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Yan L, Chen C, Wang L, Hong H, Wu C, Huang J, Jiang J, Chen J, Xu G, Cui Z. Analysis of gene expression in microglial apoptotic cell clearance following spinal cord injury based on machine learning algorithms. Exp Ther Med 2024; 28:292. [PMID: 38827468 PMCID: PMC11140288 DOI: 10.3892/etm.2024.12581] [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: 11/01/2023] [Accepted: 04/17/2024] [Indexed: 06/04/2024] Open
Abstract
Spinal cord injury (SCI) is a severe neurological complication following spinal fracture, which has long posed a challenge for clinicians. Microglia play a dual role in the pathophysiological process after SCI, both beneficial and detrimental. The underlying mechanisms of microglial actions following SCI require further exploration. The present study combined three different machine learning algorithms, namely weighted gene co-expression network analysis, random forest analysis and least absolute shrinkage and selection operator analysis, to screen for differentially expressed genes in the GSE96055 microglia dataset after SCI. It then used protein-protein interaction networks and gene set enrichment analysis with single genes to investigate the key genes and signaling pathways involved in microglial function following SCI. The results indicated that microglia not only participate in neuroinflammation but also serve a significant role in the clearance mechanism of apoptotic cells following SCI. Notably, bioinformatics analysis and lipopolysaccharide + UNC569 (a MerTK-specific inhibitor) stimulation of BV2 cell experiments showed that the expression levels of Anxa2, Myo1e and Spp1 in microglia were significantly upregulated following SCI, thus potentially involved in regulating the clearance mechanism of apoptotic cells. The present study suggested that Anxa2, Myo1e and Spp1 may serve as potential targets for the future treatment of SCI and provided a theoretical basis for the development of new methods and drugs for treating SCI.
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Affiliation(s)
- Lei Yan
- The First People's Hospital of Nantong, The Second Affiliated Hospital of Nantong University, Research Institute for Spine and Spinal Cord Disease of Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Chu Chen
- The First People's Hospital of Nantong, The Second Affiliated Hospital of Nantong University, Research Institute for Spine and Spinal Cord Disease of Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Lingling Wang
- The First People's Hospital of Nantong, The Second Affiliated Hospital of Nantong University, Research Institute for Spine and Spinal Cord Disease of Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Hongxiang Hong
- The First People's Hospital of Nantong, The Second Affiliated Hospital of Nantong University, Research Institute for Spine and Spinal Cord Disease of Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Chunshuai Wu
- The First People's Hospital of Nantong, The Second Affiliated Hospital of Nantong University, Research Institute for Spine and Spinal Cord Disease of Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Jiayi Huang
- The First People's Hospital of Nantong, The Second Affiliated Hospital of Nantong University, Research Institute for Spine and Spinal Cord Disease of Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Jiawei Jiang
- The First People's Hospital of Nantong, The Second Affiliated Hospital of Nantong University, Research Institute for Spine and Spinal Cord Disease of Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Jiajia Chen
- The First People's Hospital of Nantong, The Second Affiliated Hospital of Nantong University, Research Institute for Spine and Spinal Cord Disease of Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Guanhua Xu
- The First People's Hospital of Nantong, The Second Affiliated Hospital of Nantong University, Research Institute for Spine and Spinal Cord Disease of Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Zhiming Cui
- The First People's Hospital of Nantong, The Second Affiliated Hospital of Nantong University, Research Institute for Spine and Spinal Cord Disease of Nantong University, Nantong, Jiangsu 226019, P.R. China
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Chen Z, Zhang J, Pan Y, Hao Z, Li S. Extracellular vesicles as carriers for noncoding RNA-based regulation of macrophage/microglia polarization: an emerging candidate regulator for lung and traumatic brain injuries. Front Immunol 2024; 15:1343364. [PMID: 38558799 PMCID: PMC10978530 DOI: 10.3389/fimmu.2024.1343364] [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: 11/28/2023] [Accepted: 02/22/2024] [Indexed: 04/04/2024] Open
