (n = 12) were carried out. Real-time expression analysis of GRNs showed a similar regulatory pattern as derived from our systems biology approach. Also, our study provided several novel GRNs that regulate unique and common molecular mechanisms between MS conditions. Hence, these regulatory components of GRNs will help to understand the disease mechanism across MS classes and further insight may though light towards diagnosis.
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Affiliation(s)
- Perumal Gnanakkumaar
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Kelambakkam, 603103, India
| | - Ram Murugesan
- Drug Discovery Lab, Faculty of Allied Health Sciences, Chettinad Hospital & Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, 603103, India
| | - Shiek S S J Ahmed
- Drug Discovery Lab, Faculty of Allied Health Sciences, Chettinad Hospital & Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, 603103, India.
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Su L, Liu G, Wang J, Xu D. A rectified factor network based biclustering method for detecting cancer-related coding genes and miRNAs, and their interactions. Methods 2019; 166:22-30. [PMID: 31121299 PMCID: PMC6708461 DOI: 10.1016/j.ymeth.2019.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/14/2019] [Accepted: 05/13/2019] [Indexed: 12/12/2022] Open
Abstract
Detecting cancer-related genes and their interactions is a crucial task in cancer research. For this purpose, we proposed an efficient method, to detect coding genes, microRNAs (miRNAs), and their interactions related to a particular cancer or a cancer subtype using their expression data from the same set of samples. Firstly, biclusters specific to a particular type of cancer are detected based on rectified factor networks and ranked according to their associations with general cancers. Secondly, coding genes and miRNAs in each bicluster are prioritized by considering their differential expression and differential correlation values, protein-protein interaction data, and potential cancer markers. Finally, a rank fusion process is used to obtain the final comprehensive rank by combining multiple ranking results. We applied our proposed method on breast cancer datasets. Results show that our method outperforms other methods in detecting breast cancer-related coding genes and miRNAs. Furthermore, our method is very efficient in computing time, which can handle tens of thousands genes/miRNAs and hundreds of patients in hours on a desktop. This work may aid researchers in studying the genetic architecture of complex diseases, and improving the accuracy of diagnosis.
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Affiliation(s)
- Lingtao Su
- Department of Computer Science and Technology, Jilin University, Changchun 130012, China; Department of Electrical Engineering & Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Guixia Liu
- Department of Computer Science and Technology, Jilin University, Changchun 130012, China
| | - Juexin Wang
- Department of Electrical Engineering & Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Dong Xu
- Department of Electrical Engineering & Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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Li F, Si D, Guo X, Guo N, Li D, Zhang L, Jian X, Ma J. Aberrant expression of miR‑130a‑3p in ankylosing spondylitis and its role in regulating T‑cell survival. Mol Med Rep 2019; 20:3388-3394. [PMID: 31432140 DOI: 10.3892/mmr.2019.10573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/06/2019] [Indexed: 11/09/2022] Open
Abstract
Ankylosing spondylitis (AS) is a chronic inflammatory rheumatic disease. MicroRNAs (miRNAs) are a group of endogenous small non‑coding RNAs that regulate target genes, and play a critical role in many biological processes. However, the underlying mechanism of specific miRNA, miR‑130a‑3p, in AS remains largely unknown. Therefore, the present study aimed to explore the underlying mechanism of miR‑130a‑3p in the development of AS. In the present study, it was revealed that miR‑130a‑3p was downregulated in T cells from HLA‑B27‑positive AS patients compared with the HLA‑B27‑negative healthy controls. Next, bioinformatics software TargetScan 7.2 was used to predict the target genes of miR‑130a‑3p, and a luciferase reporter assay indicated that HOXB1 was the direct target gene of miR‑130a‑3p. Furthermore, it was determined that HOXB1 expression was upregulated in T cells from HLA‑B27‑positive AS patients. In addition, the results of the present study indicated that miR‑130a‑3p inhibitor significantly inhibited cell proliferation ability and induced cell apoptosis of Jurkat T cells, while the miR‑130a‑3p mimic promoted proliferation ability and inhibited cell apoptosis of Jurkat T cells. Notably, all the effects of the miR‑130a‑3p mimic on Jurkat T cells were reversed by HOXB1‑plasmid. Collectively, our data indicated that miR‑130a‑3p was decreased in T cells from AS patients and it could regulate T‑cell survival by targeting HOXB1.
