The translational control of oncoprotein expression is implicated in many cancers. Here we report an eIF4A RNA helicase-dependent mechanism of translational control that contributes to oncogenesis and underlies the anticancer effects of silvestrol and related compounds. For example, eIF4A promotes T-cell acute lymphoblastic leukaemia development in vivo and is required for leukaemia maintenance. Accordingly, inhibition of eIF4A with silvestrol has powerful therapeutic effects against murine and human leukaemic cells in vitro and in vivo. We use transcriptome-scale ribosome footprinting to identify the hallmarks of eIF4A-dependent transcripts. These include 5′ untranslated region (UTR) sequences such as the 12-nucleotide guanine quartet (CGG)4 motif that can form RNA G-quadruplex structures. Notably, among the most eIF4A-dependent and silvestrol-sensitive transcripts are a number of oncogenes, superenhancer-associated transcription factors, and epigenetic regulators. Hence, the 5′ UTRs of select cancer genes harbour a targetable requirement for the eIF4A RNA helicase.

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Gene Expression Omnibus

Data deposits

The ribosome footprinting and total mRNA sequencing data have been deposited in the Gene Expression Omnibus database under accession number GSE56887.


  1. 1.

    et al. Survival signalling by Akt and eIF4E in oncogenesis and cancer therapy. Nature 428, 332–337 (2004)

  2. 2.

    , , & mTOR, translation initiation and cancer. Oncogene 25, 6416–6422 (2006)

  3. 3.

    et al. Oncogenic Ras and Akt signaling contribute to glioblastoma formation by differential recruitment of existing mRNAs to polysomes. Mol. Cell 12, 889–901 (2003)

  4. 4.

    , & The mechanism of eukaryotic translation initiation and principles of its regulation. Nature Rev. Mol. Cell Biol. 11, 113–127 (2010)

  5. 5.

    , & Malignant transformation by a eukaryotic initiation factor subunit that binds to mRNA 5′ cap. Nature 345, 544–547 (1990)

  6. 6.

    et al. The translation factor eIF-4E promotes tumor formation and cooperates with c-Myc in lymphomagenesis. Nature Med. 10, 484–486 (2004)

  7. 7.

    et al. Dissecting eIF4E action in tumorigenesis. Genes Dev. 21, 3232–3237 (2007)

  8. 8.

    et al. Tumorigenic activity and therapeutic inhibition of Rheb GTPase. Genes Dev. 22, 2178–2188 (2008)

  9. 9.

    et al. mRNA helicases: the tacticians of translational control. Nature Rev. Mol. Cell Biol. 12, 235–245 (2011)

  10. 10.

    et al. Targeting cap-dependent translation blocks converging survival signals by AKT and PIM kinases in lymphoma. J. Exp. Med. 208, 1799–1807 (2011)

  11. 11.

    et al. Therapeutic suppression of translation initiation modulates chemosensitivity in a mouse lymphoma model. J. Clin. Invest. 118, 2651–2660 (2008)

  12. 12.

    et al. Topology and regulation of the human eIF4A/4G/4H helicase complex in translation initiation. Cell 136, 447–460 (2009)

  13. 13.

    et al. Translational repression and eIF4A2 activity are critical for microRNA-mediated gene regulation. Science 340, 82–85 (2013)

  14. 14.

    , , & Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218–223 (2009)

  15. 15.

    et al. A unifying model for mTORC1-mediated regulation of mRNA translation. Nature 485, 109–113 (2012)

  16. 16.

    et al. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature 485, 55–61 (2012)

  17. 17.

    et al. Mutational loss of PTEN induces resistance to NOTCH1 inhibition in T-cell leukemia. Nature Med. 13, 1203–1210 (2007)

  18. 18.

    et al. c-Myc is an important direct target of Notch1 in T-cell acute lymphoblastic leukemia/lymphoma. Genes Dev. 20, 2096–2109 (2006)

  19. 19.

    et al. Oncogenic IL7R gain-of-function mutations in childhood T-cell acute lymphoblastic leukemia. Nature Genet. 43, 932–939 (2011)

  20. 20.

    et al. Exclusive development of T cell neoplasms in mice transplanted with bone marrow expressing activated Notch alleles. J. Exp. Med. 183, 2283–2291 (1996)

  21. 21.

    et al. Control of eIF4E cellular localization by eIF4E-binding proteins, 4E-BPs. RNA 14, 1318–1327 (2008)

  22. 22.

