Skip to main content
Key Specialties
Cardiology Diabetology Endocrinology Gastroenterology Geriatrics and Gerontology Gynecology and Obstetrics Hematology Infectious Disease Internal Medicine Nephrology Neurology Oncology Pediatrics Respiratory Medicine Rheumatology Surgery
Congress Coverage
2024 ACC Congress 2023 ESMO Congress 2023 EASD Congress 2023 ERS Congress 2023 ESC Congress
Clinical Collections
Advances in Alzheimer’s

At a glance: The STEP trials

A round-up of the STEP phase 3 clinical trials evaluating semaglutide for weight loss in people with overweight or obesity.
ADVANCED SEARCH
Log in
Top
Translational Stroke Research

28-04-2024 | Stroke | Research

Integrating Bulk RNA and Single-Cell Sequencing Data Unveils Efferocytosis Patterns and ceRNA Network in Ischemic Stroke

Authors: Jing Yuan, Yu-sha Liao, Tie-chun Zhang, Yu-qi Tang, Pei Yu, Ya-ning Liu, Ding-jun Cai, Shu-guang Yu, Ling Zhao

Published in: Translational Stroke Research

Login to get access

Abstract

Excessive inflammatory response following ischemic stroke (IS) injury is a key factor affecting the functional recovery of patients. The efferocytic clearance of apoptotic cells within ischemic brain tissue is a critical mechanism for mitigating inflammation, presenting a promising avenue for the treatment of ischemic stroke. However, the cellular and molecular mechanisms underlying efferocytosis in the brain after IS and its impact on brain injury and recovery are poorly understood. This study explored the roles of inflammation and efferocytosis in IS with bioinformatics. Three Gene Expression Omnibus Series (GSE) (GSE137482-3 m, GSE137482-18 m, and GSE30655) were obtained from NCBI (National Center for Biotechnology Information) and GEO (Gene Expression Omnibus). Differentially expressed genes (DEGs) were processed for GSEA (Gene Set Enrichment Analysis), GO (Gene Ontology Functional Enrichment Analysis), and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses. Efferocytosis-related genes were identified from the existing literature, following which the relationship between Differentially Expressed Genes (DEGs) and efferocytosis-related genes was examined. The single-cell dataset GSE174574 was employed to investigate the distinct expression profiles of efferocytosis-related genes. The identified hub genes were verified using the dataset of human brain and peripheral blood sample datasets GSE56267 and GSE122709. The dataset GSE215212 was used to predict competing endogenous RNA (ceRNA) network, and GSE231431 was applied to verify the expression of differential miRNAs. At last, the middle cerebral artery (MCAO) model was established to validate the efferocytosis process and the expression of hub genes. DEGs in two datasets were significantly enriched in pathways involved in inflammatory response and immunoregulation. Based on the least absolute shrinkage and selection operator (LASSO) analyses, we identified hub efferocytosis-related genes (Abca1, C1qc, Ptx3, Irf5, and Pros1) and key transcription factors (Stat5). The scRNA-seq analysis showed that these hub genes were mainly expressed in microglia and macrophages which are the main cells with efferocytosis function in the brain. We then identified miR-125b-5p as a therapeutic target of IS based on the ceRNA network. Finally, we validated the phagocytosis and clearance of dead cells by efferocytosis and the expression of hub gene Abca1 in MCAO mice models.
Appendix
Available only for authorised users
Literature
1.
