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pmid:36300085
Identification of a dysregulated CircRNA-associated gene signature for predicting prognosis, immune landscape, and drug candidates in bladder cancer.
Chong Shen · Zhi Li · Yinglang Zhang · Zhe Zhang · Zhouliang Wu · La Da · Shaobo Yang · Zejin Wang · Yu Zhang · Yunkai Qie · Gangjian Zhao · Yuda Lin · Shiwang Huang · Mingli Zhou · Hailong Hu
Frontiers in oncology · 2022 doi:10.3389/fonc.2022.1018285
Paper
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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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However, circRNAs have rarely been studied in bladder cancer (BCa). The purpose of this research is to explore new circRNAs and their potential mechanisms in BCa. A novel ceRNA-regulated network, including 87 differentially expressed circRNAs (DE-circRNAs), 126 DE-miRNAs, and 217 DE-mRNAs was constructed to better understanding the biological processes using Cytoscape 3.7.1 based on our previously high-throughput circRNA sequencing and five GEO datasets. Subsequently, five randomly selected circRNAs (upregulated circ_0001681; downregulated circ_0000643, circ_0001798, circ_0006117 and circ_0067900) in 20 pairs of BCa and paracancerous tissues were confirmed using qRT-PCR. Functional analysis results determined that 772 GO functions and 32 KEGG pathways were enriched in the ceRNA network. Ten genes (PFKFB4, EDNRA, GSN, GAS1, PAPPA, DTL, TGFBI, PRSS8, RGS1 and TCF4) were selected for signature construction among the ceRNA network. The Human Protein Atlas (HPA) expression of these genes were consistent with the above sequencing data. Notably, the model was validated in multiple external datasets (GSE13507, GSE31684, GSE48075, IMvigor210 and GSE32894). The immune-infiltration was evaluated by 7 published algorithms (i.e., TIMER, CIBERSORT, CIBERSORT-ABS, QUANTISEQ, MCPCOUNTER, XCELL and EPIC). Next, Correlations between riskscore or risk groups and clinicopathological data, overall survival, recognized immunoregulatory cells or common chemotherapeutic agents of BCa patients were performed using wilcox rank test, chi-square test, cox regression and spearman's correlation analysis; and, these results are significant. According to R package \"GSVA\" and \"clusterProfiler\", the most significantly enriched HALLMARK and KEGG pathway was separately the 'Epithelial Mesenchymal Transition' and 'Ecm Receptor Interaction' in the high- vs. low-risk group. Additionally, the functional experiments in vitro also revealed that the overexpression of has_circ_0067900 significantly impaired the proliferation, migration, and invasion capacities of BCa cells. Collectively, the results of the current study provide a novel landscape of circRNA-associated ceRNA-regulated network in BCa. The ceRNA-associated gene model which was constructed presented a high predictive performance for the prognosis, immunotherapeutic responsiveness, and chemotherapeutic sensitivity of BCa. And, has_circ_0067900 was originally proposed as tumor suppressor for patients with BCa.", "claims": [{"id": "claim-method", "statement": "Likewise, the differential miRNA expression analysis of GSE11224, GSE113786 and GSE113740 dataset respectively identified 317 (including 217 upregulated and 100 downregulated), 252 (including 76 upregulated and 176 downregulated) and 541 (including 289 upregulated and 252 downregulated) DE-miRNAs by limma R package (adjusted P < 0.05 and |log2(FC)| > 2) ( Supplementary File S3 ).