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Multiple transcriptome analysis of Piwil2-induced cancer stem cells, including piRNAs, mRNAs and miRNAs reveals the mechanism of tumorigenesis and development

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Abstract

Background

Cancer stem cells play important roles in the process of tumorigenesis. Our research group obtained cancer stem cell-like cells named Piwil2-iCSCs by reprogramming human preputial fibroblasts (FBs) with the PIWIL2 gene, but the mechanism of Piwil2-iCSCs is still unclear.

Methods

We sequenced the piRNAs, miRNAs and mRNAs of Piwil2-iCSCs and FBs, and analyzed the differences. Gene Ontology (GO) and, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses and gene set enrichment analysis (GSEA) were performed on the differentially expressed (DE) mRNAs. In addition, we analyzed the variable shear events and fusion genes in the Piwil2-iCSCs. Target gene prediction and functional enrichment analysis were performed for the DE miRNAs.

Results

A total of 1119 DE mRNAs, 220 DE piRNAs, and 440 DE miRNAs were obtained between the Piwil2-iCSCs and FBs. Functional enrichment analysis showed that the genes with upregulated expression were mainly involved in DNA repair, mismatch repair, base excision repair, and nucleotide excision repair. Genes with downregulated expression were mainly involved in the TGF-β receptor signaling pathway, senescence and autophagy in cancer. More frequent shear events occurred in Piwil2-iCSCs and FBs, especially in intron retention (IR) events. We also identified three fusion genes MCM3AP-C21orf58, LRRFIP2-CAV3 and TMEM184B-DMC1. Enrichment analysis of DE miRNAs showed that they were associated with apoptosis, the TGF-β signaling pathway, and the stem cell regulatory signaling pathway. In particular, target gene prediction of the top three miRNAs with upregulated expression showed that they targeted SMAD, GREM1 and other genes to participate in the regulation of TGF-β and other pathways.

Conclusion

PIWIL2-induced cancer stem cells have significantly altered levels of miRNAs, piRNAs and mRNAs.TGF-β, autophagy, apoptosis and other pathways may play an important role in stem cell development. The occurrence of alternative splicing and fusion genes may be related to the occurrence of cancer stem cells.

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Data availability

The datasets used or analyzed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

That all authors are in agreement with the content of the manuscript.

Funding

The present study was supported by the Special Project of Science and Technology Innovation for Social Undertakings and Livelihood Guarantee of Chongqing (Grant Nos. cstc2019jscx-tjsbX0003 and cstc2017shmsA130103).

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Authors and Affiliations

  1. Department of Urology, Children’s Hospital of Chongqing Medical University, Yuzhong District, Chongqing, 400014, People’s Republic of China

    Xiaojun Tan, Tao Mi, Zhaoxia Zhang, Liming Jin, Zhang Wang, Xin Wu, Jinkui Wang, Mujie Li, Chenghao Zhanghuang & Dawei He

  2. Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, People’s Republic of China

    Xiaojun Tan, Tao Mi, Zhaoxia Zhang, Liming Jin, Zhang Wang, Xin Wu, Jinkui Wang, Mujie Li, Chenghao Zhanghuang & Dawei He

  3. China International Science and Technology Cooperation Base of Child Development and Critical; National Clinical Research Center for Child Health and Disorders, Chongqing, Ministry of Education Key Laboratory of Child Development and Disorders; Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, People’s Republic of China

    Xiaojun Tan, Tao Mi, Zhaoxia Zhang, Liming Jin, Zhang Wang, Xin Wu, Jinkui Wang, Mujie Li, Chenghao Zhanghuang & Dawei He

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  1. Xiaojun Tan
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  2. Tao Mi
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  10. Dawei He
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Contributions

Conceptualization: [TM, XT, ZZ and DH]; Data curation: [TM, XT, ZZ and LJ]; Formal analysis: [TM, XT, JW and XW]; Funding acquisition: [DH]; Methodology: [TM, XT, ZW, ML and CZ]; Writing—original draft: [TM, XT and ZZ]; Resources: [DH]; Supervision: [DH].

Corresponding author

Correspondence to Dawei He.

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Supplementary file1 (TIF 125 KB)

Fig. SF1 The PCA of miRNAs, piRNAs and mRNAs.

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Tan, X., Mi, T., Zhang, Z. et al. Multiple transcriptome analysis of Piwil2-induced cancer stem cells, including piRNAs, mRNAs and miRNAs reveals the mechanism of tumorigenesis and development. Mol Biol Rep 49, 6885–6898 (2022). https://doi.org/10.1007/s11033-022-07237-z

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  • DOI: https://doi.org/10.1007/s11033-022-07237-z

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