Abstract
Macrophage/microglia function as immune defense and homeostatic cells that originate from bone marrow progenitor cells. Macrophage/microglia activation is historically divided into proinflammatory M1 or anti-inflammatory M2 states based on intracellular dynamics and protein production. The polarization of macrophages/microglia involves a pivotal impact in modulating the development of inflammatory disorders, namely lung and traumatic brain injuries. Recent evidence indicates shared signaling pathways in lung and traumatic brain injuries, regulated through non-coding RNAs (ncRNAs) loaded into extracellular vesicles (EVs). This packaging protects ncRNAs from degradation. These vesicles are subcellular components released through a paracellular mechanism, constituting a group of nanoparticles that involve exosomes, microvesicles, and apoptotic bodies. EVs are characterized by a double-layered membrane and are abound with proteins, nucleic acids, and other bioactive compounds. ncRNAs are RNA molecules with functional roles, despite their absence of coding capacity. They actively participate in the regulation of mRNA expression and function through various mechanisms. Recent studies pointed out that selective packaging of ncRNAs into EVs plays a role in modulating distinct facets of macrophage/microglia polarization, under conditions of lung and traumatic brain injuries. This study will explore the latest findings regarding the role of EVs in the progression of lung and traumatic brain injuries, with a specific focus on the involvement of ncRNAs within these vesicles. The conclusion of this review will emphasize the clinical opportunities presented by EV-ncRNAs, underscoring their potential functions as both biomarkers and targets for therapeutic interventions.
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Affiliation(s)
- Zhihong Chen
- Department of Respiratory Medicine, The Third People’s Hospital of Longgang District, Shenzhen, China
| | - Jingang Zhang
- Department of Orthopedic, The Third People’s Hospital of Longgang District, Shenzhen, China
| | - Yongli Pan
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Zhongnan Hao
- Department of Neurology, University Medical Center of Göttingen, Georg-August-University of Göttingen, Göttingen, Lower Saxony, Germany
| | - Shuang Li
- Department of Respiratory Medicine, The Third People’s Hospital of Longgang District, Shenzhen, China
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Hernández-Contreras KA, Martínez-Díaz JA, Hernández-Aguilar ME, Herrera-Covarrubias D, Rojas-Durán F, Chi-Castañeda LD, García-Hernández LI, Aranda-Abreu GE. Alterations of mRNAs and Non-coding RNAs Associated with Neuroinflammation in Alzheimer's Disease. Mol Neurobiol 2024:10.1007/s12035-023-03908-5. [PMID: 38236345 DOI: 10.1007/s12035-023-03908-5] [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: 04/12/2023] [Accepted: 12/27/2023] [Indexed: 01/19/2024]
Abstract
Alzheimer's disease is a neurodegenerative pathology whose pathognomonic hallmarks are increased generation of β-amyloid (Aβ) peptide, production of hyperphosphorylated (pTau), and neuroinflammation. The last is an alteration closely related to the progression of AD and although it is present in multiple neurodegenerative diseases, the pathophysiological events that characterize neuroinflammatory processes vary depending on the disease. In this article, we focus on mRNA and non-coding RNA alterations as part of the pathophysiological events characteristic of neuroinflammation in AD and the influence of these alterations on the course of the disease through interaction with multiple RNAs related to the generation of Aβ, pTau, and neuroinflammation itself.
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Affiliation(s)
- Karla Aketzalli Hernández-Contreras
- Doctorado en Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Jorge Antonio Martínez-Díaz
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - María Elena Hernández-Aguilar
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Deissy Herrera-Covarrubias
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Fausto Rojas-Durán
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Lizbeth Donají Chi-Castañeda
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Luis Isauro García-Hernández
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Gonzalo Emiliano Aranda-Abreu
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México.
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