Zhang W, et al. Macrophages reprogram after ischemic stroke and promote efferocytosis and inflammation resolution in the mouse brain. CNS Neurosci Ther. 2019;25:1329–42.PubMedPubMedCentralCrossRef
2.
3.
Greenhalgh AD, et al. Peripherally derived macrophages modulate microglial function to reduce inflammation after CNS injury. PLoS Biol. 2018;16:e2005264.PubMedPubMedCentralCrossRef
4.
Houlden A, et al. Brain injury induces specific changes in the caecal microbiota of mice via altered autonomic activity and mucoprotein production. Brain Behav Immun. 2016;57:10–20.PubMedPubMedCentralCrossRef
5.
Bustamante A, et al. The impact of post-stroke complications on in-hospital mortality depends on stroke severity. Eur Stroke J. 2017;2:54–63.PubMedCrossRef
6.
7.
8.
Nakahashi-Oda C, et al. CD300a blockade enhances efferocytosis by infiltrating myeloid cells and ameliorates neuronal deficit after ischemic stroke. Sci Immunol. 2021;6:eabe7915.PubMedCrossRef
9.
Gustavsson EK, Zhang D, Reynolds RH, Garcia-Ruiz S, Ryten M. Ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2. Bioinformatics. 2022;38:3844–6.PubMedPubMedCentralCrossRef
10.
11.
Leifman H, Kühlhorn E, Allebeck P, Andréasson S, Romelsjö A. Abstinence in late adolescence–antecedents to and covariates of a sober lifestyle and its consequences. Soc Sci Med. 1995;41:113–21.PubMedCrossRef
12.
13.
Chen W, et al. The ABCA1-efferocytosis axis: a new strategy to protect against atherosclerosis. Clin Chim Acta. 2021;518:1–8.PubMedCrossRef
14.
15.
Paraskevopoulou MD, et al. DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows. Nucleic Acids Res. 2013;41:169–73.CrossRef
16.
Chen Y, Wang X. miRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Res. 2020;48:D127–31.PubMedCrossRef
17.
18.
Li J-H, Liu S, Zhou H, Qu L-H, Yang J-H. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014;42:D92-97.PubMedCrossRef
19.
Zhu H, et al. Janus kinase inhibition ameliorates ischemic stroke injury and neuroinflammation through reducing NLRP3 inflammasome activation via JAK2/STAT3 pathway inhibition. Front Immunol. 2021;12:714943.PubMedPubMedCentralCrossRef
20.
Elliott MR, Koster KM, Murphy PS. Efferocytosis signaling in the regulation of macrophage inflammatory responses. J Immunol. 2017;198:1387–94.PubMedCrossRef
21.
Tokumaru Y, et al. KRAS signaling enriched triple negative breast cancer is associated with favorable tumor immune microenvironment and better survival. Am J Cancer Res. 2020;10:897–907.PubMedPubMedCentral
22.
An C, et al. Molecular dialogs between the ischemic brain and the peripheral immune system: dualistic roles in injury and repair. Prog Neurobiol. 2014;115:6–24.PubMedCrossRef
23.
24.
Dreikorn M, et al. Immunotherapy of experimental and human stroke with agents approved for multiple sclerosis: a systematic review. Ther Adv Neurol Disord. 2018;11:1756286418770626.PubMedPubMedCentralCrossRef
25.
Maïer B, et al. Neuroimaging is the new ‘spatial omic’: multi-omic approaches to neuro-inflammation and immuno-thrombosis in acute ischemic stroke. Semin Immunopathol. 2023;45:125–43.PubMedPubMedCentralCrossRef
26.
Gheibi Hayat SM, Bianconi V, Pirro M, Sahebkar A. Efferocytosis: molecular mechanisms and pathophysiological perspectives. Immunol Cell Biol. 2019;97:124–33.PubMedCrossRef
27.
28.
Babashamsi MM, Koukhaloo SZ, Halalkhor S, Salimi A, Babashamsi M. ABCA1 and metabolic syndrome; a review of the ABCA1 role in HDL-VLDL production, insulin-glucose homeostasis, inflammation and obesity. Diabetes Metab Syndr. 2019;13:1529–34.PubMedCrossRef
29.
