Identification and Analysis of Biomarkers Associated with Lipophagy and Therapeutic Agents for COVID-19.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38932215", "kind": "science-record", "revision": 4, "content_hash": "sha256:35139e709d3bef89b88c4bdc71d34f054e25b70912ef0d55fa29808a3eb259ff", "created_at": "2026-11-01T20:29:00Z", "updated_at": "2026-11-01T22:54:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Analysis of Biomarkers Associated with Lipophagy and Therapeutic Agents for COVID-19.", "doi": "10.3390/v16060923", "pmid": "38932215", "authors": ["Yujia Wu", "Zhenlin Wu", "Qiying Jin", "Jinyuan Liu", "Peiping Xu"], "journal": "Viruses", "year": 2024, "abstract": "BACKGROUND: Lipids, as a fundamental cell component, play an regulating role in controlling the different cellular biological processes involved in viral infections. A notable feature of coronavirus disease 2019 (COVID-19) is impaired lipid metabolism. The function of lipophagy-related genes in COVID-19 is unknown. The present study aimed to investigate biomarkers and drug targets associated with lipophagy and lipophagy-based therapeutic agents for COVID-19 through bioinformatics analysis.\nMETHODS: Lipophagy-related biomarkers for COVID-19 were identified using machine learning algorithms such as random forest, Support Vector Machine-Recursive Feature Elimination, Generalized Linear Model, and Extreme Gradient Boosting in three COVID-19-associated GEO datasets: scRNA-seq (GSE145926) and bulk RNA-seq (GSE183533 and GSE190496). The cMAP database was searched for potential COVID-19 medications.\nRESULTS: The lipophagy pathway was downregulated, and the lipid droplet formation pathway was upregulated, resulting in impaired lipid metabolism. Seven lipophagy-related genes, including ACADVL, HYOU1, DAP, AUP1, PRXAB2, LSS, and PLIN2, were used as biomarkers and drug targets for COVID-19. Moreover, lipophagy may play a role in COVID-19 pathogenesis. As prospective drugs for treating COVID-19, seven potential downregulators (phenoxybenzamine, helveticoside, lanatoside C, geldanamycin, loperamide, pioglitazone, and trichostatin A) were discovered. These medication candidates showed remarkable binding energies against the seven biomarkers.\nCONCLUSIONS: The lipophagy-related genes ACADVL, HYOU1, DAP, AUP1, PRXAB2, LSS, and PLIN2 can be used as biomarkers and drug targets for COVID-19. Seven potential downregulators of these seven biomarkers may have therapeutic effects for treating COVID-19.", "claims": [{"id": "claim-method", "statement": "DEGs between COVID-19 patients and the control group derived from the scRNA cells and RNAseq were identified using the DEG analysis in Seurat and the edgeR package in R, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38932215", "locator": "sections[5] \"2.3. Identification of Differentially Expressed Genes (DEGs)\" paragraph 2", "quote": "DEGs between COVID-19 patients and the control group derived from the scRNA cells and RNAseq were identified using the DEG analysis in Seurat and the edgeR package in R, respectively."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this article/Supplementary Materials.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38932215", "locator": "sections[30] \"Data Availability Statement\" paragraph 2", "quote": "All data generated or analyzed during this study are included in this article/Supplementary Materials."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Seven lipophagy-related genes, including ACADVL, HYOU1, DAP, AUP1, PRXAB2, LSS, and PLIN2, were used as biomarkers and drug targets for COVID-19.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38932215", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Seven lipophagy-related genes, including ACADVL, HYOU1, DAP, AUP1, PRXAB2, LSS, and PLIN2, were used as biomarkers and drug targets for COVID-19."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Seven lipophagy-related genes, including ACADVL, HYOU1, DAP, AUP1, PRXAB2, LSS, and PLIN2, were used as biomarkers and drug targets for COVID-19.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38932215"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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