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Aravindraja C, Jeepipalli S, Duncan WD, Vekariya KM, Rahaman SO, Chan EKL, Kesavalu L. Streptococcus gordonii Supragingival Bacterium Oral Infection-Induced Periodontitis and Robust miRNA Expression Kinetics. Int J Mol Sci 2024; 25:6217. [PMID: 38892405 PMCID: PMC11172800 DOI: 10.3390/ijms25116217] [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: 04/30/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Streptococcus gordonii (S. gordonii, Sg) is one of the early colonizing, supragingival commensal bacterium normally associated with oral health in human dental plaque. MicroRNAs (miRNAs) play an important role in the inflammation-mediated pathways and are involved in periodontal disease (PD) pathogenesis. PD is a polymicrobial dysbiotic immune-inflammatory disease initiated by microbes in the gingival sulcus/pockets. The objective of this study is to determine the global miRNA expression kinetics in S. gordonii DL1-infected C57BL/6J mice. All mice were randomly divided into four groups (n = 10 mice/group; 5 males and 5 females). Bacterial infection was performed in mice at 8 weeks and 16 weeks, mice were euthanized, and tissues harvested for analysis. We analyzed differentially expressed (DE) miRNAs in the mandibles of S. gordonii-infected mice. Gingival colonization/infection by S. gordonii and alveolar bone resorption (ABR) was confirmed. All the S. gordonii-infected mice at two specific time points showed bacterial colonization (100%) in the gingival surface, and a significant increase in mandible and maxilla ABR (p < 0.0001). miRNA profiling revealed 191 upregulated miRNAs (miR-375, miR-34b-5p) and 22 downregulated miRNAs (miR-133, miR-1224) in the mandibles of S. gordonii-infected mice at the 8-week mark. Conversely, at 16 weeks post-infection, 10 miRNAs (miR-1902, miR-203) were upregulated and 32 miRNAs (miR-1937c, miR-720) were downregulated. Two miRNAs, miR-210 and miR-423-5p, were commonly upregulated, and miR-2135 and miR-145 were commonly downregulated in both 8- and 16-week-infected mice mandibles. Furthermore, we employed five machine learning (ML) algorithms to assess how the number of miRNA copies correlates with S. gordonii infections in mice. In the ML analyses, miR-22 and miR-30c (8-week), miR-720 and miR-339-5p (16-week), and miR-720, miR-22, and miR-339-5p (combined 8- and 16-week) emerged as the most influential miRNAs.
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Affiliation(s)
- Chairmandurai Aravindraja
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA; (C.A.); (S.J.); (K.M.V.)
| | - Syam Jeepipalli
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA; (C.A.); (S.J.); (K.M.V.)
| | - William D. Duncan
- Department of Community Dentistry and Behavioral Science, College of Dentistry, University of Florida, Gainesville, FL 32610, USA;
| | - Krishna Mukesh Vekariya
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA; (C.A.); (S.J.); (K.M.V.)
| | - Shaik O. Rahaman
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA;
| | - Edward K. L. Chan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA;
| | - Lakshmyya Kesavalu
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA; (C.A.); (S.J.); (K.M.V.)
