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NUDT21 negatively regulates PSMB2 and CXXC5 by alternative polyadenylation and contributes to hepatocellular carcinoma suppression

Oncogenevolume 37pages48874900 (2018) | Download Citation

Abstract

Alternative polyadenylation (APA) is an important post-transcriptional regulatory mechanism and involved in many diseases, including cancer. CFIm25, a subunit of the cleavage factor I encoded by NUDT21, is required for 3′RNA cleavage and polyadenylation. Although it has been recently reported to be involved in glioblastoma tumor suppression, its roles and the underlying functional mechanism remain unclear in other types of cancer. In this study, we characterized NUDT21 in hepatocellular carcinoma (HCC). Reduced expression of NUDT21 was observed in HCC tissue compared to adjacent non-tumorous compartment. HCC patients with lower NUDT21 expression have shorter overall and disease-free survival times than those with higher NUDT21 expression after surgery. Knockdown of NUDT21 promotes HCC cell proliferation, metastasis, and tumorigenesis, whereas forced expression of NUDT21 exhibits the opposite effects. We then performed global APA site profiling analysis in HCC cells and identified considerable number of genes with shortened 3′UTRs upon the modulation of NUDT21 expression. In particular, we further characterized the NUDT21-regulated genes PSMB2 and CXXC5. We found NUDT21 knockdown increases usage of the proximal polyadenylation site in the PSMB2 and CXXC5 3′ UTRs, resulting in marked increase in the expression of PSMB2 and CXXC5. Moreover, knockdown of PSMB2 or CXXC5 suppresses HCC cell proliferation and invasion. Taken together, our study demonstrated that NUDT21 inhibits HCC proliferation, metastasis and tumorigenesis, at least in part, by suppressing PSMB2 and CXXC5, and thereby provided a new insight into understanding the connection of HCC suppression and APA machinery.

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References

  1. 1.

    Di Giammartino DC, Nishida K, Manley JL. Mechanisms and consequences of alternative polyadenylation. Mol Cell. 2011;43:853–66.

  2. 2.

    Tian B, Manley JL. Alternative polyadenylation of mRNA precursors. Nat Rev Mol Cell Biol. 2017;18:18–30.

  3. 3.

    Elkon R, Ugalde AP, Agami R. Alternative cleavage and polyadenylation: extent, regulation and function. Nat Rev Genet. 2013;14:496–506.

  4. 4.

    Mayr C, Bartel DP. Widespread shortening of 3’UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell. 2009;138:673–84.

  5. 5.

    Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB. Proliferating cells express mRNAs with shortened 3’ untranslated regions and fewer microRNA target sites. Science. 2008;320:1643–7.

  6. 6.

    Morris AR, Bos A, Diosdado B, Rooijers K, Elkon R, Bolijn AS, et al. Alternative cleavage and polyadenylation during colorectal cancer development. Clin Cancer Res. 2012;18:5256–66.

  7. 7.

    Erson-Bensan AE, Can T. Alternative polyadenylation: another foe in cancer. Mol Cancer Res. 2016;14:507–17.

  8. 8.

    Singh P, Alley TL, Wright SM, Kamdar S, Schott W, Wilpan RY, et al. Global changes in processing of mRNA 3’ untranslated regions characterize clinically distinct cancer subtypes. Cancer Res. 2009;69:9422–30.

  9. 9.

    Fu Y, Sun Y, Li Y, Li J, Rao X, Chen C, et al. Differential genome-wide profiling of tandem 3’ UTRs among human breast cancer and normal cells by high-throughput sequencing. Genome Res. 2011;21:741–7.

  10. 10.

    Xia Z, Donehower LA, Cooper TA, Neilson JR, Wheeler DA, Wagner EJ, et al. Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3’-UTR landscape across seven tumour types. Nat Commun. 2014;5:5274.

  11. 11.

    Lembo A, Di Cunto F, Provero P. Shortening of 3’UTRs correlates with poor prognosis in breast and lung cancer. PLoS One. 2012;7:e31129.

  12. 12.

    Miles WO, Lembo A, Volorio A, Brachtel E, Tian B, Sgroi D, et al. Alternative polyadenylation in triple-negative breast tumors allows NRAS and c-JUN to bypass PUMILIO posttranscriptional regulation. Cancer Res. 2016;76:7231–41.

  13. 13.

    Shi Y, Di Giammartino DC, Taylor D, Sarkeshik A, Rice WJ, Yates JR 3rd, et al. Molecular architecture of the human pre-mRNA 3’ processing complex. Mol Cell. 2009;33:365–76.

  14. 14.

