Characterization of Modification Patterns, Biological Function, Clinical Implication, and Immune Microenvironment Association of m6A Regulators in Pancreatic Cancer.
ABSTRACT: Objective: N6-methyladenosine (m6A) modification may modulate various biological processes. Nonetheless, clinical implications of m6A modification in pancreatic cancer are undefined. Herein, this study comprehensively characterized the m6A modification patterns in pancreatic cancer based on m6A regulators. Methods: Genetic mutation and expression pattern of 21 m6A regulators and their correlations were assessed in pancreatic cancer from TCGA dataset. m6A modification patterns were clustered using unsupervised clustering analysis in TCGA and ICGC datasets. Differences in survival, biological functions and immune cell infiltrations were assessed between modification patterns. A m6A scoring system was developed by principal component analysis. Genetic mutations and TIDE scores were compared between high and low m6A score groups. Results: ZC3H13 (11%), RBM15B (9%), YTHDF1 (8%), and YTHDC1 (6%) frequently occurred mutations among m6A regulators. Also, most of regulators were distinctly dysregulated in pancreatic cancer. There were tight crosslinks between regulators. Two m6A modification patterns were constructed, with distinct prognoses, immune cell infiltration and biological functions. Furthermore, we quantified m6A score in each sample. High m6A scores indicated undesirable clinical outcomes. There were more frequent mutations in high m6A score samples. Lower TIDE score was found in high m6A score group, with AUC = 0.61, indicating that m6A scores might be used for predicting the response to immunotherapy. Conclusion: Collectively, these data demonstrated that m6A modification participates pancreatic cancer progress and ornaments immune microenvironment, providing an insight into pancreatic cancer pathogenesis and facilitating precision medicine development.
Project description:N<sup>6</sup>-methyladenosine (m<sup>6</sup>A), the most abundant RNA modification in eukaryotes, plays a pivotal role in regulating many cellular and biological processes. Aberrant m<sup>6</sup>A modification has recently been involved in carcinogenesis in various cancers, including pancreatic cancer. Pancreatic cancer is one of the deadliest cancers. It is a heterogeneous malignant disease characterized by a plethora of diverse genetic and epigenetic events. Increasing evidence suggests that dysregulation of m<sup>6</sup>A regulatory factors, such as methyltransferases, demethylases, and m<sup>6</sup>A-binding proteins, profoundly affects the development and progression of pancreatic cancer. In addition, m<sup>6</sup>A regulators and m<sup>6</sup>A target transcripts may be promising early diagnostic and prognostic cancer biomarkers, as well as therapeutic targets. In this review, we highlight the biological functions and mechanisms of m<sup>6</sup>A in pancreatic cancer and discuss the potential of m<sup>6</sup>A modification in clinical applications.
Project description:Recent studies have highlighted the biological significance of RNA N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) modification in tumorigenicity and progression. However, it remains unclear whether m<sup>6</sup>A modifications also have potential roles in immune regulation and tumor microenvironment (TME) formation. <b>Methods</b>: In this study, we curated 23 m<sup>6</sup>A regulators and performed consensus molecular subtyping with NMF algorithm to determine m<sup>6</sup>A modification patterns and the m<sup>6</sup>A-related gene signature in colon cancer (CC). The ssGSEA and CIBERSORT algorithms were employed to quantify the relative infiltration levels of various immune cell subsets. An PCA algorithm based m<sup>6</sup>Sig scoring scheme was used to evaluate the m<sup>6</sup>A modification patterns of individual tumors with an immune response. <b>Results</b>: Three distinct m6A modification patterns were identified among 1307 CC samples, which were also associated with different clinical outcomes and biological pathways. The TME characterization revealed that the identified m<sup>6</sup>A patterns were highly consistent with three known immune profiles: immune-inflamed, immune-excluded, and immune-desert, respectively. Based on the m<sup>6</sup>Sig score, which was extracted from the m<sup>6</sup>A-related signature genes, CC patients can be divided into high and low score subgroups. Patients with lower m<sup>6</sup>Sig score was characterized by prolonged survival time and enhanced immune infiltration. Further analysis indicated that lower m<sup>6</sup>Sig score also correlated with greater tumor mutation loads, PD-L1 expression, and higher mutation rates in SMGs (e.g., <i>PIK3CA</i> and <i>SMAD4</i>). In addition, patients with lower m<sup>6</sup>Sig scores showed a better immune responses and durable clinical benefits in three independent immunotherapy cohorts. <b>Conclusions</b>: This study highlights that m<sup>6</sup>A modification is significantly associated with TME diversity and complexity. Quantitatively evaluating the m<sup>6</sup>A modification patterns of individual tumors will strengthen our understanding of TME characteristics and promote more effective immunotherapy strategies.
Project description:N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) RNA modification is a reversible mechanism that regulates eukaryotic gene expression. Growing evidence has demonstrated an association between m<sup>6</sup>A modification and tumorigenesis and response to immunotherapy. However, the overall influence of m<sup>6</sup>A regulators on the tumor microenvironment and their effect on the response to immunotherapy in lung adenocarcinoma remains to be explored. Here, we comprehensively analyzed the m<sup>6</sup>A modification patterns of 936 lung adenocarcinoma samples based on 24 m<sup>6</sup>A regulators. First, we described the features of genetic variation in these m<sup>6</sup>A regulators. Many m<sup>6</sup>A regulators were aberrantly expressed in tumors and negatively correlated with most tumor-infiltrating immune cell types. Furthermore, we identified three m<sup>6</sup>A modification patterns using a consensus clustering method. m<sup>6</sup>A cluster B was preferentially associated with a favorable prognosis and enriched in metabolism-associated pathways. In contrast, m<sup>6</sup>A cluster A was associated with the worst prognosis and was enriched in the process of DNA repair. m<sup>6</sup>A cluster C was characterized by activation of the immune system and a higher stromal cell score. Surprisingly, patients who received radiotherapy had a better prognosis than patients without radiotherapy only in the m<sup>6</sup>A cluster C group. Subsequently, we constructed an m<sup>6</sup>A score model that qualified the m<sup>6</sup>A modification level of individual samples by using principal component analysis algorithms. Patients with high m<sup>6</sup>A score were characterized by enhanced immune cell infiltration and prolonged survival time and were associated with lower tumor mutation burden and PD-1/CTLA4 expression. The combination of the m<sup>6</sup>A score and tumor mutation burden could accurately predict the prognosis of patients with lung adenocarcinoma. Furthermore, patients with high m<sup>6</sup>A score exhibited greater prognostic benefits from radiotherapy and immunotherapy. This study demonstrates that m<sup>6</sup>A modification is significantly associated with tumor microenvironment diversity and prognosis. A comprehensive evaluation of m<sup>6</sup>A modification patterns in single tumors will