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Avila-Bonilla RG, Salas-Benito JS. Computational Screening to Predict MicroRNA Targets in the Flavivirus 3' UTR Genome: An Approach for Antiviral Development. Int J Mol Sci 2024; 25:10135. [PMID: 39337625 DOI: 10.3390/ijms251810135] [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: 08/27/2024] [Revised: 09/16/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
MicroRNAs (miRNAs) are molecules that influence messenger RNA (mRNA) expression levels by binding to the 3' untranslated region (3' UTR) of target genes. Host miRNAs can influence flavivirus replication, either by inducing changes in the host transcriptome or by directly binding to viral genomes. The 3' UTR of the flavivirus genome is a conserved region crucial for viral replication. Cells might exploit this well-preserved region by generating miRNAs that interact with it, ultimately impacting viral replication. Despite significant efforts to identify miRNAs capable of arresting viral replication, the potential of all these miRNAs to interact with the flavivirus 3' UTR is still poorly characterised. In this context, bioinformatic tools have been proposed as a fundamental part of accelerating the discovery of interactions between miRNAs and the 3' UTR of viral genomes. In this study, we performed a computational analysis to reveal potential miRNAs from human and mosquito species that bind to the 3' UTR of flaviviruses. In humans, miR-6842 and miR-661 were found, while in mosquitoes, miR-9-C, miR-2945-5p, miR-11924, miR-282-5p, and miR-79 were identified. These findings open new avenues for studying these miRNAs as antivirals against flavivirus infections.
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Affiliation(s)
- Rodolfo Gamaliel Avila-Bonilla
- Laboratorio de Genómica y Biología Molecular de ARNs, Departamento de Genética y Biología Molecular, Cinvestav, Av. IPN 2508, Mexico City 07360, Mexico
| | - Juan Santiago Salas-Benito
- Laboratorio de Biomedicina Molecular 3, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07320, Mexico
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2
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Omes C, Conti A, Benedetti L, Tomasoni V, De Marchi D, Nappi RE, Cusella De Angelis MG, Ceccarelli G. Expression of miRNA from spent pre-implantation embryos culture media. Reprod Biol 2024; 24:100847. [PMID: 38776743 DOI: 10.1016/j.repbio.2023.100847] [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: 04/29/2023] [Revised: 12/04/2023] [Accepted: 12/22/2023] [Indexed: 05/25/2024]
Abstract
This study examines the expression of three microRNAs (hsa-miR-661, hsa-miR-21-5p, hsa-miR-372-5p) in spent pre-implantation embryos culture media to identify possible new non-invasive biomarkers of embryo competence, predictive of development to the blastocyst stage. A preliminary analysis on 16 patients undergoing IVF cycles was performed by collecting and stored spent culture media on the fifth/sixth day of embryo culture. Expression of miRNAs was evaluated according to the embryos' fate: 1) NE/DG: non-evolved or degenerate embryos; 2) BLOK: embryos developed to the blastocyst stage. Preliminary results revealed a higher miRNAs expression in NE/DG spent media. To elucidate the roles of these miRNAs, we employed a robust bioinformatics pipeline involving: 1) in-silico miRNA Target Prediction using RNAHybrid, which identified the most-likely gene targets; 2) Construction of a Protein-Protein Interaction network via GeneMania, linking genes with significant biological correlations; 3) application of modularity-based clustering with the gLay app in Cytoscape, resulting in three size-adapted subnets for focused analysis; 4) Enrichment Analysis to discern the biological pathways influenced by the miRNAs. Our bioinformatics analysis revealed that hsa-miR-661 was closely associated with pathways regulating cell shape and morphogenesis of the epithelial sheet. These data suggest the potential use of certain miRNAs to identify embryos with a higher likelihood of developing to the blastocyst stage. Further analysis will be necessary to explore the reproducibility of these findings and to understand if miRNAs here investigated can be used as biomarkers for embryo selection before implantation into the uterus or if they may be reliable predictors of IVF outcome.
