U1 snRNP điều chỉnh sự di chuyển và xâm nhập của tế bào ung thư trong ống nghiệm

Nature Communications - Tập 11 Số 1
Jung‐Min Oh1, Christopher C. Venters1, Chao Di1, Anna Maria Pinto1, Lili Wan1, Ihab Younis1, Zhiqiang Cai1, Chie Arai1, Byung Ran So1, Jingqi Duan1, Gideon Dreyfuss1
1Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104-6148, USA

Tóm tắt

Tóm tắt

Các tế bào được kích thích và tế bào ung thư có sự rút ngắn phổ biến các vùng không dịch mã 3’- (3’UTR) và chuyển sang các isoform mRNA ngắn hơn do việc sử dụng các tín hiệu polyadenylation (PAS) gần hơn trong các intron và exon cuối. U1 snRNP (U1), RNA hạt nhỏ không mã hóa (spliceosomal) phong phú nhất ở động vật có xương sống, làm tắt các PAS gần và việc ức chế nó bằng các oligonucleotide morpholino chống nghĩa (U1 AMO) sẽ gây ra việc ngừng phiên mã sớm rộng rãi và sự rút ngắn mRNA. Ở đây, chúng tôi cho thấy rằng liều lượng thấp của U1 AMO làm tăng sự di chuyển và xâm nhập của tế bào ung thư in vitro lên tới 500%, trong khi sự biểu hiện quá mức của U1 có tác động ngược lại. Ngoài chiều dài 3’UTR, nhiều thay đổi trong toàn bộ transcriptome có thể góp phần vào kiểu hình này được quan sát, bao gồm việc cắt nối thay thế và mức độ biểu hiện mRNA của các proto-oncogen và các gen ức chế khối u. Những phát hiện này tiết lộ một vai trò bất ngờ của sự cân bằng U1 (U1 có sẵn so với phiên mã) trong các trạng thái tế bào ung thư và được kích hoạt, và gợi ý U1 như một mục tiêu tiềm năng cho việc điều chỉnh chúng.

Từ khóa


Tài liệu tham khảo

Flavell, S. W. et al. Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection. Neuron 60, 1022–1038 (2008).

Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A. & Burge, C. B. Proliferating cells express mRNAs with shortened 3’ untranslated regions and fewer microRNA target sites. Science 320, 1643–1647 (2008).

Ji, Z. & Tian, B. Reprogramming of 3’ untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types. PLoS ONE 4, e8419 (2009).

Mayr, C. & Bartel, D. P. Widespread shortening of 3’UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138, 673–684 (2009).

Singh, I. et al. Widespread intronic polyadenylation diversifies immune cell transcriptomes. Nat. Commun. 9, 1716 (2018).

Lee, S. H. et al. Widespread intronic polyadenylation inactivates tumour suppressor genes in leukaemia. Nature 561, 127–131 (2018).

Oh, J. M. et al. U1 snRNP telescripting regulates a size-function-stratified human genome. Nat. Struct. Mol. Biol. 24, 993–999 (2017).

Kaida, D. et al. U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature 468, 664–648 (2010).

Berg, M. G. et al. U1 snRNP determines mRNA length and regulates isoform expression. Cell 150, 53–64 (2012).

Matera, A. G. & Wang, Z. A day in the life of the spliceosome. Nat. Rev. Mol. Cell Biol. 15, 108–121 (2014).

Niibori, Y., Hayashi, F., Hirai, K., Matsui, M. & Inokuchi, K. Alternative poly(A) site-selection regulates the production of alternatively spliced vesl-1/homer1 isoforms that encode postsynaptic scaffolding proteins. Neurosci. Res 57, 399–410 (2007).

Matter, N. & Konig, H. Targeted ‘knockdown’ of spliceosome function in mammalian cells. Nucleic Acids Res 33, e41 (2005).

Li, W. et al. Systematic profiling of poly(A)+ transcripts modulated by core 3’ end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation. PLoS Genet. 11, e1005166 (2015).

Masamha, C. P. et al. CFIm25 links alternative polyadenylation to glioblastoma tumour suppression. Nature 510, 412–416 (2014).

Wang, Q. & Rio, D. C. JUM is a computational method for comprehensive annotation-free analysis of alternative pre-mRNA splicing patterns. Proc. Natl Acad. Sci. USA 115, E8181–E8190 (2018).

Gilad, S. et al. Genotype-phenotype relationships in ataxia-telangiectasia and variants. Am. J. Hum. Genet. 62, 551–561 (1998).

Alsafadi, S. et al. Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage. Nat. Commun. 7, 10615 (2016).

Seiler, M. et al. Somatic mutational landscape of splicing factor genes and their functional consequences across 33 cancer types. Cell Rep. 23, 282–296 e4 (2018).

Ntini, E. et al. Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality. Nat. Struct. Mol. Biol. 20, 923–928 (2013).

Almada, A. E., Wu, X., Kriz, A. J., Burge, C. B. & Sharp, P. A. Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature 499, 360–363 (2013).

Ogami, K. et al. An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression. Genes Dev. 31, 1257–1271 (2017).

