mRNA CD95/Fas ligand có khả năng độc hại đối với tế bào thông qua nhiều cơ chế khác nhau

Ashley Haluck-Kangas1, Madelaine Fink1, Elizabeth Bartom2, Peter Marynen1
1Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Chicago, IL, USA
2Department of Biochemistry and Molecular Genetics, Chicago, IL, USA

Tóm tắt

Tóm tắtCD95/Fas ligand (CD95L) kích thích quá trình apoptosis thông qua sự liên kết protein với thụ thể CD95. Tuy nhiên, mRNA CD95L cũng gây độc cho tế bào mà không cần có CD95, thông qua việc kích thích DISE (Chết do loại bỏ gen sinh tồn), một hình thức chết tế bào được trung gian bởi sự can thiệp RNA (RNAi). Chúng tôi báo cáo rằng quá trình xử lý mRNA CD95L tạo ra một loại RNA ngắn (s)RNA gần như đồng nhất với shL3, một loại shRNA nhắm vào CD95L thương mại đã dẫn đến sự phát hiện của DISE. Cả hai protein sinh tổng hợp miRNA, Drosha và Dicer, đều không cần thiết cho quá trình xử lý này. Thú vị thay, khả năng độc hại của CD95L phụ thuộc vào thành phần cốt lõi của RISC, Ago2, ở một số dòng tế bào, nhưng không ở những dòng khác. Trong dòng tế bào ung thư đại tràng HCT116, Ago 1–4 dường như hoạt động lặp lại trong RNAi. Trên thực tế, các tế bào knockout Ago 1/2/3 vẫn giữ được độ nhạy với độc tính của mRNA CD95L. Sự độc hại chỉ bị chặn lại khi có đột biến tất cả các codon khởi đầu khung đọc trong ORF của CD95L. Các tế bào đang chết cho thấy sự gia tăng RISC bị liên kết với các (R)-sRNAs có chuỗi hạt độc hại 6mer, trong khi biểu hiện của đột biến CD95L không độc hại lại gia tăng việc nạp các R-sRNAs có chuỗi hạt không độc hại 6mer. Tuy nhiên, CD95L không phải là nguồn duy nhất của các R-sRNAs này. Chúng tôi phát hiện rằng mRNA CD95L có thể kích thích DISE một cách trực tiếp và gián tiếp, và rằng các cơ chế khác nhau có thể liên quan đến quá trình xử lý và độc tính của mRNA CD95L.

Từ khóa


Tài liệu tham khảo

Schneider P, Bodmer JL, Holler N, Mattmann C, Scuderi P, Terskikh A, et al. Characterization of Fas (Apo-1, CD95)-Fas ligand interaction. J Biol Chem. 1997;272:18827–33. https://doi.org/10.1074/jbc.272.30.18827.

Algeciras-Schimnich A, Shen L, Barnhart BC, Murmann AE, Burkhardt JK, Peter ME. Molecular ordering of the initial signaling events of CD95. Mol Cell Biol. 2002;22:207–20. https://doi.org/10.1128/MCB.22.1.207-220.2002.

Nagata S. Apoptosis by death factor. Cell. 1997;88:355–65. https://doi.org/10.1016/s0092-8674(00)81874-7.

Fulda S, Scaffidi C, Pietsch T, Krammer PH, Peter ME, Debatin KM. Activation of the CD95 (APO-1/Fas) pathway in drug- and gamma-irradiation-induced apoptosis of brain tumor cells. Cell Death Differ. 1998;5:884–93. https://doi.org/10.1038/sj.cdd.4400419.

Muller M, Strand S, Hug H, Heinemann EM, Walczak H, Hofmann WJ, et al. Drug-induced apoptosis in hepatoma cells is mediated by the CD95 (APO-1/Fas) receptor/ligand system and involves activation of wild-type p53. J Clin Invest. 1997;99:403–13. https://doi.org/10.1172/JCI119174.

