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pmid:38077322
Construction of an acute myeloid leukemia prognostic model based on m6A-related efferocytosis-related genes.
Ying Wang · Ting Bin · Jing Tang · Xiao-Jun Xu · Chao Lin · Bo Lu · Tian-Tian Sun
Frontiers in immunology · 2023 doi:10.3389/fimmu.2023.1268090
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Experiment
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Data
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Analysis
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Execution
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Complete file
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Efferocytosis-related genes (ERGs) and N6-methyladenosine (m6A) have an important significance in the progression of cancer, and the metastasis of tumors.\nMethods: The AML-related data were collected from The Cancer Genome Atlas (TCGA; TCGA-AML) database and Gene Expression Omnibus (GEO; GSE9476, GSE71014, and GSE13159) database. The \"limma\" R package and Venn diagram were adopted to identify differentially expressed ERGs (DE-ERGs). The m6A related-DE-ERGs were obtained by Spearman analysis. Subsequently, univariate Cox and Least Absolute Shrinkage and Selection Operator (LASSO) were used to construct an m6A related-ERGs risk signature for AML patients. The possibility of immunotherapy for AML was explored. The pRRophetic package was adopted to calculate the IC50 of drugs for the treatment of AML. Finally, the expression of characterized genes was validated by quantitative reverse transcription-PCR (qRT-PCR).\nResults: Based on m6A related-DE-ERGs, a prognostic model with four characteristic genes (UCP2, DOCK1, SLC14A1, and SLC25A1) was constructed. The risk score of model was significantly associated with the immune microenvironment of AML, with four immune cell types, 14 immune checkpoints, 20 HLA family genes and, immunophenoscore (IPS) all showing differences between the high- and low-risk groups. A total of 56 drugs were predicted to differ between the two groups, of which Erlotinib, Dasatinib, BI.2536, and bortezomib have been reported to be associated with AML treatment. The qRT-PCR results showed that the expression trends of DOCK1, SLC14A1 and SLC25A1 were consistent with the bioinformatics analysis.\nConclusion: In summary, 4 m6A related- ERGs were identified and the corresponding prognostic model was constructed for AML patients. This prognostic model effectively stratified the risk of AML patients.", "claims": [{"id": "claim-method", "statement": "By using univariate Cox analysis of m6A -related DE-ERGs in the TCGA-AML dataset, the prognosis-related genes were acquired (P < 0.05). Subsequently, the most predictive characteristic genes were identified by the least absolute shrinkage and selection operator (LASSO) (27).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38077322", "locator": "sections[6] \"Constructing a new AML prognostic risk model based on m6A -related DE-ERGs\" paragraph 2", "quote": "By using univariate Cox analysis of m6A -related DE-ERGs in the TCGA-AML dataset, the prognosis-related genes were acquired (P < 0.05). Subsequently, the most predictive characteristic genes were identified by the least absolute shrinkage and selection operator (LASSO) (27)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38077322", "locator": "sections[21] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material ."