Expression of immune related genes and possible regulatory mechanisms in different stages of non-alcoholic fatty liver disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38524129", "kind": "science-record", "revision": 4, "content_hash": "sha256:ffc418e99255e87eaf9be401b7143aee3c60befe32fcbfa07e8f89611ada1de9", "created_at": "2026-11-01T19:20:28Z", "updated_at": "2026-11-01T22:53:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Expression of immune related genes and possible regulatory mechanisms in different stages of non-alcoholic fatty liver disease.", "doi": "10.3389/fimmu.2024.1364442", "pmid": "38524129", "authors": ["Risheng He", "Canghai Guan", "Xudong Zhao", "Liang Yu", "Yunfu Cui"], "journal": "Frontiers in immunology", "year": 2024, "abstract": "Background: Non-alcoholic fatty liver disease (NAFLD), which includes simple steatosis (SS) and non-alcoholic steatohepatitis (NASH), is a significant contributor to liver disease on a global scale. The change of immunity-related genes (IRGs) expression level leads to different immune infiltrations. However, the expression of IRGs and possible regulatory mechanisms involved in NAFLD remain unclear. The objective of our research is to investigate crucial genes linked to the development of NAFLD and the transition from SS to NASH.\nMethods: Dataset GSE89632, which includes healthy controls, SS patients, and NASH patients, was obtained using the GEO database. To examine the correlation between sets of genes and clinical characteristics, we employed weighted gene co-expression network analysis (WGCNA) and differential expression analysis. Hub genes were extracted using a network of protein-protein interactions (PPI) and three different machine learning algorithms. To validate the findings, another dataset that is publicly accessible and mice that were subjected to a high-fat diet (HFD) or MCD diet were utilized. Furthermore, the ESTIMATE algorithm and ssGSEA were employed to investigate the immune landscape in the normal versus SS group and SS versus NASH group, additionally, the relationship between immune infiltration and the expression of hub genes was also examined.\nResults: A total of 28 immune related key genes were selected. Most of these genes expressed reverse patterns in the initial and progressive stages of NAFLD. GO and KEGG analyses showed that they were focused on the cytokine related pathways and immune cell activation and chemotaxis. After screening by various algorithms, we obtained two hub genes, including JUN and CCL20. Validation of these findings was confirmed by analyzing gene expression patterns in both the validation dataset and the mouse model. Ultimately, two hub genes were discovered to have a significant correlation with the infiltration of immune cells.\nConclusion: We proposed that there were dynamic changes in the expression levels of IRGs in different stages of NAFLD disease, which led to different immune landscapes in SS and NASH. The findings of our research could serve as a guide for the accurate management of various phases of NAFLD.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) were selected from the SS vs. NASH group using the R limma package (15), based on the threshold criteria of |log2FC| > 0.25 and p-value < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38524129", "locator": "sections[5] \"Identification of differentially expressed genes between SS samples and NASH samples\" paragraph 2", "quote": "Differentially expressed genes (DEGs) were selected from the SS vs. NASH group using the R limma package (15), based on the threshold criteria of |log2FC| > 0.25 and p-value < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38524129", "locator": "sections[25] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "After screening by various algorithms, we obtained two hub genes, including JUN and CCL20.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38524129", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "After screening by various algorithms, we obtained two hub genes, including JUN and CCL20."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "After screening by various algorithms, we obtained two hub genes, including JUN and CCL20.", "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:38524129"], "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:GSE135251"], "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:GSE135251"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38524129", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2024.1364442", "sha256": "sha256:1ce17295e81bd8580a7d1ba9584a9b9b9a4fd6677b598ce479554af7648eb75b", "bytes": 51439, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2024.1364442", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10957650", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE135251", "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=GSE135251", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE135251", "version": null, "note": "The original contributions presented in the study are included in the article/supplementary material. 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