Identification of RNA Methylation-Related lncRNAs Signature for Predicting Hot and Cold Tumors and Prognosis in Colon Cancer

Abstract

N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), and 7-methylguanosine (m7G) are the major forms of RNA methylation modifications, which are closely associated with the development of many tumors. However, the prognostic value of RNA methylation-related long non-coding RNAs (lncRNAs) in colon cancer (CC) has not been defined. This study summarised 50 m6A/m1A/m5C/m7G-related genes and downloaded 41 normal and 471 CC tumor samples with RNA-seq data and clinicopathological information from The Cancer Genome Atlas (TCGA) database. A total of 1057 RNA methylation-related lncRNAs (RMlncRNAs) were identified with Pearson correlation analysis. Twenty-three RMlncRNAs with prognostic values were screened using univariate Cox regression analysis. By consensus clustering analysis, CC patients were classified into two molecular subtypes (Cluster 1 and Cluster 2) with different clinical outcomes and immune microenvironmental infiltration characteristics. Cluster 2 was considered to be the “hot tumor” with a better prognosis, while cluster 1 was regarded as the “cold tumor” with a poorer prognosis. Subsequently, we constructed a seven-lncRNA prognostic signature using the least absolute shrinkage and selection operator (LASSO) Cox regression. In combination with other clinical traits, we found that the RNA methylation-related lncRNA prognostic signature (called the “RMlnc-score”) was an independent prognostic factor for patients with colon cancer. In addition, immune infiltration, immunotherapy response analysis, and half-maximum inhibitory concentration (IC50) showed that the low RMlnc-score group was more sensitive to immunotherapy, while the high RMlnc-score group was sensitive to more chemotherapeutic agents. In summary, the RMlnc-score we developed could be used to predict the prognosis, immunotherapy response, and drug sensitivity of CC patients, guiding more accurate, and personalized treatment regimens.

Identification of N1 methyladenosine‐related biomarker predicting overall survival outcomes and experimental verification in ovarian cancer

“…23,24 The latest research demonstrated that m1A methylation modification is an essential driver in the prognosis of OVCA. 10 Considering the potential prognostic value of various RNA methylation modifications in OVCA, [25][26][27] we used the NMF algorithm for the first time to cluster OVCA samples and screened out four hub genes (AADAC, CD38, CACNA1C, and ATP1A3) for building a risk score model in this study. AADAC is a glycoprotein and is associated with lower rifapentine clearance.…”

m6A/ m1A /m5C/m7G-related methylation modification patterns and immune characterization in prostate cancer

“…The stromal score, CD4 memory resting T cells, CD4 memory activated T cells, follicular helper T cells, M0 macrophages, M1 macrophages, and resting mast cells were linked with the risk score. This implies that PCa immune cell infiltration is related to the risk model created using MRGs ( He et al, 2022 ). Our study shows that differentially expressed ASPN,COL1A1, PCGEM1 and PHYHD1 was associated with immune infiltration.…”

Combining Bulk and Single-Cell RNA Sequencing Data to Identify RNA methylation and Autophagy-Related Signatures in Patients with Chronic Obstructive Pulmonary Disease

“…GO enrichment analysis (22) of RNA-modified genes in the GSE76705 dataset was performed by using the R package clusterProfiler (23). For each GO entry, the differential gene count was tallied, and a hypergeometric distribution technique was used to determine the importance of the differential gene enrichment in each entry.…”