    , , , & Synthesis of rocaglamide hydroxamates and related compounds as eukaryotic translation inhibitors: synthetic and biological studies. J. Med. Chem. 55, 558–562 (2012)

  23. 23.

    , , , & Rapamycin differentially inhibits S6Ks and 4E-BP1 to mediate cell-type-specific repression of mRNA translation. Proc. Natl Acad. Sci. USA 105, 17414–17419 (2008)

  24. 24.

    , & Detecting differential usage of exons from RNA-seq data. Genome Res. 22, 2008–2017 (2012)

  25. 25.

    et al. Accurate detection of differential RNA processing. Nucleic Acids Res. 41, 5189–5198 (2013)

  26. 26.

    Synthesis of the translational apparatus is regulated at the translational level. Eur. J. Biochem. 267, 6321–6330 (2000)

  27. 27.

    & Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA. Nature 334, 320–325 (1988)

  28. 28.

    DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 27, 1653–1659 (2011)

  29. 29.

    & 5′-UTR RNA G-quadruplexes: translation regulation and targeting. Nucleic Acids Res. 40, 4727–4741 (2012)

  30. 30.

    et al. The RNA helicase RHAU (DHX36) unwinds a G4-quadruplex in human telomerase RNA and promotes the formation of the P1 helix template boundary. Nucleic Acids Res. 40, 4110–4124 (2012)

  31. 31.

    & Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes. DNA Repair (Amst.) 10, 654–665 (2011)

  32. 32.

    et al. ETV6 mutations in early immature human T cell leukemias. J. Exp. Med. 208, 2571–2579 (2011)

  33. 33.

    et al. Evidence for a functionally relevant rocaglamide binding site on the eIF4A-RNA complex. ACS Chem. Biol. 8, 1519–1527 (2013)

  34. 34.

    et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934–947 (2013)

  35. 35.

    , , & Negative autoregulation of c-myc transcription. EMBO J. 9, 1113–1121 (1990)

  36. 36.

    , , & An RNA G-quadruplex in the 5′ UTR of the NRAS proto-oncogene modulates translation. Nature Chem. Biol. 3, 218–221 (2007)

  37. 37.

    , & The BCL-2 5′ untranslated region contains an RNA G-quadruplex-forming motif that modulates protein expression. Biochemistry 49, 8300–8306 (2010)

  38. 38.

    , , , & An RNA G-quadruplex is essential for cap-independent translation initiation in human VEGF IRES. J. Am. Chem. Soc. 132, 17831–17839 (2010)

  39. 39.

    , , & G-quadruplexes: the beginning and end of UTRs. Nucleic Acids Res. 36, 6260–6268 (2008)

  40. 40.

    et al. Small-molecule inhibition of the interaction between the translation initiation factors eIF4E and eIF4G. Cell 128, 257–267 (2007)

  41. 41.

    , , , & Ribavirin suppresses eIF4E-mediated oncogenic transformation by physical mimicry of the 7-methyl guanosine mRNA cap. Proc. Natl Acad. Sci. USA 101, 18105–18110 (2004)

  42. 42.

    , , , & RNA-Seq read alignments with PALMapper. Curr. Protoc. Bioinformatics 32, 11.6.1–11.6.37 (2010)

  43. 43.

    et al. Ensembl 2013. Nucleic Acids Res. 41, D48–D55 (2013)

  44. 44.

    et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013)

  45. 45.

