m6A regulators featured by tumor immune microenvironment landscapes and correlated with immunotherapy in non-small cell lung cancer (NSCLC)
IntroductionRecent research has confirmed the critical role that epigenetic factors play in regulating the immune response. Nonetheless, what role m6A methylation modification might play in the immune response of non-small cell lung cancer (NSCLC) remains vague.MethodsHerein, the gene expression, co...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-12-01
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| Series: | Frontiers in Oncology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fonc.2022.1087753/full |
| _version_ | 1798006014215192576 |
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| author | Baowen Yuan Hao Qin Jingyao Zhang Min Zhang Yunkai Yang Xu Teng Hefen Yu Wei Huang Yan Wang |
| author_facet | Baowen Yuan Hao Qin Jingyao Zhang Min Zhang Yunkai Yang Xu Teng Hefen Yu Wei Huang Yan Wang |
| author_sort | Baowen Yuan |
| collection | DOAJ |
| description | IntroductionRecent research has confirmed the critical role that epigenetic factors play in regulating the immune response. Nonetheless, what role m6A methylation modification might play in the immune response of non-small cell lung cancer (NSCLC) remains vague.MethodsHerein, the gene expression, copy number variations (CNVs), and somatic mutations of 31 m6A regulators in NSCLC and adjacent control samples from the GEO and TCGA databases were comprehensively explored. Using consensus clustering, m6A modification patterns were identified. Correlations between m6A modification patterns and immune cell infiltration traits in the tumor immune microenvironment (TME) were systematically analyzed. Differentially expressed genes were verified and screened by random forest and cox regression analysis by comparing different m6A modification patterns. Based on the retained gene panel, a risk model was built, and m6Ascore for each sample was calculated. The function of m6Ascore in NSCLC prognosis, tumor somatic mutations, and chemotherapy/immunotherapy response prediction were evaluated.ResultsConsensus clustering classified all NSCLC samples into two m6A clusters (m6A_clusterA and m6A_clusterB) according to the expression levels of 25 m6A regulator genes. Hierarchical clustering further divides the NSCLC samples into two m6A gene clusters: m6AgeneclusterA and m6AgeneclusterB. A panel of 83 genes was screened from the 194 differentially expressed genes between m6A gene clusters. Based on this, a risk score model was established. m6A modification clusters, m6A gene clusters, and m6Ascore calculated from the risk model were able to predict tumor stages, immune cell infiltration, clinical prognosis, and tumor somatic mutations. NSCLC patients with high m6Ascore have poor drug resistance to chemotherapy drugs (Cisplatin and Gemcitabine) and exhibit considerable therapeutic benefits and favorable clinical responses to anti-PD1 or anti-CTLA4 immunotherapy.DiscussionIn conclusion, methylation modification patterns mediated by the m6A regulators in individuals play a non-negligible role in prognosis prediction and immunotherapy response, which will facilitate personalized treatment and immunotherapeutic strategies for NSCLC patients in the future. |
| first_indexed | 2024-04-11T12:48:11Z |
| format | Article |
| id | doaj.art-11ea6bc135ba4941af14e86adaa7adda |
| institution | Directory Open Access Journal |
| issn | 2234-943X |
| language | English |
| last_indexed | 2024-04-11T12:48:11Z |
| publishDate | 2022-12-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Oncology |
| spelling | doaj.art-11ea6bc135ba4941af14e86adaa7adda2022-12-22T04:23:16ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2022-12-011210.3389/fonc.2022.10877531087753m6A regulators featured by tumor immune microenvironment landscapes and correlated with immunotherapy in non-small cell lung cancer (NSCLC)Baowen Yuan0Hao Qin1Jingyao Zhang2Min Zhang3Yunkai Yang4Xu Teng5Hefen Yu6Wei Huang7Yan