Identification of Key Biomarkers and Immune Infiltration in Liver Tissue after Bariatric Surgery.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35789605", "kind": "science-record", "revision": 5, "content_hash": "sha256:43d03fc05dacf6cc2b378936c458af8727ecdcc26637141c7a7b69532df80154", "created_at": "2026-11-01T18:14:50Z", "updated_at": "2026-11-01T22:49:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Key Biomarkers and Immune Infiltration in Liver Tissue after Bariatric Surgery.", "doi": "10.1155/2022/4369329", "pmid": "35789605", "authors": ["Xiaoyan Zhang", "Jingxin Li", "Tiancai Liu", "Min Zhao", "Baozhu Liang", "Hong Chen", "Zhen Zhang"], "journal": "Disease markers", "year": 2022, "abstract": "Background: Few drugs are clearly available for nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH); nevertheless, mounting studies have provided sufficient evidence that bariatric surgery is efficient for multiple metabolic diseases, including NAFLD and NASH, while the molecular mechanisms are still poorly understood.\nMethods: The mRNA expression profiling of GSE48452 and GSE83452 were retrieved and obtained from the Gene Expression Omnibus (GEO) database. The limma package was employed for identifying differentially expressed genes (DEGs), followed by clusterProfiler for performing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and GSEA software for performing GSEA analyses. The PPI network analyses were constructed using Metascape online analyses. WGCNA was also utilized to identify and verify the hub genes. CIBERSORT tools contributed to the analysis of immune cell infiltration of liver diseases.\nResults: We identify coexpressed differential genes including 10 upregulated and 55 downregulated genes in liver tissue after bariatric surgery. GO and KEGG enrichment analyses indicated that DEGs were remarkably involved in the immune response. GSEA demonstrated that DEGs were markedly enriched in the immune response before surgery, while most were enriched in metabolism after surgery. Seven genes were screened through the MCC algorithm and KME values, including SRGN, CD53, EVI2B, MPEG1, NCKAP1L, LCP1, and TYROBP. The mRNA levels of these genes were verified in the Attie Lab Diabetes Database, and only LCP1 was found to have significant differences and correlation with certain immune cells.\nConclusion: Our knowledge of the mechanisms by which bariatric surgery benefits the liver and the discovery of LCP1 is expected to serve as potential biomarkers or therapeutic targets for NAFLD and NASH.", "claims": [{"id": "claim-method", "statement": "DEGs in liver tissue of postoperative samples were screened out by performing the limma V3.42.0 package with criteria of |log FC| > 0.5 and adj P < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35789605", "locator": "sections[4] \"2.2. Identification of Differentially Expressed Genes\" paragraph 2", "quote": "DEGs in liver tissue of postoperative samples were screened out by performing the limma V3.42.0 package with criteria of |log FC| > 0.5 and adj P < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the data used to support the research are included within this article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35789605", "locator": "sections[25] \"Data Availability\" paragraph 2", "quote": "All the data used to support the research are included within this article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identify coexpressed differential genes including 10 upregulated and 55 downregulated genes in liver tissue after bariatric surgery.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35789605", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identify coexpressed differential genes including 10 upregulated and 55 downregulated genes in liver tissue after bariatric surgery."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identify coexpressed differential genes including 10 upregulated and 55 downregulated genes in liver tissue after bariatric surgery.", "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:35789605"], "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:GSE48452"], "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:GSE48452"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35789605", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/4369329", "sha256": 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