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pmid:38903927
Analysis of prognostic biomarker models of TXNIP/NLRP3/IL1B inflammasome pathway in patients with acute myeloid leukemia.
Junjie Chen · Qi Hou · Tao Chang · Jiamian Zheng · Chao Yao · Junyi He · Shengting Chen · Xiuli Wu · Zhenyi Jin
International journal of medical sciences · 2024 doi:10.7150/ijms.96627
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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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This study aimed to investigate the expression pattern of the thioredoxin-interacting protein (TXNIP)/nucleotide-binding oligomerization domain (NOD)-like receptor protein 3 (NLRP3) pathway and its role in the prognosis of AML patients. Methods: In this study, we examined the prognostic value of TXNIP/NLRP3 pathway in AML patients using microarray data from Gene Expression Omnibus (GEO) and transcriptome data from the Cancer Genome Atlas (TCGA) to develop a prognostic model and validated the results by quantitative real-time PCR (qRT-PCR) in a validation cohort of 26 AML patients and 18 healthy individuals from Jinan University (JNU) database. Results: Analysis of the GSE13159 database revealed that TXNIP, interleukin 1 beta (IL1B) within the TXNIP/NLRP3 pathway were significantly upregulated and caspase1 (CASP1) was downregulated in AML patients (TXNIP, P = 0.031; IL1B, P = 0.042; CASP1, P = 0.038). Compared to high NLRP3 expression, AML patients with low NLRP3 expression had a longer overall survival (OS) in the GSE12417 dataset (P = 0.004). Moreover, both the training and validation results indicated that lower TXNIP, NLRP3, and IL1B expression were associated with favorable prognosis (GSE12417, P = 0.009; TCGA, P = 0.050; JNU, P = 0.026). According to the receiver operating characteristic curve analysis, this model demonstrated a sensitivity of 84% for predicting three-year survival. These data might provide novel predictors for AML outcome and direction for further investigation of the possibility of using TXNIP/NLRP3/IL1B genes in novel targeted therapies for AML.", "claims": [{"id": "claim-method", "statement": "The log-rank test conducted by R package “survminer” was used to compare differences in Kaplan-Meier curves.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38903927", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "The log-rank test conducted by R package “survminer” was used to compare differences in Kaplan-Meier curves."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material. 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"GSM329850", "GSM329851", "GSM329852", "GSM329853", "GSM329854", "GSM329855", "GSM329856", "GSM329857", "GSM329858", "GSM329859", "GSM329860", "GSM329861", "GSM329862", "GSM329863", "GSM329864", "GSM329865", "GSM329866", "GSM329867", "GSM329868", "GSM329869", "GSM329870", "GSM329871", "GSM329872", "GSM329873", "GSM329874", "GSM329875", "GSM329876", "GSM329877", "GSM329878", "GSM329879", "GSM329880", "GSM329881", "GSM329882", "GSM329883", "GSM329884", "GSM329885", "GSM329886", "GSM329887", "GSM329888", "GSM329889", "GSM329890", "GSM329891", "GSM329892", "GSM329893", "GSM329894", "GSM329895", "GSM329896", "GSM329897", "GSM329898", "GSM329899", "GSM329900", "GSM329901", "GSM329902", "GSM329903", "GSM329904", "GSM329905", "GSM329906", "GSM329907", "GSM329908", "GSM329909", "GSM329910", "GSM329911", "GSM329912", "GSM329913", "GSM329914", "GSM329915", "GSM329916", "GSM329917", "GSM329918", "GSM329919", "GSM329920", "GSM329921", "GSM329922", "GSM329923", "GSM329924", "GSM329925", "GSM329926", "GSM329927", "GSM329928", "GSM329929", "GSM329930", "GSM329931", "GSM329932", "GSM329933", "GSM329934", "GSM329935", "GSM329936", "GSM329937", "GSM329938", "GSM329939", "GSM329940", "GSM329941", "GSM329942", "GSM329943", "GSM329944", "GSM329945", "GSM329946", "GSM329947", "GSM329948", "GSM329949", "GSM329950", "GSM329951", "GSM329952", "GSM329953", "GSM329954", "GSM329955", "GSM329956", "GSM329957", "GSM329958", "GSM329959", "GSM329960", "GSM329961", "GSM329962", "GSM329963", "GSM329964", "GSM329965", "GSM329966", "GSM329967", "GSM329968", "GSM329969", "GSM329970", "GSM329971", "GSM329972", "GSM329973", "GSM329974", "GSM329975", "GSM329976", "GSM329977", "GSM329978", "GSM329979", "GSM329980", "GSM329981", "GSM329982", "GSM329983", "GSM329984", "GSM329985", "GSM329986", "GSM329987", "GSM329988", "GSM329989", "GSM329990", "GSM329991", "GSM329992", "GSM329993", "GSM329994", "GSM329995", "GSM329996", "GSM329997", "GSM329998", "GSM329999", "GSM330000", "GSM330001", "GSM330002", "GSM330003", "GSM330004", "GSM330005", "GSM330006", "GSM330007", "GSM330008", "GSM330009", "GSM330010", "GSM330011", "GSM330012", "GSM330013", "GSM330014", "GSM330