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pmid:35203505
Relationship between Macrophage and Radiosensitivity in Human Primary and Recurrent Glioblastoma: In Silico Analysis with Publicly Available Datasets.
Bum-Sup Jang · In Ah Kim
Biomedicines · 2022 doi:10.3390/biomedicines10020292
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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We investigated the relationship between tumor radiosensitivity and infiltrating M1/M2 macrophage profiles in public datasets of primary and recurrent glioblastoma. We estimated the radiosensitivity index (RSI) score based on gene expression rankings. Macrophages were profiled using the deconvolution algorithm CIBERSORTx. Samples from The Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), the Ivy Glioblastoma Atlas Project dataset, a single-cell RNA sequencing dataset (GSE84465), Glioma Longitudinal Analysis Consortium (GLASS), and an immunotherapy trial dataset (GSE121810) were included. RSI-high radioresistant tumors were associated with worse overall survival in TCGA and CGGA than RSI-low tumors. M1/M2 macrophage ratios and RSI scores were inversely associated, indicating that radioresistant glioblastoma tumor microenvironments contain more M2 than M1 macrophages. In the single-cell RNA sequencing dataset, the mean RSI of neoplastic cells was positively correlated with high M2 macrophages proportions. A favorable response to programmed cell death protein 1 (PD-1) therapy was observed in recurrent glioblastomas with high M1/M2 macrophage ratios and low RSI scores. In patients with recurrent glioblastoma, fewer M2 macrophages and low RSI scores were associated with improved overall survival. High M2 macrophage proportions may be involved in radioresistant glioblastoma.", "claims": [{"id": "claim-method", "statement": "Available survival data were analyzed with the Cox proportional hazards model. A Kaplan–Meier curve was plotted, and the log-rank test was performed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35203505", "locator": "sections[5] \"2.3. Statistical Analysis\" paragraph 2", "quote": "Available survival data were analyzed with the Cox proportional hazards model. A Kaplan–Meier curve was plotted, and the log-rank test was performed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data analyzed during this study are available from the publicly available repository. Data from TCGA can be downloaded from the Genomic Data Commons Data Portal (https://portal.gdc.cancer.gov (accessed on 6 January 2021)) and CGCA from the website (http://cgga.org.cn (accessed on 6 May 2020)). Data for the Ivy Glioblastoma Atlas Project can be retrieved from the website (https://glioblastoma.alleninstitute.org (accessed on 1 April 2021)). Single-cell RNA sequencing data are available using identifier GSE84465 in the GEO database. The brain immune atlas is available from the website (https://www.brainimmuneatlas.org (accessed on 8 May 2021)). 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Paired bulk tumor RNA sequencing data were retrieved from the GLASS Consortium (https://github.com/fpbarthel/GLASS (accessed on 15 May 2021))."}], "state": "complete"}, {"id": "claim-target-result", "statement": "These results indicate that RSI is predictive for overall survival among patients who are treated with radiation therapy.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35203505", "locator": "sections[8] \"3.1. 