Systematic Analysis of Autophagy-Related Signature Uncovers Prognostic Predictor for Acute Myeloid Leukemia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32783661", "kind": "science-record", "revision": 4, "content_hash": "sha256:ba84404efa2da96f3090b29f87ef0112d68f1c470551b257e7af79f47fd9ab12", "created_at": "2026-11-01T17:33:57Z", "updated_at": "2026-11-01T22:02:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Systematic Analysis of Autophagy-Related Signature Uncovers Prognostic Predictor for Acute Myeloid Leukemia.", "doi": "10.1089/dna.2020.5667", "pmid": "32783661", "authors": ["Xue-Xing Chen", "Zi-Ping Li", "Jian-Hua Zhu", "Hai-Tao Xia", "Hao Zhou"], "journal": "DNA and cell biology", "year": 2020, "abstract": "Autophagy, a highly conserved cellular protein degradation process, has been involved in acute myeloid leukemia (AML). The present study aims to establish a novel, autophagy-related prognostic signature for prediction of AML prognosis. Differentially expressed autophagy-related genes in AML and healthy samples were screened using GSE1159. Univariate Cox regression analysis was applied to determine survival-associated autophagy-related genes in The Cancer Genome Atlas (TCGA) AML cohort. Lasso regression was performed to develop multiple-gene prognostic signatures. A novel six-gene signature (including CASP3, CHAF1B, KLHL24, OPTN, VEGFA, and VPS37C) DC was established for AML prognosis prediction. The Kaplan-Meier survival analysis revealed that patients in the high-risk score group had poorer overall survival (OS). The receiver operating characteristic (ROC) curve validated its good performance in survival prediction in TCGA AML cohort, and the area under the curve value was 0.817. Moreover, our signature could independently predict OS. A nomogram was constructed, including the six-gene signature and other clinical parameters, and predictive efficiency was confirmed using the ROC curve and calibration curve. Furthermore, gene set enrichment analyses identified several tumor-associated pathways that may contribute to explain the potential molecular mechanisms of our signature. Overall, we developed a new autophagy-associated gene signature and nomogram to predict OS of AML patients, which may help in clinical decision-making for AML treatment.", "claims": [{"id": "claim-method", "statement": "Univariate Cox regression analysis was applied to determine survival-associated autophagy-related genes in The Cancer Genome Atlas (TCGA) AML cohort. Lasso regression was performed to develop multiple-gene prognostic signatures. The Kaplan–Meier survival analysis revealed that patients in the high-risk score group had poorer overall survival (OS). The receiver operating characteristic (ROC) curve validated its good performance in survival prediction in TCGA AML cohort, and the area under the curve value was 0.817. Furthermore, gene set enrichment analyses identified several tumor-associated pathways that may contribute to explain the potential molecular mechanisms of our signature.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32783661", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Univariate Cox regression analysis was applied to determine survival-associated autophagy-related genes in The Cancer Genome Atlas (TCGA) AML cohort."}, {"asset": "source:pmid:32783661", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Lasso regression was performed to develop multiple-gene prognostic signatures."}, {"asset": "source:pmid:32783661", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The Kaplan–Meier survival analysis revealed that patients in the high-risk score group had poorer overall survival (OS)."}, {"asset": "source:pmid:32783661", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The receiver operating characteristic (ROC) curve validated its good performance in survival prediction in TCGA AML cohort, and the area under the curve value was 0.817."}, {"asset": "source:pmid:32783661", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Furthermore, gene set enrichment analyses identified several tumor-associated pathways that may contribute to explain the potential molecular mechanisms of our signature."