Abstract

Clear cell renal cell carcinoma (ccRCC) is characterized by inactivation of the von Hippel-Lindau tumour suppressor gene (VHL)1,2. Because no other gene is mutated as frequently in ccRCC and VHL mutations are truncal3, VHL inactivation is regarded as the governing event4. VHL loss activates the HIF-2 transcription factor, and constitutive HIF-2 activity restores tumorigenesis in VHL-reconstituted ccRCC cells5. HIF-2 has been implicated in angiogenesis and multiple other processes6,7,8,9, but angiogenesis is the main target of drugs such as the tyrosine kinase inhibitor sunitinib10. HIF-2 has been regarded as undruggable11. Here we use a tumourgraft/patient-derived xenograft platform12,13 to evaluate PT2399, a selective HIF-2 antagonist that was identified using a structure-based design approach. PT2399 dissociated HIF-2 (an obligatory heterodimer of HIF-2α–HIF-1β)14 in human ccRCC cells and suppressed tumorigenesis in 56% (10 out of 18) of such lines. PT2399 had greater activity than sunitinib, was active in sunitinib-progressing tumours, and was better tolerated. Unexpectedly, some VHL-mutant ccRCCs were resistant to PT2399. Resistance occurred despite HIF-2 dissociation in tumours and evidence of Hif-2 inhibition in the mouse, as determined by suppression of circulating erythropoietin, a HIF-2 target15 and possible pharmacodynamic marker. We identified a HIF-2-dependent gene signature in sensitive tumours. Gene expression was largely unaffected by PT2399 in resistant tumours, illustrating the specificity of the drug. Sensitive tumours exhibited a distinguishing gene expression signature and generally higher levels of HIF-2α. Prolonged PT2399 treatment led to resistance. We identified binding site and second site suppressor mutations in HIF-2α and HIF-1β, respectively. Both mutations preserved HIF-2 dimers despite treatment with PT2399. Finally, an extensively pretreated patient whose tumour had given rise to a sensitive tumourgraft showed disease control for more than 11 months when treated with a close analogue of PT2399, PT2385. We validate HIF-2 as a target in ccRCC, show that some ccRCCs are HIF-2 independent, and set the stage for biomarker-driven clinical trials.

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Acknowledgements

We thank the patients who generously provided tissues and participated in our studies. PT2399 was provided by Peloton Therapeutics, Inc. Funding was provided by Peloton Therapeutics, Inc. (OTD-105466), CPRIT (RP160440) and philanthropy, including the Tom Green memorial. W.C. is supported by grants from the National Natural Science Foundation of China (No. 811011934) and the Science and Technology Program of Guangzhou, China (No. 2012J5100031). M.S.K. and H.Z. are supported by a grant from CPRIT (RP150596). I.P. is supported by grants from the NIH (R01CA154475, P50CA196516). X.S. is supported by a grant from CPRIT (RP110771). J.B. is a Virginia Murchison Linthicum endowed scholar and is supported by grants from the NIH (R01CA175754, P50CA196516, P30CA142543) and CPRIT (RP130603). R.K.B. is the Michael L. Rosenberg Scholar in Medical Research and was supported by CPRIT (RP130513). Histology equipment was purchased with funding from the National Center for Advancing Translational Sciences (Center for Translational Medicine UL1TR001105).

Author information

Author notes

    • Wenfang Chen
    • , Haley Hill
    • , Alana Christie
    •  & Min Soo Kim

    These authors contributed equally to this work.

Affiliations

  1. Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.

    • Wenfang Chen
    • , Haley Hill
    • , Alana Christie
    • , Min Soo Kim
    • , Eboni Holloman
    • , Andrea Pavia-Jimenez
    • , Farrah Homayoun
    • , Yuanqing Ma
    • , Nirav Patel
    • , Qurratulain Yousuf
    • , Allison Joyce
    • , Ivan Pedrosa
    • , He Zhang
    • , Jenny Chang
    • , Richard K. Bruick
    • , Tae Hyun Hwang
    • , Kevin Courtney
    • , Eugene Frenkel
    • , Xiankai Sun
    • , Yang Xie
    • , Xian-Jin Xie
    • , Payal Kapur
    • , Renée M. McKay
    •  & James Brugarolas
  2. Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.