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Based on m6A related-DE-ERGs, a prognostic model with four characteristic genes (UCP2, DOCK1, SLC14A1, and SLC25A1) was constructed.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38077322", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Based on m6A related-DE-ERGs, a prognostic model with four characteristic genes (UCP2, DOCK1, SLC14A1, and SLC25A1) was constructed."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Based on m6A related-DE-ERGs, a prognostic model with four characteristic genes (UCP2, DOCK1, SLC14A1, and SLC25A1) was constructed.", "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:38077322"], "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:GSE13159"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE13159"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38077322", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2023.1268090", "sha256": "sha256:8d3789986bfdbba1e9ee054a68cad713e8863d3c6e5f63b9af3068df58570fe3", "bytes": 40476, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2023.1268090", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10704160", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13159", "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=GSE13159", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13159", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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"GSM330308", "GSM330309", "GSM330310", "GSM330317", "GSM330318", "GSM330319", "GSM330320", "GSM330321", "GSM330322", "GSM330323", "GSM330324", "GSM330325", "GSM330326", "GSM330327", "GSM330328", "GSM330329", "GSM330330", "GSM330331", "GSM330332", "GSM330333", "GSM330334", "GSM330335", "GSM330336", "GSM330337", "GSM330338", "GSM330339", "GSM330340", "GSM330341", "GSM330342", "GSM330343", "GSM330344", "GSM330345", "GSM330346", "GSM330347", "GSM330348", "GSM330349", "GSM330350", "GSM330351", "GSM330352", "GSM330353", "GSM330354", "GSM330355", "GSM330356", "GSM330357", "GSM330358", "GSM330359", "GSM330360", "GSM330361", "GSM330362", "GSM330363", "GSM330364", "GSM330365", "GSM330366", "GSM330367", "GSM330368", "GSM330369", "GSM330370", "GSM330371", "GSM330372", "GSM330373", "GSM330374", "GSM330375", "GSM330376", "GSM330377", "GSM330378", "GSM330379", "GSM330380", "GSM330381", "GSM330382", "GSM330383", "GSM330384", "GSM330385", "GSM330386", "GSM330387", "GSM330388", "GSM330389", "GSM330390", "GSM330391", "GSM330392", "GSM330393", "GSM330394", "GSM330395", "GSM330396", "GSM330397", "GSM330398", "GSM330399", "GSM330400", "GSM330401", "GSM330402", "GSM330403", "GSM330404", "GSM330405", "GSM330406", "GSM330407", "GSM330408", "GSM330409", "GSM330410", "GSM330411", "GSM330412", "GSM330413", "GSM330414", "GSM330415", "GSM330416", "GSM330417", "GSM330418", "GSM330419", "GSM330420", "GSM330421", "GSM330422", "GSM330423", "GSM330424", "GSM330425", "GSM330426", "GSM330427", "GSM330428", "GSM330429", "GSM330430", "GSM330431", "GSM330432", "GSM330433", "GSM330434", "GSM330435", "GSM330436", "GSM330437", "GSM330438", "GSM330439", "GSM330440", "GSM330441", "GSM330442", "GSM330443", "GSM330444", "GSM330445", "GSM330446", "GSM330447", "GSM330448", "GSM330449", "GSM330450", "GSM330451", "GSM330452", "GSM330453", "GSM330454", "GSM330455", "GSM330456", "GSM330457", "GSM330458", "GSM330459", "GSM330460", "GSM330461", "GSM330462", "GSM330463", "GSM330464", "GSM330465", "GSM330466", "GSM330467", "GSM330468", "