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

  46. 46.

    et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009)

  47. 47.

    , , & Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods 7, 1009–1015 (2010)

  48. 48.

    , & FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017–1018 (2011)

  49. 49.

    Vienna RNA secondary structure server. Nucleic Acids Res. 31, 3429–3431 (2003)

  50. 50.

    et al. C9orf72 hexanucleotide repeat associated with amyotrophic lateral sclerosis and frontotemporal dementia forms RNA G-quadruplexes. Sci. Rep. 2, 1016 (2012)

  51. 51.

    Using circular dichroism collected as a function of temperature to determine the thermodynamics of protein unfolding and binding interactions. Nature Protocols 1, 2527–2535 (2007)

  52. 52.

    et al. A cooperative microRNA-tumor suppressor gene network in acute T-cell lymphoblastic leukemia (T-ALL). Nature Genet. 43, 673–678 (2011)

  53. 53.

    et al. Gain-of-function mutations in interleukin-7 receptor-α (IL7R) in childhood acute lymphoblastic leukemias. J. Exp. Med. 208, 901–908 (2011)

  54. 54.

    et al. The significance of PTEN and AKT aberrations in pediatric T-cell acute lymphoblastic leukemia. Haematologica 97, 1405–1413 (2012)

  55. 55.

    et al. arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays. BMC Bioinformatics 6, 124 (2005)

  56. 56.

    , , , & A cellular response linking eIF4AI activity to eIF4AII transcription. RNA 18, 1373–1384 (2012)

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We thank the members of A.L.W.’s thesis committee: N. Rosen, A. M. Brown and S. W. Lowe. For reagents and advice we thank J. T. Barata, W. S. Pear, R. Cencic, S. Shuman, J. Cools, A. A. Ferrando, C. S. Fraser, N. J. Lajkiewicz, A. Luz, J. F. Glickman, C. Y. Park, P. Yellen, A. Heguy, K. Huberman and A. Viale. H.-G.W. is a Scholar of the Leukemia and Lymphoma Society. This research was supported by National Cancer Institute R01-CA142798-01 (H.-G.W.), the Leukemia Research Foundation (H.-G.W.), the Experimental Therapeutics Center (H.-G.W.), the American Cancer Society 10284 (H.-G.W.), European Union grant no. PITN-GA-2012-316861 (Y.Z.), the Fund for Scientific Research FWO Flanders (J.V.d.M. and P.R.), grants G.0198.08 and G.0869.10N (F.S.), the GOA-UGent 12051203 (F.S.), Stichting tegen Kanker (F.S.), the Belgian Program of Interuniversity Poles of Attraction (F.S.), the Belgian Foundation Against Cancer (F.S.), the American Cancer Society PF-11-077-01-CDD (C.M.R.), the Lymphoma Research Foundation (J.H.S.), National Institutes of Health grants GM-067041 and GM-073855 (J.A.P.), and the Canadian Institutes of Health Research MOP-10653 (J.P.).

Author information

Author notes

    • Andrew L. Wolfe
    •  & Kamini Singh

    These authors contributed equally to this work.

    • Konstantinos J. Mavrakis
    •  & Jonathan H. Schatz

    Present addresses: Novartis, Cambridge, Massachusetts 02139, USA (K.J.M.); The University of Arizona Cancer Center, Tucson, Arizona 85719, USA (J.H.S.).


