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pmid:38532996
Prognostic insights and immune microenvironment delineation in acute myeloid leukemia by ferroptosis-derived signature.
Lijun Jing · Biyu Zhang · Jinghui Sun · Jueping Feng · Denggang Fu
Heliyon · 2024 doi:10.1016/j.heliyon.2024.e28237
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Experiment
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Data
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Analysis
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Complete file
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Ferroptosis has been found to be correlated with cancer initiation, therapeutic response, and clinical outcome. Nevertheless, the involvement of Ferroptosis-related genes (FRGs) in AML remains ambiguous. Five independent AML cohorts totaling 1,470 (GSE37642, GSE12417, GSE10358, Beat-AML, and TCGA-AML) patients with clinical information were used to systematically investigated the influence of these FRGs expression on outcome and tumor microenvironment. The integration of these datasets led to the subdivision into training and validation sets. Nineteen FRGs were identified as correlated with the overall survival (OS) of AML patients, primarily enriched in ferroptosis, fatty acid metabolism, and leukemia-related signaling pathways. The prognostic signature, consisting of 11 FRGs, was formulated using LASSO-Cox stepwise regression analysis. Patients with high-risk scores exhibited reduced survival compared to those in the low-risk group. The receiver operating characteristic (ROC) analysis underscored the signature's robust predictive accuracy. The high predictive efficacy was confirmed by both internal and external validation datasets. Leukemia and signaling related to immune regulation were mainly enriched pathways of the differentially expressed genes by comparing high- and low-risk groups. The immune composition deconvolution might indicate an immunosuppressive niche in the high-risk patients. The pRRophetic algorithm exploration unveiled chemical drugs with potentially sensitivity among patients in both groups. 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"GSM311865", "GSM311866", "GSM311867", "GSM311868", "GSM311869", "GSM311870", "GSM311871", "GSM311872", "GSM311873", "GSM311874", "GSM311875", "GSM311876", "GSM311877", "GSM311878", "GSM311879", "GSM311880", "GSM311881", "GSM311882", "GSM311883", "GSM311884", "GSM311885", "GSM311886", "GSM311887", "GSM311888", "GSM311889", "GSM311890", "GSM311891", "GSM311892", "GSM311893", "GSM311894", "GSM311895", "GSM311896", "GSM311897", "GSM311898", "GSM311899", "GSM311900", "GSM311901", "GSM311902", "GSM311903", "GSM311904", "GSM311905", "GSM311906", "GSM311907", "GSM311908", "GSM311909", "GSM311910", "GSM311911", "GSM311912", "GSM311913", "GSM311914", "GSM311915", "GSM311916", "GSM311917", "GSM311918", "GSM311919", "GSM311920", "GSM311921", "GSM311922", "GSM311923", "GSM316652", "GSM316653", "GSM316654", "GSM316655", "GSM316656", "GSM316657", "GSM316658", "GSM316659", "GSM316660", "GSM316661", "GSM316662", "GSM316663", "GSM316664", "GSM316665", "GSM316666", "GSM316667", "GSM316668", "GSM316669", "GSM316670", "GSM316671", "GSM316672", "GSM316673", "GSM316674", "GSM316675", "GSM316676", "GSM316677", "GSM316678", "GSM316679", "GSM316680", "GSM316681", "GSM316682", "GSM316683", "GSM316684", "GSM316685", "GSM316686", "GSM316687", "GSM316688", "GSM316689", "GSM316690", "GSM316691", "GSM316692", "GSM316693", "GSM316694", "GSM316695", "GSM316696", "GSM316697", "GSM316698", "GSM316699", "GSM316700", "GSM316701", "GSM316702", "GSM316703", "GSM316704", "GSM316705", "GSM316706", "GSM316707", "GSM316708", "GSM316709", "GSM316710", "GSM316711", "GSM316712", "GSM316713", "GSM316714", "GSM316715", "GSM316716", "GSM316717", "GSM316718", "GSM316719", "GSM316720", "GSM316721", "GSM316722", "GSM316723", "GSM316724", "GSM316725", "GSM316726", "GSM316727", "GSM316728", "GSM316729", "GSM316730"], "sample_count": 405, "group_sizes": null, "group_sizes_basis": null, "platform": "570;96;97", "taxon": "Homo sapiens", "title": "Prognostic gene signature for normal karyotype AML", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE37642", "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=GSE37642", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37642", "version": null, "note": "The data used in this work are from the following databases.\n1.TCGA: https://portal.gdc.cancer.gov/.2.GEO: https://www.ncbi.nlm.nih.gov/geo/including GSE37642, GSE12417, and GSE10358.3.UCSC Xena database: https://xenabrowser.net/datapages/.4.Beat-AML: http://www.vizome.org/aml/.5.STRING: https://string-db.org/cgi/input.pl.6.FerrDb database: http://www.zhounan.org/ferrdb/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used in this work are from the following databases.\n1.TCGA: https://portal.gdc.cancer.gov/.2.GEO: https://www.ncbi.nlm.nih.gov/geo/including GSE37642, GSE12417, and GSE10358.3.UCSC Xena database: https://xenabrowser.net/datapages/.4.Beat-AML: http://www.vizome.org/aml/.5.STRING: https://string-db.org/cgi/input.pl.6.FerrDb database: http://www.zhounan.org/ferrdb/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM923596", "GSM923597", "GSM923598", "GSM923599", "GSM923600", "GSM923601", "GSM923602", "GSM923603", "GSM923604", "GSM923605", "GSM923606", "GSM923607", "GSM923608", "GSM923609", "GSM923610", "GSM923611", "GSM923612", "GSM923613", "GSM923614", "GSM923615", "GSM923616", "GSM923617", "GSM923618", "GSM923619", "GSM923620", "GSM923621", "GSM923622", "GSM923623", "GSM923624", "GSM923625", "GSM923626", "GSM923627", "GSM923628", "GSM923629", "GSM923630", "GSM923631", "GSM923632", "GSM923633", "GSM923634", "GSM923635", "GSM923636", "GSM923637", 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:38532996", "data:geo:GSE10358"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10358"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:13:21Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15713, "completion_tokens": 2282, "cached_tokens": 264}}, "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:38532996", "type": "paper", "label": "pmid:38532996"}, {"id": "source:pmid:38532996", "type": "manuscript", "label": "PMID 38532996 full text"}, {"id": "data:geo:GSE10358", "type": "dataset", "label": "GEO GSE10358"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38532996", "type": "paper", "label": "pmid:38532996"}, {"id": "source:pmid:38532996", "type": "manuscript", "label": "PMID 38532996 full text"}, {"id": "data:geo:GSE10358", "type": "dataset", "label": "GEO GSE10358"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38532996", "type": "extraction", "used": ["source:pmid:38532996"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10358", "type": "accession_resolution", "used": ["data:geo:GSE10358"], "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:38532996", "parent_hash": "sha256:a457d55902b1984f8278c9938a461d75ac41063e5586019bbfe767fcad038e52", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE10358 licence not read", "asset:data:geo:GSE10358 not downloaded", "asset:data:geo:GSE12417 licence not read", "asset:data:geo:GSE12417 not downloaded", "asset:data:geo:GSE37642 licence not read", "asset:data:geo:GSE37642 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Cox regression"], "order_basis": "analysis_only", "id": "assay:1"}]}