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Differentially expressed autophagy-related genes in AML and healthy samples were screened using GSE1159.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32783661", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Differentially expressed autophagy-related genes in AML and healthy samples were screened using GSE1159."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:32783661"], "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:GSE1159"], "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:GSE1159"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32783661", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1089/dna.2020.5667", "sha256": "sha256:babdb37cde405e859916b3ff34b41c3f00ba3fe129bc0065bc2d8b653e8ac63c", "bytes": 1580, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1089/dna.2020.5667", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7482110", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE1159", "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=GSE1159", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE1159", "version": null, "note": "Differentially expressed autophagy-related genes in AML and healthy samples were screened using GSE1159.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Differentially expressed autophagy-related genes in AML and healthy samples were screened using GSE1159.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM19382", "GSM19383", "GSM20684", "GSM20685", "GSM20686", "GSM20687", "GSM20688", "GSM20689", "GSM20690", "GSM20691", "GSM20692", "GSM20693", "GSM20694", "GSM20695", "GSM20696", "GSM20697", "GSM20698", "GSM20699", "GSM20700", "GSM20701", "GSM20702", "GSM20703", "GSM20704", "GSM20705", "GSM20706", "GSM20707", "GSM20708", "GSM20709", "GSM20710", "GSM20711", "GSM20712", "GSM20713", "GSM20714", "GSM20715", "GSM20716", "GSM20717", "GSM20718", "GSM20719", "GSM20720", "GSM20721", "GSM20722", "GSM20723", "GSM20724", "GSM20725", "GSM20726", "GSM20727", "GSM20728", "GSM20729", "GSM20730", "GSM20731", "GSM20732", "GSM20733", "GSM20734", "GSM20735", "GSM20736", "GSM20737", "GSM20738", "GSM20739", "GSM20740", "GSM20741", "GSM20742", "GSM20743", "GSM20744", "GSM20745", "GSM20746", "GSM20747", "GSM20748", "GSM20749", "GSM20750", "GSM20751", "GSM20752", "GSM20753", "GSM20754", "GSM20755", "GSM20756", "GSM20757", "GSM20758", "GSM20759", "GSM20760", "GSM20761", "GSM20762", "GSM20763", "GSM20764", "GSM20765", "GSM20766", "GSM20767", "GSM20768", "GSM20769", "GSM20770", "GSM20771", "GSM20772", "GSM20773", "GSM20774", "GSM20775", "GSM20776", "GSM20777", "GSM20778", "GSM20779", "GSM20780", "GSM20781", "GSM20782", "GSM20783", "GSM20784", "GSM20785", "GSM20786", "GSM20787", "GSM20788", "GSM20789", "GSM20790", "GSM20791", "GSM20792", "GSM20793", "GSM20794", "GSM20795", "GSM20796", "GSM20797", "GSM20798", "GSM20799", "GSM20800", "GSM20801", "GSM20802", "GSM20803", "GSM20804", "GSM20805", "GSM20806", "GSM20807", "GSM20808", "GSM20809", "GSM20810", "GSM20811", "GSM20812", "GSM20813", "GSM20814", "GSM20815", "GSM20816", "GSM20817", "GSM20818", "GSM20819", "GSM20820", "GSM20821", "GSM20822", "GSM20823", "GSM20824", "GSM20825", "GSM20826", "GSM20827", "GSM20828", "GSM20829", "GSM20830", "GSM20831", "GSM20832", "GSM20833", "GSM20834", "GSM20835", "GSM20836", "GSM20837", "GSM20838", "GSM20839", "GSM20840", "GSM20841", "GSM20842", "GSM20843", "GSM20844", "GSM20845", "GSM20846", "GSM20847", "GSM20848", "GSM20849", "GSM20850", "GSM20851", "GSM20852", "GSM20853", "GSM20854", "GSM20855", "GSM20856", "GSM20857", "GSM20858", "GSM20859", "GSM20860", "GSM20861", "GSM20862", "GSM20863", "GSM20864", "GSM20865", "GSM20866", "GSM20867", "GSM20868", "GSM20869", "GSM20870", "GSM20871", "GSM20872", "GSM20873", "GSM20874", "GSM20875", "GSM20876", "GSM20877", "GSM20878", "GSM20879", "GSM20880", "GSM20881", "GSM20882", "GSM20883", "GSM20884", "GSM20885", "GSM20886", "GSM20887", "GSM20888", "GSM20889", "GSM20890", "GSM20891", "GSM20892", "GSM20893", "GSM20894", "GSM20895", "GSM20896", "GSM20897", "GSM20898", "GSM20899", "GSM20900", "GSM20901", "GSM20902", "GSM20903", "GSM20904", "GSM20905", "GSM20906", "GSM20907", "GSM20908", "GSM20909", "GSM20910", "GSM20911", "GSM20912", "GSM20913", "GSM20914", "GSM20915", "GSM20916", "GSM20917", "GSM20918", "GSM20919", "GSM20920", "GSM20921", "GSM20922", "GSM20923", "GSM20924", "GSM20925", "GSM20926", "GSM20927", "GSM20928", "GSM20929", "GSM20930", "GSM20931", "GSM20932", "GSM20933", "GSM20934", "GSM20935", "GSM20936", "GSM20937", "GSM20938", "GSM20939", "GSM20940", "GSM20941", "GSM20942", "GSM20943", "GSM20944", "GSM20945", "GSM20946", "GSM20947", "GSM20948", "GSM20949", "GSM20950", "GSM20951", "GSM20952", "GSM20953", "GSM20954", "GSM20955", "GSM20956", "GSM20957", "GSM20958", "GSM20959", "GSM20960", "GSM20961", "GSM20962", "GSM20963", "GSM20964", "GSM20965", "GSM20966", "GSM20967", "GSM20968", "GSM20969", "GSM20970", "GSM20971", "GSM20972", "GSM20973", "GSM20974"], "sample_count": 293, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Expression profiles of acute myeloid leukemia patient samples", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE1159 not downloaded", "asset:data:geo:GSE1159 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "reordered", "quote": "Univariate Cox regression analysis was applied to determine survival-associated autophagy-related genes in The Cancer Genome Atlas (TCGA) AML cohort. Lasso regression was performed to develop multiple-gene prognostic signatures. The Kaplan–Meier survival analysis revealed that patients in the high-risk score group had poorer overall survival (OS). The receiver operating characteristic (ROC) curve validated its good performance in survival prediction in TCGA AML cohort, and the area under the curve value was 0.817. Furthermore, gene set enrichment analyses identified several tumor-associated pathways that may contribute to explain the potential molecular mechanisms of our signature."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC curve"}}], "targets": [], "gaps": []}, "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE1159"], "resolved_accessions": ["GSE1159"], "statements": ["Differentially expressed autophagy-related genes in AML and healthy samples were screened using GSE1159."], "basis": "The paper names GSE1159 in GSE1159 and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:32783661", "data:geo:GSE1159"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE1159"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:00:21Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 1929, "completion_tokens": 1140, "cached_tokens": 188}}, "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:32783661", "type": "paper", "label": "pmid:32783661"}, {"id": "source:pmid:32783661", "type": "manuscript", "label": "PMID 32783661 full text"}, {"id": "data:geo:GSE1159", "type": "dataset", "label": "GEO GSE1159"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32783661", "type": "paper", "label": "pmid:32783661"}, {"id": "source:pmid:32783661", "type": "manuscript", "label": "PMID 32783661 full text"}, {"id": "data:geo:GSE1159", "type": "dataset", "label": "GEO GSE1159"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32783661", "type": "extraction", "used": ["source:pmid:32783661"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE1159", "type": "accession_resolution", "used": ["data:geo:GSE1159"], "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:32783661", "parent_hash": "sha256:10785c88fd3a7104d810931fc7da80b93c4ee8b3ed6fdc90ed95d2387e24947f", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE1159 licence not read", "asset:data:geo:GSE1159 not downloaded", "execution.not_run", "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": 1.0, "evidence": ["Univariate Cox regression analysis was applied to determine survival-associated autophagy-related genes in The Cancer Genome Atlas (TCGA) AML cohort. Lasso regression was performed to develop multiple-gene prognostic signatures. The Kaplan–Meier survival analysis revealed that patients in the high-risk score group had poorer overall survival (OS). The receiver operating characteristic (ROC) curve validated its good performance in survival prediction in TCGA AML cohort, and the area under the curve value was 0.817. Furthermore, gene set enrichment analyses identified several tumor-associated pathways that may contribute to explain the potential molecular mechanisms of our signature."], "order_basis": "analysis_only", "id": "assay:1"}]}