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Affiliation(s)
- Fengju Li
- Department of Rheumatism and Immunology, Puyang Oilfield General Hospital, Puyang, Henan 457001, P.R. China
| | - Dingran Si
- Department of Cardiovascular Medicine, Puyang Oilfield General Hospital, Puyang, Henan 457001, P.R. China
| | - Xuejun Guo
- Department of Hematology, Puyang Oilfield General Hospital, Puyang, Henan 457001, P.R. China
| | - Ningru Guo
- Department of Rheumatism and Immunology, Puyang Oilfield General Hospital, Puyang, Henan 457001, P.R. China
| | - Dandan Li
- Department of Rheumatism and Immunology, Puyang Oilfield General Hospital, Puyang, Henan 457001, P.R. China
| | - Liujing Zhang
- Department of Rheumatism and Immunology, Puyang Oilfield General Hospital, Puyang, Henan 457001, P.R. China
| | - Xianan Jian
- Department of Rheumatism and Immunology, Puyang Oilfield General Hospital, Puyang, Henan 457001, P.R. China
| | - Jiasheng Ma
- Department of Rheumatism and Immunology, Puyang Oilfield General Hospital, Puyang, Henan 457001, P.R. China
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Goodall EF, Leach V, Wang C, Cooper-Knock J, Heath PR, Baker D, Drew DR, Saffrey MJ, Simpson JE, Romero IA, Wharton SB. Age-Associated mRNA and miRNA Expression Changes in the Blood-Brain Barrier. Int J Mol Sci 2019; 20:ijms20123097. [PMID: 31242592 PMCID: PMC6627814 DOI: 10.3390/ijms20123097] [Citation(s) in RCA: 15] [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: 06/06/2019] [Revised: 06/21/2019] [Accepted: 06/22/2019] [Indexed: 02/04/2023] Open
Abstract
Functional and structural age-associated changes in the blood-brain barrier (BBB) may affect the neurovascular unit and contribute to the onset and progression of age-associated neurodegenerative pathologies, including Alzheimer’s disease. The current study interrogated the RNA profile of the BBB in an ageing human autopsy brain cohort and an ageing mouse model using combined laser capture microdissection and expression profiling. Only 12 overlapping genes were altered in the same direction in the BBB of both ageing human and mouse cohorts. These included genes with roles in regulating vascular tone, tight junction protein expression and cell adhesion, all processes prone to dysregulation with advancing age. Integrated mRNA and miRNA network and pathway enrichment analysis of the datasets identified 15 overlapping miRNAs that showed altered expression. In addition to targeting genes related to DNA binding and/or autophagy, many of the miRNAs identified play a role in age-relevant processes, including BBB dysfunction and regulating the neuroinflammatory response. Future studies have the potential to develop targeted therapeutic approaches against these candidates to prevent vascular dysfunction in the ageing brain.
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Affiliation(s)
- Emily F Goodall
- Sheffield Institute for Translational Neuroscience, 385a Glossop Road, University of Sheffield, Sheffield S10 2HQ, UK.
| | - Vicki Leach
- Sheffield Institute for Translational Neuroscience, 385a Glossop Road, University of Sheffield, Sheffield S10 2HQ, UK.
| | - Chunfang Wang
- School of Life Science, Health and Chemical Sciences, Faculty of Science, Technology Engineering and Mathematics, The Open University, Walton Hall, Milton Keynes MK7 6AA, UK.
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience, 385a Glossop Road, University of Sheffield, Sheffield S10 2HQ, UK.
| | - Paul R Heath
- Sheffield Institute for Translational Neuroscience, 385a Glossop Road, University of Sheffield, Sheffield S10 2HQ, UK.
| | - David Baker
- Sheffield Institute for Translational Neuroscience, 385a Glossop Road, University of Sheffield, Sheffield S10 2HQ, UK.
| | - David R Drew
- Sheffield Institute for Translational Neuroscience, 385a Glossop Road, University of Sheffield, Sheffield S10 2HQ, UK.
| | - M Jill Saffrey
- School of Life Science, Health and Chemical Sciences, Faculty of Science, Technology Engineering and Mathematics, The Open University, Walton Hall, Milton Keynes MK7 6AA, UK.
| | - Julie E Simpson
- Sheffield Institute for Translational Neuroscience, 385a Glossop Road, University of Sheffield, Sheffield S10 2HQ, UK.
| | - Ignacio A Romero
- School of Life Science, Health and Chemical Sciences, Faculty of Science, Technology Engineering and Mathematics, The Open University, Walton Hall, Milton Keynes MK7 6AA, UK.
| | - Stephen B Wharton
- Sheffield Institute for Translational Neuroscience, 385a Glossop Road, University of Sheffield, Sheffield S10 2HQ, UK.
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Gene Expression and miRNAs Profiling: Function and Regulation in Human Epidermal Growth Factor Receptor 2 (HER2)-Positive Breast Cancer. Cancers (Basel) 2019; 11:cancers11050646. [PMID: 31083383 PMCID: PMC6562440 DOI: 10.3390/cancers11050646] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the second most common cause of cancer-related deaths among women worldwide. It is a heterogeneous disease with four major molecular subtypes. One of the subtypes, human epidermal growth factor receptor 2 (HER2)-enriched (HER2-positive) is characterized by the absence of estrogen and progesterone receptors and overexpression of HER2 receptor, and accounts for 15–20% of all breast cancers. Despite the anti-HER2 and cytotoxic chemotherapy, HER2 subtype is an aggressive disease with significant mortality. Recent advances in molecular biology techniques, including gene expression profiling, proteomics, and microRNA analysis, have been extensively used to explore the underlying mechanisms behind human breast carcinogenesis and metastasis including HER2-positive breast cancer, paving the way for developing new targeted therapies. This review focuses on recent advances on gene expression and miRNA status in HER2-positive breast cancer.