GSM330469", "GSM330470", "GSM330471", "GSM330472", "GSM330473", "GSM330474", "GSM330475", "GSM330476", "GSM330477", "GSM330478", "GSM330479", "GSM330480", "GSM330481", "GSM330482", "GSM330483", "GSM330484", "GSM330485", "GSM330486", "GSM330487", "GSM330488", "GSM330489", "GSM330490", "GSM330491", "GSM330492", "GSM330493", "GSM330494", "GSM330495", "GSM330496", "GSM330497", "GSM330498", "GSM330499", "GSM330500", "GSM330501", "GSM330502", "GSM330503", "GSM330504", "GSM330505", "GSM330506", "GSM330507", "GSM330508", "GSM330509", "GSM330510", "GSM330511", "GSM330512", "GSM330513", "GSM330514", "GSM330515", "GSM330516", "GSM330517", "GSM330518", "GSM330519", "GSM330520", "GSM330521", "GSM330522", "GSM330523", "GSM330524", "GSM330525", "GSM330526", "GSM330527", "GSM330528", "GSM330529", "GSM330530", "GSM330531", "GSM330532", "GSM330533", "GSM330534", "GSM330535", "GSM330536", "GSM330537", "GSM330538", "GSM330539", "GSM330540", "GSM330541", "GSM330542", "GSM330543", "GSM330544", "GSM330545", "GSM330546", "GSM330547", "GSM330548", "GSM330549", "GSM330550", "GSM330551", "GSM330552", "GSM330553", "GSM330554", "GSM330555", "GSM330556", "GSM330557", "GSM330558", "GSM330559", "GSM330560", "GSM330561", "GSM330562", "GSM330563", "GSM330564", "GSM330565", "GSM330566", "GSM330567", "GSM330568", "GSM330569", "GSM330570", "GSM330571", "GSM330572", "GSM330573", "GSM330574", "GSM330575", "GSM330576", "GSM330577", "GSM330578", "GSM330579", "GSM330580", "GSM330581", "GSM330582", "GSM330583", "GSM330584", "GSM330585", "GSM330586", "GSM330587", "GSM330588", "GSM330589", "GSM330590", "GSM330591", "GSM330592", "GSM330593", "GSM330594", "GSM330595", "GSM330596", "GSM330597", "GSM330598", "GSM330599", "GSM330600", "GSM330601", "GSM330602", "GSM330603", "GSM330604", "GSM330605", "GSM330606", "GSM330607", "GSM330608", "GSM330609", "GSM330610", "GSM330611", "GSM330612", "GSM330613", "GSM330614", "GSM330615", "GSM330616", "GSM330617", "GSM330618", "GSM330619", "GSM330620", "GSM330621", "GSM330622", "GSM330623", "GSM330624", "GSM330625", "GSM330626", "GSM330627", "GSM330628", "GSM330629", "GSM330630", "GSM330631", "GSM330632", "GSM330633", "GSM330634", "GSM330635", "GSM330636", "GSM330637", "GSM330638", "GSM330639", "GSM330640", "GSM330641", "GSM330642", "GSM330643", "GSM330644", "GSM330645", "GSM330646", "GSM330647", "GSM330648", "GSM330649", "GSM330650", "GSM330651", "GSM330652", "GSM330653", "GSM330654", "GSM330655", "GSM330656", "GSM330657", "GSM330658", "GSM330659", "GSM330660", "GSM330661", "GSM330662", "GSM330663", "GSM330664", "GSM330665", "GSM330666", "GSM330667", "GSM330668", "GSM330669", "GSM330670", "GSM330671", "GSM330672", "GSM330673", "GSM330674", "GSM330675", "GSM330676", "GSM330677", "GSM330678", "GSM330679", "GSM330680", "GSM330681", "GSM330682", "GSM330683", "GSM330684", "GSM330685", "GSM330686", "GSM330687", "GSM330688", "GSM330689", "GSM330690", "GSM330691", "GSM330692", "GSM330693", "GSM330694", "GSM330695", "GSM330696", "GSM330697", "GSM330698", "GSM330699", "GSM330700", "GSM330701", "GSM330702", "GSM330703", "GSM330704", "GSM330705", "GSM330706", "GSM330707", "GSM330708", "GSM330709", "GSM330710", "GSM330711", "GSM330712", "GSM330713", "GSM330714", "GSM330715", "GSM330716", "GSM330717", "GSM330718", "GSM330719", "GSM330720", "GSM330721", "GSM330722", "GSM330723", "GSM330724", "GSM330725", "GSM330726", "GSM330727", "GSM330728", "GSM330729", "GSM330730", "GSM330731", "GSM330732", "GSM330733", "GSM330734", "GSM330735", "GSM330736