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36300085", "locator": "sections[19] \"Identification of DE-circRNAs, DE-miRNAs, DE-mRNAs\" paragraph 2", "quote": "Likewise, the differential miRNA expression analysis of GSE11224, GSE113786 and GSE113740 dataset respectively identified 317 (including 217 upregulated and 100 downregulated), 252 (including 76 upregulated and 176 downregulated) and 541 (including 289 upregulated and 252 downregulated) DE-miRNAs by limma R package (adjusted P < 0.05 and |log2(FC)| > 2) ( Supplementary File S3 )."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36300085", "locator": "sections[30] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Collectively, the results of the current study provide a novel landscape of circRNA-associated ceRNA-regulated network in BCa.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36300085", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Collectively, the results of the current study provide a novel landscape of circRNA-associated ceRNA-regulated network in BCa."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Collectively, the results of the current study provide a novel landscape of circRNA-associated ceRNA-regulated network in BCa.", "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:36300085"], "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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"GSM3616303", "GSM3616304", "GSM3616305", "GSM3616306", "GSM3616307", "GSM3616308", "GSM3616309", "GSM3616310", "GSM3616311", "GSM3616312", "GSM3616313", "GSM3616314", "GSM3616315", "GSM3616316", "GSM3616317", "GSM3616318", "GSM3616319", "GSM3616320", "GSM3616321", "GSM3616322", "GSM3616323", "GSM3616324", "GSM3616325", "GSM3616326", "GSM3616327", "GSM3616328", "GSM3616329", "GSM3616330", "GSM3616331", "GSM3616332", "GSM3616333", "GSM3616334", "GSM3616335", "GSM3616336", "GSM3616337", "GSM3616338", "GSM3616339", "GSM3616340", "GSM3616341", "GSM3616342", "GSM3616343", "GSM3616344", "GSM3616345", "GSM3616346", "GSM3616347", "GSM3616348", "GSM3616349", "GSM3616350", "GSM3616351", "GSM3616352", "GSM3616353", "GSM3616354", "GSM3616355", "GSM3616356", "GSM3616357", "GSM3616358", "GSM3616359", "GSM3616360", "GSM3616361", "GSM3616362", "GSM3616363", "GSM3616364", "GSM3616365", "GSM3616366", "GSM3616367", "GSM3616368", "GSM3616369", "GSM3616370", "GSM3616371", "GSM3616372", "GSM3616373", 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"GSM3616587", "GSM3616588", "GSM3616589", "GSM3616590", "GSM3616591", "GSM3616592", "GSM3616593", "GSM3616594", "GSM3616595", "GSM3616596", "GSM3616597", "GSM3616598", "GSM3616599", "GSM3616600", "GSM3616601", "GSM3616602", "GSM3616603", "GSM3616604", "GSM3616605", "GSM3616606", "GSM3616607", "GSM3616608", "GSM3616609", "GSM3616610", "GSM3616611", "GSM3616612", "GSM3616613", "GSM3616614", "GSM3616615", "GSM3616616", "GSM3616617", "GSM3616618", "GSM3616619", "GSM3616620", "GSM3616621", "GSM3616622", "GSM3616623", "GSM3616624", "GSM3616625", "GSM3616626", "GSM3616627", "GSM3616628", "GSM3616629", "GSM3616630", "GSM3616631", "GSM3616632", "GSM3616633", "GSM3616634", "GSM3616635", "GSM3616636", "GSM3616637", "GSM3616638", "GSM3616639", "GSM3616640", "GSM3616641", "GSM3616642", "GSM3616643", "GSM3616644", "GSM3616645", "GSM3616646", "GSM3616647", "GSM3616648", "GSM3616649", "GSM3616650", "GSM3616651", "GSM3616652", "GSM3616653", "GSM3616654", "GSM3616655", "GSM3616656", "GSM3616657", "GSM3616658", "GSM3616659", "GSM3616660", "GSM3616661", "GSM3616662", "GSM3616663", "GSM3616664", "GSM3616665", "GSM3616666", "GSM3616667", "GSM3616668", "GSM3616669", "GSM3616670", "GSM3616671", "GSM3616672", "GSM3616673", "GSM3616674", "GSM3616675