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Gharibi S, Moghimi B, Haghmorad D, Mahmoudi MB, Shahvazian E, Yadegari M, Yazd EF, Tahoori MT. Altered expression patterns of complement factor H and miR‐146a genes in acute‐chronic phases in experimental autoimmune encephalomyelitis mouse. J Cell Physiol 2019; 234:19842-19851. [DOI: 10.1002/jcp.28583] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/10/2019] [Accepted: 03/19/2019] [Indexed: 01/10/2023]
Affiliation(s)
- Saba Gharibi
- Department of Genetics, Faculty of Medicine, International Campus Shahid Sadoughi University of Medical Sciences and Health Services Yazd Iran
| | - Bahram Moghimi
- Department of Genetics, Faculty of Medicine Shahid Sadoughi University of Medical Sciences and Health Services Yazd Iran
| | - Dariush Haghmorad
- Department of Pathology and Laboratory Medicine, School of Medicine Semnan University of Medical Sciences Semnan Iran
- Department of Immunology, School of Medicine Semnan University of Medical Sciences and Health Services Semnan Iran
| | - Mohammad Bagher Mahmoudi
- Department of Genetics, Faculty of Medicine Shahid Sadoughi University of Medical Sciences and Health Services Yazd Iran
| | - Ensieh Shahvazian
- Department of Genetics, Faculty of Medicine, International Campus Shahid Sadoughi University of Medical Sciences and Health Services Yazd Iran
| | - Maryam Yadegari
- Department of Biology & Anatomical Sciences, Shahid Sadoughi University of Medical Sciences and Health Services Faculty of Medicine Yazd Iran
| | - Ehsan Farashahi Yazd
- Department of Genetics, Faculty of Medicine Shahid Sadoughi University of Medical Sciences and Health Services Yazd Iran
- Genetic Engineering and Genome Editing Laboratory, Stem Cell Biology Research Center Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences Yazd Iran
| | - Mohammad Taher Tahoori
- Department of Immunology, Faculty of Medicine Shahid Sadoughi University of Medical Sciences and Health Services Yazd Iran
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Hassani A, Khan G. Epstein-Barr Virus and miRNAs: Partners in Crime in the Pathogenesis of Multiple Sclerosis? Front Immunol 2019; 10:695. [PMID: 31001286 PMCID: PMC6456696 DOI: 10.3389/fimmu.2019.00695] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/13/2019] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that modulate gene expression post transcriptionally. In healthy individuals, miRNAs contribute to maintaining gene expression homeostasis. However, the level of miRNAs expressed is markedly altered in different diseases, including multiple sclerosis (MS). The impact of such changes is being investigated, and thought to shape the immune system into the inflammatory autoimmune phenotype. Much is yet to be learned about the contribution of miRNAs in the molecular pathology of MS. Epstein-Barr virus (EBV) infection is a major risk factor for the development of MS. EBV encodes more than 40 miRNAs, most of which have been studied in the context of EBV associated cancers. These viral miRNAs regulate genes involved in cell apoptosis, antigen presentation and recognition, as well as B cell transformation. If EBV infection contributes to the pathology of MS, it is plausible that EBV miRNAs may be involved. Unfortunately, there are limited studies addressing how EBV miRNAs are involved in the pathogenesis of MS. This review summarizes what has been reported regarding cellular and viral miRNA profiles in MS and proposes possible interactions between the two in the development of MS.
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Affiliation(s)
- Asma Hassani
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Gulfaraz Khan
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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Tripathi A, Volsko C, Datta U, Regev K, Dutta R. Expression of disease-related miRNAs in white-matter lesions of progressive multiple sclerosis brains. Ann Clin Transl Neurol 2019; 6:854-862. [PMID: 31139683 PMCID: PMC6530016 DOI: 10.1002/acn3.750] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/26/2019] [Accepted: 02/11/2019] [Indexed: 01/15/2023] Open
Abstract
Background MicroRNA (miRNA) expression in the serum of multiple sclerosis (MS) patients has been correlated with white matter (WM) magnetic resonance imaging (MRI) abnormalities. The expression levels and cellular specificity of the target genes of these miRNAs are unknown in MS brain. Objective The aim of this study was to analyze and validate the expression of miRNAs, previously reported as dysregulated in sera of MS patients, in white‐matter lesions (WMLs) of progressive MS brains. Methods We performed global miRNA expression profiling analysis in demyelinated WMLs of progressive MS brains (n = 5) and compared the significantly altered miRNAs to previously identified miRNAs from sera of MS patients. Top dysregulated miRNAs common between the two datasets were validated in an independent cohort of MS brains by quantitative PCR (qPCR) and in situ hybridization. Results Among the miRNAs that were significantly changed in WML tissues, 11 were similar to pathogenic and 12 were common to protective miRNAs previously identified in sera and correlating with WM MRI abnormalities. Importantly, the expression levels of 58% of the protective miRNAs (7 of 12) were decreased in MS lesions compared to surrounding normal‐appearing tissue. Target genes of these miRNAs were also altered in MS lesions and queries of cell‐specific databases identified astrocytes and microglia as the key cellular expressers of these genes in MS brains. Conclusions We identified miRNAs that correlate with MRI abnormalities in lesioned tissue from MS brains.