015", "GSM330016", "GSM330017", "GSM330018", "GSM330019", "GSM330020", "GSM330021", "GSM330022", "GSM330023", "GSM330024", "GSM330025", "GSM330026", "GSM330027", "GSM330028", "GSM330029", "GSM330030", "GSM330031", "GSM330032", "GSM330033", "GSM330034", "GSM330035", "GSM330036", "GSM330037", "GSM330038", "GSM330039", "GSM330040", "GSM330041", "GSM330042", "GSM330043", "GSM330044", "GSM330045", "GSM330046", "GSM330047", "GSM330048", "GSM330049", "GSM330050", "GSM330051", "GSM330052", "GSM330053", "GSM330054", "GSM330055", "GSM330056", "GSM330057", "GSM330058", "GSM330059", "GSM330060", "GSM330061", "GSM330062", "GSM330063", "GSM330064", "GSM330065", "GSM330066", "GSM330067", "GSM330068", "GSM330069", "GSM330070", "GSM330071", "GSM330072", "GSM330073", "GSM330074", "GSM330075", "GSM330076", "GSM330077", "GSM330078", "GSM330079", "GSM330080", "GSM330081", "GSM330082", "GSM330083", "GSM330084", "GSM330085", "GSM330086", "GSM330087", "GSM330088", "GSM330089", "GSM330090", "GSM330091", "GSM330092", "GSM330093", "GSM330094", "GSM330095", "GSM330096", "GSM330097", "GSM330098", "GSM330099", "GSM330100", "GSM330101", "GSM330102", "GSM330103", "GSM330104", "GSM330105", "GSM330106", "GSM330107", "GSM330108", "GSM330109", "GSM330110", "GSM330111", "GSM330112", "GSM330113", "GSM330114", "GSM330115", "GSM330116", "GSM330117", "GSM330118", "GSM330119", "GSM330120", "GSM330121", "GSM330122", "GSM330123", "GSM330124", "GSM330125", "GSM330126", "GSM330127", "GSM330128", "GSM330129", "GSM330130", "GSM330131", "GSM330132", "GSM330133", "GSM330134", "GSM330135", "GSM330136", "GSM330137", "GSM330138", "GSM330139", "GSM330140", "GSM330141", "GSM330142", "GSM330143", "GSM330144", "GSM330145", "GSM330146", "GSM330147", "GSM330148", "GSM330149", "GSM330150", "GSM330151", "GSM330152", "GSM330153", "GSM330154", "GSM330155", "GSM330156", "GSM330157", "GSM330158", "GSM330159", "GSM330160", "GSM330161", "GSM330162", "GSM330163", "GSM330164", "GSM330165", "GSM330166", "GSM330167", "GSM330168", "GSM330169", "GSM330170", "GSM330171", "GSM330172", "GSM330173", "GSM330174", "GSM330175", "GSM330176", "GSM330177", "GSM330178", "GSM330179", "GSM330180", "GSM330181", "GSM330182", "GSM330183", "GSM330184", "GSM330185", "GSM330186", "GSM330187", "GSM330188", "GSM330189", "GSM330190", "GSM330191", "GSM330192", "GSM330193", "GSM330194", "GSM330195", "GSM330196", "GSM330197", "GSM330198", "GSM330199", "GSM330200", "GSM330201", "GSM330202", "GSM330203", "GSM330204", "GSM330205", "GSM330206", "GSM330207", "GSM330208", "GSM330209", "GSM330210", "GSM330211", "GSM330212", "GSM330213", "GSM330214", "GSM330215", "GSM330216", "GSM330217", "GSM330218", "GSM330219", "GSM330220", "GSM330221", "GSM330222", "GSM330223", "GSM330224", "GSM330225", "GSM330226", "GSM330227", "GSM330228", "GSM330229", "GSM330230", "GSM330231", "GSM330232", "GSM330233", "GSM330234", "GSM330235", "GSM330236", "GSM330237", "GSM330238", "GSM330239", "GSM330240", "GSM330241", "GSM330242", "GSM330243", "GSM330244", "GSM330245", "GSM330246", "GSM330247", "GSM330248", "GSM330249", "GSM330250", "GSM330251", "GSM330252", "GSM330253", "GSM330254", "GSM330255", "GSM330256", "GSM330257", "GSM330258", "GSM330259", "GSM330260", "GSM330261", "GSM330262", "GSM330263", "GSM330264", "GSM330265", "GSM330266", "GSM330267", "GSM330268", "GSM330269", "GSM330270", "GSM330271", "GSM330272", "GSM330273", "GSM330274", "GSM330275", "GSM330276", "GSM330277", "GSM330278", "GSM330279", "GSM330280", "GSM330281", "GSM330282", "GSM330283", "GSM330284", "GSM330285", "GSM330286", "GSM330287", "GSM330288", "GSM330289", "GSM330290", "GSM330291", "GSM330292", "GSM330293", "GSM330294", "GSM330295", "GSM330296", "GSM330297", "GSM330298", "GSM330299", "GSM330300", "GSM330301", "GSM330302", "GSM330303", "GSM330304", "GSM330305", "GSM330306", "GSM330307", "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", 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"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": 1.0, "band": "verbatim", "quote": "The log-rank test conducted by R package “survminer” was used to compare differences in Kaplan-Meier curves."}}, {"id": "method-2", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Mann Whitney"}}, {"id": "method-3", "family": "survival_analysis", "specific": "restricted_mean_survival", "label": "Survival analysis", "dsl_operations": ["restricted_mean_survival"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "restricted mean survival"}}, {"id": "method-4", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE13159", "GSE12417"], "resolved_accessions": ["GSE13159", "GSE12417"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE13159, GSE12417 in GEO database and the accession resolves in the repository. 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