Prognostic significance and immune landscape of a fatty acid metabolism-related gene signature in colon adenocarcinoma
Background: Fatty acid metabolism (FAM), as a hallmark of caner, plays important roles in tumor initiation and carcinogenesis. However, the significance of fatty acid metabolism-related genes in colon adenocarcinoma (COAD) are largely unknown.Methods: RNA sequencing data and clinical information wer...
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| Format: | Article |
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Frontiers Media S.A.
2022-12-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.996625/full |
| _version_ | 1811178412322062336 |
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| author | Xia Liu Xisheng Fang Lin Lu Guolong Liu |
| author_facet | Xia Liu Xisheng Fang Lin Lu Guolong Liu |
| author_sort | Xia Liu |
| collection | DOAJ |
| description | Background: Fatty acid metabolism (FAM), as a hallmark of caner, plays important roles in tumor initiation and carcinogenesis. However, the significance of fatty acid metabolism-related genes in colon adenocarcinoma (COAD) are largely unknown.Methods: RNA sequencing data and clinical information were downloaded from the Cancer Genome Atlas (TCGA) cohort. Univariate and multivariate Cox regression analyses were utilized to construct a fatty acid metabolism-related gene signature. Kaplan-Meier survival and receiver operating characteristic (ROC) analyses were used to verify the performance of this signature. GEO datasets were applied to validate the signature. Maftools package was utilized to analyze the mutation profiles of this signature. Correlation between the risk signature and stemness scores was compared by RNA stemness score (RNAss). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set variation analysis (GSVA) were performed to explore the potential functions and signaling pathways. Immune landscape of the signature was explored by analyzing different immune cells infiltration, immune functions and microsatellite instability. A nomogram was constructed by combining the risk signature and multiple clinical factors. Expression levels and prognostic values of the risk genes were revealed in the cancer genome atlas and GEO databases. Moreover, the expression the risk genes were measured in cell lines using real time quantitative PCR (qRT-PCR).Results: Eight fatty acid metabolism-related genes (CD36, ENO3, MORC2, PTGR1, SUCLG2, ELOVL3, ELOVL6 and CPT2) were used to construct a risk signature. This signature demonstrated better prognostic value than other clinicopathological parameters, with AUC value was 0.734 according to the cancer genome atlas database. There was negative correlation between the riskscore and RNA stemness score. The patients in the high-risk group demonstrated higher infiltration of M0 macrophages, and less infiltration of activated CD4 memory T cells and Eosinophils. There were more MSI patients in the high-risk group than those in the low-risk group (38% vs. 30%). The risk scores of patients in the MSI group were slightly higher than those in the microsatellite stability group. Gene ontology, kyoto encyclopedia of genes and genomes and gene set variation analysis enrichment analyses showed that several metabolism-related functions and signaling pathways were enriched. A nomogram showed good predictive capability of the signature. Moreover, qRT-PCR revealed upregulated expression of ENO3, MORC2, SUCLG2 and ELOVL6, and downregulated expression of CPT2 in all examined colon adenocarcinoma cell lines.Conclusion: This study provided novel insights into a fatty acid metabolism-related signature in the prognosis an immune landscape of colon adenocarcinoma patients. |
| first_indexed | 2024-04-11T06:17:54Z |
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| id | doaj.art-d455402e7020402f9993f6faad5c099d |
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| language | English |
| last_indexed | 2024-04-11T06:17:54Z |
| publishDate | 2022-12-01 |
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| series | Frontiers in Genetics |
| spelling | doaj.art-d455402e7020402f9993f6faad5c099d2022-12-22T04:40:59ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-12-011310.3389/fgene.2022.996625996625Prognostic significance and immune landscape of a fatty acid metabolism-related gene signature in colon adenocarcinomaXia LiuXisheng FangLin LuGuolong LiuBackground: Fatty acid metabolism (FAM), as a hallmark of caner, plays important roles in tumor initiation and carcinogenesis. However, the significance of fatty acid metabolism-related genes in colon adenocarcinoma (COAD) are largely unknown.Methods: RNA sequencing data and clinical information were downloaded from the Cancer Genome Atlas (TCGA) cohort. Univariate and multivariate Cox regression analyses were utilized to construct a fatty acid metabolism-related gene signature. Kaplan-Meier survival and receiver operating characteristic (ROC) analyses were used to verify the performance of this signature. GEO datasets were applied to validate the signature. Maftools package was utilized to analyze the mutation profiles of this signature. Correlation between the risk signature and stemness scores was compared by RNA stemness score (RNAss). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set variation analysis (GSVA) were performed to explore the potential functions and signaling pathways. Immune landscape of the signature was explored by analyzing different immune cells infiltration, immune functions and microsatellite instability. A nomogram was constructed by combining the risk signature and multiple clinical factors. Expression levels and prognostic values of the risk genes were revealed in the cancer genome atlas and GEO databases. Moreover, the expression the risk genes were measured in cell lines using real time quantitative PCR (qRT-PCR).Results: Eight fatty acid metabolism-related genes (CD36, ENO3, MORC2, PTGR1, SUCLG2, ELOVL3, ELOVL6 and CPT2) were used to construct a risk signature. This signature demonstrated better prognostic value than other clinicopathological parameters, with AUC value was 0.734 according to the cancer genome atlas database. There was negative correlation between the riskscore and RNA stemness score. The patients in the high-risk group demonstrated higher infiltration of M0 macrophages, and less infiltration of activated CD4 memory T cells and Eosinophils. There were more MSI patients in the high-risk group than those in the low-risk group (38% vs. 30%). The risk scores of patients in the MSI group were slightly higher than those in the microsatellite stability group. Gene ontology, kyoto encyclopedia of genes and genomes and gene set variation analysis enrichment analyses showed that several metabolism-related functions and signaling pathways were enriched. A nomogram showed good predictive capability of the signature. Moreover, qRT-PCR revealed upregulated expression of ENO3, MORC2, SUCLG2 and ELOVL6, and downregulated expression of CPT2 in all examined colon adenocarcinoma cell lines.Conclusion: This study provided novel insights into a fatty acid metabolism-related signature in the prognosis an immune landscape of colon adenocarcinoma patients.https://www.frontiersin.org/articles/10.3389/fgene.2022.996625/fullcolon adenocarcinomafatty acid metabolism geneprognosisrisk signatureimmune microenvironment |
| spellingShingle | Xia Liu Xisheng Fang Lin Lu Guolong Liu Prognostic significance and immune landscape of a fatty acid metabolism-related gene signature in colon adenocarcinoma Frontiers in Genetics colon adenocarcinoma fatty acid metabolism gene prognosis risk signature immune microenvironment |
| title | Prognostic significance and immune landscape of a fatty acid metabolism-related gene signature in colon adenocarcinoma |
| title_full | Prognostic significance and immune landscape of a fatty acid metabolism-related gene signature in colon adenocarcinoma |
| title_fullStr | Prognostic significance and immune landscape of a fatty acid metabolism-related gene signature in colon adenocarcinoma |
| title_full_unstemmed | Prognostic significance and immune landscape of a fatty acid metabolism-related gene signature in colon adenocarcinoma |
| title_short | Prognostic significance and immune landscape of a fatty acid metabolism-related gene signature in colon adenocarcinoma |
| title_sort | prognostic significance and immune landscape of a fatty acid metabolism related gene signature in colon adenocarcinoma |
| topic | colon adenocarcinoma fatty acid metabolism gene prognosis risk signature immune microenvironment |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.996625/full |
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