    • Wenfang Chen
    • , Haley Hill
    • , Eboni Holloman
    • , Andrea Pavia-Jimenez
    • , Farrah Homayoun
    • , Yuanqing Ma
    • , Nirav Patel
    • , Qurratulain Yousuf
    • , Allison Joyce
    • , Kevin Courtney
    • , Eugene Frenkel
    • , Renée M. McKay
    •  & James Brugarolas
  3. Department of Pathology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, People’s Republic of China.

    • Wenfang Chen
  4. Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.

    • Min Soo Kim
    • , He Zhang
    • , Tae Hyun Hwang
    • , Yang Xie
    •  & Xian-Jin Xie
  5. Parkland Health and Hospital System, Dallas, Texas 75235, USA.

    • Paul Yell
  6. Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.

    • Guiyang Hao
    • , Ivan Pedrosa
    •  & Xiankai Sun
  7. New York Genome Center, New York, New York 10013, USA.

    • Heather Geiger
    •  & Catherine Reeves
  8. Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York 10031, USA.

    • Kevin H. Gardner
  9. Department of Chemistry and Biochemistry, City College of New York, New York, New York 10031, USA.

    • Kevin H. Gardner
  10. Biochemistry, Chemistry and Biology Ph.D. Programs, Graduate Center, City University of New York, New York, New York 10016, USA.

    • Kevin H. Gardner
  11. Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.

    • Richard K. Bruick
  12. Peloton Therapeutics Inc., Dallas, Texas 75235, USA.

    • Naseem Zojwalla
    • , Tai Wong
    • , James P. Rizzi
    • , Eli M. Wallace
    •  & John A. Josey
  13. Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.

    • Payal Kapur

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Contributions

W.C. designed and performed biochemical experiments; H.H., E.H., A.P.-J., Q.Y., and A.J. performed tumourgraft experiments; A.C. performed extensive statistical analyses with the supervision of X.-J.X.; M.S.K. performed RNA-seq analyses under the supervision of T.H.H. and Y.X., who also supervised H.Z. on sequencing analysis; Y.M. and N.P. performed experiments; F.H. and P.Y. performed histological analyses under the supervision of P.K.; G.H. performed PET studies under the supervision of X.S.; I.P. performed patient imaging analyses; H.G. and C.R. performed RNA-seq validation studies at the New York Genome Center; J.C. is the clinical research coordinator of the PT2385 phase 1 trial overseen by K.C. and N.Z.; K.H.G., R.K.B., and E.F. participated in discussions; T.W., J.P.R., E.M.W., and J.A.J. oversaw the development and characterization of PT2399 and provided the drug; R.M.M. assisted with manuscript preparation, writing and submission; and J.B. conceived and supervised the project, and wrote the manuscript with input from R.M.M. and the other authors.

Competing interests

T.W., J.P.R., E.M.W., N.Z. and J.A.J. are employees and own equity in Peloton Therapeutics, Inc. and K.H.G. and R.K.B. have licensed intellectual property, consult for and own equity in Peloton Therapeutics, Inc. M.S.K., T.H.H, Y.X. and J.B. are authors on a filed patent pertaining to a biomarker of PT2399. J.B. is a member of the advisory board for Bethyl Laboratories.

Corresponding author

Correspondence to James Brugarolas.

RNAseq was released to NCBI Sequence Read Archive (SRA). ID: SRP073253.

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    Supplementary Information

    This file contains Supplementary Figure 1(gel source data) and Supplementary Figure 2 (Tumor dimensions).

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https://doi.org/10.1038/nature19796

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