", "GSM3616676", "GSM3616677", "GSM3616678", "GSM3616679", "GSM3616680", "GSM3616681", "GSM3616682", "GSM3616683", "GSM3616684", "GSM3616685", "GSM3616686", "GSM3616687", "GSM3616688", "GSM3616689", "GSM3616690", "GSM3616691", "GSM3616692", "GSM3616693", "GSM3616694", "GSM3616695", "GSM3616696", "GSM3616697", "GSM3616698", "GSM3616699", "GSM3616700", "GSM3616701", "GSM3616702", "GSM3616703", "GSM3616704", "GSM3616705", "GSM3616706", "GSM3616707", "GSM3616708", "GSM3616709", "GSM3616710", "GSM3616711", "GSM3616712", "GSM3616713", "GSM3616714", "GSM3616715", "GSM3616716", "GSM3616717", "GSM3616718", "GSM3616719", "GSM3616720", "GSM3616721", "GSM3616722", "GSM3616723", "GSM3616724", "GSM3616725", "GSM3616726", "GSM3616727", "GSM3616728", 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"GSM3616800", "GSM3616801", "GSM3616802", "GSM3616803", "GSM3616804", "GSM3616805", "GSM3616806", "GSM3616807", "GSM3616808", "GSM3616809", "GSM3616810", "GSM3616811", "GSM3616812", "GSM3616813", "GSM3616814", "GSM3616815", "GSM3616816", "GSM3616817", "GSM3616818", "GSM3616819", "GSM3616820", "GSM3616821", "GSM3616822", "GSM3616823", "GSM3616824", "GSM3616825", "GSM3616826", "GSM3616827", "GSM3616828", "GSM3616829", "GSM3616830", "GSM3616831", "GSM3616832", "GSM3616833", "GSM3616834", "GSM3616835", "GSM3616836", "GSM3616837", "GSM3616838", "GSM3616839", "GSM3616840", "GSM3616841", "GSM3616842", "GSM3616843", "GSM3616844", "GSM3616845", "GSM3616846", "GSM3616847", "GSM3616848", "GSM3616849", "GSM3616850", "GSM3616851", "GSM3616852", "GSM3616853", "GSM3616854", "GSM3616855", "GSM3616856", "GSM3616857", "GSM3616858", "GSM3616859", "GSM3616860", "GSM3616861", "GSM3616862", "GSM3616863", "GSM3616864", "GSM3616865", "GSM3616866", "GSM3616867", "GSM3616868", "GSM3616869", "GSM3616870", "GSM3616871", "GSM3616872", "GSM3616873", "GSM3616874", "GSM3616875", "GSM3616876", "GSM3616877", "GSM3616878", "GSM3616879", "GSM3616880", "GSM3616881", "GSM3616882", "GSM3616883", "GSM3616884", "GSM3616885", "GSM3616886", "GSM3616887", "GSM3616888", "GSM3616889", "GSM3616890", "GSM3616891", "GSM3616892", "GSM3616893", "GSM3616894", "GSM3616895", "GSM3616896", "GSM3616897", "GSM3616898", "GSM3616899", "GSM3616900", "GSM3616901", "GSM3616902", "GSM3616903", "GSM3616904", "GSM3616905", "GSM3616906", "GSM3616907", "GSM3616908", "GSM3616909", "GSM3616910", "GSM3616911", "GSM3616912", "GSM3616913", "GSM3616914", "GSM3616915", "GSM3616916", "GSM3616917", "GSM3616918", "GSM3616919", "GSM3616920", "GSM3616921", "GSM3616922", "GSM3616923", "GSM3616924", "GSM3616925", "GSM3616926", "GSM3616927", "GSM3616928", "GSM3616929", "GSM3616930", "GSM3616931", "GSM3616932", "GSM3616933", "GSM3616934", "GSM3616935", "GSM3616936", "GSM3616937", "GSM3616938", "GSM3616939", "GSM3616940", "GSM3616941", "GSM3616942", "GSM3616943", "GSM3616944", "GSM3616945", "GSM3616946", "GSM3616947", "GSM3616948", "GSM3616949", "GSM3616950", "GSM3616951", "GSM3616952", "GSM3616953", "GSM3616954", "GSM3616955", "GSM3616956", "GSM3616957", "GSM3616958", "GSM3616959", "GSM3616960", "GSM3616961", "GSM3616962", "GSM3616963", "GSM3616964", "GSM3616965", "GSM3616966", "GSM3616967", "GSM3616968", "GSM3616969", "GSM3616970", "GSM3616971", "GSM3616972", "GSM3616973", "GSM3616974", "GSM3616975", "GSM3616976", "GSM3616977", "GSM3616978", "GSM3616979", "GSM3616980", "GSM3616981", "GSM3616982", "GSM3616983", "GSM3616984", "GSM3616985", "GSM3616986", "GSM3616987", "GSM3616988", "GSM3616989", "GSM3616990", "GSM3616991", "GSM3616992", "GSM3616993", "GSM3616994", "GSM3616995", "GSM3616996", "GSM3616997", "GSM3616998", "GSM3616999", "GSM3617000", "GSM3617001", "GSM3617002", "GSM3617003", "GSM3617004", "GSM3617005", "GSM3617006", "GSM3617007", "GSM3617008", "GSM3617009", "GSM3617010", "GSM3617011", "GSM3617012", "GSM3617013", "GSM3617014", "GSM3617015", "GSM3617016", "GSM3617017", "GSM3617018", "GSM3617019", "GSM3617020", "GSM3617021", "GSM3617022", "GSM3617023", "GSM3617024", "GSM3617025", "GSM3617026", "GSM3617027", "GSM3617028", "GSM3617029", "GSM3617030", "GSM3617031", "GSM3617032", "GSM3617033", "GSM3617034", "GSM3617035", "GSM3617036", "GSM3617037", "GSM3617038", "GSM3617039", "GSM3617040", "GSM3617041", "GSM3617042", "GSM3617043", "GSM3617044", "GSM3617045", "GSM3617046", "GSM3617047", "GSM3617048", "GSM3617049", "GSM3617050", "GSM3617051", "GSM3617052", "GSM3617053", "GSM3617054", "GSM3617055", "GSM3617056", "GSM3617057", "GSM3617058", "GSM3617059", "GSM3617060", "GSM3617061", "GSM3617062", "GSM3617063", "GSM3617064", "GSM3617065", "GSM3617066", "GSM3617067", "GSM3617068", "GSM3617069", "GSM3617070", "GSM3617071", "GSM3617072", "GSM3617073", "GSM3617074", "GSM3617075", "GSM3617076", "GSM3617077", "GSM3617078", "GSM3617079", "GSM3617080", "GSM3617081", "GSM3617082", "GSM3617083", "GSM3617084", "GSM3617085", "GSM3617086", "GSM3617087", "GSM3617088", "GSM3617089", "GSM3617090", "GSM3617091", "GSM3617092", "GSM3617093", "GSM3617094", "GSM3617095", "GSM3617096", "GSM3617097", "GSM3617098", "GSM3617099", "GSM3617100", "GSM3617101", "GSM3617102", "GSM3617103", "GSM3617104", "GSM3617105", "GSM3617106", "GSM3617107", "GSM3617108", "GSM3617109", "GSM3617110", "GSM3617111", "GSM3617112", "GSM3617113", "GSM3617114", "GSM3617115", "GSM3617116", "GSM3617117", "GSM3617118", "GSM3617119", "GSM3617120", "GSM3617121", "GSM3617122", "GSM3617123", "GSM3617124", "GSM3617125", "GSM3617126", "GSM3617127", "GSM3617128", "GSM3617129", "GSM3617130", "GSM3617131", "GSM3617132", "GSM3617133", "GSM3617134", "GSM3617135", "GSM3617136", "GSM3617137", "GSM3617138", "GSM3617139", "GSM3617140", "GSM3617141", "GSM3617142", "GSM3617143", "GSM3617144", "GSM3617145", "GSM3617146", "GSM3617147", "GSM3617148", "GSM3617149", "GSM3617150", "GSM3617151", "GSM3617152", "GSM3617153", "GSM3617154", 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Next, Correlations between riskscore or ri"], "order_basis": "paper_text_order:1589", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["rial and methods Cell culture and lentiviral transfection Human two bladder cancer cell lines (T24 and", ", Ltd. After 24 hours of culture, cells were transfected with the lentiviral vectors. Expression of h", "0 was observed and determined 72 hours after transfection using an inverted microscope with fluorescen"], "order_basis": "paper_text_order:2806", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["th fluorescence observation and quantitative real-time PCR. Statistical analysis Statistical analysis r", "al Supplementary Table 1The primers used for real-time PCR are designed and synthesized by Sango Biotec", "ls Supplementary Table 1The primers used for real-time PCR are designed and synthesized by Sango Biotec"], "order_basis": "paper_text_order:3545", "id": "assay:3"}, {"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": ["Likewise, the differential miRNA expression analysis of GSE11224, GSE113786 and GSE113740 dataset respectively identified 317 (including 217 upregulated and 100 downregulated), 252 (including 76 upregulated and 176 downregulated) and 541 (including 289 upregulated and 252 downregulated) DE-miRNAs by limma R package (adjusted P < 0.05 and |log2(FC)| > 2) ( Supplementary File S3 )."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}