  1. Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA

    • Andrew L. Wolfe
    • , Kamini Singh
    • , Viraj R. Sanghvi
    • , Konstantinos J. Mavrakis
    • , Man Jiang
    • , Joni Van der Meulen
    • , Jonathan H. Schatz
    • , Chunying Zhao
    •  & Hans-Guido Wendel
  2. Weill Cornell Graduate School of Medical Sciences, New York, New York 10065, USA

    • Andrew L. Wolfe
  3. Computational Biology Department, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA

    • Yi Zhong
    • , Philipp Drewe
    •  & Gunnar Rätsch
  4. Stem Cell Center and Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA

    • Vinagolu K. Rajasekhar
  5. Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 USA

    • Justine E. Roderick
    •  & Michelle A. Kelliher
  6. Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium

    • Joni Van der Meulen
    • , Pieter Rondou
    •  & Frank Speleman
  7. Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA

    • Jonathan H. Schatz
  8. Department of Chemistry, Center for Chemical Methodology and Library Development, Boston University, Boston, Massachusetts 02215, USA

    • Christina M. Rodrigo
    •  & John A. Porco
  9. Molecular Pharmacology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA

    • Elisa de Stanchina
  10. Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA

    • Julie Teruya-Feldstein
  11. Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada

    • Jerry Pelletier
  12. Department of Oncology, McGill University, Montreal, Quebec H3G 1Y6, Canada

    • Jerry Pelletier
  13. The Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec H3G 1Y6, Canada

    • Jerry Pelletier


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A.L.W. performed in vivo and treatment studies; K.S. performed ribosome footprinting and RNA structure studies; Y.Z. and P.D. analysed footprint data; V.K.R., V.R.S., K.J.M., M.J., J.E.R., J.H.S., C.Z., J.T.-F. and M.A.K. contributed to experiments; C.M.R. prepared (±)-CR-31-B; E.d.S. directed murine drug toxicity experiments; J.V.d.M., P.R. and F.S. generated genomic data on T-ALL; J.A.P. Jr and J.P. advised on all aspects of the study; G.R. supervised computational analyses; H.-G.W. designed the study and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Gunnar Rätsch or Hans-Guido Wendel.

Extended data

Supplementary information

Excel files

  1. 1.

    Supplementary Table 1

    Summary of re-sequencing data showing mutation data observed in 36 T-ALL samples.

  2. 2.

    Supplementary Table 2

    The multi-panel table provides results of a detailed analysis of the toxic effects of CR treatment in non-tumour bearing c57/B6 mice. a) Body and organ weights; b) Individual haematology; c) Bone marrow and spleen cytology; d) Individual chemistry.

  3. 3.

    Supplementary Table 3

    a) Genes with decreased Translational Efficiency (TE down); b) Genes with increased Translational Efficiency (TE up); c) Background genes with no change in Translational Efficiency (TE background); d) Complete list of genes that showed a significant change in RF distribution across the length of their transcript (rDiff positive gene set); e) Genes that are both TE down and rDiff positive.

  4. 4.

    Supplementary Table 4

    a-b) Complete lists of TE Down genes that harbour the 12-mer (a) or 9-mer (b) in their 5’UTRs; c-d) Complete lists of rDiff genes that harbour the 12-mer (c) or 9-mer (d) in their 5’UTRs; Prevalence of the TE Down 12-mer motif; e) TE Down genes with one or more predicted G-quadruplex structures; f) rDiff genes with one or more predicted G-quadruplex structures; g-h) Overlap of TE Down 12-mer motif (g) or 9-mer motif (h) with predicted G-quadruplexes. i-j) Overlap of rDiff 12-mer motif (i) or 9-mer motif (j) with predicted G-quadruplexes; k) Nucleotide-level depiction of the overlap between 9-mer motifs and G-quadruplexes. The motif is located at the positions marked X in the sequence. The middle row shows the structure. + represents that it is part of a G-quadruplex, ) ( represents a bond with another nucleotide.

  5. 5.

    Supplementary Table 5

    RNA oligos used for Circular Dichroism (CD) and thermal denaturation analysis. Note: 12-mers or 9-mers are shown in red.

  6. 6.

    Supplementary Table 6

    Overlap of TE down or rDiff genes with reported super-enhancer associated genes in the T-ALL cell lines DND41, JURKAT, or RPMI-840234. '+' indicates presence of one or more 12-mers, 9-mers, or predicted G-quadruplexes in the 5’UTR.

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