Wang8Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, ChinaKey Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, ChinaKey Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, ChinaKey Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, ChinaKey Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, ChinaBeijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, ChinaBeijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, ChinaBeijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, ChinaKey Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, ChinaIntroductionRecent research has confirmed the critical role that epigenetic factors play in regulating the immune response. Nonetheless, what role m6A methylation modification might play in the immune response of non-small cell lung cancer (NSCLC) remains vague.MethodsHerein, the gene expression, copy number variations (CNVs), and somatic mutations of 31 m6A regulators in NSCLC and adjacent control samples from the GEO and TCGA databases were comprehensively explored. Using consensus clustering, m6A modification patterns were identified. Correlations between m6A modification patterns and immune cell infiltration traits in the tumor immune microenvironment (TME) were systematically analyzed. Differentially expressed genes were verified and screened by random forest and cox regression analysis by comparing different m6A modification patterns. Based on the retained gene panel, a risk model was built, and m6Ascore for each sample was calculated. The function of m6Ascore in NSCLC prognosis, tumor somatic mutations, and chemotherapy/immunotherapy response prediction were evaluated.ResultsConsensus clustering classified all NSCLC samples into two m6A clusters (m6A_clusterA and m6A_clusterB) according to the expression levels of 25 m6A regulator genes. Hierarchical clustering further divides the NSCLC samples into two m6A gene clusters: m6AgeneclusterA and m6AgeneclusterB. A panel of 83 genes was screened from the 194 differentially expressed genes between m6A gene clusters. Based on this, a risk score model was established. m6A modification clusters, m6A gene clusters, and m6Ascore calculated from the risk model were able to predict tumor stages, immune cell infiltration, clinical prognosis, and tumor somatic mutations. NSCLC patients with high m6Ascore have poor drug resistance to chemotherapy drugs (Cisplatin and Gemcitabine) and exhibit considerable therapeutic benefits and favorable clinical responses to anti-PD1 or anti-CTLA4 immunotherapy.DiscussionIn conclusion, methylation modification patterns mediated by the m6A regulators in individuals play a non-negligible role in prognosis prediction and immunotherapy response, which will facilitate personalized treatment and immunotherapeutic strategies for NSCLC patients in the future.https://www.frontiersin.org/articles/10.3389/fonc.2022.1087753/fullm6A regulatorsm6A modificationtumor immune microenvironment (TME)immunotherapynon-small cell lung cancer (NSCLC) |
| spellingShingle | Baowen Yuan Hao Qin Jingyao Zhang Min Zhang Yunkai Yang Xu Teng Hefen Yu Wei Huang Yan Wang m6A regulators featured by tumor immune microenvironment landscapes and correlated with immunotherapy in non-small cell lung cancer (NSCLC) Frontiers in Oncology m6A regulators m6A modification tumor immune microenvironment (TME) immunotherapy non-small cell lung cancer (NSCLC) |
| title | m6A regulators featured by tumor immune microenvironment landscapes and correlated with immunotherapy in non-small cell lung cancer (NSCLC) |
| title_full | m6A regulators featured by tumor immune microenvironment landscapes and correlated with immunotherapy in non-small cell lung cancer (NSCLC) |
| title_fullStr | m6A regulators featured by tumor immune microenvironment landscapes and correlated with immunotherapy in non-small cell lung cancer (NSCLC) |
| title_full_unstemmed | m6A regulators featured by tumor immune microenvironment landscapes and correlated with immunotherapy in non-small cell lung cancer (NSCLC) |
| title_short | m6A regulators featured by tumor immune microenvironment landscapes and correlated with immunotherapy in non-small cell lung cancer (NSCLC) |
| title_sort | m6a regulators featured by tumor immune microenvironment landscapes and correlated with immunotherapy in non small cell lung cancer nsclc |
| topic | m6A regulators m6A modification tumor immune microenvironment (TME) immunotherapy non-small cell lung cancer (NSCLC) |
| url | https://www.frontiersin.org/articles/10.3389/fonc.2022.1087753/full |
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