Prognostic role of chemokine-related genes in acute myeloid leukemia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39135956", "kind": "science-record", "revision": 4, "content_hash": "sha256:0243141ded037e5e9a03335a47d96f487f3782f8c6f437f8d1cc91051d8cee9d", "created_at": "2026-11-01T20:29:14Z", "updated_at": "2026-11-01T22:54:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic role of chemokine-related genes in acute myeloid leukemia.", "doi": "10.7717/peerj.17862", "pmid": "39135956", "authors": ["Yanfei Hou", "Yu Chen", "Yaofang Zhang", "Mengyao Li", "Jianfang Chen"], "journal": "PeerJ", "year": 2024, "abstract": "Background: Chemotactic cytokines play a crucial role in the development of acute myeloid leukemia (AML). Thus, investigating the mechanisms of chemotactic cytokine-related genes (CCRGs) in AML is of paramount importance.\nMethods: Using the TCGA-AML, GSE114868, and GSE12417 datasets, differential expression analysis identified differentially expressed CCRGs (DE-CCRGs). These genes were screened by overlapping differentially expressed genes (DEGs) between AML and control groups with CCRGs. Subsequently, functional enrichment analysis and the construction of a protein-protein interaction (PPI) network were conducted to explore the functions of the DE-CCRGs. Univariate Cox regression, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses identified relevant prognostic genes and developed a prognostic model. Survival analysis of the prognostic gene was performed, followed by functional similarity analysis, immune analysis, enrichment analysis, and drug prediction analysis.\nResults: Differential expression analysis revealed 6,743 DEGs, of which 29 DE-CCRGs were selected for this study. Functional enrichment analysis indicated that DE-CCRGs were primarily involved in chemotactic cytokine-related functions and pathways. Six prognostic genes (CXCR3, CXCR2, CXCR6, CCL20, CCL4, and CCR2) were identified and incorporated into the risk model. The model's performance was validated using the GSE12417 dataset. Survival analysis showed significant differences in AML overall survival (OS) between prognostic gene high and low expression groups, indicating that prognostic gene might be significantly associated with patient survival. Additionally, nine different immune cells were identified between the two risk groups. Correlation analysis revealed that CCR2 had the most significant positive correlation with monocytes and the most significant negative correlation with resting mast cells. The tumor immune dysfunction and exclusion score was lower in the high-risk group.\nConclusion: CXCR3, CXCR2, CXCR6, CCL20, CCL4, and CCR2 were identified as prognostic genes correlated to AML and the tumor immune microenvironment. These findings offerred novel insights into the prevention and treatment of AML.", "claims": [{"id": "claim-method", "statement": "The limma package was used for differential analysis with criteria of —log2fold change (FC)— > 0.5 and adj.P.Val < 0.05 (Shen et al., 2023).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39135956", "locator": "sections[4] \"Identification and functional enrichment analysis of DEGs and DE-CCRGs\" paragraph 2", "quote": "The limma package was used for differential analysis with criteria of —log2fold change (FC)— > 0.5 and adj.P.Val < 0.05 (Shen et al., 2023)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw measurements are available in the Supplementary Files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39135956", "locator": "sections[21] \"Additional Information and Declarations\" paragraph 6", "quote": "The raw measurements are available in the Supplementary Files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differential expression analysis revealed 6,743 DEGs, of which 29 DE-CCRGs were selected for this study.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39135956", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Differential expression analysis revealed 6,743 DEGs, of which 29 DE-CCRGs were selected for this study."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Differential expression analysis revealed 6,743 DEGs, of which 29 DE-CCRGs were selected for this study.", "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:39135956"], "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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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:39135956", "data:geo:GSE114868"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE114868"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:28:04Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10103, "completion_tokens": 1548, "cached_tokens": 256}}, "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:39135956", "type": "paper", "label": "pmid:39135956"}, {"id": "source:pmid:39135956", "type": "manuscript", "label": "PMID 39135956 full text"}, {"id": "data:geo:GSE114868", "type": "dataset", "label": "GEO GSE114868"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39135956", "type": "paper", "label": "pmid:39135956"}, {"id": "source:pmid:39135956", "type": "manuscript", "label": "PMID 39135956 full text"}, {"id": "data:geo:GSE114868", "type": "dataset", "label": "GEO GSE114868"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39135956", "type": "extraction", "used": ["source:pmid:39135956"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE114868", "type": "accession_resolution", "used": ["data:geo:GSE114868"], "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:39135956", "parent_hash": "sha256:8ef6e85e3c1877687cd3fcafdee87ba91660b70b91416d869289066ebdefb1c7", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE114868 licence not read", "asset:data:geo:GSE114868 not downloaded", "asset:data:geo:GSE12417 licence not read", "asset:data:geo:GSE12417 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The limma package was used for differential analysis with criteria of —log2fold change (FC)— > 0.5 and adj.P.Val < 0.05 (Shen et al., 2023)."], "order_basis": "analysis_only", "id": "assay:1"}]}