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, USA;
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Rochín-Hernández LJ, Rochín-Hernández LS, Padilla-Cristerna ML, Duarte-García A, Jiménez-Acosta MA, Figueroa-Corona MP, Meraz-Ríos MA. Mesenchymal Stem Cells from Familial Alzheimer's Patients Express MicroRNA Differently. Int J Mol Sci 2024; 25:1580. [PMID: 38338859 PMCID: PMC10855944 DOI: 10.3390/ijms25031580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/13/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the predominant form of dementia globally. No reliable diagnostic, predictive techniques, or curative interventions are available. MicroRNAs (miRNAs) are vital to controlling gene expression, making them valuable biomarkers for diagnosis and prognosis. This study examines the transcriptome of olfactory ecto-mesenchymal stem cells (MSCs) derived from individuals with the PSEN1(A431E) mutation (Jalisco mutation). The aim is to determine whether this mutation affects the transcriptome and expression profile of miRNAs and their target genes at different stages of asymptomatic, presymptomatic, and symptomatic conditions. Expression microarrays compare the MSCs from mutation carriers with those from healthy donors. The results indicate a distinct variation in the expression of miRNAs and mRNAs among different symptomatologic groups and between individuals with the mutation. Using bioinformatics tools allows us to identify target genes for miRNAs, which in turn affect various biological processes and pathways. These include the cell cycle, senescence, transcription, and pathways involved in regulating the pluripotency of stem cells. These processes are closely linked to inter- and intracellular communication, vital for cellular functioning. These findings can enhance our comprehension and monitoring of the disease's physiological processes, identify new disorder indicators, and develop innovative treatments and diagnostic tools for preventing or treating AD.
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Affiliation(s)
- Lory J. Rochín-Hernández
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.L.P.-C.); (A.D.-G.); (M.A.J.-A.); (M.P.F.-C.)
| | - Lory S. Rochín-Hernández
- Departamento de Biotecnología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico;
| | - Mayte L. Padilla-Cristerna
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.L.P.-C.); (A.D.-G.); (M.A.J.-A.); (M.P.F.-C.)
| | - Andrea Duarte-García
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.L.P.-C.); (A.D.-G.); (M.A.J.-A.); (M.P.F.-C.)
| | - Miguel A. Jiménez-Acosta
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.L.P.-C.); (A.D.-G.); (M.A.J.-A.); (M.P.F.-C.)
| | - María P. Figueroa-Corona
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.L.P.-C.); (A.D.-G.); (M.A.J.-A.); (M.P.F.-C.)
| | - Marco A. Meraz-Ríos
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico; (L.J.R.-H.); (M.L.P.-C.); (A.D.-G.); (M.A.J.-A.); (M.P.F.-C.)
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Mohammadi-Pilehdarboni H, Shenagari M, Joukar F, Naziri H, Mansour-Ghanaei F. Alzheimer's disease and microorganisms: the non-coding RNAs crosstalk. Front Cell Neurosci 2024; 17:1256100. [PMID: 38249527 PMCID: PMC10796784 DOI: 10.3389/fncel.2023.1256100] [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: 07/10/2023] [Accepted: 10/25/2023] [Indexed: 01/23/2024] Open
Abstract
Alzheimer's disease (AD) is a complex, multifactorial disorder, influenced by a multitude of variables ranging from genetic factors, age, and head injuries to vascular diseases, infections, and various other environmental and demographic determinants. Among the environmental factors, the role of the microbiome in the genesis of neurodegenerative disorders (NDs) is gaining increased recognition. This paradigm shift is substantiated by an extensive body of scientific literature, which underscores the significant contributions of microorganisms, encompassing viruses and gut-derived bacteria, to the pathogenesis of AD. The mechanism by which microbial infection exerts its influence on AD hinges primarily on inflammation. Neuroinflammation, activated in response to microbial infections, acts as a defense mechanism for the brain but can inadvertently lead to unexpected neuropathological perturbations, ultimately contributing to NDs. Given the ongoing uncertainty surrounding the genetic factors underpinning ND, comprehensive investigations into environmental factors, particularly the microbiome and viral agents, are imperative. Recent advances in neuroscientific research have unveiled the pivotal role of non-coding RNAs (ncRNAs) in orchestrating various pathways integral to neurodegenerative pathologies. While the upstream regulators governing the pathological manifestations of microorganisms remain elusive, an in-depth exploration of the nuanced role of ncRNAs holds promise for the development of prospective therapeutic interventions. This review aims to elucidate the pivotal role of ncRNAs as master modulators in the realm of neurodegenerative conditions, with a specific focus on Alzheimer's disease.