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Affiliation(s)
- Ajai Tripathi
- Department of Neurosciences Cleveland Clinic Cleveland Ohio
| | | | - Ushasi Datta
- Department of Neurosciences Cleveland Clinic Cleveland Ohio
| | - Keren Regev
- Department of Neurology Tel Aviv Sourasky Medical Center Tel Aviv Israel
| | - Ranjan Dutta
- Department of Neurosciences Cleveland Clinic Cleveland Ohio
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40
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Teymoori-Rad M, Mozhgani SH, Zarei-Ghobadi M, Sahraian MA, Nejati A, Amiri MM, Shokri F, Marashi SM. Integrational analysis of miRNAs data sets as a plausible missing linker between Epstein-Barr virus and vitamin D in relapsing remitting MS patients. Gene 2019; 689:1-10. [DOI: 10.1016/j.gene.2018.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/21/2018] [Accepted: 12/06/2018] [Indexed: 12/14/2022]
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Liguori M, Nuzziello N, Licciulli F, Consiglio A, Simone M, Viterbo RG, Creanza TM, Ancona N, Tortorella C, Margari L, Grillo G, Giordano P, Liuni S, Trojano M. Combined microRNA and mRNA expression analysis in pediatric multiple sclerosis: an integrated approach to uncover novel pathogenic mechanisms of the disease. Hum Mol Genet 2019; 27:66-79. [PMID: 29087462 DOI: 10.1093/hmg/ddx385] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/23/2017] [Indexed: 12/12/2022] Open
Abstract
Multiple sclerosis (MS) is a complex disease of the CNS that usually affects young adults, although 3-5% of cases are diagnosed in childhood and adolescence (hence called pediatric MS, PedMS). Genetic predisposition, among other factors, seems to contribute to the risk of the onset, in pediatric as in adult ages, but few studies have investigated the genetic 'environmentally naïve' load of PedMS. The main goal of this study was to identify circulating markers (miRNAs), target genes (mRNAs) and functional pathways associated with PedMS; we also verified the impact of miRNAs on clinical features, i.e. disability and cognitive performances. The investigation was performed in 19 PedMS and 20 pediatric controls (PCs) using a High-Throughput Next-generation Sequencing (HT-NGS) approach followed by an integrated bioinformatics/biostatistics analysis. Twelve miRNAs were significantly upregulated (let-7a-5p, let-7b-5p, miR-25-3p, miR-125a-5p, miR-942-5p, miR-221-3p, miR-652-3p, miR-182-5p, miR-185-5p, miR-181a-5p, miR-320a, miR-99b-5p) and 1 miRNA was downregulated (miR-148b-3p) in PedMS compared with PCs. The interactions between the significant miRNAs and their targets uncovered predicted genes (i.e. TNFSF13B, TLR2, BACH2, KLF4) related to immunological functions, as well as genes involved in autophagy-related processes (i.e. ATG16L1, SORT1, LAMP2) and ATPase activity (i.e. ABCA1, GPX3). No significant molecular profiles were associated with any PedMS demographic/clinical features. Both miRNAs and mRNA expressions predicted the phenotypes (PedMS-PC) with an accuracy of 92% and 91%, respectively. In our view, this original strategy of contemporary miRNA/mRNA analysis may help to shed light in the genetic background of the disease, suggesting further molecular investigations in novel pathogenic mechanisms.
