HNRNPR-Mediated UPF3B mRNA Splicing Drives Hepatocellular Carcinoma Metastasis

In recent years, hepatocellular carcinoma (HCC) has become one of the leading causes of cancer-related deaths worldwide due to its highly invasive and metastatic nature. The mechanisms underlying HCC metastasis are complex, with abnormal alternative splicing (AS) playing a significant role in tumor initiation, invasion, and metastasis. UPF3B (Up-frameshift suppressor 3B), an X chromosome-linked gene, encodes a key protein in the nonsense-mediated mRNA decay (NMD) pathway. Although dysregulation of UPF3B has been associated with the progression of various cancers, its specific mechanisms in HCC remain unclear. To address this, a research team from the First Affiliated Hospital of the University of Science and Technology of China conducted a study on the role of the UPF3B splice variant (UPF3B-S) in HCC metastasis, aiming to elucidate its molecular mechanisms in HCC invasion and metastasis.

Background and Motivation

The high mortality rate of HCC is primarily attributed to its invasiveness and metastatic potential. Vascular invasion (VI) is a critical feature of HCC invasion and metastasis, providing a direct pathway for tumor cell dissemination. Studies have shown that abnormal splicing plays a significant role in tumor metastasis. While UPF3B is essential for neuronal differentiation and maturation, its function in solid tumors remains poorly understood. This study identified a truncated splice variant of UPF3B, UPF3B-S, through the analysis of splicing events in HCC tissues and investigated its role in HCC metastasis.

Research Source

This study was conducted jointly by Hong Wang, Dong Qian, Jiabei Wang, and other researchers, primarily from the First Affiliated Hospital of the University of Science and Technology of China. The paper was published in Journal of Advanced Research (Vol. 68, 2025), titled “HNRNPR-mediated UPF3B mRNA splicing drives hepatocellular carcinoma metastasis.” The research was supported by grants from the National Natural Science Foundation of China, the Anhui Provincial Natural Science Foundation, and the Guangdong Natural Science Foundation.

Research Process and Key Findings

The research team revealed the mechanism of UPF3B-S in HCC metastasis through multiple experimental steps, as outlined below:

1. Expression of UPF3B-S and Its Relationship with HCC Invasion

The study first identified elevated UPF3B-S expression in HCC tissues compared to adjacent liver tissues through RNA sequencing data analysis, with higher expression in invasive HCC than in non-invasive HCC. Using BaseScope technology, the team further validated the high expression of UPF3B-S mRNA in HCC cells and found that its expression was associated with poor prognosis in HCC patients. These results suggest that UPF3B-S may play a potential role in HCC invasion and metastasis.

2. Functional Studies of UPF3B-S

To investigate the biological function of UPF3B-S, the research team constructed HCC cell lines with UPF3B-S knockdown and overexpression, and verified its function through in vitro and in vivo experiments. In vitro experiments showed that knockdown of UPF3B-S significantly inhibited the invasive and migratory abilities of HCC cells, while overexpression enhanced these abilities. In mouse models, knockdown of UPF3B-S significantly reduced lung metastases and intrahepatic metastatic nodules, further confirming the critical role of UPF3B-S in HCC metastasis.

3. Mechanism of HNRNPR-Mediated UPF3B Splicing

The study further investigated the splicing factors regulating UPF3B-S expression and identified heterogeneous nuclear ribonucleoprotein R (HNRNPR) as a key regulator of UPF3B-S. Through RNA immunoprecipitation experiments, the study confirmed that HNRNPR binds to UPF3B pre-mRNA via its RNA recognition motif (RRM2) domain, inducing the skipping of exon 8 and generating UPF3B-S. Additionally, HNRNPR expression was significantly elevated in invasive HCC and positively correlated with UPF3B-S expression.

4. UPF3B-S Promotes HCC Metastasis via the Hippo/YAP Signaling Pathway

To elucidate the molecular mechanism by which UPF3B-S promotes HCC metastasis, the research team performed RNA sequencing analysis and found that the Hippo signaling pathway was significantly altered upon UPF3B-S knockdown. UPF3B-S degrades CDH1 mRNA, suppresses E-cadherin expression, and subsequently activates the Hippo signaling pathway. Overexpression of UPF3B-S enhances the nuclear accumulation of YAP1 and upregulates its downstream target gene BIRC5, while inhibition of BIRC5 significantly reduces UPF3B-S-induced HCC cell invasion and migration.

Research Value and Significance

This study is the first to reveal the critical role of the HNRNPR-mediated UPF3B splice variant UPF3B-S in HCC metastasis and to elucidate its molecular mechanism in promoting HCC invasion and metastasis through the Hippo/YAP signaling pathway. These findings provide new potential therapeutic targets for HCC, and UPF3B-S may serve as a prognostic biomarker for the invasive phenotype of HCC. Additionally, the study highlights the importance of splicing factors in tumor metastasis, offering a theoretical foundation for future therapeutic strategies targeting splicing processes.

Research Highlights

1. Novel Splice Variant: The study is the first to identify the high expression of the truncated splice variant UPF3B-S in HCC and its close association with the invasive phenotype.
   
2. Innovative Experimental Methods: The research combines BaseScope technology, RNA immunoprecipitation, and in vitro and in vivo models to comprehensively evaluate the function of UPF3B-S.
   
3. In-Depth Mechanistic Insights: The study elucidates the mechanism by which UPF3B-S indirectly regulates the Hippo/YAP signaling pathway through the degradation of CDH1 mRNA.
   
4. Clinical Application Potential: UPF3B-S and HNRNPR may serve as potential therapeutic targets for HCC, providing directions for the development of new treatment strategies.

Conclusion

Through multi-level experimental design and in-depth mechanistic analysis, this study reveals the critical role of the HNRNPR-mediated UPF3B splice variant in HCC metastasis. These findings not only enhance the understanding of HCC metastasis mechanisms but also provide a theoretical basis for the development of new therapeutic strategies. In the future, targeted therapies against UPF3B-S and HNRNPR may offer new hope for HCC patients.