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"GSM2245275", "GSM2245276", "GSM2245277", "GSM2245278", "GSM2245279", "GSM2245280", "GSM2245281", "GSM2245282", "GSM2245283", "GSM2245284", "GSM2245285", "GSM2245286", "GSM2245287", "GSM2245288", "GSM2245289", "GSM2245290", "GSM2245291", "GSM2245292", "GSM2245293", "GSM2245294", "GSM2245295", "GSM2245296", "GSM2245297", "GSM2245298", "GSM2245299", "GSM2245300", "GSM2245301", "GSM2245302", "GSM2245303", "GSM2245304", "GSM2245305", "GSM2245306", "GSM2245307", "GSM2245308", "GSM2245309", "GSM2245310", "GSM2245311", "GSM2245312", "GSM2245313", "GSM2245314", "GSM2245315", "GSM2245316", "GSM2245317", "GSM2245318", "GSM2245319", "GSM2245320", "GSM2245321", "GSM2245322", "GSM2245323", "GSM2245324", "GSM2245325", "GSM2245326", "GSM2245327", "GSM2245328", "GSM2245329", "GSM2245330", "GSM2245331", "GSM2245332", "GSM2245333", "GSM2245334", "GSM2245335", "GSM2245336", "GSM2245337", "GSM2245338", "GSM2245339", "GSM2245340", "GSM2245341", "GSM2245342", "GSM2245343", "GSM2245344", "GSM2245345", "GSM2245346", "GSM2245347", "GSM2245348", "GSM2245349", "GSM2245350", "GSM2245351", "GSM2245352", "GSM2245353", "GSM2245354", "GSM2245355", "GSM2245356", "GSM2245357", "GSM2245358", "GSM2245359", "GSM2245360", "GSM2245361", "GSM2245362", "GSM2245363", "GSM2245364", "GSM2245365", "GSM2245366", "GSM2245367", "GSM2245368", "GSM2245369", "GSM2245370", "GSM2245371", "GSM2245372", "GSM2245373", "GSM2245374", "GSM2245375", "GSM2245376", "GSM2245377", "GSM2245378", "GSM2245379", "GSM2245380", "GSM2245381", "GSM2245382", "GSM2245383", "GSM2245384", "GSM2245385", "GSM2245386", "GSM2245387", "GSM2245388", "GSM2245389", "GSM2245390", "GSM2245391", "GSM2245392", "GSM2245393", "GSM2245394", "GSM2245395", "GSM2245396", "GSM2245397", "GSM2245398", "GSM2245399", "GSM2245400", "GSM2245401", "GSM2245402", "GSM2245403", "GSM2245404", "GSM2245405", "GSM2245406", "GSM2245407", "GSM2245408", "GSM2245409", "GSM2245410", "GSM2245411", "GSM2245412", "GSM2245413", "GSM2245414", "GSM2245415", "GSM2245416", "GSM2245417", "GSM2245418", "GSM2245419", "GSM2245420", "GSM2245421", "GSM2245422", "GSM2245423", "GSM2245424", "GSM2245425", "GSM2245426", "GSM2245427", "GSM2245428", "GSM2245429", "GSM2245430", "GSM2245431", "GSM2245432", "GSM2245433", "GSM2245434", "GSM2245435", "GSM2245436", "GSM2245437", "GSM2245438", "GSM2245439", "GSM2245440", "GSM2245441", "GSM2245442", "GSM2245443", "GSM2245444", "GSM2245445", "GSM2245446", "GSM2245447", "GSM2245448", "GSM2245449", "GSM2245450", "GSM2245451", "GSM2245452", "GSM2245453", "GSM2245454", "GSM2245455", "GSM2245456", "GSM2245457", "GSM2245458", "GSM2245459", "GSM2245460", "GSM2245461", "GSM2245462", "GSM2245463", "GSM2245464", "GSM2245465", "GSM2245466", "GSM2245467", "GSM2245468", "GSM2245469", "GSM2245470", "GSM2245471", "GSM2245472", "GSM2245473", "GSM2245474", "GSM2245475", "GSM2245476", "GSM2245477", "GSM2245478", "GSM2245479", "GSM2245480", "GSM2245481", "GSM2245482", "GSM2245483", "GSM2245484", "GSM2245485", "GSM2245486", "GSM2245487", "GSM2245488", "GSM2245489", "GSM2245490", "GSM2245491", "GSM2245492", "GSM2245493", "GSM2245494", "GSM2245495", "GSM2245496", "GSM2245497", "GSM2245498", "GSM2245499", "GSM2245500", "GSM2245501", "GSM2245502", "GSM2245503", "GSM2245504", "GSM2245505", "GSM2245506", "GSM2245507", "GSM2245508", "GSM2245509", "GSM2245510", "GSM2245511", "GSM2245512", "GSM2245513", "GSM2245514", "GSM2245515", "GSM2245516", "GSM2245517", "GSM2245518", "GSM2245519", "GSM2245520", "GSM2245521", "GSM2245522", "GSM2245523", "GSM2245524", "GSM2245525", "GSM2245526", "GSM2245527", "GSM2245528", "GSM2245529", "GSM2245530", "GSM2245531", "GSM2245532", "GSM2245533", "GSM2245534", "GSM2245535", "GSM2245536", "GSM2245537", "GSM2245538", "GSM2245539", "GSM2245540", "GSM2245541", "GSM2245542", "GSM2245543", "GSM2245544", "GSM2245545", "GSM2245546", "GSM2245547", "GSM2245548", "GSM2245549", "GSM2245550", "GSM2245551", "GSM2245552", "GSM2245553", "GSM2245554", "GSM2245555", "GSM2245556", "GSM2245557", "GSM2245558", "GSM2245559", "GSM2245560", "GSM2245561", "GSM2245562", "GSM2245563", "GSM2245564", "GSM2245565", "GSM2245566", "GSM2245567", "GSM2245568", "GSM2245569", "GSM2245570", "GSM2245571", "GSM2245572", "GSM2245573", "GSM2245