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Affiliation(s)
- Claudia Omes
- Center for Reproductive Medicine - Obstetrics and Gynecology Unit 2, Woman and Child Health Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
| | - Alice Conti
- Human Anatomy Unit, Department of Public Health, Experimental Medicine and Forensic, University of Pavia, Pavia, Italy
| | - Laura Benedetti
- Human Anatomy Unit, Department of Public Health, Experimental Medicine and Forensic, University of Pavia, Pavia, Italy
| | - Veronica Tomasoni
- Center for Reproductive Medicine - Obstetrics and Gynecology Unit 2, Woman and Child Health Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Davide De Marchi
- Centre for Health Technologies (CHT), University of Pavia, Pavia, Italy; Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Rossella E Nappi
- Center for Reproductive Medicine - Obstetrics and Gynecology Unit 2, Woman and Child Health Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - M Gabriella Cusella De Angelis
- Human Anatomy Unit, Department of Public Health, Experimental Medicine and Forensic, University of Pavia, Pavia, Italy; Centre for Health Technologies (CHT), University of Pavia, Pavia, Italy
| | - Gabriele Ceccarelli
- Human Anatomy Unit, Department of Public Health, Experimental Medicine and Forensic, University of Pavia, Pavia, Italy; Centre for Health Technologies (CHT), University of Pavia, Pavia, Italy
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Llera-Oyola J, Carceller H, Andreu Z, Hidalgo MR, Soler-Sáez I, Gordillo F, Gómez-Cabañes B, Roson B, de la Iglesia-Vayá M, Mancuso R, Guerini FR, Mizokami A, García-García F. The role of microRNAs in understanding sex-based differences in Alzheimer's disease. Biol Sex Differ 2024; 15:13. [PMID: 38297404 PMCID: PMC10832236 DOI: 10.1186/s13293-024-00588-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND The incidence of Alzheimer's disease (AD)-the most frequent cause of dementia-is expected to increase as life expectancies rise across the globe. While sex-based differences in AD have previously been described, there remain uncertainties regarding any association between sex and disease-associated molecular mechanisms. Studying sex-specific expression profiles of regulatory factors such as microRNAs (miRNAs) could contribute to more accurate disease diagnosis and treatment. METHODS A systematic review identified six studies of microRNA expression in AD patients that incorporated information regarding the biological sex of samples in the Gene Expression Omnibus repository. A differential microRNA expression analysis was performed, considering disease status and patient sex. Subsequently, results were integrated within a meta-analysis methodology, with a functional enrichment of meta-analysis results establishing an association between altered miRNA expression and relevant Gene Ontology terms. RESULTS Meta-analyses of miRNA expression profiles in blood samples revealed the alteration of sixteen miRNAs in female and 22 miRNAs in male AD patients. We discovered nine miRNAs commonly overexpressed in both sexes, suggesting a shared miRNA dysregulation profile. Functional enrichment results based on miRNA profiles revealed sex-based differences in biological processes; most affected processes related to ubiquitination, regulation of different kinase activities, and apoptotic processes in males, but RNA splicing and translation in females. Meta-analyses of miRNA expression profiles in brain samples revealed the alteration of six miRNAs in female and four miRNAs in male AD patients. We observed a single underexpressed miRNA in female and male AD patients (hsa-miR-767-5p); however, the functional enrichment analysis for brain samples did not reveal any specifically affected biological process. CONCLUSIONS Sex-specific meta-analyses supported the detection of differentially expressed miRNAs in female and male AD patients, highlighting the relevance of sex-based information in biomedical data. Further studies on miRNA regulation in AD patients should meet the criteria for comparability and standardization of information.
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Affiliation(s)
- Jaime Llera-Oyola
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
- Carlos Simon Foundation-INCLIVA Instituto de Investigación Sanitaria, Valencia, Spain
| | - Héctor Carceller
- Neurobiology Unit, Program in Neurosciences and Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, Burjassot, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spanish National Network for Research in Mental Health, Madrid, Spain
- Joint Unit in Biomedical Imaging FISABIO-CIPF, Foundation for the Promotion of Health and Biomedical Research of Valencia Region, València, Spain
| | - Zoraida Andreu
- Foundation Valencian Institute of Oncology (FIVO), 46009, Valencia, Spain
| | - Marta R Hidalgo
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
| | - Irene Soler-Sáez
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
| | - Fernando Gordillo
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
| | - Borja Gómez-Cabañes
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
| | - Beatriz Roson
- Carlos Simon Foundation-INCLIVA Instituto de Investigación Sanitaria, Valencia, Spain
| | - Maria de la Iglesia-Vayá
- Joint Unit in Biomedical Imaging FISABIO-CIPF, Foundation for the Promotion of Health and Biomedical Research of Valencia Region, València, Spain
| | - Roberta Mancuso
- IRCCS Fondazione Don Carlo Gnocchi ONLUS, 20148, Milan, Italy
| | | | - Akiko Mizokami
- Oral Health/Brain Health/Total Health (OBT) Research Center, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Francisco García-García
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain.
