A novel immune-related genes signature after bariatric surgery is histologically associated with non-alcoholic fatty liver disease.

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We identified differentially expressed immune-related genes (DEIRGs) of adipose tissue after BS by analysing the two expression profiles of GEO (GSE59034 and GSE29409). Subsequently, enrichment analysis, GSEA and PPI networks were examined to identify the hub IRGs and related pathways. The performance of the signature was evaluated by area under the curve (AUC) of the receiver operating characteristic (ROC). CIBERSORT algorithm was used to evaluate the relative abundance of infiltrated immune cells.42 DEIRGs were found between the GSE59034 and GSE29409 datasets. The AUC of the signature was 0.904 and 0.865 in the GSE58979 and GSE48452, respectively. Interestingly, the signature also showed good performance in diagnosing non-alcoholic fatty liver disease (NAFLD) (AUC was 0.834 and 0.800, respectively). The number of neutrophils, macrophages M2, macrophages M0 and dendritic cells activated decreased significantly. After BS, the infiltration of T cells regulatory, monocytes, mast cells resting and plasma cells in adipose tissue increased. The novel proposed IRGs signature reveals the underlying immune mechanism of BS and is a promising biomarker for distinguishing the severity of NAFLD. This will provide new insights into strategies for treating obesity and NAFLD.", "claims": [{"id": "claim-method", "statement": "GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/) is the tool used to identify DEGs in the GEO database. GEO2R was used to identify DEGs before and after BS. |log FC| >0.5 and p < 0.05 were used as the threshold for DEGs screening.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34506234", "locator": "sections[4] \"Identification of differentially expressed genes (DEGs)\" paragraph 2", "quote": "GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/) is the tool used to identify DEGs in the GEO database. GEO2R was used to identify DEGs before and after BS. |log FC| >0.5 and p < 0.05 were used as the threshold for DEGs screening."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available in GEO database (http://www.ncbi.nlm.nih.gov/geo), reference number [GSE59034, GSE29409, GSE83452, GSE58979 and GSE48452].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34506234", "locator": "sections[24] \"Data availability statement\" paragraph 2", "quote": "The data that support the findings of this study are available in GEO database (http://www.ncbi.nlm.nih.gov/geo), reference number [GSE59034, GSE29409, GSE83452, GSE58979 and GSE48452]."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34506234"], "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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"row_count": 12, "column_count": 4}, "table": {"label": "Table 3.", "caption": "GSEA analysis of GSE59034", "rows": [["Pathway", "P-value", "NES", "Size"], ["KEGG_GRAFT_VERSUS_HOST_DISEASE", "6.67E-04", "−1.71E+00", "29"], ["KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS", "5.44E-04", "−1.70E+00", "33"], ["KEGG_TOLL_LIKE_RECEPTOR_SIGNALLING_PATHWAY", "1.03E-04", "−1.67E+00", "66"], ["KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION", "1.29E-03", "−1.65E+00", "39"], ["KEGG_TYPE_I_DIABETES_MELLITUS", "1.89E-03", "−1.64E+00", "29"], ["KEGG_CHEMOKINE_SIGNALLING_PATHWAY", "1.01E-04", "−1.64E+00", "109"], ["KEGG_VIRAL_MYOCARDITIS", "2.21E-03", "−1.64E+00", "30"], ["KEGG_HAEMATOPOIETIC_CELL_LINEAGE", "1.26E-03", "−1.63E+00", "48"], ["KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION", "3.49E-03", "−1.51E+00", "64"], ["KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION", "2.80E-03", "−1.33E+00", "229"], ["KEGG_RENIN_ANGIOTENSIN_SYSTEM", "2.91E-03", "1.80E+00", "5"]], "row_count": 12, "column_count": 4, "numeric_cells": 33, "header_rows": 1, "locator": "section[15]/table-wrap[1]#t0003"}}], "gaps": ["asset:data:geo:GSE29409 not downloaded", "asset:data:geo:GSE29409 licence not read", "asset:data:geo:GSE48452 not downloaded", "asset:data:geo:GSE48452 licence not read", "asset:data:geo:GSE58979 not downloaded", "asset:data:geo:GSE58979 licence not read", "asset:data:geo:GSE59034 not downloaded", "asset:data:geo:GSE59034 licence not read", "asset:data:geo:GSE83452 not downloaded", "asset:data:geo:GSE83452 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-2", "family": null, "specific": null, "label": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/) is the tool used to identify DEGs in the GEO database. GEO2R was used to identify DEGs before and after BS. |log FC| >0.5 and p < 0.05 were used as the threshold for DEGs screening."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE59034", "GSE29409", "GSE83452", "GSE58979", "GSE48452"], "resolved_accessions": ["GSE59034", "GSE29409", "GSE83452", "GSE58979", "GSE48452"], "statements": ["The data that support the findings of this study are available in GEO database (http://www.ncbi.nlm.nih.gov/geo), reference number [GSE59034, GSE29409, GSE83452, GSE58979 and GSE48452]."], "basis": "The paper names GSE59034, GSE29409, GSE83452, GSE58979, GSE48452 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:34506234", "data:geo:GSE29409", "asset:table:pmid:34506234:1", "asset:table:pmid:34506234:2", "asset:table:pmid:34506234:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE29409"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:33Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 29035, "completion_tokens": 2077, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:34506234", "type": "paper", "label": "pmid:34506234"}, {"id": "source:pmid:34506234", "type": "manuscript", "label": "PMID 34506234 full text"}, {"id": "data:geo:GSE29409", "type": "dataset", "label": "GEO GSE29409"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34506234", "type": "paper", "label": "pmid:34506234"}, {"id": "source:pmid:34506234", "type": "manuscript", "label": "PMID 34506234 full text"}, {"id": "data:geo:GSE29409", "type": "dataset", "label": "GEO GSE29409"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34506234", "type": "extraction", "used": ["source:pmid:34506234"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE29409", "type": "accession_resolution", "used": ["data:geo:GSE29409"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:34506234", "parent_hash": "sha256:a9ec1d64d13d2652045bb9179f011d6e55c00a3f27d6bce8f079e81eb022fda6", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE29409 licence not read", "asset:data:geo:GSE29409 not downloaded", "asset:data:geo:GSE48452 licence not read", "asset:data:geo:GSE48452 not downloaded", "asset:data:geo:GSE58979 licence not read", "asset:data:geo:GSE58979 not downloaded", "asset:data:geo:GSE59034 licence not read", "asset:data:geo:GSE59034 not downloaded", "asset:data:geo:GSE83452 licence not read", "asset:data:geo:GSE83452 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["PPI"], "order_basis": "analysis_only", "id": "assay:1"}]}