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Affiliation(s)
- Maria Liguori
- National Research Council of Italy, Department of Biomedicine, Institute of Biomedical Technologies, Bari Section, 70125 Bari, Italy
| | - Nicoletta Nuzziello
- National Research Council of Italy, Department of Biomedicine, Institute of Biomedical Technologies, Bari Section, 70125 Bari, Italy.,Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, 70125 Bari, Italy
| | - Flavio Licciulli
- National Research Council of Italy, Department of Biomedicine, Institute of Biomedical Technologies, Bari Section, 70125 Bari, Italy
| | - Arianna Consiglio
- National Research Council of Italy, Department of Biomedicine, Institute of Biomedical Technologies, Bari Section, 70125 Bari, Italy
| | - Marta Simone
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, 70125 Bari, Italy
| | - Rosa Gemma Viterbo
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, 70125 Bari, Italy
| | - Teresa Maria Creanza
- National Research Council of Italy, Department of Engineering, ICT and Technology for Energy and Transportation, Institute of Intelligent Systems for Automation, 70125 Bari, Italy
| | - Nicola Ancona
- National Research Council of Italy, Department of Engineering, ICT and Technology for Energy and Transportation, Institute of Intelligent Systems for Automation, 70125 Bari, Italy
| | - Carla Tortorella
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, 70125 Bari, Italy.,Department of Neurosciences, San Camillo Forlanini Hospital, 00185 Rome, Italy
| | - Lucia Margari
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, 70125 Bari, Italy
| | - Giorgio Grillo
- National Research Council of Italy, Department of Biomedicine, Institute of Biomedical Technologies, Bari Section, 70125 Bari, Italy
| | - Paola Giordano
- General Paediatric Unit "B. Trambusti", Azienda Policlinico-Giovanni XXIII and University of Bari, 70125 Bari, Italy
| | - Sabino Liuni
- National Research Council of Italy, Department of Biomedicine, Institute of Biomedical Technologies, Bari Section, 70125 Bari, Italy
| | - Maria Trojano
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, 70125 Bari, Italy
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Islam T, Rahman MR, Karim MR, Huq F, Quinn JM, Moni MA. Detection of multiple sclerosis using blood and brain cells transcript profiles: Insights from comprehensive bioinformatics approach. INFORMATICS IN MEDICINE UNLOCKED 2019. [DOI: 10.1016/j.imu.2019.100201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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43
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Plasma miR-21, miR-155, miR-10b, and Let-7a as the potential biomarkers for the monitoring of breast cancer patients. Sci Rep 2018; 8:17981. [PMID: 30568292 PMCID: PMC6299272 DOI: 10.1038/s41598-018-36321-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/19/2018] [Indexed: 12/19/2022] Open
Abstract
There is a pressing need for further studies to categorize and validate circulating microRNAs (miRs) in breast cancer patients that can be one of the novel strategies for cancer screening and monitoring. The present study is aimed to investigate the expression of the circulating candidate microRNAs after the operation, chemotherapy, and radiotherapy in the non-metastatic breast cancer patients. Tumor tissue and plasma samples were collected from the 30 patients with recently diagnosed Luminal A breast cancer. Control plasma samples were collected from the 10 healthy subjects. A panel of four miRs including miR-21, miR-55, miR-10b, and Let-7a were selected and their expression levels were measured before and after the operation, chemotherapy, and radiotherapy by using Real-Time PCR technique. The plasma expression of the miR-21, miR-155, and miR-10b was significantly increased and the Let-7a plasma expression decreased in the breast cancer patients compromised to the control ones. There was a similar expression pattern of the miRs between the tissue and plasma samples. The plasma levels of the miR-21, miR-155, and miR-10b were significantly down-regulated and the Let-7a plasma level was up-regulated after the operation, chemotherapy, and radiotherapy compromised to the pre-treatment. There was a significant difference in the miR-155 plasma level after the operation, chemotherapy, and radiotherapy compromised with each other. Moreover, there was no significant difference between the plasma levels of the miRs after the radiotherapy compromised to the control cases. The operation, chemotherapy, and radiotherapy led to a more reduction in the oncomiRs and an increase in the tumor suppressor-miRs. It seems that monitoring miRs during treatment might be considered as a respectable diagnostic tool for monitoring of breast cancer patients.
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Nuzziello N, Vilardo L, Pelucchi P, Consiglio A, Liuni S, Trojano M, Liguori M. Investigating the Role of MicroRNA and Transcription Factor Co-regulatory Networks in Multiple Sclerosis Pathogenesis. Int J Mol Sci 2018; 19:ijms19113652. [PMID: 30463275 PMCID: PMC6274935 DOI: 10.3390/ijms19113652] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/15/2018] [Accepted: 11/16/2018] [Indexed: 01/04/2023] Open
Abstract
MicroRNAs (miRNAs) and transcription factors (TFs) play key roles in complex multifactorial diseases like multiple sclerosis (MS). Starting from the miRNomic profile previously associated with a cohort of pediatric MS (PedMS) patients, we applied a combined molecular and computational approach in order to verify published data in patients with adult-onset MS (AOMS). Six out of the 13 selected miRNAs (miR-320a, miR-125a-5p, miR-652-3p, miR-185-5p, miR-942-5p, miR-25-3p) were significantly upregulated in PedMS and AOMS patients, suggesting that they may be considered circulating biomarkers distinctive of the disease independently from age. A computational and unbiased miRNA-based screening of target genes not necessarily associated to MS was then performed in order to provide an extensive view of the genetic mechanisms underlying the disease. A comprehensive MS-specific miRNA-TF co-regulatory network was hypothesized; among others, SP1, RELA, NF-κB, TP53, AR, MYC, HDAC1, and STAT3 regulated the transcription of 61 targets. Interestingly, NF-κB and STAT3 cooperatively regulate the expression of immune response genes and control the cross-talk between inflammatory and immune cells. Further functional analysis will be performed on the identified critical hubs. Above all, in our view, this approach supports the need of multidisciplinary strategies for shedding light into the pathogenesis of MS.