    Masamha CP, Xia Z, Yang J, Albrecht TR, Li M, Shyu AB, et al. CFIm25 links alternative polyadenylation to glioblastoma tumour suppression. Nature. 2014;510:412–6.

  15. 15.

    Martin G, Gruber AR, Keller W, Zavolan M. Genome-wide analysis of pre-mRNA 3’ end processing reveals a decisive role of human cleavage factor I in the regulation of 3’ UTR length. Cell Rep. 2012;1:753–63.

  16. 16.

    Brown KM, Gilmartin GM. A mechanism for the regulation of pre-mRNA 3’ processing by human cleavage factor Im. Mol Cell. 2003;12:1467–76.

  17. 17.

    Venkataraman K, Brown KM, Gilmartin GM. Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition. Genes Dev. 2005;19:1315–27.

  18. 18.

    Coseno M, Martin G, Berger C, Gilmartin G, Keller W, Doublie S. Crystal structure of the 25 kDa subunit of human cleavage factor Im. Nucleic Acids Res. 2008;36:3474–83.

  19. 19.

    Yang Q, Gilmartin GM, Doublie S. Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3’ processing. Proc Natl Acad Sci USA. 2010;107:10062–7.

  20. 20.

    Gennarino VA, Alcott CE, Chen CA, Chaudhury A, Gillentine MA, Rosenfeld JA, et al. NUDT21-spanning CNVs lead to neuropsychiatric disease and altered MeCP2 abundance via alternative polyadenylation. Elife 2015;4;e10782.

  21. 21.

    Lai DP, Tan S, Kang YN, Wu J, Ooi HS, Chen J, et al. Genome-wide profiling of polyadenylation sites reveals a link between selective polyadenylation and cancer metastasis. Hum Mol Genet. 2015;24:3410–7.

  22. 22.

    Forner A, Llovet JM, Bruix J. Hepatocellular carcinoma. Lancet. 2012;379:1245–55.

  23. 23.

    Llovet JM, Zucman-Rossi J, Pikarsky E, Sangro B, Schwartz M, Sherman M, et al. Hepatocellular carcinoma. Nat Rev Dis Prim. 2016;2:16018.

  24. 24.

    Llovet JM. Liver cancer: time to evolve trial design after everolimus failure. Nat Rev Clin Oncol. 2014;11:506–7.

  25. 25.

    Collavoli A, Comelli L, Cervelli T, Galli A. The over-expression of the beta2 catalytic subunit of the proteasome decreases homologous recombination and impairs DNA double-strand break repair in human cells. J Biomed Biotechnol. 2011;2011:757960.

  26. 26.

    Knappskog S, Myklebust LM, Busch C, Aloysius T, Varhaug JE, Lonning PE, et al. RINF (CXXC5) is overexpressed in solid tumors and is an unfavorable prognostic factor in breast cancer. Ann Oncol. 2011;22:2208–15.

  27. 27.

    Tan S, Ding K, Li R, Zhang W, Li G, Kong X, et al. Identification of miR-26 as a key mediator of estrogen stimulated cell proliferation by targeting CHD1, GREB1 and KPNA2. Breast Cancer Res. 2014;16:R40.

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Acknowledgements

This work was supported by The National Key Scientific Programme of China (2016YFC1302305), The National Natural Science Foundation of China (81672609, 31671299, 81502282, 81472494,) and the Shenzhen Development and Reform Commission Subject Construction Project [2017] 1434. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

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Author notes

  1. These authors contributed equally: Sheng Tan, Hua Li, Weijie Zhang.

Affiliations

  1. Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China

    • Sheng Tan
    • , Weijie Zhang
    • , Yunying Shao
    • , Yuan Liu
    • , Haiyang Guan
    • , Junsong Zhao
    • , Qing Yu
    • , Min Zhang
    • , Wenchang Qian
    • , Yong Zhu
    • , Huayong Cai
    •  & Tao Zhu
  2. School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, 200240, China

    • Hua Li
    • , Jun Wu
    • , Yani Kang
    •  & Yunzhao Gu
  3. Department of Pathology, Anhui Medical University, Meishan Road, Hefei, Anhui, 230031, China

    • Keshuo Ding
  4. First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Meishan Road, Hefei, Anhui, 230031, China

    • Changyu Chen
  5. Tsinghua-Berkeley Shenzhen Institute, Precision Medicine & Healthcare Research Center, Tsinghua University, Shenzhen, 518055, China

    • Peter E. Lobie
  6. Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China

    • Xiaodong Zhao
    •  & Jielin Sun

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Conflict of interest

The authors declare that they have no conflict of interest.

Corresponding authors

Correspondence to Xiaodong Zhao or Jielin Sun or Tao Zhu.

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DOI

https://doi.org/10.1038/s41388-018-0280-6