Luciani MF, Chimini G. The ATP binding cassette transporter ABC1, is required for the engulfment of corpses generated by apoptotic cell death. EMBO J. 1996;15:226–35.PubMedPubMedCentralCrossRef
30.
31.
Yan W, et al. PTX3 alleviates hard metal-induced acute lung injury through potentiating efferocytosis. Ecotoxicol Environ Saf. 2022;230:113139.PubMedCrossRef
32.
Nebuloni M, et al. PTX3 expression in the heart tissues of patients with myocardial infarction and infectious myocarditis. Cardiovasc Pathol. 2011;20:e27-35.PubMedCrossRef
33.
Rolph MS, et al. Production of the long pentraxin PTX3 in advanced atherosclerotic plaques. Arterioscler Thromb Vasc Biol. 2002;22:e10-14.PubMedCrossRef
34.
Guo T, et al. PTX3 is located at the membrane of late apoptotic macrophages and mediates the phagocytosis of macrophages. J Clin Immunol. 2012;32:330–9.PubMedCrossRef
35.
Bohlson SS, Fraser DA, Tenner AJ. Complement proteins C1q and MBL are pattern recognition molecules that signal immediate and long-term protective immune functions. Mol Immunol. 2007;44:33–43.PubMedCrossRef
36.
Schartz ND, Tenner AJ. The good, the bad, and the opportunities of the complement system in neurodegenerative disease. J Neuroinflammation. 2020;17:354.PubMedPubMedCentralCrossRef
37.
Nauta AJ, et al. Biochemical and functional characterization of the interaction between pentraxin 3 and C1q. Eur J Immunol. 2003;33:465–73.PubMedCrossRef
38.
Kravitz MS, Pitashny M, Shoenfeld Y. Protective molecules–C-reactive protein (CRP), serum amyloid P (SAP), pentraxin3 (PTX3), mannose-binding lectin (MBL), and apolipoprotein A1 (Apo A1), and their autoantibodies: prevalence and clinical significance in autoimmunity. J Clin Immunol. 2005;25:582–91.PubMedCrossRef
39.
Krausgruber T, et al. IRF5 promotes inflammatory macrophage polarization and TH1-TH17 responses. Nat Immunol. 2011;12:231–8.PubMedCrossRef
40.
Seneviratne AN, et al. Interferon regulatory factor 5 controls necrotic core formation in atherosclerotic lesions by impairing efferocytosis. Circulation. 2017;136:1140–54.PubMedPubMedCentralCrossRef
41.
Lai Y-S, Putra RBDS, Aui S-P, Chang K-T. M2C polarization by baicalin enhances efferocytosis via upregulation of MERTK receptor. Am J Chin Med. 2018;46:1899–914.PubMedCrossRef
42.
43.
44.
45.
46.
Fan J, et al. Investigating the AC079305/DUSP1 axis as oxidative stress-related signatures and immune infiltration characteristics in ischemic stroke. Oxid Med Cell Longev. 2022;2022:8432352.PubMedPubMedCentralCrossRef
47.
Karagkouni D, et al. DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts. Nucleic Acids Res. 2020;48:D101–10.PubMed
48.
Ritter A. Modified shifted angular spectrum method for numerical propagation at reduced spatial sampling rates. Opt Express. 2014;22:26265–76.PubMedCrossRef
49.
50.
Li S, et al. Construction of lncRNA-mediated ceRNA network for investigating immune pathogenesis of ischemic stroke. Mol Neurobiol. 2021;58:4758–69.PubMedCrossRef
51.
Ma Z, et al. The construction and analysis of immune infiltration and competing endogenous RNA network in acute ischemic stroke. Front Aging Neurosci. 2022;14:806200.PubMedPubMedCentralCrossRef
Metadata
Title
Integrating Bulk RNA and Single-Cell Sequencing Data Unveils Efferocytosis Patterns and ceRNA Network in Ischemic Stroke
Authors
Jing Yuan
Yu-sha Liao
Tie-chun Zhang
Yu-qi Tang
Pei Yu
Ya-ning Liu
Ding-jun Cai
Shu-guang Yu
Ling Zhao
Publication date
28-04-2024
Publisher
Springer US
Keyword
Stroke
Published in
Translational Stroke Research
Print ISSN: 1868-4483
Electronic ISSN: 1868-601X
DOI
https://doi.org/10.1007/s12975-024-01255-8