Friesen C, Herr I, Krammer PH, Debatin KM. Involvement of the CD95 (APO-1/FAS) receptor/ligand system in drug-induced apoptosis in leukemia cells. Nat Med. 1996;2:574–7.

Muller M, Wilder S, Bannasch D, Israeli D, Lehlbach K, Li-Weber M, et al. p53 activates the CD95 (APO-1/Fas) gene in response to DNA damage by anticancer drugs. J Exp Med. 1998;188:2033–45.

Kischkel FC, Hellbardt S, Behrmann I, Germer M, Pawlita M, Krammer PH, et al. Cytotoxicity-dependent APO-1 (Fas/CD95)-associated proteins form a death-inducing signaling complex (DISC) with the receptor. EMBO J. 1995;14:5579–88. https://doi.org/10.1002/j.1460-2075.1995.tb00245.x.

Muzio M, Chinnaiyan AM, Kischkel FC, O’Rourke K, Shevchenko A, Ni J, et al. FLICE, a novel FADD-homologous ICE/CED-3-like protease, is recruited to the CD95 (Fas/APO-1) death-inducing signaling complex. Cell. 1996;85:817–27. https://doi.org/10.1016/s0092-8674(00)81266-0.

Gao QQ, Putzbach WE, Murmann AE, Chen S, Ambrosini G, Peter JM, et al. 6mer seed toxicity in tumor suppressive miRNAs. Nature Comm. 2018;9:4504. https://doi.org/10.1038/s41467-018-06526-1.

Putzbach W, Gao QQ, Patel M, van Dongen S, Haluck-Kangas A, Sarshad AA, et al. Many si/shRNAs can kill cancer cells by targeting multiple survival genes through an off-target mechanism. eLife. 2017;6:e29702. https://doi.org/10.7554/eLife.29702.

Hadji A, Ceppi P, Murmann AE, Brockway S, Pattanayak A, Bhinder B, et al. Death induced by CD95 or CD95 ligand elimination. Cell Rep. 2014;7:208–22. https://doi.org/10.1016/j.celrep.2014.02.035.

Patel M, Bartom ET, Paudel B, Kocherginsky M, O’Shea KL, Murmann AE, et al. Identification of the toxic 6mer seed consensus in human cancer cells. Sci Rep. 2022;12:5130. https://doi.org/10.1038/s41598-022-09051-w.

Bartom ET, Kocherginsky M, Baudel B, Vaidyanathan A, Haluck-Kangas A, Patel M, et al. SPOROS: A pipeline to analyze DISE/6mer seed toxicity. PLOS Comp Biol. 2021;18:e1010022. https://doi.org/10.1371/journal.pcbi.1010022.

Patel M, Wang Y, Bartom ET, Dhir R, Nephew KP, Adli M, et al. The ratio of toxic-to-nontoxic microRNAs predicts platinum sensitivity in ovarian cancer. Can Res. 2021;81:385–4000. https://doi.org/10.1158/0008-5472.CAN-21-0953.

Putzbach W, Haluck-Kangas A, Gao QQ, Sarshad AA, Bartom ET, Stults A, et al. CD95/Fas ligand mRNA is toxic to cells. eLife. 2018;7:e38621. https://doi.org/10.7554/eLife.38621.

Wang D, Zhang Z, O’Loughlin E, Lee T, Houel S, O’Carroll D, et al. Quantitative functions of Argonaute proteins in mammalian development. Genes Dev. 2012;26:693–704. https://doi.org/10.1101/gad.182758.111.

Haluck-Kangas A, Patel M, Paudel B, Vaidyanathan A, Murmann AE, Peter MP. DISE/6mer Seed Toxicity - a powerful anti-cancer mechanism with implications for other diseases. J Exp Clin Cancer Res. 2021;40:389. https://doi.org/10.1186/s13046-021-02177-1.

Rybak-Wolf A, Jens M, Murakawa Y, Herzog M, Landthaler M, Rajewsky N. A variety of dicer substrates in human and C. elegans. Cell. 2014;159:1153–67. https://doi.org/10.1016/j.cell.2014.10.040.

