RNA modifications are chemical changes that occur on RNA molecules after they are transcribed from DNA. They can regulate the stability, translation, and localization of RNA, and thus affect the expression of genes and proteins. RNA modifications are involved in various biological processes and diseases, including cancer.
In this article, we will focus on three types of RNA modifications: m6A, m5C, and m1A, which are the most abundant and well-studied modifications in eukaryotic mRNA. We will also discuss how these modifications affect the prognosis and immune status of hepatocellular carcinoma (HCC), which is the most common type of liver cancer and one of the leading causes of cancer-related deaths worldwide.
The Role of m6A, m5C, and m1A in RNA Regulation
m6A, m5C, and m1A are methylations that occur on the nitrogen or carbon atoms of the RNA bases adenine, cytosine, and adenine, respectively. These modifications are reversible and dynamic, meaning that they can be added or removed by specific enzymes. These enzymes are called writers, erasers, and readers, depending on their functions. Writers are the enzymes that catalyze the methylation of RNA, erasers are the enzymes that demethylate RNA, and readers are the proteins that recognize and bind to the methylated RNA and mediate its downstream effects.
The effects of m6A, m5C, and m1A on RNA depend on the context and location of the modifications, as well as the interactions with the readers. Generally speaking, these modifications can influence the following aspects of RNA regulation:
- RNA stability: m6A, m5C, and m1A can affect the degradation of RNA by altering its susceptibility to exonucleases or endonucleases. For example, m6A can recruit the YTHDF2 reader, which promotes the decay of m6A-modified mRNA by transporting it to the processing bodies (P-bodies), where RNA degradation occurs. m5C can also induce RNA degradation by recruiting the NSUN2 reader, which cleaves the m5C-modified RNA. On the other hand, m1A can enhance RNA stability by preventing the cleavage of the m1A-modified RNA by the endonuclease ANGEL2.
- RNA translation: m6A, m5C, and m1A can affect the translation of RNA by altering its interaction with the ribosome or the initiation factors. For example, m6A can recruit the YTHDF1 reader, which enhances the translation of m6A-modified mRNA by facilitating its association with the eIF4F complex and the ribosome. m5C can also increase RNA translation by recruiting the ALYREF reader, which promotes the export of m5C-modified mRNA from the nucleus to the cytoplasm, where translation occurs. Conversely, m1A can inhibit RNA translation by interfering with the binding of the eIF3 complex and the ribosome to the m1A-modified RNA.
- RNA localization: m6A, m5C, and m1A can affect the localization of RNA by altering its transport or retention in different cellular compartments or regions. For example, m6A can recruit the YTHDF3 reader, which facilitates the transport of m6A-modified mRNA to the dendrites of neurons, where local translation occurs. m5C can also modulate RNA localization by recruiting the NOP2 reader, which sequesters the m5C-modified RNA in the nucleolus, where ribosome biogenesis occurs. Similarly, m1A can regulate RNA localization by recruiting the YTHDC1 reader, which mediates the nuclear export of m1A-modified mRNA.
The Impact of m6A, m5C, and m1A on HCC Prognosis and Immune Status
Recent studies have revealed that m6A, m5C, and m1A regulated genes play important roles in the prognosis and immune status of HCC patients. These genes include the writers, erasers, and readers of these modifications, as well as the target genes that are modified by them. By analyzing the gene expression profiles and clinical data of HCC patients from various databases, such as The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), researchers have identified several m6A, m5C, and m1A regulated gene signatures that can predict the survival and correlate with the immune status of HCC patients. Some of the main findings are summarized below:
- m6A regulated gene signature: A study by Li et al found that eight of the 13 core m6A-related regulators were overexpressed in HCC tissues, including METTL3, METTL14, WTAP, KIAA1429, YTHDC1, YTHDC2, YTHDF1, and YTHDF2. These genes were involved in mRNA and RNA modifications, mRNA and RNA methylation, mRNA and RNA stability, and other processes. The study also identified two clusters of HCC patients based on the expression of these genes, and found that cluster 1 had a significantly better prognosis than cluster 2. Moreover, the study revealed that the m6A regulated gene signature was associated with the immune status of HCC patients, such as the infiltration of immune cells, the expression of immune checkpoints, and the immune subtypes.
- m5C regulated gene signature: A study by Zhang et al found that six of the 11 core m5C-related regulators were differentially expressed in HCC tissues, including NSUN2, NSUN5, NSUN6, NSUN7, TRDMT1, and ALYREF. These genes were involved in mRNA and RNA modifications, mRNA and RNA methylation, mRNA and RNA transport, and other processes. The study also identified a risk model based on the expression of these genes, and found that the high-risk group had a significantly worse prognosis than the low-risk group. Furthermore, the study showed that the m5C regulated gene signature was related to the immune status of HCC patients, such as the infiltration of immune cells, the expression of immune checkpoints, and the immune subtypes.
- m1A regulated gene signature: A study by Wang et al found that four of the six core m1A-related regulators were differentially expressed in HCC tissues, including TRMT6, TRMT10C, YTHDF1, and YTHDF2. These genes were involved in mRNA and RNA modifications, mRNA and RNA methylation, mRNA and RNA stability, and other processes. The study also identified a risk model based on the expression of these genes, and found that the high-risk group had a significantly worse prognosis than the low-risk group. Additionally, the study indicated that the m1A regulated gene signature was associated with the immune status of HCC patients, such as the infiltration of immune cells, the expression of immune checkpoints, and the immune subtypes.
The Implications and Challenges of RNA Modifications for HCC Therapy
The discovery of the role of m6A, m5C, and m1A in HCC prognosis and immune status has important implications for the diagnosis, treatment, and prevention of HCC. By analyzing the expression of m6A, m5C, and m1A regulated genes in HCC tissues or blood samples, clinicians can stratify HCC patients into different risk groups and provide personalized and precise therapeutic strategies. Moreover, by targeting the writers, erasers, and readers of these modifications, researchers can develop novel drugs or interventions that can modulate the expression and function of m6A, m5C, and m1A regulated genes and proteins, and thus affect the growth, invasion, metastasis, and immune evasion of HCC cells. For example, some small molecule inhibitors or activators of m6A-related enzymes, such as METTL3, FTO, and ALKBH5, have been identified and tested in preclinical or clinical studies for various cancers, including HCC .
However, there are also many challenges and limitations in the study and application of RNA modifications for HCC therapy. First, the mechanisms and functions of m6A, m5C, and m1A in HCC are still not fully understood, and the interactions and crosstalk among these modifications and other epigenetic or genetic factors are still unclear. Second, the detection and quantification of m6A, m5C, and m1A in HCC tissues or blood samples are still technically difficult and costly, and the standardization and validation of these methods are still lacking. Third, the specificity and efficacy of the inhibitors or activators of m6A, m5C, and m1A related enzymes are still not satisfactory, and the potential side effects and toxicity of these drugs are still unknown. Therefore, more in-depth and comprehensive studies on RNA modifications, their roles in HCC, and their inhibitors or activators are needed for a better understanding and utilization of epitranscriptomics for HCC therapy.