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Affiliation(s)
- Hanieh Mohammadi-Pilehdarboni
- Faculty of Medicine and Dentistry and the School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Shenagari
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Farahnaz Joukar
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Hamed Naziri
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Fariborz Mansour-Ghanaei
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
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Miao B, Xing X, Bazylianska V, Madden P, Moszczynska A, Zhang B. Methamphetamine-induced region-specific transcriptomic and epigenetic changes in the brain of male rats. Commun Biol 2023; 6:991. [PMID: 37758941 PMCID: PMC10533900 DOI: 10.1038/s42003-023-05355-3] [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: 07/13/2022] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Psychostimulant methamphetamine (METH) is neurotoxic to the brain and, therefore, its misuse leads to neurological and psychiatric disorders. The gene regulatory network (GRN) response to neurotoxic METH binge remains unclear in most brain regions. Here we examined the effects of binge METH on the GRN in the nucleus accumbens, dentate gyrus, Ammon's horn, and subventricular zone in male rats. At 24 h after METH, ~16% of genes displayed altered expression and over a quarter of previously open chromatin regions - parts of the genome where genes are typically active - showed shifts in their accessibility. Intriguingly, most changes were unique to each area studied, and independent regulation between transcriptome and chromatin accessibility was observed. Unexpectedly, METH differentially impacted gene activity and chromatin accessibility within the dentate gyrus and Ammon's horn. Around 70% of the affected chromatin-accessible regions in the rat brain have conserved DNA sequences in the human genome. These regions frequently act as enhancers, ramping up the activity of nearby genes, and contain mutations linked to various neurological conditions. By sketching out the gene regulatory networks associated with binge METH in specific brain regions, our study offers fresh insights into how METH can trigger profound, region-specific molecular shifts.
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Affiliation(s)
- Benpeng Miao
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Genetics, Center for Genomic Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Center for Genomic Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Viktoriia Bazylianska
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Pamela Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anna Moszczynska
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, 48201, USA.
| | - Bo Zhang
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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Xie G, Chen H, He C, Hu S, Xiao X, Luo Q. The dysregulation of miRNAs in epilepsy and their regulatory role in inflammation and apoptosis. Funct Integr Genomics 2023; 23:287. [PMID: 37653173 PMCID: PMC10471759 DOI: 10.1007/s10142-023-01220-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/22/2023] [Accepted: 08/26/2023] [Indexed: 09/02/2023]
Abstract
Epilepsy is a neurological disorder that impacts millions of people worldwide, and it is characterized by the occurrence of recurrent seizures. The pathogenesis of epilepsy is complex, involving dysregulation of various genes and signaling pathways. MicroRNAs (miRNAs) are a group of small non-coding RNAs that play a vital role in the regulation of gene expression. They have been found to be involved in the pathogenesis of epilepsy, acting as key regulators of neuronal excitability and synaptic plasticity. In recent years, there has been a growing interest in exploring the miRNA regulatory network in epilepsy. This review summarizes the current knowledge of the regulatory miRNAs involved in inflammation and apoptosis in epilepsy and discusses its potential as a new avenue for developing targeted therapies for the treatment of epilepsy.
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Affiliation(s)
- Guoping Xie
- Department of Clinical Laboratory, The Second Staff Hospital of Wuhan Iron and Steel (Group) Corporation, Wuhan, Hubei, China
| | - Huan Chen
- Department of Clinical Laboratory, Wuhan Institute of Technology Hospital, Wuhan Institute of Technology, Wuhan, China
| | - Chan He
- Department of Clinical Laboratory, Maternal and Child Health Hospital in Wuchang District, Wuhan, Hubei, China
| | - Siheng Hu
- Department of Clinical Laboratory, Honggangcheng Street Community Health Service Center, Qingshan District, Wuhan, Hubei, China
| | - Xue Xiao
- Department of Clinical Laboratory, Gongrencun Street Community Health Service Center, Wuhan, China
| | - Qunying Luo
- Department of Neurology, Huarun Wuhan Iron and Steel General Hospital, Wuhan, Hubei, China.