", "GSM330737", "GSM330738", "GSM330739", "GSM330740", "GSM330741", "GSM330742", "GSM330743", "GSM330744", "GSM330745", "GSM330746", "GSM330747", "GSM330748", "GSM330749", "GSM330750", "GSM330751", "GSM330752", "GSM330753", "GSM330754", "GSM330755", "GSM330756", "GSM330757", "GSM330758", "GSM330759", "GSM330760", "GSM330761", "GSM330762", "GSM330763", "GSM330764", "GSM330765", "GSM330766", "GSM330767", "GSM330768", "GSM330769", "GSM330770", "GSM330771", "GSM330772", "GSM330773", "GSM330774", "GSM330775", "GSM330776", "GSM330777", "GSM330778", "GSM330779", "GSM330780", "GSM330781", "GSM330782", "GSM330783", "GSM330784", "GSM330785", "GSM330786", "GSM330787", "GSM330788", "GSM330789", "GSM330790", "GSM330791", "GSM330792", "GSM330793", "GSM330794", "GSM330795", "GSM330796", "GSM330797", "GSM330798", "GSM330799", "GSM330800", "GSM330801", "GSM330802", "GSM330803", "GSM330804", "GSM330805", "GSM330806", "GSM330807", "GSM330808", "GSM330809", "GSM330810", "GSM330811", "GSM330812", "GSM330813", "GSM330814", "GSM330815", "GSM330816", "GSM330817", "GSM330818", "GSM330819", "GSM330820", "GSM330821", "GSM330822", "GSM330823", "GSM330824", "GSM330825", "GSM330826", "GSM330827", "GSM330828", "GSM330829", "GSM330830", "GSM330831", "GSM330832", "GSM330833", "GSM330834", "GSM330835", "GSM330836", "GSM330837", "GSM330838", "GSM330839", "GSM330840", "GSM330841", "GSM330842", "GSM330843", "GSM330844", "GSM330845", "GSM330846", "GSM330847", "GSM330848", "GSM330849", "GSM330850", "GSM330851", "GSM330852", "GSM330853", "GSM330854", "GSM330855", "GSM330856", "GSM330857", "GSM330858", "GSM330859", "GSM330860", "GSM330861", "GSM330862", "GSM330863", "GSM330864", "GSM330865", "GSM330866", "GSM330867", "GSM330868", "GSM330869", "GSM330870", "GSM330871", "GSM330872", "GSM330873", "GSM330874", "GSM330875", "GSM330876", "GSM330877", "GSM330878", "GSM330879", "GSM330880", "GSM330881", "GSM330882", "GSM330883", "GSM330884", "GSM330885", "GSM330886", "GSM330887", "GSM330888", "GSM330889", "GSM330890", "GSM330891", "GSM330892", "GSM330893", "GSM330894", "GSM330895", "GSM330896", "GSM330897", "GSM330898", "GSM330899", "GSM330900", "GSM330901", "GSM330902", "GSM330903", "GSM330904", "GSM330905", "GSM330906", "GSM330907", "GSM330908", "GSM330909", "GSM330910", "GSM330911", "GSM330912", "GSM330913", "GSM330914", "GSM330915", "GSM330916", "GSM330917", "GSM330918", "GSM330919", "GSM330920", "GSM330921", "GSM330922", "GSM330923", "GSM330924", "GSM330925", "GSM330926", "GSM330927", "GSM330928", "GSM330929", "GSM330930", "GSM330931", "GSM330932", "GSM330933", "GSM330934", "GSM330935", "GSM330936", "GSM330937", "GSM330938", "GSM330939", "GSM330940", "GSM330941", "GSM330942", "GSM330943", "GSM330944", "GSM330945", "GSM330946", "GSM330947", "GSM330948", "GSM330949", "GSM330950", "GSM330951", "GSM330952", "GSM330953", "GSM330954", "GSM330955", "GSM330956", "GSM330957", "GSM330958", "GSM330959", "GSM330960", "GSM330961", "GSM330962", "GSM330963", "GSM330964", "GSM330965", "GSM330966", "GSM330967", "GSM330968", "GSM330969", "GSM330970", "GSM330971", "GSM330972", "GSM330973", "GSM330974", "GSM330975", "GSM330976", "GSM330977", "GSM330978", "GSM330979", "GSM330980", "GSM330981", "GSM330982", "GSM330983", "GSM330984", "GSM330985", "GSM330986", "GSM330987", "GSM330988", "GSM330989", "GSM330990", "GSM330991", "GSM330992", "GSM330993", "GSM330994", "GSM330995", "GSM330996", "GSM330997", "GSM330998", "GSM330999", "GSM331000", "GSM331001", "GSM331002", "GSM331003", "GSM331004", "GSM331005", "GSM331006", "GSM331007", "GSM331008", "GSM331009", "GSM331010", "GSM331011", "GSM331012", "GSM331013", "GSM331014", "GSM331015", "GSM331016", "GSM331017", "GSM331018", "GSM331019", "GSM331020", "GSM331021", "GSM331022", "GSM331023", "GSM331024", "GSM331025", "GSM331026", "GSM331027", "GSM331028", "GSM331029", "GSM331030", "GSM331031", "GSM331032", "GSM331033", "GSM331034", "GSM331035", "GSM331036", "GSM331037", "GSM331038", "GSM331039", "GSM331040", "GSM331041", "GSM331042", "GSM331043", "GSM331044", "GSM331045", "GSM331046", "GSM331047", "GSM331048", "GSM331049", "GSM331050", "GSM331051", "GSM331052", "GSM331053", "GSM331054", "GSM331055", "GSM331056", "GSM331057", "GSM331058", "GSM331059", "GSM331060", "GSM331061", "GSM331062", "GSM331063", "GSM331064", "GSM331065", "GSM331066", "GSM331067", "GSM331068", "GSM331069", "GSM331070", "GSM331071", "GSM331072", "GSM331073", "GSM331074", "GSM331075", "GSM331076", "GSM331077", "GSM331078", "GSM331079", "GSM331080", "GSM331081", "GSM331082", "GSM331083", "GSM331084", "GSM331085", "GSM331086", "GSM331087", "GSM331088", "GSM331089", "GSM331090", "GSM331091", "GSM331092", "GSM331093", "GSM331094", "GSM331095", "GSM331096", "GSM331097", "GSM331098", "GSM331099", "GSM331100", "GSM331101", "GSM331102", "GSM331103", "GSM331104", "GSM331105", "GSM331106", "GSM331107", "GSM331108", "GSM331109", "GSM331110", "GSM331111", "GSM331112", "GSM331113", "GSM331114", "GSM331115", "GSM331116", "GSM331117", "GSM331118", "GSM331119", "GSM331120", "GSM331121", "GSM331122", "GSM331123", "GSM331124", "GSM331125", "GSM331126", "GSM331127", "GSM331128", "GSM331129", "GSM331130", "GSM331131", "GSM331132", "GSM331133", "GSM331134", "GSM331135", "GSM331136", "GSM331137", "GSM331138", "GSM331139", "GSM331140", "GSM331141", "GSM331142", "GSM331143", "GSM331144", "GSM331145", "GSM331146", "GSM331147", "GSM331148", "GSM331149", "GSM331150", "GSM331151", "GSM331152", "GSM331153", "GSM331154", "GSM331155", "GSM331156", "GSM331157", "GSM331158", "GSM331159", "GSM331160", "GSM331161", "GSM331162", "GSM331163", "GSM331164", "GSM331165", "GSM331166", "GSM331167", "GSM331168", "GSM331169", "GSM331170", "GSM331171", "GSM331172", "GSM331173", "GSM331174", "GSM331175", "GSM331176", "GSM331177", "GSM331178", "GSM331179", "GSM331180", "GSM331181", "GSM331182", "GSM331183", "GSM331184", "GSM331185", "GSM331186", "GSM331187", "GSM331188", "GSM331189", "GSM331190", "GSM331191", "GSM331192", "GSM331193", "GSM331194", "GSM331195", "GSM331196", "GSM331197", "GSM331198", "GSM331199", "GSM331200", "GSM331201", "GSM331202", "GSM331203", "GSM331204", "GSM331205", "GSM331206", "GSM331207", "GSM331208", "GSM331209", "GSM331210", "GSM331211", "GSM331212", "GSM331213", "GSM331214", "GSM331215", "GSM331216", "GSM331217", "GSM331218", "GSM331219", "GSM331220", "GSM331221", "GSM331222", "GSM331223", "GSM331224", "GSM331225", "GSM331226", "GSM331227", "GSM331228", "GSM331229", "GSM331230", "GSM331231", "GSM331232", "GSM331233", "GSM331234", "GSM331235", "GSM331236", "GSM331237", 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Subsequently, the most predictive characteristic genes were identified by the least absolute shrinkage and selection operator (LASSO) (27)."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.group_comparison_wilcoxon"]}, "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": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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