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VIRMA facilitates intrahepatic cholangiocarcinoma progression through epigenetic augmentation of TMED2 and PARD3B mRNA stabilization

  • Original Article—Liver, Pancreas, and Biliary Tract
  • Published:
Journal of Gastroenterology Aims and scope Submit manuscript

Abstract

Background

N6-methyladenine modification of RNA, a critical component of the regulatory role at the post-transcriptional level, has a crucial effect on tumor development and progression. vir-Like m6A methyltransferase associated (VIRMA) has been recently discovered as an N6-methyladenine methyltransferase; however, its specific role in intrahepatic cholangiocarcinoma (ICC) remains to be investigated in-depth.

Methods

VIRMA expression and its association with clinicopathological characteristics were evaluated using The Cancer Genome Atlas (TCGA) dataset and tissue microarrays. In vivo and in vitro assays were performed to determine the role of VIRMA in ICC proliferation and metastasis. The underlying mechanism by which VIRMA influences ICC was clarified by RNA sequencing (RNA-seq), methylated RNA immunoprecipitation sequencing (MeRIP-seq), SLAM sequencing (SLAM-seq), RNA immunoprecipitation, a luciferase reporter assay, and chromatin immunoprecipitation assay.

Results

VIRMA showed high expression in ICC tissues, and this finding predicted a dismal prognostic outcome. The high expression of VIRMA in ICC was due to the demethylation of H3K27me3 modification in the promoter region. Functionally, VIRMA is required for the endothelial–mesenchymal transition (EMT) process in ICC cells, as shown by multiple ICC models in in vitro and in vivo experiments. Mechanistically, multi-omics analysis using ICC cells demonstrated that TMED2 and PARD3B were the direct downstream target of VIRMA. The methylated TMED2 and PARD3B transcripts were directly recognized by HuR, which exerted stabilizing effects on its bound RNA. VIRMA-induced expression of TMED2 and PARD3B activated the Akt/GSK/β-catenin and MEK/ERK/Slug signaling pathways, thereby promoting ICC proliferation and metastasis.

Conclusions

The present study showed that VIRMA plays a critical role in ICC development by stabilizing TMED2 and PARD3B expression through the m6A–HuR-mediated mechanism. Thus, demonstrating VIRMA and its pathway as candidate therapeutic targets for ICC treatment.

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Abbreviations

ICC:

Intrahepatic cholangiocarcinoma

TCGA:

The Cancer Genome Atlas

RT-qPCR:

Quantitative reverse transcription polymerase chain reaction

DMSO:

Dimethyl sulfoxide

RNA-seq:

RNA sequencing

MeRIP-seq:

Methylated RNA immunoprecipitation sequencing

SLAM-seq:

Thiol (SH)-linked alkylation for metabolic sequencing of RNA

EMT:

Endothelial–mesenchymal transition

HuR:

Hu-antigen R

RIP:

RNA immunoprecipitation

ChIP:

Chromatin immunoprecipitation

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Acknowledgements

This study was supported by the National Natural Science Foundation of China (82272103, 82230067), the Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment (2021B1212040004), the Natural Science Foundation of Guangdong Province of China (2022B1515020010), and Scientific Research Foundation of Guangdong Medical University of China (2021113808, 2021093728).

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Author notes

  1. Hongfa Xu, Xiaowen Lin, and Zhongliang Li have contributed equally to this work.

Authors and Affiliations

  1. Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, 519000, Guangdong, China

    Hongfa Xu, Xiaowen Lin, Zhongliang Li, Xu He, Yong Li, Lige Qiu, Ligong Lu, Bing Liu & Meixiao Zhan

  2. Oncology Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, Guangdong, China

    Hongfa Xu

  3. Minimally Invasive Tumor Therapies Center, Guangdong Second Provincial General Hospital, Guangzhou, 510310, Guangdong, China

    Ke He

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Contributions

The studies were designed by MXZ, HFX, KH, XWL, and BL. Experiments were performed by HFX, XWL, ZLL, and KH. Dara analysis was carried out by HFX, XWL, ZLL, KH, BL, XH, YL, LGL, and LGQ. The manuscript was written by HFX and XWL, and revised by HFX, XWL, and KH. All authors revised and approved the manuscript.

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Correspondence to Meixiao Zhan or Ke He.

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Xu, H., Lin, X., Li, Z. et al. VIRMA facilitates intrahepatic cholangiocarcinoma progression through epigenetic augmentation of TMED2 and PARD3B mRNA stabilization. J Gastroenterol 58, 925–944 (2023). https://doi.org/10.1007/s00535-023-02015-5

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