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Ryu IS, Kim DH, Ro JY, Park BG, Kim SH, Im JY, Lee JY, Yoon SJ, Kang H, Iwatsubo T, Teunissen CE, Cho HJ, Ryu JH. The microRNA-485-3p concentration in salivary exosome-enriched extracellular vesicles is related to amyloid β deposition in the brain of patients with Alzheimer's disease. Clin Biochem 2023:110603. [PMID: 37355215 DOI: 10.1016/j.clinbiochem.2023.110603] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
OBJECTIVES Alzheimer's disease (AD) is an irreversible neurodegenerative disease characterized by progressive long-term memory loss and cognitive dysfunction. Neuroimaging tests for abnormal amyloid-β (Aβ) deposition are considered the most reliable methods for the diagnosis of AD; however, the cost for such testing is very high and generally not covered by national insurance systems. Accordingly, it is only recommended for individuals exhibiting clinical symptoms of AD supported by clinical cognitive assessments. Recently, it was suggested that dysregulated microRNA-485-3p (miRNA-485-3p) in the brain and cerebrospinal fluid is closely related to pathogenesis of AD. However, a relationship between circulating miRNA-485-3p in salivary exosome-enriched extracellular vesicles (EE-EV) and Aβ deposition in the brain has not been observed. DESIGN & METHODS Using quantitative real-time polymerase chain reaction, we analyzed miRNA-485-3p concentration in salivary EE-EV. We used receiver operating characteristic (ROC) curve analysis to evaluate its predictive value for Aβ positron emission tomography (Aβ-PET) positivity in patients with AD. RESULTS Our results showed that the miRNA-485-3p concentration in salivary EE-EV isolated from patients with AD was significantly increased compared with that in the healthy controls (p<0.0001). In the analysis of all participants, the miRNA-485-3p concentration was significantly increased in Aβ-PET-positive participants compared to Aβ-PET-negative participants (p<0.0001). Further analysis using only AD patients also showed that the miRNA-485-3p concentration was significantly increased in Aβ-PET-positive AD patients vs. Aβ-PET-negative AD patients (p=0.0063). The ROC curve analysis for differentiating Aβ-PET-positive and negative participants showed that the area under the curve for miRNA-485-3p was 0.9217. CONCLUSION These findings suggested that the miRNA-485-3p concentration in salivary EE-EV was closely related to Aβ deposition in the brain and had high diagnostic accuracy for predicting Aβ-PET positivity.
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Affiliation(s)
- In Soo Ryu
- BIORCHESTRA Co. Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Dae Hoon Kim
- BIORCHESTRA Co. Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Ju-Ye Ro
- BIORCHESTRA Co. Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Byeong-Gyu Park
- BIORCHESTRA Co. Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Seo Hyun Kim
- BIORCHESTRA Co. Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Jong-Yeop Im
- BIORCHESTRA Co. Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea
| | - Jun-Young Lee
- Borame Medical Center 20, Boramae-ro 5-gil, Dongjak-gu, Seoul 07061, South Korea
| | - Soo Jin Yoon
- Daejeon Eulji Medical Center, 95, Dunsanseo-ro, Seo-gu, Daejeon 35233, South Korea
| | - Heeyoung Kang
- Gyeongsang National University Hospital, 501, Jinju-daero, Jinju 52828, South Korea
| | - Takeshi Iwatsubo
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam 1081, Netherlands
| | - Hyun-Jeong Cho
- Department of Biomedical Laboratory Science, College of Medical Science, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, South Korea.
| | - Jin-Hyeob Ryu
- BIORCHESTRA Co. Ltd., 17, Techno 4-ro, Yuseong-gu, Daejeon 34013, South Korea; BIORCHESTRA US., Inc., 1 Kendall square, Building 200, Suite 2-103, Cambridge, MA, 02139, United States.
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