The translation of oncogenic mRNAs regulated by pseudouridylation: A new player in HCC
Authors: Hayato Nakagawa, Aifu Lin
Journal: Hepatology (2024)

In recent years, novel drugs for HCC have been consistently approved, leading to a significant expansion of treatment options. However, the targets primarily focus on angiogenesis and immune checkpoints. While precision medicine, which selects treatment based on genomic abnormalities, is advancing in other cancers, it lags considerably in HCC. One of the reasons for this lag is the limited presence of driver mutations, which could serve as treatment targets in HCC. TERT promoter mutations are observed in ~60%, while mutations in CTNNB1 and TP53 occur in 30%–50%.1 However, none of these are currently targeted for treatment, and the formation of HCC seems to result from the accumulation of low-frequency mutations. On the other hand, at the expression level, activation of various pathways related to carcinogenesis is noted.2 Specific chemical modifications serve as an efficient method for regulating molecular function, impacting a diverse array of downstream signaling pathways through the modification of DNA and proteins. Numerous enzymes responsible for overseeing these modifications are targeted by current cancer therapies. The study of RNA modifications, known as RNA epitranscriptomics, represents a new frontier in this field.3 RNA modification provides a highly specific and effective method for regulating the expression and function of RNA without altering the underlying sequence.1 The most prevalent RNA modification is N6-methyladenosine.4 Studies on enzymes and factors involved in the catalysis, recognition, and removal of N6-methyladenosine have revealed its extensive involvement in various aspects of mRNA metabolism and physiological processes, including HCC.5 Recent advancements in high-throughput detection of RNA modification sites have revealed the presence of other modifications, such as pseudouridine, within mRNA. However, their functions and modifiers have not been extensively explored. Although the elevation of pseudouridine levels in serum and urine has been reported in HCC,6 the regulatory mechanism and its relevance to the pathophysiology have been largely unknown. In this issue of Hepatology, Hu et al have unveiled a novel mechanism of increased expression of oncogenic proteins through RNA modification with pseudouridine.7 Consistent with previous studies showing that pseudouridine synthase 1 (PUS1) is a potential prognostic biomarker in cancers, they observed an increase in PUS1 levels in HCC samples from The Cancer Genome Atlas or collected, suggesting that PUS1 likely plays an oncogenic function in HCC. Indeed, in their study, in vitro cell line assays, in vivo subcutaneous xenograft, and hydrodynamic tail vein injection mouse HCC models clearly showed that PUS1 promotes the development of HCC. Interestingly, this oncogenic effect is dependent on the pseudouridylation catalytic activity of PUS1. Thus, it is straightforward that identifying the target RNAs of PUS1 will lead to deciphering its underlying mechanism. To comprehensively profile the target RNAs of PUS1, Hu and colleagues employed a recently developed approach termed Surveying Targets by Apolipoprotein B mRNA editing enzyme catalytic subunit 1-Mediated Profiling,8 which has been shown to identify the landscape of a specific RNA binding protein. By overexpressing a PUS1-Apolipoprotein B mRNA editing enzyme catalytic subunit 1 fusion construct and subsequently using RNA-seq to identify the C-to-U editing events, the landscape of target mRNAs of PUS1 was revealed by Surveying Targets by Apolipoprotein B mRNA editing enzyme catalytic subunit 1-Mediated Profiling. Surprisingly, PUS1-interacting mRNAs were found to be significantly enriched with oncogenic mRNAs. Further experiments showed that PUS1 pseudouridates these oncogenic mRNAs, enhancing their translation capacity without affecting mRNA levels. These findings suggest that PUS1 promotes the development of HCC by increasing oncogenic protein synthesis through mRNA pseudouridylation (Figure 1).FIGURE 1: PUS1 promotes HCC by enhancing the translation of oncogenic mRNAs through pseudouridylation. Pseudouridylation is a posttranscriptional RNA modification that occurs after the formation of RNA. The protein responsible for this modification is called PUS. Hu and colleagues identified increased expression of PUS1 in HCC and revealed that PUS1 induces pseudouridylation of oncogenic mRNAs such as c-Myc and IRS1, thereby enhancing their translation and promoting hepatocarcinogenesis. Abbreviation: PUS1, pseudouridine synthase 1.Despite advancing our understanding of mRNA pseudouridylation in HCC, this study has raised more interesting questions. PUS1, a typical pseudouridine synthase, was found to be significantly up-regulated in several cancers, including HCC. However, mutations and amplifications of PUS1 were rare. Further investigation is needed to understand how PUS1 is regulated in HCC. While various reader proteins are known to recognize and bind to N6-methyladenosine–modified sites in mRNA, their recognition of pseudouridylation remains largely unknown. It is important to identify the proteins that recognize pseudouridylation and understand how they modulate mRNA fates. Additionally, it is unclear whether pseudouridylation is a reversible and dynamic epigenetic modification. Identifying potential erasers for pseudouridylation would be of great interest. From a clinical perspective, PUS1 has been reported to exhibit high expression in steatotic liver disease-related HCC, along with its association with the metabolic pathway.9 Given the escalating incidence of steatotic liver disease-related HCC, there is an interest in unraveling the intricate relationship between PUS1 and the etiology of HCC, as well as its active participation in the carcinogenic process. Furthermore, immunotherapy currently plays a central role in drug therapy for HCC, and a report suggested a potential connection between PUS1 and immune response.10 Currently, there is a lack of useful biomarkers in drug therapy for HCC. Therefore, there is not only the potential for PUS1 to be a therapeutic target, but also for serum or urine pseudouridine levels to be utilized as a biomarker for early detection of HCC and for guiding treatment decisions within drug therapy. The future development in this field is eagerly anticipated. In conclusion, Hu and colleagues have made significant contributions to our understanding of the role of PUS1 and RNA pseudouridylation in the development of HCC. They have also provided valuable insights into the molecular mechanisms underlying PUS1-mediated HCC development. Further research will be necessary to investigate the regulation of PUS1 in HCC and to understand how pseudouridylation is recognized and reversed.