574", "GSM2245575", "GSM2245576", "GSM2245577", "GSM2245578", "GSM2245579", "GSM2245580", "GSM2245581", "GSM2245582", "GSM2245583", "GSM2245584", "GSM2245585", "GSM2245586", "GSM2245587", "GSM2245588", "GSM2245589", "GSM2245590", "GSM2245591", "GSM2245592", "GSM2245593", "GSM2245594", "GSM2245595", "GSM2245596", "GSM2245597", "GSM2245598", "GSM2245599", "GSM2245600", "GSM2245601", "GSM2245602", "GSM2245603", "GSM2245604", "GSM2245605", "GSM2245606", "GSM2245607", "GSM2245608", "GSM2245609", "GSM2245610", "GSM2245611", "GSM2245612", "GSM2245613", "GSM2245614", "GSM2245615", "GSM2245616", "GSM2245617", "GSM2245618", "GSM2245619", "GSM2245620", "GSM2245621", "GSM2245622", "GSM2245623", "GSM2245624", "GSM2245625", "GSM2245626", "GSM2245627", "GSM2245628", "GSM2245629", "GSM2245630", "GSM2245631", "GSM2245632", "GSM2245633", "GSM2245634", "GSM2245635", "GSM2245636", "GSM2245637", "GSM2245638", "GSM2245639", "GSM2245640", "GSM2245641", "GSM2245642", "GSM2245643", "GSM2245644", "GSM2245645", "GSM2245646", "GSM2245647", "GSM2245648", "GSM2245649", "GSM2245650", "GSM2245651", "GSM2245652", "GSM2245653", "GSM2245654", "GSM2245655", "GSM2245656", "GSM2245657", "GSM2245658", "GSM2245659", "GSM2245660", "GSM2245661", "GSM2245662", "GSM2245663", "GSM2245664", "GSM2245665", "GSM2245666", "GSM2245667", "GSM2245668", "GSM2245669", "GSM2245670", "GSM2245671", "GSM2245672", "GSM2245673", "GSM2245674", "GSM2245675", "GSM2245676", "GSM2245677", "GSM2245678", "GSM2245679", "GSM2245680", "GSM2245681", "GSM2245682", "GSM2245683", "GSM2245684", "GSM2245685", "GSM2245686", "GSM2245687", "GSM2245688", "GSM2245689", "GSM2245690", "GSM2245691", "GSM2245692", "GSM2245693", "GSM2245694", "GSM2245695", "GSM2245696", "GSM2245697", "GSM2245698", "GSM2245699", "GSM2245700", "GSM2245701", "GSM2245702", "GSM2245703", "GSM2245704", "GSM2245705", "GSM2245706", "GSM2245707", "GSM2245708", "GSM2245709", "GSM2245710", "GSM2245711", "GSM2245712", "GSM2245713", "GSM2245714", "GSM2245715", "GSM2245716", "GSM2245717", "GSM2245718", "GSM2245719", "GSM2245720", "GSM2245721", "GSM2245722", "GSM2245723", "GSM2245724", "GSM2245725", "GSM2245726", "GSM2245727", "GSM2245728", "GSM2245729", "GSM2245730", "GSM2245731", "GSM2245732", "GSM2245733", "GSM2245734", "GSM2245735", "GSM2245736", "GSM2245737", "GSM2245738", "GSM2245739", "GSM2245740", "GSM2245741", "GSM2245742", "GSM2245743", "GSM2245744", "GSM2245745", "GSM2245746", "GSM2245747", "GSM2245748", "GSM2245749", "GSM2245750", "GSM2245751", "GSM2245752", "GSM2245753", "GSM2245754", "GSM2245755", "GSM2245756", "GSM2245757", "GSM2245758", "GSM2245759", "GSM2245760", "GSM2245761", "GSM2245762", "GSM2245763", "GSM2245764", "GSM2245765", "GSM2245766", "GSM2245767", "GSM2245768", "GSM2245769", "GSM2245770", "GSM2245771", 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE84465", "GSE121810"], "resolved_accessions": ["GSE84465", "GSE121810"], "statements": ["All data analyzed during this study are available from the publicly available repository. Data from TCGA can be downloaded from the Genomic Data Commons Data Portal (https://portal.gdc.cancer.gov (accessed on 6 January 2021)) and CGCA from the website (http://cgga.org.cn (accessed on 6 May 2020)). Data for the Ivy Glioblastoma Atlas Project can be retrieved from the website (https://glioblastoma.alleninstitute.org (accessed on 1 April 2021)). Single-cell RNA sequencing data are available using identifier GSE84465 in the GEO database. The brain immune atlas is available from the website (https://www.brainimmuneatlas.org (accessed on 8 May 2021)). Paired bulk tumor RNA sequencing data were retrieved from the GLASS Consortium (https://github.com/fpbarthel/GLASS (accessed on 15 May 2021))."], "basis": "The paper names GSE84465, GSE121810 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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