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DNA damage-induced cell death relies on SLFN11-dependent cleavage of distinct type II tRNAs



Transcriptome analysis reveals a strong positive correlation between human Schlafen family member 11 (SLFN11) expression and the sensitivity of tumor cells to DNA-damaging agents (DDAs). Here, we show that SLFN11 preferentially inhibits translation of the serine/threonine kinases ATR and ATM upon DDA treatment based on distinct codon usage without disrupting early DNA damage response signaling. Type II transfer RNAs (tRNAs), which include all serine and leucine tRNAs, are cleaved in a SLFN11-dependent manner in response to DDAs. Messenger RNAs encoded by genes with high TTA (Leu) codon usage, such as ATR, display utmost susceptibility to translational suppression by SLFN11. Specific attenuation of tRNA-Leu-TAA sufficed to ablate ATR protein expression and restore the DDA sensitivity of SLFN11-deficient cells. Our study uncovered a novel mechanism of codon-specific translational inhibition via SLFN11-dependent tRNA cleavage in the DNA damage response and supports the notion that SLFN11-deficient tumor cells can be resensitized to DDAs by targeting ATR or tRNA-Leu-TAA.

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Fig. 1: SLFN11 selectively inhibits ATR/ATM protein expression and sensitizes cells to death on treatment with DDAs.
Fig. 2: Selective inhibition of ATR sensitizes SLFN11-deficient cells to CPT treatment.
Fig. 3: SLFN11 selectively inhibits ATR protein synthesis on CPT treatment.
Fig. 4: CRISPR–Cas9 mediated SLFN11 gene knockout confers significant resistance to CPT-induced apoptosis on cells without affecting cell proliferation.
Fig. 5: SLFN11 mediates the downregulation of type II tRNAs on DDA treatment.
Fig. 6: SLFN11-mediated type II tRNAs cleavage inhibits mRNA translation of genes with high frequency of codon TTA (Leu) usage.
Fig. 7: Ablation of tRNA-Leu-TAA via gapmer antisense oligonucleotides resensitizes SLFN11-deficient FG cells to CPT-induced apoptosis.
Fig. 8: Gapmer antisense oligonucleotides directed at tRNA-Leu-TAA sensitize intrinsically SLFN11-deficient MIA PaCa-2 cells to CPT-induced apoptosis.

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All data generated and analyzed in this study are available with the paper online.


  1. Li, M. et al. Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11. Nature 491, 125–128 (2012).

    Article  CAS  Google Scholar 

  2. Zoppoli, G. et al. Putative DNA/RNA helicase Schlafen-11 (SLFN11) sensitizes cancer cells to DNA-damaging agents. Proc. Natl Acad. Sci. USA 109, 15030–15035 (2012).

    Article  CAS  Google Scholar 

  3. Barretina, J. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603–607 (2012).

    Article  CAS  Google Scholar 

  4. Schwarz, D. A., Katayama, C. D. & Hedrick, S. M. Schlafen, a new family of growth regulatory genes that affect thymocyte development. Immunity 9, 657–668 (1998).

    Article  CAS  Google Scholar 

  5. Bustos, O. et al. Evolution of the Schlafen genes, a gene family associated with embryonic lethality, meiotic drive, immune processes and orthopoxvirus virulence. Gene 447, 1–11 (2009).

    Article  CAS  Google Scholar 

  6. Sharp, P. M. & Li, W. H. The codon Adaptation Index: a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15, 1281–1295 (1987).

    Article  CAS  Google Scholar 

  7. Puigbò, P., Bravo, I. G. & Garcia-Vallve, S. CAIcal: a combined set of tools to assess codon usage adaptation. Biol. Direct. 3, 38 (2008).

    Article  Google Scholar 

  8. Jalal, S., Earley, J. N. & Turchi, J. J. DNA repair: from genome maintenance to biomarker and therapeutic target. Clin. Cancer Res. 17, 6973–6984 (2011).

    Article  CAS  Google Scholar 

  9. Brown, J. S., O’Carrigan, B., Jackson, S. P. & Yap, T. A. Targeting DNA repair in cancer: beyond PARP inhibitors. Cancer Discov. 7, 20–37 (2017).

    Article  CAS  Google Scholar 

  10. Beck, M. et al. The quantitative proteome of a human cell line. Mol. Syst. Biol. 7, 549 (2011).

    Article  Google Scholar 

  11. Blackford, A. N. & Jackson, S. P. ATM, ATR, and DNA-PK: the trinity at the heart of the DNA damage response. Mol. Cell 66, 801–817 (2017).

    Article  CAS  Google Scholar 

  12. Cimprich, K. A. & Cortez, D. ATR: an essential regulator of genome integrity. Nat. Rev. Mol. Cell Biol. 9, 616–627 (2008).