Luo QJ, Zhang J, Li P, Wang Q, Zhang Y, Roy-Chaudhuri B, et al. RNA structure probing reveals the structural basis of Dicer binding and cleavage. Nat Commun. 2021;12:3397. https://doi.org/10.1038/s41467-021-23607-w.

Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JW, et al. Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA. 2009;15:2147–60. https://doi.org/10.1261/rna.1738409.

Landthaler M, Gaidatzis D, Rothballer A, Chen PY, Soll SJ, Dinic L, et al. Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA. 2008;14:2580–96. https://doi.org/10.1261/rna.1351608.

Hauptmann J, Kater L, Loffler P, Merkl R, Meister G. Generation of catalytic human Ago4 identifies structural elements important for RNA cleavage. RNA. 2014;20:1532–8. https://doi.org/10.1261/rna.045203.114.

Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science. 2004;305:1437–41. https://doi.org/10.1126/science.1102513.

Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G, Tuschl T. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol Cell. 2004;15:185–97. https://doi.org/10.1016/j.molcel.2004.07.007.

Chu Y, Kilikevicius A, Liu J, Johnson KC, Yokota S, Corey DR. Argonaute binding within 3’-untranslated regions poorly predicts gene repression. Nucleic Acids Res. 2020;48:7439–53. https://doi.org/10.1093/nar/gkaa478.

Popp MW, Maquat LE. Nonsense-mediated mRNA Decay and Cancer. Curr Opin Genet Dev. 2018;48:44–50. https://doi.org/10.1016/j.gde.2017.10.007.

Paudel B, Jeong SY, Pena Martinez C, Rickman A, Haluck-Kangas A, T. BE, et al. Death induced by survival gene elimination (DISE) contributes to neurotoxicity in Alzheimer's disease. 2022; https://www.biorxiv.org/content/10.1101/2022.09.08.507157v1.

Vaidyanathan A, Taylor HE, Hope TJ, D’Aquilla RT, Bartom ET, Hultquist JF, et al. Contribution of 6mer seed toxicity to HIV-1 induced cytopacitity. 2022; https://www.biorxiv.org/content/10.1101/2022.09.08.507157v1.

Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, et al. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science. 2010;328:1694–8. https://doi.org/10.1126/science.1190809.

Cheloufi S, Dos Santos CO, Chong MM, Hannon GJ. A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature. 2010;465:584–9. https://doi.org/10.1038/nature09092.

Su H, Trombly MI, Chen J, Wang X. Essential and overlapping functions for mammalian Argonautes in microRNA silencing. Genes Dev. 2009;23:304–17. https://doi.org/10.1101/gad.1749809.

Adiliaghdam F, Basavappa M, Saunders TL, Harjanto D, Prior JT, Cronkite DA, et al. A requirement for Argonaute 4 in mammalian antiviral defense. Cell Rep. 2020;30:1690-1701.e4. https://doi.org/10.1016/j.celrep.2020.01.021.

Modzelewski AJ, Holmes RJ, Hilz S, Grimson A, Cohen PE. AGO4 regulates entry into meiosis and influences silencing of sex chromosomes in the male mouse germline. Dev Cell. 2012;23:251–64. https://doi.org/10.1016/j.devcel.2012.07.003.

Ruda VM, Chandwani R, Sehgal A, Bogorad RL, Akinc A, Charisse K, et al. The roles of individual mammalian argonautes in RNA interference in vivo. PLoS One. 2014;9:e101749. https://doi.org/10.1371/journal.pone.0101749.

Houseley J, Tollervey D. The many pathways of RNA degradation. Cell. 2009;136:763–76. https://doi.org/10.1016/j.cell.2009.01.019.

Pule MN, Glover ML, Fire AZ, Arribere JA. Ribosome clearance during RNA interference. RNA. 2019;25:963–74. https://doi.org/10.1261/rna.070813.119.

