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pmid:32117736
A 6 lncRNA-Based Risk Score System for Predicting the Recurrence of Colon Adenocarcinoma Patients.
Haojie Yang · Hong-Cheng Lin · Hua Liu · Dan Gan · Wei Jin · Can Cui · Yixin Yan · Yiming Qian · Changpeng Han · Zhenyi Wang
Frontiers in oncology · 2020 doi:10.3389/fonc.2020.00081
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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 is designed to build a risk score system for COAD patients. The Cancer Genome Atlas (TCGA) dataset of COAD (the training set) was downloaded, and GSE17538 and GSE39582 (the validation sets) from Gene Expression Omnibus database were obtained. The differentially expressed RNAs (DERs) were analyzed by limma package. Using survival package, the independent prognosis-associated long non-coding RNAs (lncRNAs) were selected for constructing risk score system. After the independent clinical prognostic factors were screened out using survival package, a nomogram survival model was constructed using rms package. Furthermore, competitive endogenous RNA (ceRNA) regulatory network and enrichment analyses separately were performed using Cytoscape software and DAVID tool. Totally 404 DERs between recurrence and non-recurrence groups were identified. Based on the six independent prognosis-associated lncRNAs (including H19, KCNJ2-AS1, LINC00899, LINC01503, PRKAG2-AS1, and SRRM2-AS1), the risk score system was constructed. After the independent clinical prognostic factors (Pathologic M, pathologic T, and RS model status) were identified, the nomogram survival model was built. In the ceRNA regulatory network, there were three lncRNAs, four miRNAs, and 77 mRNAs. Additionally, PPAR signaling pathway and hedgehog signaling pathway were enriched for the mRNAs in the ceRNA regulatory network. The risk score system and the nomogram survival model might be used for predicting COAD recurrence. 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"0.417", "0.435", "−2.01", "4.40E-02"], ["PRR7-AS1", "0.669", "1.95", "0.334", "2", "4.50E-02"]], "row_count": 22, "column_count": 6, "numeric_cells": 112, "header_rows": 1, "locator": "section[4]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32117736:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2a037df7f6cd8167beb0ec7ab23c8e2e90646476a8460793850cb4a37bb45a57", "bytes": 640, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[2]#T2", "version": null, "note": "The information of the six independent prognosis-associated long non-coding RNAs (lncRNAs).", "structure": {"pmcid": "PMC7015976", "section_index": 4, "section_title": "Construction of Risk Score System", "row_count": 7, "column_count": 5}, "table": {"label": "Table 2", "caption": "The information of the six independent prognosis-associated long non-coding RNAs (lncRNAs).", "rows": [["Symbol", "Coef", "P-value", "Hazard ratio", "95% CI"], ["H19", "0.1647", "2.23E-02", "1.179", "1.024–1.358"], ["KCNJ2-AS1", "−1.1438", "1.60E-02", "0.319", "0.126–0.808"], ["LINC00899", "1.4922", "1.65E-03", "4.447", "1.755–6.265"], ["LINC01503", "0.8525", "1.22E-03", "2.346", "1.399–3.932"], ["PRKAG2-AS1", "−0.8100", "6.73E-04", "0.445", "0.279–0.710"], ["SRRM2-AS1", "3.8523", "1.35E-02", "7.100", "2.213–10.431"]], "row_count": 7, "column_count": 5, "numeric_cells": 28, "header_rows": 1, "locator": "section[4]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:32117736:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fb401248eb213953e5fb7331be86bb7ca247d1a7f5aa6b0286e7f6da85679206", "bytes": 1453, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#T3", "version": null, "note": "The selection of independent clinical prognostic factors.", "structure": {"pmcid": "PMC7015976", "section_index": 5, "section_title": "Establishment and Validation of Nomogram Survival Model", "row_count": 13, "column_count": 6}, "table": {"label": "Table 3", "caption": "The selection of independent clinical prognostic factors.", "rows": [["Clinical characteristics", "TCGA (N = 310)", "Univariable cox", "Multivariable cox"], ["", "", "HR (95% CI)", "P-value", "HR (95% CI)", "P-value"], ["Age (years, mean ± SD)", "65.73 ± 12.71", "0.994 [0.975–1.014]", "5.549E-01", "–", "–"], ["Gender (Male/Female)", "169/141", "1.802 [0.885–2.993]", "2.103E-01", "–", "–"], ["Pathologic M (M0/M1/–)", "226/43/41", "3.550 [1.969–6.400]", "7.051E-06", "3.450 [1.107–10.76]", "3.280E-02"], ["Pathologic N (N0/N1/N2)", "180/77/53", "1.948 [1.449–2.619]", "4.638E-06", "1.317 [0.749–2.314]", "3.378E-01"], ["Pathologic T (T1/T2/T3/T4)", "8/55/212/35", "2.461 [1.507–4.019]", "5.105E-04", "1.775 [1.167–3.259]", "4.640E-02"], ["Pathologic stage (I/II/III/IV/–)", "51/118/88/43/10", "1.761 [1.329–2.334]", "6.207E-05", "0.717 [0.334–1.542]", "3.947E-01"], ["Lymphatic invasion (Yes/No/–)", "109/175/26", "2.401 [0.441–3.997]", "5.247E-02", "–", "–"], ["Colon polyps history (Yes/No/–)", "78/176/56", "0.836 [0.443–1.578]", "5.801E-01", "–", "–"], ["RS model status (High/Low)", "155/155", "4.396 [2.467–7.832]", "5.164E-08", "3.793 [2.009–7.161]", "3.940E-05"], ["Recurrence (Yes/No)", "66/244", "–", "–", "–", "–"], ["Recurrence free survival time (months, mean ± SD)", "29.66 ± 25.46", "–", "–", "–", "–"]], "row_count": 13, "column_count": 6, "numeric_cells": 42, "header_rows": 2, "locator": "section[5]/table-wrap[1]#T3"}}, {"id": "asset:table:pmid:32117736:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8afa0aa93d79b9b47d6869a3746fa3b74c4ab4d96da23b451d0cbbf0a75dd661", "bytes": 1936, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#T4", "version": null, "note": "The enrichment results for the mRNAs in the competitive endogenous RNA (ceRNA) regulatory network.", "structure": {"pmcid": "PMC7015976", "section_index": 6, "section_title": "CeRNA Regulatory Network Construction and Enrichment Analysis", "row_count": 19, "column_count": 5}, "table": {"label": "Table 4", "caption": "The enrichment results for the mRNAs in the competitive endogenous RNA (ceRNA) regulatory network.", "rows": [["Category", "Term", "Count", "P-value", "Genes"], ["GO_Biology process", "GO:0045664~regulation of neuron differentiation", "5", "1.68E-03", "ATOH1, BCL2, PAX6, SEMA3A, DBN1"], ["", "GO:0050767~regulation of neurogenesis", "5", "3.74E-03", "ATOH1, BCL2, PAX6, SEMA3A, DBN1"], ["", "GO:0015698~inorganic anion transport", "4", "5.45E-03", "GABRA2, ENPP1, GLRA2, SLC26A2"], ["", "GO:0051960~regulation of nervous system development", "5", "6.26E-03", "ATOH1, BCL2, PAX6, SEMA3A, DBN1"], ["", "GO:0060284~regulation of cell development", "5", "7.86E-03", "ATOH1, BCL2, PAX6, SEMA3A, DBN1"], ["", "GO:0006820~anion transport", "4", "1.75E-02", "GABRA2, ENPP1, GLRA2, SLC26A2"], ["", "GO:0007015~actin filament organization", "3", "3.12E-02", "ARHGAP6, BCL2, DBN1"], ["", "GO:0045017~glycerolipid biosynthetic process", "3", "3.79E-02", "MOGAT2, SEMA6D, PCK1"], ["", "GO:0007409~axonogenesis", "4", "3.79E-02", "ATOH1, BCL2, PAX6, SEMA3A"], ["", "GO:0048878~chemical homeostasis", "6", "4.61E-02", "DHH, ENPP1, BCL2, NR3C2, CCL28, PCK1"], ["", "GO:0048667~cell morphogenesis involved in neuron differentiation", "4", "4.62E-02", "ATOH1, BCL2, PAX6, SEMA3A"], ["", "GO:0048812~neuron projection morphogenesis", "4", "4.84E-02", "ATOH1, BCL2, PAX6, SEMA3A"], ["", "GO:0030308~negative regulation of cell growth", "3", "4.87E-02", "ENPP1, BCL2, SEMA3A"], ["KEGG pathway", "hsa03320:PPAR signaling pathway", "3", "3.82E-03", "SLC27A1, FABP2, PCK1"], ["", "hsa04080:Neuroactive 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"reader_status": "available", "identifier": "section[4]/table-wrap[2]#T2", "version": null, "note": "The information of the six independent prognosis-associated long non-coding RNAs (lncRNAs).", "structure": {"pmcid": "PMC7015976", "section_index": 11, "section_title": "Construction of Risk Score System", "row_count": 7, "column_count": 5}, "table": {"label": "Table 2", "caption": "The information of the six independent prognosis-associated long non-coding RNAs (lncRNAs).", "rows": [["Symbol", "Coef", "P-value", "Hazard ratio", "95% CI"], ["H19", "0.1647", "2.23E-02", "1.179", "1.024–1.358"], ["KCNJ2-AS1", "−1.1438", "1.60E-02", "0.319", "0.126–0.808"], ["LINC00899", "1.4922", "1.65E-03", "4.447", "1.755–6.265"], ["LINC01503", "0.8525", "1.22E-03", "2.346", "1.399–3.932"], ["PRKAG2-AS1", "−0.8100", "6.73E-04", "0.445", "0.279–0.710"], ["SRRM2-AS1", "3.8523", "1.35E-02", "7.100", "2.213–10.431"]], "row_count": 7, "column_count": 5, "numeric_cells": 28, "header_rows": 1, "locator": 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