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pmid:34623759
New insights into genetic characteristics between multiple myeloma and COVID-19: An integrative bioinformatics analysis of gene expression omnibus microarray and the cancer genome atlas data.
Fei Wang · Ran Liu · Jie Yang · Baoan Chen
International journal of laboratory hematology · 2021 doi:10.1111/ijlh.13717
Paper
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Experiment
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Analysis
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Complete file
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This study aimed to identify MM prognostic biomarkers with potential association with COVID-19.\nMETHODS: Differentially expressed genes (DEGs) in five MM data sets (GSE47552, GSE16558, GSE13591, GSE6477, and GSE39754) with the same expression trends were screened out. Functional enrichment analysis and the protein-protein interaction network were performed for all DEGs. Prognosis-associated DEGs were screened using the stepwise Cox regression analysis in the cancer genome atlas (TCGA) MMRF-CoMMpass cohort and the GSE24080 data set. Prognosis-associated DEGs associated with COVID-19 infection in the GSE164805 data set were also identified.\nRESULTS: A total of 98 DEGs with the same expression trends in five data sets were identified, and 83 DEGs were included in the protein-protein interaction network. Cox regression analysis identified 16 DEGs were associated with MM prognosis in the TCGA cohort, and only the cytochrome c oxidase subunit 6C (COX6C) gene (HR = 1.717, 95% CI 1.231-2.428, p = .002) and the nucleotide-binding oligomerization domain containing 2 (NOD2) gene (HR = 0.882, 95% CI 0.798-0.975, p = .014) were independent factors related to MM prognosis in the GSE24080 data set. Both of them were downregulated in patients with mild COVID-19 infection compared with controls but were upregulated in patients with severe COVID-19 compared with patients with mild illness.\nCONCLUSIONS: The NOD2 and COX6C genes might be used as prognostic biomarkers in MM. The two genes might be associated with the development of COVID-19 infection.", "claims": [{"id": "claim-method", "statement": "Prognosis‐associated DEGs were screened using the stepwise Cox regression analysis in the cancer genome atlas (TCGA) MMRF‐CoMMpass cohort and the GSE24080 data set.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34623759", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Prognosis‐associated DEGs were screened using the stepwise Cox regression analysis in the cancer genome atlas (TCGA) MMRF‐CoMMpass cohort and the GSE24080 data set."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Differentially expressed genes (DEGs) in five MM data sets (GSE47552, GSE16558, GSE13591, GSE6477, and GSE39754) with the same expression trends were screened out.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34623759", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Differentially expressed genes (DEGs) in five MM data sets (GSE47552, GSE16558, GSE13591, GSE6477, and GSE39754) with the same expression trends were screened out."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Cox regression analysis identified 16 DEGs were associated with MM prognosis in the TCGA cohort, and only the cytochrome c oxidase subunit 6C (COX6C) gene (HR = 1.717, 95% CI 1.231–2.428, p = .002) and the nucleotide‐binding oligomerization domain containing 2 (NOD2) gene (HR = 0.882, 95% CI 0.798–0.975, p = .014) were independent factors related to MM prognosis in the GSE24080 data set.", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "Cox regression analysis identified 16 DEGs were associated with MM prognosis in the TCGA cohort, and only the cytochrome c oxidase subunit 6C (COX6C) gene (HR = 1.717, 95% CI 1.231–2.428, p = .002) and the nucleotide‐binding oligomerization domain containing 2 (NOD2) gene (HR = 0.882, 95% CI 0.798–0.975, p = .014) were independent factors related to MM prognosis in the GSE24080 data set."}, "evidence": [{"asset": "source:pmid:34623759", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Cox regression analysis identified 16 DEGs were associated with MM prognosis in the TCGA cohort, and only the cytochrome c oxidase subunit 6C (COX6C) gene (HR = 1.717, 95% CI 1.231–2.428, p = .002) and the nucleotide‐binding oligomerization domain containing 2 (NOD2) gene (HR = 0.882, 95% CI 0.798–0.975, p = .014) were independent factors related to MM prognosis in the GSE24080 data set."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Cox regression analysis identified 16 DEGs were associated with MM prognosis in the TCGA cohort, and only the cytochrome c oxidase subunit 6C (COX6C) gene (HR = 1.717, 95% CI 1.231–2.428, p = .002) and the nucleotide‐binding oligomerization domain containing 2 (NOD2) gene (HR = 0.882, 95% CI 0.798–0.975, p = .014) were independent factors related to MM prognosis in the GSE24080 data set.", "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:34623759"], "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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