Identification and validation of three diagnostic autophagy-related genes associated with advanced plaques and immune cell infiltration in carotid atherosclerosis based on integrated bioinformatics analyses.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39588003", "kind": "science-record", "revision": 3, "content_hash": "sha256:5489f9d63af79bd5e2e02c1b443b128fcea478d7194d9beef2e798be65d0292e", "created_at": "2026-11-01T20:29:51Z", "updated_at": "2026-11-01T22:13:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of three diagnostic autophagy-related genes associated with advanced plaques and immune cell infiltration in carotid atherosclerosis based on integrated bioinformatics analyses.", "doi": "10.7717/peerj.18543", "pmid": "39588003", "authors": ["Tiegen Huang", "Chen Su", "Quanli Su", "Yali Nie", "Zhenni Xiao", "Yao Tang", "Jiahao Wang", "Xiaotian Luo", "Yixin Tang"], "journal": "PeerJ", "year": 2024, "abstract": "Background: Autophagy plays a key role in the development of carotid atherosclerosis (CAS). This study aimed to identify key autophagy-related genes (ATGs) related with CAS using bioinformatics analysis, in vivo AS mouse model, and in vitro experiments.\nMethods: The GSE100927 and GSE28829 datasets were downloaded from the Gene Expression Omnibus (GEO) database. An integrated bioinformatics analyses of differentially expressed ATGs (DE-ATGs) was conducted. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to identify the biological processes and pathways associated with DE-ATGs. Protein-protein interaction (PPI) network was constructed with the DE-ATGs to identify the key CAS-related DE-ATGs. Receiver operating characteristic (ROC) curve analysis was used to determine the diagnostic value of the key CAS-related DE-ATGs. CIBERSORT analysis was performed to determine the infiltration status of 22 immune cell types and their correlation with the expression levels of the key CAS-related DE-ATGs. Hematoxylin and eosin (HE) staining was used to estimate the plaque histology in the AS mouse model. Western blotting, quantitative real-time PCR (qRT-PCR), and immunohistochemistry (IHC) were performed to validate the protein and mRNA expression levels of the key CAS-related DE-ATGs in the in vitro and in vivo models.\nResults: We compared transcriptome profiles of 12 early CAS plaques and 29 advanced CAS plaques in the GSE100927 dataset and identified 41 DE-ATGs (33 up-regulated and eight down-regulated). Functional enrichment analysis showed that the DE-ATGs were closely related with apoptosis, autophagy, and immune activation. ROC curve analysis showed that the area under the curve (AUC) values for the three key CAS-related DE-ATGs (CCL2, LAMP2, and CTSB) were 0.707, 0.977, and 0.951, respectively. CIBERSORT analyses showed close association between the three key CAS-related DE-ATGs and the infiltration of immune cell types in the plaques. Finally, the western blot, qRT-PCR, and IHC staining confirmed that CCL2, LAMP2, and CTSB were highly expressed in the plaques of the AS model mice or ox-LDL-treated human umbilical vein endothelial cells (HUVECs) and human aorta vascular smooth muscle cells (HAoSMCs).\nConclusion: We identified and validated three key CAS-associated ATGs, namely, CCL2, LAMP2, and CTSB with high diagnostic value. These three key CAS-associated ATGs are promising diagnostic markers and therapeutic targets for patients with CAS.", "claims": [{"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nThe genomics data is available at NCBI: GSE100927 and GSE28829.\nThe raw data is available at figshare: Tang, Yixin (2024). Identification and validation of three diagnostic autophagy-related genes associated with advanced plaques and immune cell infiltration in carotid atherosclerosis based on integrated bioinformatics analyses. figshare. Dataset. https://doi.org/10.6084/m9.figshare.26075161.v1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39588003", "locator": "sections[39] \"Data Availability Statement\" paragraphs 1-4", "quote": "The following information was supplied regarding data availability:\nThe genomics data is available at NCBI: GSE100927 and GSE28829.\nThe raw data is available at figshare: Tang, Yixin (2024). Identification and validation of three diagnostic autophagy-related genes associated with advanced plaques and immune cell infiltration in carotid atherosclerosis based on integrated bioinformatics analyses. figshare. Dataset. https://doi.org/10.6084/m9.figshare.26075161.v1."}], "state": "complete"}, {"id": "claim-target-result", "statement": "ROC curve analysis showed that the area under the curve (AUC) values for the three key CAS-related DE-ATGs (CCL2, LAMP2, and CTSB) were 0.707, 0.977, and 0.951, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39588003", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "ROC curve analysis showed that the area under the curve (AUC) values for the three key CAS-related DE-ATGs (CCL2, LAMP2, and CTSB) were 0.707, 0.977, and 0.951, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "ROC curve analysis showed that the area under the curve (AUC) values for the three key CAS-related DE-ATGs (CCL2, LAMP2, and CTSB) were 0.707, 0.977, and 0.951, respectively.", "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:39588003"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE100927"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE100927"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39588003", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.18543", "sha256": "sha256:cc8cb9c545a3f69c7f45eb71ae8e1981bf4cead09a5dd2c90b95c7aab364a176", "bytes": 50512, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.18543", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11587871", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE100927", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100927", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE100927", "version": null, "note": "The following information was supplied regarding data availability:\nThe genomics data is available at NCBI: GSE100927 and GSE28829.\nThe raw data is available at figshare: Tang, Yixin (2024). 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Methods: The GSE1", "d to estimate the plaque histology in the AS mouse model. Western blotting, quantitative real-time PC", "ated with CAS using bioinformatics analysis, in vivo AS mouse model, and in vitro experiments. Me", "key CAS-related DE-ATGs in the in vitro and in vivo models. Results: We compared transcriptome p"], "order_basis": "paper_text_order:367", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["the plaque histology in the AS mouse model. Western blotting, quantitative real-time PCR (qRT-PCR), and i", "mune cell types in the plaques. Finally, the western blot, qRT-PCR, and IHC staining confirmed that CC"], "order_basis": "paper_text_order:1326", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["mouse model. Western blotting, quantitative real-time PCR (qRT-PCR), and immunohistochemistry (IHC) we"], "order_basis": "paper_text_order:1357", "id": "assay:3"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["g, quantitative real-time PCR (qRT-PCR), and immunohistochemistry (IHC) were performed to validate the protein", "ime PCR (qRT-PCR), and immunohistochemistry (IHC) were performed to validate the protein and", "ues. Finally, the western blot, qRT-PCR, and IHC staining confirmed that CCL2, LAMP2, and CTS", "upp-9 Supplemental Information 10Raw data of IHC staining of CCL2 in the aortic root of the c"], "order_basis": "paper_text_order:1385", "id": "assay:4"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["d that the DE-ATGs were closely related with apoptosis, autophagy, and immune activation. ROC curve", "Gs were NOD-like receptor signaling pathway, apoptosis, autophagy, and immune activation (Fig. 4B;", "the CAS-related DE-ATGs were associated with apoptosis, autophagy, and immune activation. GO and KE"], "order_basis": "paper_text_order:1817", "id": "assay:5"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}