    Article  CAS  Google Scholar 

  13. Morgan, R. T. et al. Human cell line (COLO 357) of metastatic pancreatic adenocarcinoma. Int. J. Cancer 25, 591–598 (1980).

    Article  CAS  Google Scholar 

  14. Chan, P. P. & Lowe, T. M. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 37, D93–D97 (2009).

    Article  CAS  Google Scholar 

  15. Chan, P. P. & Lowe, T. M. GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucleic Acids Res. 44, D184–D189 (2016).

    Article  CAS  Google Scholar 

  16. Zheng, G. et al. Efficient and quantitative high-throughput tRNA sequencing. Nat. Methods 12, 835–837 (2015).

    Article  CAS  Google Scholar 

  17. Cozen, A. E. et al. ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. Nat. Methods 12, 879–884 (2015).

    Article  CAS  Google Scholar 

  18. Hinnebusch, A. G. Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes. Microbiol. Mol. Biol. Rev. 75, 434–467 (2011).

    Article  CAS  Google Scholar 

  19. Kolitz, S. E. & Lorsch, J. R. Eukaryotic initiator tRNA: finely tuned and ready for action. FEBS Lett. 584, 396–404 (2010).

    Article  CAS  Google Scholar 

  20. Grünweller, A. et al. Comparison of different antisense strategies in mammalian cells using locked nucleic acids, 2′-O-methyl RNA, phosphorothioates and small interfering RNA. Nucleic Acids Res. 31, 3185–3193 (2003).

    Article  Google Scholar 

  21. Kurreck, J., Wyszko, E., Gillen, C. & Erdmann, V. A. Design of antisense oligonucleotides stabilized by locked nucleic acids. Nucleic Acids Res. 30, 1911–1918 (2002).

    Article  CAS  Google Scholar 

  22. Cheung-Ong, K., Giaever, G. & Nislow, C. DNA-damaging agents in cancer chemotherapy: serendipity and chemical biology. Chem. Biol. 20, 648–659 (2013).

    Article  CAS  Google Scholar 

  23. Gardner, E. E. et al. Chemosensitive relapse in small cell lung cancer proceeds through an EZH2-SLFN11 axis. Cancer Cell 31, 286–299 (2017).

    Article  CAS  Google Scholar 

  24. Mu, Y. et al. SLFN11 inhibits checkpoint maintenance and homologous recombination repair. EMBO Rep. 17, 94–109 (2016).

    Article  CAS  Google Scholar 

  25. Murai, J. et al. SLFN11 blocks stressed replication forks independently of ATR. Mol. Cell 69, 371–384.e6 (2018).

    Article  CAS  Google Scholar 

  26. Pisareva, V. P., Muslimov, I. A., Tcherepanov, A. & Pisarev, A. V. Characterization of novel ribosome-associated endoribonuclease SLFN14 from rabbit reticulocytes. Biochemistry 54, 3286–3301 (2015).

    Article  CAS  Google Scholar 

  27. Yang, J. Y. et al. Structure of Schlafen13 reveals a new class of tRNA/rRNA- targeting RNase engaged in translational control. Nat. Commun. 9, 1165 (2018).

    Article  Google Scholar 

  28. Hopper, A. K. & Huang, H. Y. Quality control pathways for nucleus-encoded eukaryotic tRNA biosynthesis and subcellular trafficking. Mol. Cell. Biol. 35, 2052–2058 (2015).

    Article  CAS  Google Scholar 

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The authors wish to thank R. Lardelli and M. Arribas-Layton for assistance with northern blot and polysome profile analyses. This work was supported by grants R01-GM101982 and R21-AI124199 to M.D.

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Authors and Affiliations



M.L., J.Y.W. and M.D. conceived the experiments. E.K. and X.G. performed the cell viability studies, ATR experiments and polysome analysis. M.L., X.G. and D.M. are responsible for all tRNA data and codon usage studies. M.L. and X.G. designed and performed all gapmer related studies. M.L., E.K. and D.M. generated the figures. M.L. and M.D. wrote the manuscript.

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Correspondence to Manqing Li or Michael David.

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Supplementary information

Supplementary Tables

Supplementary Tables 1–6

Reporting Summary

Supplementary Dataset 1

Uncropped blots

Supplementary Dataset 2

Source data for Fig. 6a

Supplementary Dataset 3

Source data for Fig. 6b

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Li, M., Kao, E., Malone, D. et al. DNA damage-induced cell death relies on SLFN11-dependent cleavage of distinct type II tRNAs. Nat Struct Mol Biol 25, 1047–1058 (2018).

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