Quantification of m6A RNA methylation modulators pattern was a potential biomarker for prognosis and associated with tumor immune microenvironment of pancreatic adenocarcinoma

• Published in: BMC cancer 2021-07, Vol.21 (1), p.1-876, Article 876
• Main Authors: Wang, Lianzi, Zhang, Shubing, Li, Huimin, Xu, Yang, Wu, Qiang, Shen, Jilong, Li, Tao, Xu, Yuanhong
• Format: Article
• Language: English
• Subjects: Adenocarcinoma; Bioinformatics; Biomarkers; Care and treatment; CD4 antigen; CD8 antigen; Colorectal cancer; CTLA-4 protein; DNA methylation; Drug resistance; Gene expression; Gene set enrichment analysis; Genetic aspects; Genomes; Health aspects; Immune cell infiltration; Immunomodulation; Immunotherapy; Infiltration; Lymphocytes T; m6A RNA methylation modulators; m6Ascore; Medical prognosis; Metastases; Mortality; mRNA; Mutation; N6-methyladenosine; Pancreatic adenocarcinoma; Pancreatic cancer; Patients; PD-1 protein; Prediction models; Prognosis; Prognostic; Proteins; RNA sequencing; Tumor microenvironment; Tumorigenesis; Tumors; Writers
• ISSN: 1471-2407; 1471-2407
• DOI: 10.1186/s12885-021-08550-9

Background m6A is the most prevalent and abundant form of mRNA modifications and is closely related to tumor proliferation, differentiation, and tumorigenesis. In this study, we try to conduct an effective prediction model to investigated the function of m6A RNA methylation modulators in pancreatic adenocarcinoma and estimated the potential association between m6A RNA methylation modulators and tumor microenvironment infiltration for optimization of treatment. Methods Expression of 28 m6A RNA methylation modulators and clinical data of patients with pancreatic adenocarcinoma and normal samples were obtained from TCGA and GTEx database. Differences in the expression of 28 m6A RNA methylation modulators between tumour (n = 40) and healthy (n = 167) samples were compared by Wilcoxon test. LASSO Cox regression was used to select m6A RNA methylation modulators to analyze the relationship between expression and clinical characteristics by univariate and multivariate regression. A risk score prognosis model was conducted based on the expression of select m6A RNA methylation modulators. Bioinformatics analysis was used to explore the association between the m6Ascore and the composition of infiltrating immune cells between high and low m6Ascore group by CIBERSORT algorithm. Evaluation of m6Ascore for immunotherapy was analyzed via the IPS and three immunotherapy cohort. Besides, the biological signaling pathways of the m6A RNA methylation modulators were examined by gene set enrichment analysis (GSEA). Results Expression of 28 m6A RNA methylation modulators were upregulated in patients with PAAD except for MTEEL3. An m6Ascore prognosis model was established, including KIAA1429, IGF2BP2, IGF2BP3, METTL3, EIF3H and LRPPRC was used to predict the prognosis of patients with PAAD, the high risk score was an independent prognostic indicator for pancreatic adenocarcinoma, and a high risk score presented a lower overall survival. In addition, m6Ascore was related with the immune cell infiltration of PAAD. Patients with a high m6Ascore had lower infiltration of Tregs and CD8.sup.+T cells but a higher resting CD4.sup.+ T infiltration. Patients with a low m6Ascore displayed a low abundance of PD-1, CTLA-4 and TIGIT, however, the IPS showed no difference between the two groups. The m6Ascore applied in three immunotherapy cohort (GSE78220, TCGA-SKCM, and IMvigor210) did not exhibit a good prediction for estimating the patients' response to immunotherapy, so it may need more res