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CX3CR1–TLR4 Axis as a Shared Neuroimmune Target in COVID-19 and Epilepsy: Integrative Transcriptomics and Gabapentin Repositioning

Pan et al., Biomedicines, doi:10.3390/biomedicines13092133, Aug 2025
https://c19early.org/pan5.html
In silico study showing that gabapentin may be beneficial for COVID-19 treatment through shared neuroinflammatory pathways with epilepsy. Authors performed integrative transcriptomic analysis of COVID-19 peripheral blood mononuclear cells and epilepsy hippocampal tissue, identifying 25 shared differentially expressed genes including upregulated CX3CR1, TLR4, TNF, and CCL3 involved in cytokine signaling and immune cell recruitment.
Pan et al., 31 Aug 2025, peer-reviewed, 6 authors. Contact: ningjeny@126.com (corresponding author), 2024360094@gzhmu.edu.com.
In silico studies are an important part of preclinical research, however results may be very different in vivo.
CX3CR1–TLR4 Axis as a Shared Neuroimmune Target in COVID-19 and Epilepsy: Integrative Transcriptomics and Gabapentin Repositioning
Nannan Pan, Penghui Cao, Ben Chen, Li Chen, Xuezhen Liao, Yuping Ning
Biomedicines, doi:10.3390/biomedicines13092133
Introduction: Neuroinflammation is a common pathological hallmark of Coronavirus Disease 2019 (COVID-19) and epilepsy; however, their shared immunogenomic mechanisms remain poorly defined. This study explores shared immune-inflammatory transcriptomic signatures and identifies potential repositioning therapeutics. Methods: We integrated single-cell RNA-seq data from peripheral blood mononuclear cells (PBMCs) of COVID-19 patients and healthy donors (GSE149689), and bulk RNA-seq data from hippocampal tissue of patients with Temporal Lobe Epilepsy with Hippocampal Sclerosis (TLE-HS) and healthy controls (GSE256068). Common Differentially Expressed Genes (DEGs) were identified and subjected to GO/KEGG enrichment, a PPI network, hub gene detection (cytoHubba), and transcriptional regulation analysis (ENCODE-based TF/miRNA networks). Drug repositioning was performed using the LINCS L1000 database. Results: We identified 25 DEGs shared across datasets, including 22 upregulated genes enriched in cytokine-cytokine receptor interaction, NF-κB, and Toll-like receptor pathways. PPI analysis revealed a CX3CR1-TLR4-centered immune module. Gabapentin emerged as a promising repositioning candidate with potential to downregulate CX3CR1, TLR4, and selectin P ligand (SELPLG). Receiver Operating Characteristic (ROC) analysis confirmed the diagnostic value of these targets (AUC > 0.90 in epilepsy). A mechanistic model was proposed to illustrate Gabapentin's dual action on microglial polarization and cytokine suppression. Conclusions: Our results reveal a shared CX3CR1-TLR4-NF-κB inflammatory axis in COVID-19 and epilepsy, supporting Gabapentin as a potential dual-action immunomodulator. These findings reveal a previously underappreciated immunomodulatory role for Gabapentin, providing mechanistic rationale for its repositioning in neuroinflammatory conditions beyond seizure control.
Supplementary Materials: The following supporting information can be downloaded at: https: //www.mdpi.com/article/10.3390/biomedicines13092133/s1 , Supplementary File S1: Common upregulated DEGs with statistical details; Supplementary File S2:
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DOI record: { "DOI": "10.3390/biomedicines13092133", "ISSN": [ "2227-9059" ], "URL": "http://dx.doi.org/10.3390/biomedicines13092133", "abstract": "<jats:p>Introduction: Neuroinflammation is a common pathological hallmark of Coronavirus Disease 2019 (COVID-19) and epilepsy; however, their shared immunogenomic mechanisms remain poorly defined. This study explores shared immune-inflammatory transcriptomic signatures and identifies potential repositioning therapeutics. Methods: We integrated single-cell RNA-seq data from peripheral blood mononuclear cells (PBMCs) of COVID-19 patients and healthy donors (GSE149689), and bulk RNA-seq data from hippocampal tissue of patients with Temporal Lobe Epilepsy with Hippocampal Sclerosis (TLE-HS) and healthy controls (GSE256068). Common Differentially Expressed Genes (DEGs) were identified and subjected to GO/KEGG enrichment, a PPI network, hub gene detection (cytoHubba), and transcriptional regulation analysis (ENCODE-based TF/miRNA networks). Drug repositioning was performed using the LINCS L1000 database. Results: We identified 25 DEGs shared across datasets, including 22 upregulated genes enriched in cytokine–cytokine receptor interaction, NF-κB, and Toll-like receptor pathways. PPI analysis revealed a CX3CR1–TLR4-centered immune module. Gabapentin emerged as a promising repositioning candidate with potential to downregulate CX3CR1, TLR4, and selectin P ligand (SELPLG). Receiver Operating Characteristic (ROC) analysis confirmed the diagnostic value of these targets (AUC &gt; 0.90 in epilepsy). A mechanistic model was proposed to illustrate Gabapentin’s dual action on microglial polarization and cytokine suppression. Conclusions: Our results reveal a shared CX3CR1–TLR4–NF-κB inflammatory axis in COVID-19 and epilepsy, supporting Gabapentin as a potential dual-action immunomodulator. These findings reveal a previously underappreciated immunomodulatory role for Gabapentin, providing mechanistic rationale for its repositioning in neuroinflammatory conditions beyond seizure control.