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RNA bisulfite sequencing reveals NSUN2-mediated suppression of epithelial differentiation in pancreatic cancer

Oncogene volume 41, pages 3162–3176 (2022)Cite this article

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Abstract

Posttranscriptional modifications in RNA have been considered to contribute to disease pathogenesis and tumor progression. NOL1/NOP2/Sun domain family member 2 (NSUN2) is an RNA methyltransferase that promotes tumor progression in several cancers. Pancreatic cancer relapse inevitably occurs even in cases where primary tumors have been successfully treated. Associations of cancer progression due to reprogramming of the cancer methyl-metabolome and the cancer genome have been noted, but the effect of base modifications, namely 5-methylcytosine (m5C), in the transcriptome remains unclear. Aberrant regulation of 5-methylcytosine turnover in cancer may affect posttranscriptional modifications in coding and noncoding RNAs in disease pathogenesis. Mutations in NSUN2 have been reported as drivers of neurodevelopmental disorders in mice, and upregulated expression of NSUN2 in tumors of the breast, bladder, and pancreas has been reported. In this study, we conducted mRNA whole transcriptomic bisulfite sequencing to categorize NSUN2 target sites in the mRNA of human pancreatic cancer cells. We identified a total of 2829 frequent m5C sites in mRNA from pancreatic cancer cells. A total of 90.9% (2572/2829) of these m5C sites were mapped to annotated genes in autosomes and sex chromosomes X and Y. Immunohistochemistry staining confirmed that the NSUN2 expression was significantly upregulated in cancer lesions in the LSL-KrasG12D/+;Trp53fl/fl;Pdx1-Cre (KPC) spontaneous pancreatic cancer mouse model induced by Pdx1-driven Cre/lox system expressing mutant KrasG12D and p53 deletion. The in vitro phenotypic analysis of NSUN2 knockdown showed mild effects on pancreatic cancer cell 2D/3D growth, morphology and gemcitabine sensitivity in the early phase of tumorigenesis, but cumulative changes after multiple cell doubling passages over time were required for these mutations to accumulate. Syngeneic transplantation of NSUN2-knockdown KPC cells via subcutaneous injection showed decreased stromal fibrosis and restored differentiation of ductal epithelium in vivo.

Significance

  • Transcriptome-wide mRNA bisulfite sequencing identified candidate m5C sites of mRNAs in human pancreatic cancer cells.

  • NSUN2-mediated m5C mRNA metabolism was observed in a mouse model of pancreatic cancer.

  • NSUN2 regulates cancer progression and epithelial differentiation via mRNA methylation.

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Fig. 1: Overexpressed NSUN2 in pancreatic cancer associated with patient’s survival and tumorigenesis.
Fig. 2: Identification of NSUN2-m5C sites.
Fig. 3: The functional analysis of NSUN2-m5C sites.
Fig. 4: Integrated protein expression and candidate genes with differentially methylated m5C mRNA in NSUN2 knockdown cells.
Fig. 5: NSUN2 participates in cellular proliferation in 3D organoid culture and in DNA repair of DSBs.
Fig. 6: NSUN2 knockdown diminished the growth of high-grade tumor in immunocompetent mice.

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Data availability

GSE182148.

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Acknowledgements

The authors acknowledge technical services from core facilities: Research Center of Clinical Medicine, Center of Cell Therapy, and the Human Biobank and the Cancer Data Bank of National Cheng Kung University Hospital. The authors thank the Core Research Laboratory and the Laboratory Animal Center, College of Medicine, National Cheng Kung University; and Taiwan Animal Consortium. We thank the technical services provided by the following National Core Facilities: Bioimaging Core Facility; and the International Institute for Macromolecular Analysis and Nanomedicine Innovations, National Core Facility for Biopharmaceuticals, Ministry of Science and Technology, Taiwan. Sequencing run, computational analyses and data mining were performed using the system provided by the Center for Bioinformatics and Digital Health at the National Cheng Kung University, supported by Ministry of Science and Technology, Taiwan. The authors acknowledge the mass spectrometry technical research services from NTU Consortia of Key Technologies and NTU Instrumentation Center. We thank the National RNAi Core Facility at Academia Sinica in Taiwan for providing shRNA reagents and related services. This work is supported by grant support from the MOST (110-2320-B-006-038- and 110-2314-B-006-107-) to PHH.

Author information

Author notes

  1. These authors contributed equally: Szu-Ying Chen, Kuan-Lin Chen, Li-Yun Ding.

Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan

    Szu-Ying Chen, Kuan-Lin Chen, Chien-Hung Yu, Ya-Yi Chou & Po-Hsien Huang

  2. Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan

    Szu-Ying Chen, Li-Yun Ding, Chien-Hung Yu & Po-Hsien Huang

  3. Instrumentation Center, College of Science, National Taiwan University, Tainan, Taiwan

    Hsin-Yi Wu

  4. Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan

    Chia-Jung Chang & Chih-Han Chang

  5. Medical Device Innovation Center, National Cheng Kung University, Tainan, Taiwan

    Chih-Han Chang

  6. Center for Corporate Relations and Technology Transfer, National Cheng Kung University, Tainan, Taiwan

    Chih-Han Chang

  7. International Institute for Macromolecular Analysis and Nanomedicine Innovations, Tainan, Taiwan

    Ya-Na Wu & Shang-Rung Wu

  8. Institute of Oral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan

    Shang-Rung Wu

  9. Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan

    Ya-Chin Hou, Peng-Chieh Chen & Yan-Shen Shan

  10. Division of General Surgery, Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan

    Ya-Chin Hou & Yan-Shen Shan

  11. Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan

    Chung-Ta Lee

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  1. Szu-Ying Chen
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Contributions

Investigation: experiments, library construction, mapping of reads to genome and transcriptome, and m5C site analysis: SYC; Bioinformatics: SYC, KLC, CJC, CHC; Sequencing assistance: PCC. Investigation: cellular and animal experiments: SYC, LYD, YYC, KLC; Transmission electron microscopy experiments: YYC, YNW, SRW; Formal analysis: SYC, PHH. Clinical specimen analysis: CTL, PHH, YCH, YSS. Concept and experiment design: SYC, CHY, and PHH. Writing of initial draft: SYC. Writing: SYC and PHH with proof-read and inputs from all authors. Supervision: PHH. All authors read and approve the final version of the manuscript.

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Correspondence to Yan-Shen Shan or Po-Hsien Huang.

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Chen, SY., Chen, KL., Ding, LY. et al. RNA bisulfite sequencing reveals NSUN2-mediated suppression of epithelial differentiation in pancreatic cancer. Oncogene 41, 3162–3176 (2022). https://doi.org/10.1038/s41388-022-02325-7

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