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4
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Awuson-David B, Williams AC, Wright B, Hill LJ, Di Pietro V. Common microRNA regulated pathways in Alzheimer's and Parkinson's disease. Front Neurosci 2023; 17:1228927. [PMID: 37719162 PMCID: PMC10502311 DOI: 10.3389/fnins.2023.1228927] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/02/2023] [Indexed: 09/19/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in gene regulation. Recently, miRNA dysregulation has been found in neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). The diagnosis of Alzheimer's and Parkinson's is currently challenging, mainly occurring when pathology is already present, and although treatments are available for both diseases, the role of treatment is primarily to prevent or delay the progress of the diseases instead of fully overcoming the diseases. Therefore, the challenge in the near future will be to determine effective drugs to tackle the dysregulated biological pathways in neurodegenerative diseases. In the present study, we describe the dysregulation of miRNAs in blood of Alzheimer's and Parkinson's patients with the aim to identify common mechanisms between the 2 pathologies and potentially to identify common therapeutic targets which can stop or delay the progression of two most frequent neuropathologies. Two independent systematic reviews, bioinformatic analysis, and experiment validation were performed to identify whether AD and PD share common pathways. A total of 15 common miRNAs were found in the literature and 13 common KEGG pathways. Among the common miRNAs, two were selected for validation in a small cohort of AD and PD patients. Let-7f-5p and miR-29b-3p showed to be good predictors in blood of PD patients.
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Affiliation(s)
- Betina Awuson-David
- School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Adrian C. Williams
- Department of Neurology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Benjamin Wright
- Department of Neurology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Lisa J. Hill
- School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Valentina Di Pietro
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
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Ma X, Feng Y, Quan X, Geng B, Li G, Fu X, Zeng L. Multi-omics analysis revealed the role of CCT2 in the induction of autophagy in Alzheimer's disease. Front Genet 2023; 13:967730. [PMID: 36704351 PMCID: PMC9871314 DOI: 10.3389/fgene.2022.967730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/07/2022] [Indexed: 01/12/2023] Open
Abstract
Chaperonin containing TCP1 subunit 2 (CCT2) is essential in various neurodegenerative diseases, albeit its role in the pathogenesis of Alzheimer's disease (AD) remains elusive. This study aimed to evaluate the role of CCT2 in Alzheimer's disease. First, bioinformatics database analysis revealed that CCT2 was significantly downregulated in patients with Alzheimer's disease and associated with autophagic clearance of β-amyloid. The 789 differentially expressed genes overlapped in AD-group and CCT2-low/high group, and the CCT2-high-associated genes screened by Pearson coefficients were enriched in protein folding, autophagy, and messenger RNA stability regulation pathways. These results suggest that CCT2 is significantly and positively associated with multiple pathways linked to autophagy and negatively associated with neuronal death. The logistic prediction model with 13 key genes, such as CCT2, screened in this study better predicts Alzheimer's disease occurrence (AUC = 0.9671) and is a favorable candidate for predicting potential biological targets of Alzheimer's disease. Additionally, this study predicts reciprocal micro RNAs and small molecule drugs for hub genes. Our findings suggest that low CCT2 expression may be responsible for the autophagy suppression in Alzheimer's disease, providing an accurate explanation for its pathogenesis and new targets and small molecule inhibitors for its treatment.
