Abstract
BackgroundN6-methyladenosine (m6A) and 5-methylcytosine (m5C) can modify long non-coding RNAs (lncRNAs), thereby affecting tumorigenesis and tumor progression. However, there is a lack of knowledge regarding the potential roles and cross-talk of m6A- and m5C-related lncRNAs in the tumor microenvironment (TME) and their effect on prognosis.MethodsWe systematically evaluated the expression patterns of m6A- and m5C-related lncRNAs in 1358 colorectal cancer (CRC) samples from four datasets. Consensus clustering was conducted to identify molecular subtypes of CRC, and the clinical significance, TME, tumor-infiltrating immune cells (TIICs), and immune checkpoints in the different molecular subtypes were analyzed. Finally, we established a m6A- and m5C-related lncRNA signature and a prognostic nomogram.ResultsWe identified 141 m6A- and m5C-related lncRNAs by co-expression analysis, among which 23 lncRNAs were significantly associated with the overall survival (OS) of CRC patients. Two distinct molecular subtypes (cluster A and cluster B) were identified, and these two distinct molecular subtypes could predict clinicopathological features, prognosis, TME stromal activity, TIICs, immune checkpoints. Next, a m6A- and m5C-related lncRNA signature for predicting OS was constructed, and its predictive capability in CRC patients was validated. We then constructed a highly accurate nomogram for improving the clinical applicability of the signature. Analyses of clinicopathological features, prognosis, TIICs, cancer stem cell (CSC), and drug response revealed significant differences between two risk groups. In addition, we found that patients with a low-risk score exhibited enhanced response to anti-PD-1/L1 immunotherapy. Functional enrichment analysis showed that these lncRNAs related to the high-risk group were involved in the development and progression of CRC.ConclusionsWe conducted a comprehensive analysis of m6A- and m5C-related lncRNAs in CRC and revealed their potential functions in predicting tumor-immune-stromal microenvironment, clinicopathological features, and prognosis, and determined their role in immunotherapy. These findings may improve our understanding of the cross-talk between m6A- and m5C-related lncRNAs in CRC and pave a new road for prognosis assessment and more effective immunotherapy strategies.
Highlights
Colorectal cancer (CRC) is one of the most common and lethal cancers of the digestive system, and it remains a challenging issue globally [1]
We explored genomic alterations in 1358 CRC samples from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets to comprehensively evaluate the roles of m6A- and m5C-related Long non-coding RNAs (lncRNAs)
To gain a comprehensive understanding of the expression patterns of the m6A- and m5C-related lncRNAs involved in tumorigenesis, 1364 CRC samples from four eligible CRC cohorts, namely TCGA-COAD/READ (n = 486), GSE39582 (n = 579), GSE17536 (n = 177), and GSE38832 (n = 122), were integrated in our study for further analysis
Summary
Colorectal cancer (CRC) is one of the most common and lethal cancers of the digestive system, and it remains a challenging issue globally [1]. CRC is characterized by inherent biological invasiveness as well as specific radiological and chemical resistance that result in high recurrence rates and progression in patients. Different treatments, such as surgery, chemotherapy, radiotherapy, and some new immunotherapies, are currently applied, their clinical benefits remain unsatisfactory [4]. Long non-coding RNAs (lncRNAs), a sequence made up of more than 200 bp but lacking protein encoding capability, are transcribed by RNA polymerase II; they play a crucial regulatory role at the transcriptional, post-transcriptional, and epigenetic levels, and are involved in multiple aspects of gene regulation and numerous biological processes [5]. There is a lack of knowledge regarding the potential roles and cross-talk of m6Aand m5C-related lncRNAs in the tumor microenvironment (TME) and their effect on prognosis
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