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Affiliation(s)
- Nicoletta Nuzziello
- National Research Council, Institute of Biomedical Technologies, Bari Unit, 70126 Bari, Italy.
| | - Laura Vilardo
- National Research Council, Institute of Biomedical Technologies, Segrate Unit, 20090 Milan, Italy.
| | - Paride Pelucchi
- National Research Council, Institute of Biomedical Technologies, Segrate Unit, 20090 Milan, Italy.
| | - Arianna Consiglio
- National Research Council, Institute of Biomedical Technologies, Bari Unit, 70126 Bari, Italy.
| | - Sabino Liuni
- National Research Council, Institute of Biomedical Technologies, Bari Unit, 70126 Bari, Italy.
| | - Maria Trojano
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, 70124 Bari, Italy.
| | - Maria Liguori
- National Research Council, Institute of Biomedical Technologies, Bari Unit, 70126 Bari, Italy.
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Annibali V, Umeton R, Palermo A, Severa M, Etna MP, Giglio S, Romano S, Ferraldeschi M, Buscarinu MC, Vecchione A, Annese A, Policano C, Mechelli R, Pizzolato Umeton R, Fornasiero A, Angelini DF, Guerrera G, Battistini L, Coccia EM, Salvetti M, Ristori G. Analysis of coding and non-coding transcriptome of peripheral B cells reveals an altered interferon response factor (IRF)-1 pathway in multiple sclerosis patients. J Neuroimmunol 2018; 324:165-171. [PMID: 30270021 DOI: 10.1016/j.jneuroim.2018.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 08/13/2018] [Accepted: 09/10/2018] [Indexed: 01/15/2023]
Abstract
Several evidences emphasize B-cell pathogenic roles in multiple sclerosis (MS). We performed transcriptome analyses on peripheral B cells from therapy-free patients and age/sex-matched controls. Down-regulation of two transcripts (interferon response factor 1-IRF1, and C-X-C motif chemokine 10-CXCL10), belonging to the same pathway, was validated by RT-PCR in 26 patients and 21 controls. IRF1 and CXCL10 transcripts share potential seeding sequences for hsa-miR-424, that resulted up-regulated in MS patients. We confirmed this interaction and its functional effect by transfection experiments. Consistent findings indicate down-regulation of IRF1/CXCL10 axis, that may plausibly contribute to a pro-survival status of B cells in MS.
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Affiliation(s)
- Viviana Annibali
- Center for Experimental Neurological Therapies, Sant'Andrea Hospital, Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Renato Umeton
- Department of Informatics, Dana-Farber Cancer Institute, Boston, MA, United States; Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Antonia Palermo
- Department of Mathematics and Computer Science, University of Calabria
| | - Martina Severa
- Department of Infectious, Parasitic and Immune-mediated Disease, Istituto Superiore di Sanità, Rome, Italy
| | - Marilena Paola Etna
- Department of Infectious, Parasitic and Immune-mediated Disease, Istituto Superiore di Sanità, Rome, Italy
| | - Simona Giglio
- Division of Pathology, Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Silvia Romano
- Center for Experimental Neurological Therapies, Sant'Andrea Hospital, Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Michela Ferraldeschi
- Center for Experimental Neurological Therapies, Sant'Andrea Hospital, Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Maria Chiara Buscarinu
- Center for Experimental Neurological Therapies, Sant'Andrea Hospital, Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Andrea Vecchione
- Division of Pathology, Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Anita Annese
- Center for Experimental Neurological Therapies, Sant'Andrea Hospital, Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Claudia Policano
- Center for Experimental Neurological Therapies, Sant'Andrea Hospital, Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Rosella Mechelli
- Center for Experimental Neurological Therapies, Sant'Andrea Hospital, Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | | | - Arianna Fornasiero
- Center for Experimental Neurological Therapies, Sant'Andrea Hospital, Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | | | | | | | - Eliana Marina Coccia
- Department of Infectious, Parasitic and Immune-mediated Disease, Istituto Superiore di Sanità, Rome, Italy
| | - Marco Salvetti
- Center for Experimental Neurological Therapies, Sant'Andrea Hospital, Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy; IRCCS Istituto Neurologico Mediterraneo (INM) Neuromed (M.S.), Pozzilli, IS, Italy.
| | - Giovanni Ristori
- Center for Experimental Neurological Therapies, Sant'Andrea Hospital, Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy.