So, B. R. et al. A complex of U1 snRNP with cleavage and polyadenylation factors controls telescripting, regulating mRNA transcription in human cells. Mol. Cell 76, 590–599 e4 (2019).

Yoshida, K. et al. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature 478, 64–69 (2011).

Ilagan, J. O. et al. U2AF1 mutations alter splice site recognition in hematological malignancies. Genome Res 25, 14–26 (2015).

Kim, E. et al. SRSF2 mutations contribute to myelodysplasia by mutant-specific effects on exon recognition. Cancer Cell 27, 617–630 (2015).

Futreal, P. A. et al. A census of human cancer genes. Nat. Rev. Cancer 4, 177–183 (2004).

Nicoloso, M. S., Spizzo, R., Shimizu, M., Rossi, S. & Calin, G. A. MicroRNAs–the micro steering wheel of tumour metastases. Nat. Rev. Cancer 9, 293–302 (2009).

Nana-Sinkam, S. P. & Croce, C. M. Non-coding RNAs in cancer initiation and progression and as novel biomarkers. Mol. Oncol. 5, 483–491 (2011).

Ebert, M. S. & Sharp, P. A. Roles for MicroRNAs in conferring robustness to biological processes. Cell 149, 515–524 (2012).

Mendell, J. T. & Olson, E. N. MicroRNAs in stress signaling and human disease. Cell 148, 1172–1187 (2012).

Johnson, C. D. et al. The let-7 microRNA represses cell proliferation pathways in human cells. Cancer Res. 67, 7713–7722 (2007).

Lee, S. O. et al. MicroRNA15a modulates expression of the cell-cycle regulator Cdc25A and affects hepatic cystogenesis in a rat model of polycystic kidney disease. J. Clin. Invest. 118, 3714–3724 (2008).

Wang, P. et al. microRNA-21 negatively regulates Cdc25A and cell cycle progression in colon cancer cells. Cancer Res. 69, 8157–8165 (2009).

Paranjape, T. et al. A 3’-untranslated region KRAS variant and triple-negative breast cancer: a case-control and genetic analysis. Lancet Oncol. 12, 377–386 (2011).

Milde-Langosch, K. The Fos family of transcription factors and their role in tumourigenesis. Eur. J. Cancer 41, 2449–2461 (2005).

Silvestre, D. C., Gil, G. A., Tomasini, N., Bussolino, D. F. & Caputto, B. L. Growth of peripheral and central nervous system tumors is supported by cytoplasmic c-Fos in humans and mice. PLoS ONE 5, e9544 (2010).

Takagaki, Y., Seipelt, R. L., Peterson, M. L. & Manley, J. L. The polyadenylation factor CstF-64 regulates alternative processing of IgM heavy chain pre-mRNA during B cell differentiation. Cell 87, 941–952 (1996).

Di Giammartino, D. C., Nishida, K. & Manley, J. L. Mechanisms and consequences of alternative polyadenylation. Mol. Cell 43, 853–866 (2011).

de Klerk, E. et al. Poly(A) binding protein nuclear 1 levels affect alternative polyadenylation. Nucl. Acids Res. 40, 9089–9101 (2012).

Martin, G., Gruber, A. R., 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. 1, 753–763 (2012).

Yao, C. et al. Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation. Proc. Natl Acad. Sci. USA 109, 18773–18778 (2012).

Jenal, M. et al. The poly(a)-binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites. Cell 149, 538–553 (2012).

Gruber, A. R., Martin, G., Keller, W. & Zavolan, M. Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors. Wiley Interdiscip. Rev. RNA 5, 183–196 (2014).

Yu, K. et al. A precisely regulated gene expression cassette potently modulates metastasis and survival in multiple solid cancers. PLoS Genet. 4, e1000129 (2008).

Park, H. J. et al. 3’ UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk. Nat. Genet. 50, 783–789 (2018).

Cheng, Z. et al. Gene expression profiling reveals U1 snRNA regulates cancer gene expression. Oncotarget 8, 112867–112874 (2017).

Henrich, K. O., Schwab, M. & Westermann, F. 1p36 tumor suppression–a matter of dosage? Cancer Res. 72, 6079–6088 (2012).

Chiu, A. C. et al. Transcriptional pause sites delineate stable nucleosome-associated premature polyadenylation suppressed by U1 snRNP. Mol. Cell 69, 648–663 e7 (2018).

Vorlova, S. et al. Induction of antagonistic soluble decoy receptor tyrosine kinases by intronic polyA activation. Mol. Cell 43, 927–939 (2011).

Langemeier, J. et al. A complex immunodeficiency is based on U1 snRNP-mediated poly(A) site suppression. EMBO J. 31, 4035–4044 (2012).

Tsujii, M. et al. Cyclooxygenase regulates angiogenesis induced by colon cancer cells. Cell 93, 705–716 (1998).

Kramer, N. et al. In vitro cell migration and invasion assays. Mutat. Res. 752, 10–24 (2012).

Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628 (2008).

Feng, J. et al. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics 28, 2782–2788 (2012).