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pmid:33626208
Construction of a robust prognostic model for adult adrenocortical carcinoma: Results from bioinformatics and real-world data.
Xi Tian · Wen-Hao Xu · Aihetaimujiang Anwaier · Hong-Kai Wang · Fang-Ning Wan · Da-Long Cao · Wen-Jie Luo · Guo-Hai Shi · Yuan-Yuan Qu · Hai-Liang Zhang · Ding-Wei Ye
Journal of cellular and molecular medicine · 2021 doi:10.1111/jcmm.16323
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Complete file
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The RPPA data, gene expression profiles and clinical information of adult ACC patients were obtained from The Cancer Proteome Atlas (TCPA), Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). Integrated prognosis-related proteins (IPRPs) model was constructed. Immunohistochemistry was used to validate the prognostic value of the IPRPs model in Fudan University Shanghai Cancer Center (FUSCC) cohort. 76 ACC cases from TCGA and 22 ACC cases from GSE10927 in NCBI's GEO database with full data for clinical information and gene expression were utilized to validate the effectiveness of the IPRPs model. Higher FASN (P = .039), FIBRONECTIN (P < .001), TFRC (P < .001), TSC1 (P < .001) expression indicated significantly worse overall survival for adult ACC patients. Risk assessment suggested significantly a strong predictive capacity of IPRPs model for poor overall survival (P < .05). IPRPs model showed a little stronger ability for predicting prognosis than Ki-67 protein in FUSCC cohort (P = .003, HR = 3.947; P = .005, HR = 3.787). In external validation of IPRPs model using gene expression data, IPRPs model showed strong ability for predicting prognosis in TCGA cohort (P = .005, HR = 3.061) and it exhibited best ability for predicting prognosis in GSE10927 cohort (P = .0898, HR = 2.318). This research constructed IPRPs model for predicting adult ACC patients' prognosis using proteomic data, gene expression data and real-world data and this prognostic model showed stronger predictive value than other biomarkers (Ki-67, Beta-catenin, etc) in multi-cohorts.", "claims": [{"id": "claim-data-access", "statement": "The datasets analysed during the current study available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33626208", "locator": "sections[27] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The datasets analysed during the current study available from the corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33626208"], "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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["M Stage a"], ["M0", "21 (53.8)"], ["M1", "18 (46.2)"], ["Necrosis"], ["Present", "25 (64.1)"], ["Absent", "14 (35.9)"]], "row_count": 23, "column_count": 2, "numeric_cells": 17, "header_rows": 1, "locator": "section[7]/table-wrap[1]#jcmm16323-tbl-0003"}}, {"id": "asset:table:pmid:33626208:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c5a86a9efd339f0d39a5c3c2f17f4d242fe363944fa6909280b25994b289d549", "bytes": 2387, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#jcmm16323-tbl-0004", "version": null, "note": "Kaplan‐Meier analysis and univariate Cox regression analysis of proteins (both P‐value < .05)", "structure": {"pmcid": "PMC8051734", "section_index": 12, "section_title": "Selection for candidate proteins with significant prognostic value", "row_count": 43, "column_count": 4}, "table": {"label": "Table 4", "caption": 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"section_title": "External validation of the IPRPs model and comparison with other biomarkers using gene expression data", "row_count": 8, "column_count": 13}, "table": {"label": "Table 5", "caption": "Evaluating biomarkers of ACC in multiple cohorts", "rows": [["Biomarker evaluation", "AUC", "C‐index", "NRI"], ["Cohorts", "TCGA (RPPA)", "TCGA (RNAseq)", "GSE10927 (RNA seq)", "FUSCC IHC)", "TCGA (RPPA)", "TCGA (RNAseq)", "GSE10927 (RNAseq)", "FUSCC (IHC)", "TCGA (RPPA)", "TCGA (RNAseq)", "GSE10927 (RNAseq)", "FUSCC (IHC)"], ["CTNNB1", "0.4", "0.704", "0.732", "‐", "0.564", "0.659", "0.657", "‐", "ns", "‐0.02", "0.06", "‐"], ["IGF2", "‐", "0.313", "‐", "‐", "‐", "0.575", "‐", "‐", "‐", "ns", "‐", "‐"], ["TP53", "0.489", "0.87", "0.571", "‐", "0.676", "0.659", "0.551", "‐", "‐0.02", "ns", "ns", "‐"], ["MKI67", "‐", "0.862", "0.786", "0.621", "‐", "0.853", "0.671", "0.694", "‐", "0.37", "ns", "ns"], ["SF‐1", "‐", "0.71", "‐", "‐", "‐", "0.665", "‐", "‐", "‐", "‐0.07", "ns", "‐"], ["Risk 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"Description", "Count in gene set", "P value"], ["GO:0 140 014", "Mitotic nuclear division", "21", "1.26E‐30"], ["GO:0 000 280", "Nuclear division", "22", "1.81E‐28"], ["GO:0 048 285", "Organelle fission", "22", "1.61E‐27"], ["GO:0 000 775", "Chromosome, centromeric region", "24", "5.20E‐41"], ["GO:0 000 776", "Kinetochore", "21", "1.48E‐37"], ["GO:0 098 687", "Chromosomal region", "25", "1.04E‐36"], ["GO:0 008 017", "Microtubule binding", "8", "1.65E‐08"], ["GO:0 035 173", "Histone kinase activity", "4", "2.65E‐08"], ["GO:0 015 631", "Tubulin binding", "8", "1.83E‐07"], ["hsa04110", "Cell cycle", "8", "7.26E‐12"], ["hsa04914", "Progesterone‐mediated oocyte maturation", "7", "1.13E‐10"], ["hsa04114", "Oocyte meiosis", "7", "7.02E‐10"]], "row_count": 13, "column_count": 4, "numeric_cells": 36, "header_rows": 1, "locator": "section[18]/table-wrap[1]#jcmm16323-tbl-0006"}}], "gaps": ["asset:data:geo:GSE10927 not downloaded", "asset:data:geo:GSE10927 licence not read"]}, "analysis": 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