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Liguori M, Nuzziello N, Introna A, Consiglio A, Licciulli F, D’Errico E, Scarafino A, Distaso E, Simone IL. Dysregulation of MicroRNAs and Target Genes Networks in Peripheral Blood of Patients With Sporadic Amyotrophic Lateral Sclerosis. Front Mol Neurosci 2018; 11:288. [PMID: 30210287 PMCID: PMC6121079 DOI: 10.3389/fnmol.2018.00288] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 07/31/2018] [Indexed: 01/01/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease. While genetics and other factors contribute to ALS pathogenesis, critical knowledge is still missing and validated biomarkers for monitoring the disease activity have not yet been identified. To address those aspects we carried out this study with the primary aim of identifying possible miRNAs/mRNAs dysregulation associated with the sporadic form of the disease (sALS). Additionally, we explored miRNAs as modulating factors of the observed clinical features. Study included 56 sALS and 20 healthy controls (HCs). We analyzed the peripheral blood samples of sALS patients and HCs with a high-throughput next-generation sequencing followed by an integrated bioinformatics/biostatistics analysis. Results showed that 38 miRNAs (let-7a-5p, let-7d-5p, let-7f-5p, let-7g-5p, let-7i-5p, miR-103a-3p, miR-106b-3p, miR-128-3p, miR-130a-3p, miR-130b-3p, miR-144-5p, miR-148a-3p, miR-148b-3p, miR-15a-5p, miR-15b-5p, miR-151a-5p, miR-151b, miR-16-5p, miR-182-5p, miR-183-5p, miR-186-5p, miR-22-3p, miR-221-3p, miR-223-3p, miR-23a-3p, miR-26a-5p, miR-26b-5p, miR-27b-3p, miR-28-3p, miR-30b-5p, miR-30c-5p, miR-342-3p, miR-425-5p, miR-451a, miR-532-5p, miR-550a-3p, miR-584-5p, miR-93-5p) were significantly downregulated in sALS. We also found that different miRNAs profiles characterized the bulbar/spinal onset and the progression rate. This observation supports the hypothesis that miRNAs may impact the phenotypic expression of the disease. Genes known to be associated with ALS (e.g., PARK7, C9orf72, ALS2, MATR3, SPG11, ATXN2) were confirmed to be dysregulated in our study. We also identified other potential candidate genes like LGALS3 (implicated in neuroinflammation) and PRKCD (activated in mitochondrial-induced apoptosis). Some of the downregulated genes are involved in molecular bindings to ions (i.e., metals, zinc, magnesium) and in ions-related functions. The genes that we found upregulated were involved in the immune response, oxidation-reduction, and apoptosis. These findings may have important implication for the monitoring, e.g., of sALS progression and therefore represent a significant advance in the elucidation of the disease's underlying molecular mechanisms. The extensive multidisciplinary approach we applied in this study was critically important for its success, especially in complex disorders such as sALS, wherein access to genetic background is a major limitation.
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Affiliation(s)
- Maria Liguori
- National Research Council, Institute of Biomedical Technologies, Bari Unit, Bari, Italy
| | - Nicoletta Nuzziello
- National Research Council, Institute of Biomedical Technologies, Bari Unit, Bari, Italy
| | - Alessandro Introna
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, Bari, Italy
| | - Arianna Consiglio
- National Research Council, Institute of Biomedical Technologies, Bari Unit, Bari, Italy
| | - Flavio Licciulli
- National Research Council, Institute of Biomedical Technologies, Bari Unit, Bari, Italy
| | - Eustachio D’Errico
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, Bari, Italy
| | - Antonio Scarafino
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, Bari, Italy
| | - Eugenio Distaso
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, Bari, Italy
| | - Isabella L. Simone
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, Bari, Italy
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A workflow for the integrative transcriptomic description of molecular pathology and the suggestion of normalizing compounds, exemplified by Parkinson's disease. Sci Rep 2018; 8:7937. [PMID: 29784986 PMCID: PMC5962550 DOI: 10.1038/s41598-018-25754-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 04/06/2018] [Indexed: 12/13/2022] Open
Abstract
The volume of molecular observations on human diseases in public databases is continuously increasing at accelerating rates. A bottleneck is their computational integration into a coherent description, from which researchers may derive new well-founded hypotheses. Also, the need to integrate data from different technologies (genetics, coding and regulatory RNA, proteomics) emerged in order to identify biomarkers for early diagnosis and prognosis of complex diseases and therefore facilitating the development of novel treatment approaches. We propose here a workflow for the integrative transcriptomic description of the molecular pathology in Parkinsons’s Disease (PD), including suggestions of compounds normalizing disease-induced transcriptional changes as a paradigmatic example. We integrated gene expression profiles, miRNA signatures, and publicly available regulatory databases to specify a partial model of the molecular pathophysiology of PD. Six genetic driver elements (2 genes and 4 miRNAs) and several functional network modules that are associated with PD were identified. Functional modules were assessed for their statistical significance, cellular functional homogeneity, literature evidence, and normalizing small molecules. In summary, our workflow for the joint regulatory analysis of coding and non-coding RNA, has the potential to yield clinically as well as biologically relevant information, as demonstrated here on PD data.