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Affiliation(s)
- Xueting Ma
- Edmond H. Fischer Signal Transduction laboratory, School of Life Sciences, Jilin University, Changchun, China
| | - Yuxin Feng
- Edmond H. Fischer Signal Transduction laboratory, School of Life Sciences, Jilin University, Changchun, China
| | - Xiangyu Quan
- Edmond H. Fischer Signal Transduction laboratory, School of Life Sciences, Jilin University, Changchun, China
| | - Bingyu Geng
- Edmond H. Fischer Signal Transduction laboratory, School of Life Sciences, Jilin University, Changchun, China
| | - Guodong Li
- Department of General Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Xueqi Fu
- Edmond H. Fischer Signal Transduction laboratory, School of Life Sciences, Jilin University, Changchun, China
| | - Linlin Zeng
- Edmond H. Fischer Signal Transduction laboratory, School of Life Sciences, Jilin University, Changchun, China,*Correspondence: Linlin Zeng,
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Scheper M, Romagnolo A, Besharat ZM, Iyer AM, Moavero R, Hertzberg C, Weschke B, Riney K, Feucht M, Scholl T, Petrak B, Maulisova A, Nabbout R, Jansen AC, Jansen FE, Lagae L, Urbanska M, Ferretti E, Tempes A, Blazejczyk M, Jaworski J, Kwiatkowski DJ, Jozwiak S, Kotulska K, Sadowski K, Borkowska J, Curatolo P, Mills JD, Aronica E. miRNAs and isomiRs: Serum-Based Biomarkers for the Development of Intellectual Disability and Autism Spectrum Disorder in Tuberous Sclerosis Complex. Biomedicines 2022; 10:biomedicines10081838. [PMID: 36009385 PMCID: PMC9405248 DOI: 10.3390/biomedicines10081838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/22/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is a rare multi-system genetic disorder characterized by a high incidence of epilepsy and neuropsychiatric manifestations known as tuberous-sclerosis-associated neuropsychiatric disorders (TANDs), including autism spectrum disorder (ASD) and intellectual disability (ID). MicroRNAs (miRNAs) are small regulatory non-coding RNAs that regulate the expression of more than 60% of all protein-coding genes in humans and have been reported to be dysregulated in several diseases, including TSC. In the current study, RNA sequencing analysis was performed to define the miRNA and isoform (isomiR) expression patterns in serum. A Receiver Operating Characteristic (ROC) curve analysis was used to identify circulating molecular biomarkers, miRNAs, and isomiRs, able to discriminate the development of neuropsychiatric comorbidity, either ASD, ID, or ASD + ID, in patients with TSC. Part of our bioinformatics predictions was verified with RT-qPCR performed on RNA isolated from patients’ serum. Our results support the notion that circulating miRNAs and isomiRs have the potential to aid standard clinical testing in the early risk assessment of ASD and ID development in TSC patients.
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Affiliation(s)
- Mirte Scheper
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.R.); (A.M.I.)
| | - Alessia Romagnolo
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.R.); (A.M.I.)
| | - Zein Mersini Besharat
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (Z.M.B.); (E.F.)
| | - Anand M. Iyer
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.R.); (A.M.I.)
- Internal Medicine, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Romina Moavero
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University, 00133 Rome, Italy; (R.M.); (P.C.)
- Child Neurology Unit, Neuroscience Department, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Christoph Hertzberg
- Diagnose-und Behandlungszentrum für Kinder, Vivantes-Klinikum Neukölln, 12351 Berlin, Germany;
| | - Bernhard Weschke
- Department of Neuropediatrics, Charité University Medicine Berlin, 13353 Berlin, Germany;
| | - Kate Riney
- Faculty of Medicine, The University of Queensland, Herston, QLD 4029, Australia;
- Neurosciences Unit, Queensland Children’s Hospital, South Brisbane, QLD 4101, Australia
| | - Martha Feucht
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, “Member of ERN EpiCARE”, 1090 Vienna, Austria; (M.F.); (T.S.)
| | - Theresa Scholl
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, “Member of ERN EpiCARE”, 1090 Vienna, Austria; (M.F.); (T.S.)
| | - Borivoj Petrak
- Motol University Hospital, Charles University, 15000 Prague, Czech Republic; (B.P.); (A.M.)
| | - Alice Maulisova
- Motol University Hospital, Charles University, 15000 Prague, Czech Republic; (B.P.); (A.M.)
| | - Rima Nabbout
- Reference Centre for Rare Epilepsies, Department of Pediatric Neurology, Necker Enfants Malades University Hospital, APHP, Member of ERN EpiCARE, Université de Paris, 149 Rue de Sèvres, 75015 Paris, France;
| | - Anna C. Jansen
- Department of Translational Neurosciences, University of Antwerp, 2000 Antwerp, Belgium;
| | - Floor E. Jansen
- Department of Child Neurology, Brain Center University Medical Center, Member of ERN EpiCare, 3584 BA Utrecht, The Netherlands;
| | - Lieven Lagae
- Department of Development and Regeneration Section Pediatric Neurology, University Hospitals KU Leuven, 3000 Leuven, Belgium;
| | - Malgorzata Urbanska
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.U.); (S.J.); (K.K.); (K.S.); (J.B.)
| | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (Z.M.B.); (E.F.)
| | - Aleksandra Tempes
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland; (A.T.); (M.B.); (J.J.)
| | - Magdalena Blazejczyk
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland; (A.T.); (M.B.); (J.J.)
| | - Jacek Jaworski
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland; (A.T.); (M.B.); (J.J.)
| | | | - Sergiusz Jozwiak
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.U.); (S.J.); (K.K.); (K.S.); (J.B.)