</jats:p>", "alternative-id": [ "biomedicines13092133" ], "author": [ { "affiliation": [ { "name": "Department of Neurology, Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou 510370, China" } ], "family": "Pan", "given": "Nannan", "sequence": "first" }, { "affiliation": [ { "name": "Department of Psychiatry, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China" } ], "family": "Cao", "given": "Penghui", "sequence": "additional" }, { "affiliation": [ { "name": "Geriatric Neuroscience Center, Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou 510370, China" } ], "family": "Chen", "given": "Ben", "sequence": "additional" }, { "affiliation": [ { "name": "Department of Neurology, Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou 510370, China" } ], "family": "Chen", "given": "Li", "sequence": "additional" }, { "affiliation": [ { "name": "Department of Neurology, Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou 510370, China" } ], "family": "Liao", "given": "Xuezhen", "sequence": "additional" }, { "ORCID": "https://orcid.org/0000-0002-5727-2782", "affiliation": [ { "name": "Geriatric Neuroscience Center, Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou 510370, China" }, { "name": "Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou Medical University, Guangzhou 511436, China" } ], "authenticated-orcid": false, "family": "Ning", "given": "Yuping", "sequence": "additional" } ], "container-title": "Biomedicines", "container-title-short": "Biomedicines", "content-domain": { "crossmark-restriction": false, "domain": [] }, "created": { "date-parts": [ [ 2025, 9, 1 ] ], "date-time": "2025-09-01T13:27:44Z", "timestamp": 1756733264000 }, "deposited": { "date-parts": [ [ 2025, 9, 1 ] ], "date-time": "2025-09-01T13:59:01Z", "timestamp": 1756735141000 }, "funder": [ { "DOI": "10.13039/501100001809", "award": [ "82371428", "82171533" ], "doi-asserted-by": "publisher", "id": [ { "asserted-by": "publisher", "id": "10.13039/501100001809", "id-type": "DOI" } ], "name": "National Natural Science Foundation of China" }, { "DOI": "10.13039/501100003453", "award": [ "2022A1515011623", "2024A1515011035" ], "doi-asserted-by": "publisher", "id": [ { "asserted-by": "publisher", "id": "10.13039/501100003453", "id-type": "DOI" } ], "name": "Natural Science Foundation of Guangdong Province" }, { "award": [ "202201003" ], "name": "Science and Technology Program of Liwan District, Guangzhou" }, { "award": [ "2023A03J0852", "2023A03J0853", "2023A03J0850" ], "name": "Guangzhou Science and Technology Plan Project—University-Enterprise Joint Funding" }, { "award": [ "2021ZD0201800" ], "name": "National Brain Science and Brain-Like Intelligence Technology Project" } ], "indexed": { "date-parts": [ [ 2025, 9, 1 ] ], "date-time": "2025-09-01T14:40:01Z", "timestamp": 1756737601461, "version": "3.44.0" }, "is-referenced-by-count": 0, "issue": "9", "issued": { "date-parts": [ [ 2025, 8, 31 ] ] }, "journal-issue": { "issue": "9", "published-online": { "date-parts": [ [ 2025, 9 ] ] } }, "language": "en", "license": [ { "URL": "https://creativecommons.org/licenses/by/4.0/", "content-version": "vor", "delay-in-days": 0, "start": { "date-parts": [ [ 2025, 8, 31 ] ], "date-time": "2025-08-31T00:00:00Z", "timestamp": 1756598400000 } } ], "link": [ { "URL": "https://www.mdpi.com/2227-9059/13/9/2133/pdf", "content-type": "unspecified", "content-version": "vor", "intended-application": "similarity-checking" } ], "member": "1968", "original-title": [], "page": "2133", "prefix": "10.3390", "published": { "date-parts": [ [ 2025, 8, 31 ] ] }, "published-online": { "date-parts": [ [ 2025, 8, 31 ] ] }, "publisher": "MDPI AG", "reference": [ { "DOI": "10.1001/jama.2022.10594", "article-title": "Review of Antiseizure Medications for Adults With Epilepsy", "author": "Majeed", "doi-asserted-by": "crossref", "first-page": "680", "journal-title": "JAMA", "key": "ref_1", "volume": "328", "year": "2022" }, { "DOI": "10.1038/s41573-024-00981-w", "article-title": "New epilepsy therapies in development", "author": "Klein", "doi-asserted-by": "crossref", "first-page": "682", "journal-title": "Nat. 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