Ibrahim F, Maragkakis M, Alexiou P, Mourelatos Z. Ribothrypsis, a novel process of canonical mRNA decay, mediates ribosome-phased mRNA endonucleolysis. Nat Struct Mol Biol. 2018;25:302–10. https://doi.org/10.1038/s41594-018-0042-8.

Glover ML, Burroughs AM, Monem PC, Egelhofer TA, Pule MN, Aravind L, et al. NONU-1 Encodes a Conserved Endonuclease Required for mRNA Translation Surveillance. Cell Rep. 2020;30:4321-4331.e4. https://doi.org/10.1016/j.celrep.2020.03.023.

D'Orazio KN, Wu CC, Sinha N, Loll-Krippleber R, Brown GW and Green R. The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during No Go Decay. Elife. 2019;8. https://doi.org/10.7554/eLife.49117.

Tuck AC, Rankova A, Arpat AB, Liechti LA, Hess D, Iesmantavicius V, et al. Mammalian RNA decay pathways are highly specialized and widely linked to translation. Mol Cell. 2020;77:1222-1236.e13. https://doi.org/10.1016/j.molcel.2020.01.007.

Behm-Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P, Izaurralde E. mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev. 2006;20:1885–98. https://doi.org/10.1101/gad.1424106.

Rehwinkel J, Behm-Ansmant I, Gatfield D, Izaurralde E. A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing. RNA. 2005;11:1640–7. https://doi.org/10.1261/rna.2191905.

Hashimoto Y, Takahashi M, Sakota E, Nakamura Y. Nonstop-mRNA decay machinery is involved in the clearance of mRNA 5’-fragments produced by RNAi and NMD in Drosophila melanogaster cells. Biochem Biophys Res Commun. 2017;484:1–7. https://doi.org/10.1016/j.bbrc.2017.01.092.

Orban TI, Izaurralde E. Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome. RNA. 2005;11:459–69. https://doi.org/10.1261/rna.7231505.

Lima WF, De Hoyos CL, Liang XH, Crooke ST. RNA cleavage products generated by antisense oligonucleotides and siRNAs are processed by the RNA surveillance machinery. Nucleic Acids Res. 2016;44:3351–63. https://doi.org/10.1093/nar/gkw065.

Algeciras-Schimnich A, Pietras EM, Barnhart BC, Legembre P, Vijayan S, Holbeck SL, et al. Two CD95 tumor classes with different sensitivities to antitumor drugs. Proc Natl Acad Sci U S A. 2003;100:11445–50. https://doi.org/10.1073/pnas.2034995100.

Golden RJ, Chen B, Li T, Braun J, Manjunath H, Chen X, et al. An Argonaute phosphorylation cycle promotes microRNA-mediated silencing. Nature. 2017;542:197–202. https://doi.org/10.1038/nature21025.

Hauptmann J, Schraivogel D, Bruckmann A, Manickavel S, Jakob L, Eichner N, et al. Biochemical isolation of Argonaute protein complexes by Ago-APP. Proc Natl Acad Sci U S A. 2015;112:11841–5. https://doi.org/10.1073/pnas.1506116112.

Hafner M, Renwick N, Farazi TA, Mihailovic A, Pena JT, Tuschl T. Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing. Methods. 2012;58:164–70. https://doi.org/10.1016/j.ymeth.2012.07.030.

Lorenz R, Bernhart SH, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, et al. ViennaRNA Package 2.0. Algorithms Mol Biol. 2011;6:26. https://doi.org/10.1186/1748-7188-6-26.

Hulsen T, de Vlieg J, Alkema W. BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. BMC Genomics. 2008;9:488. https://doi.org/10.1186/1471-2164-9-488.

da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44–57. https://doi.org/10.1038/nprot.2008.211.

Sherman BT, Hao M, Qiu J, Jiao X, Baseler MW, Lane HC, et al. DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Res. 2022. https://doi.org/10.1093/nar/gkac194.