- Department of Child Neurology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Katarzyna Kotulska
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.U.); (S.J.); (K.K.); (K.S.); (J.B.)
| | - Krzysztof Sadowski
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.U.); (S.J.); (K.K.); (K.S.); (J.B.)
| | - Julita Borkowska
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.U.); (S.J.); (K.K.); (K.S.); (J.B.)
| | - Paolo Curatolo
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University, 00133 Rome, Italy; (R.M.); (P.C.)
| | - James D. Mills
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.R.); (A.M.I.)
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London WC1E 6BT, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter SL9 0RJ, UK
- Correspondence: (J.D.M.); (E.A.)
| | - Eleonora Aronica
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.R.); (A.M.I.)
- Correspondence: (J.D.M.); (E.A.)
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Dysregulated miRNAs in Progression and Pathogenesis of Alzheimer's Disease. Mol Neurobiol 2022; 59:6107-6124. [PMID: 35867206 DOI: 10.1007/s12035-022-02950-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 06/28/2022] [Indexed: 10/17/2022]
Abstract
Alzheimer's disease (AD) is a progressive degeneration of neurons due to the accumulation of amyloid-β peptide (Aβ) and hyper-phosphorylation of tau protein in the neuronal milieu leading to increased oxidative stress and apoptosis. Numerous factors contribute towards the progression of AD, including miRNA, which are 22-24 nucleotides long sequence which acts as critical regulators of cellular processes by binding to 3' UTR of mRNA, regulating its expression post-transcriptionally. This review aims to determine the miRNA with the most significant dysregulation in the brain and cerebrospinal fluid (CSF) of human patients. A systemized inclusion/exclusion criterion has been utilized based on selected keywords followed by screening of those articles to conclude a list of 8 highly dysregulated miRNAs based on the fold change of AD vs control patients, which could be used in clinical testing as these miRNAs play central role in the pathophysiology of AD. Furthermore, a network study of highly dysregulated miRNA estimated the association of these miRNA in the mediation of Aβ generation and aggregation, inhibition of autophagy, reduction of Aβ clearance, microglial and astrocytic activation, neuro-inflammation, tau hyper-phosphorylation, and synaptic loss.
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8
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Peña-Bautista C, Álvarez-Sánchez L, Cañada-Martínez AJ, Baquero M, Cháfer-Pericás C. Epigenomics and Lipidomics Integration in Alzheimer Disease: Pathways Involved in Early Stages. Biomedicines 2021; 9:1812. [PMID: 34944628 PMCID: PMC8698767 DOI: 10.3390/biomedicines9121812] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/23/2021] [Accepted: 11/29/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Alzheimer Disease (AD) is the most prevalent dementia. However, the physiopathological mechanisms involved in its development are unclear. In this sense, a multi-omics approach could provide some progress. METHODS Epigenomic and lipidomic analysis were carried out in plasma samples from patients with mild cognitive impairment (MCI) due to AD (n = 22), and healthy controls (n = 5). Then, omics integration between microRNAs (miRNAs) and lipids was performed by Sparse Partial Least Squares (s-PLS) regression and target genes for the selected miRNAs were identified. RESULTS 25 miRNAs and 25 lipids with higher loadings in the sPLS regression were selected. Lipids from phosphatidylethanolamines (PE), lysophosphatidylcholines (LPC), ceramides, phosphatidylcholines (PC), triglycerides (TG) and several long chain fatty acids families were identified as differentially expressed in AD. Among them, several fatty acids showed strong positive correlations with miRNAs studied. In fact, these miRNAs regulated genes implied in fatty acids metabolism, as elongation of very long-chain fatty acids (ELOVL), and fatty acid desaturases (FADs). CONCLUSIONS The lipidomic-epigenomic integration showed that several lipids and miRNAs were differentially expressed in AD, being the fatty acids mechanisms potentially involved in the disease development. However, further work about targeted analysis should be carried out in a larger cohort, in order to validate these preliminary results and study the proposed pathways in detail.
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Affiliation(s)
- Carmen Peña-Bautista
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (M.B.)
| | - Lourdes Álvarez-Sánchez
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (M.B.)
- Division of Neurology, University and Polytechnic Hospital La Fe, 46026 Valencia, Spain
| | | | - Miguel Baquero
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (M.B.)
- Division of Neurology, University and Polytechnic Hospital La Fe, 46026 Valencia, Spain
| | - Consuelo Cháfer-Pericás
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (M.B.)
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