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Habib R, Noureen N, Nadeem N. Decoding Common Features of Neurodegenerative Disorders: From Differentially Expressed Genes to Pathways. Curr Genomics 2018; 19:300-312. [PMID: 29755292 PMCID: PMC5930451 DOI: 10.2174/1389202918666171005100549] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Neurodegeneration is a progressive/irreversible loss of neurons, building blocks of our nervous system. Their degeneration gradually collapses the entire structural and functional system manifesting in myriads of clinical disorders categorized as Neurodegenerative Disorders (NDs) such as Alzheimer's Disease, (AD), Parkinson's Disease (PD), Frontotemporal Dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS). NDs are characterized by a puzzling interplay of molecular and cellular defects affecting subset of neuronal populations in specific affected brain areas. OBJECTIVE In present study, comparative in silico analysis was performed by utilizing gene expression datasets of AD, PD, FTD and ALS to identify potential common features to gain insights into complex molecular pathophysiology of the selected NDs. METHODS Gene expression data of four disorders were subjected to the identification of Differential Gene Expression (DEG) and their mapping on biological processes, KEGG pathways and molecular functions. Detailed comparative analysis was performed to highlight the common grounds of these dis-orders at various stages. RESULTS Astoundingly, 106 DEGs were found to be common across all disorders. Alongwith in total 100 GO terms and 7 KEGG pathways were found to be significantly enriched across all disorders. EGFR, CDC42 and CREBBP have been identified as the significantly interacting nodes in gene-gene in-teraction and in Protein-Protein Interaction (PPI) network as well. Furthermore, interaction of common DEGs targets with miRNA's has been scrutinized. CONCLUSION The complex molecular underpinnings of these disorders are currently elusive. Despite heterogeneous clinical and pathological expressions, common features have been recognized in many NDs which provide evidence of their convergence.
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Affiliation(s)
| | - Nighat Noureen
- Address correspondence to this author at the Biosciences Department, COMSATS Institute of Information Technology, Islamabad, Pakistan; Tel: + (051) 9247000-6104; E-mail:
| | - Neha Nadeem
- Biosciences Department, COMSATS Institute of Information Technology, Islamabad, Pakistan
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Kucherenko MM, Shcherbata HR. miRNA targeting and alternative splicing in the stress response - events hosted by membrane-less compartments. J Cell Sci 2018; 131:131/4/jcs202002. [PMID: 29444950 DOI: 10.1242/jcs.202002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Stress can be temporary or chronic, and mild or acute. Depending on its extent and severity, cells either alter their metabolism, and adopt a new state, or die. Fluctuations in environmental conditions occur frequently, and such stress disturbs cellular homeostasis, but in general, stresses are reversible and last only a short time. There is increasing evidence that regulation of gene expression in response to temporal stress happens post-transcriptionally in specialized subcellular membrane-less compartments called ribonucleoprotein (RNP) granules. RNP granules assemble through a concentration-dependent liquid-liquid phase separation of RNA-binding proteins that contain low-complexity sequence domains (LCDs). Interestingly, many factors that regulate microRNA (miRNA) biogenesis and alternative splicing are RNA-binding proteins that contain LCDs and localize to stress-induced liquid-like compartments. Consequently, gene silencing through miRNAs and alternative splicing of pre-mRNAs are emerging as crucial post-transcriptional mechanisms that function on a genome-wide scale to regulate the cellular stress response. In this Review, we describe the interplay between these two post-transcriptional processes that occur in liquid-like compartments as an adaptive cellular response to stress.
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Affiliation(s)
- Mariya M Kucherenko
- Max Planck Research Group of Gene Expression and Signaling, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Halyna R Shcherbata
- Max Planck Research Group of Gene Expression and Signaling, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
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Mie Y, Hirano Y, Kowata K, Nakamura A, Yasunaga M, Nakajima Y, Komatsu Y. Function Control of Anti-microRNA Oligonucleotides Using Interstrand Cross-Linked Duplexes. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 10:64-74. [PMID: 29499957 PMCID: PMC5734696 DOI: 10.1016/j.omtn.2017.11.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 11/08/2017] [Accepted: 11/08/2017] [Indexed: 12/11/2022]
Abstract
MicroRNA (miRNA)-guided argonaute (Ago) controls gene expression upon binding to the 3′ UTR of mRNA. The miRNA function can be competitively inhibited by single-stranded anti-miRNA oligonucleotides (AMOs). In this study, we constructed a novel type of AMO flanked by interstrand cross-linked 2′-O-methylated RNA duplexes (CLs) that confer a stable helical conformation. Compared with other structured AMOs, AMO flanked by CLs at the 5′ and 3′ termini exhibited much higher inhibitory activity in cells. Anti-miRNA activity, nuclease resistance, and miRNA modification pattern distinctly differed according to the CL-connected positions in AMOs. Moreover, we found that the 3′-side CL improves nuclease resistance, whereas the 5′-side CL contributes to stable binding with miRNA in Ago upon interaction with the 3′ part of miRNA. These structure-function relationship analyses of AMOs provide important insights into the function control of Ago-miRNA complexes, which will be useful for basic miRNA research as well as for determining therapeutic applications of AMO.
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Affiliation(s)
- Yasuhiro Mie
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yu Hirano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Keiko Kowata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Akiyoshi Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Mayu Yasunaga
- Health Research Institute, AIST, 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan
| | - Yoshihiro Nakajima
- Health Research Institute, AIST, 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
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