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Abstract

Lung cancer is a devastating disease that remains a top cause of cancer mortality. Despite improvements with targeted and immunotherapies, the majority of patients with lung cancer lack effective therapies, underscoring the need for additional treatment approaches. Genomic studies have identified frequent alterations in components of the SWI/SNF chromatin remodeling complex including SMARCA4 and ARID1A. To understand the mechanisms of tumorigenesis driven by mutations in this complex, we developed a genetically engineered mouse model of lung adenocarcinoma by ablating Smarca4 in the lung epithelium. We demonstrate that Smarca4 acts as a bona fide tumor suppressor and cooperates with p53 loss and Kras activation. Gene expression analyses revealed the signature of enhanced oxidative phosphorylation (OXPHOS) in SMARCA4 mutant tumors. We further show that SMARCA4 mutant cells have enhanced oxygen consumption and increased respiratory capacity. Importantly, SMARCA4 mutant lung cancer cell lines and xenograft tumors have marked sensitivity to inhibition of OXPHOS by a novel small molecule, IACS-010759, that is under clinical development. Mechanistically, we show that SMARCA4-deficient cells have a blunted transcriptional response to energy stress creating a therapeutically exploitable synthetic lethal interaction. These findings provide the mechanistic basis for further development of OXPHOS inhibitors as therapeutics against SWI/SNF mutant tumors.

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Acknowledgements

We thank T. Tieu for vector cloning; the MD Anderson core facilities, including the Sequencing and Microarray Facility (SMF), the Non-coding RNA and Sequencing Facility, the Genetically Engineered Mouse Facility (GEMF), S. Jiang and K. Zhao for assistance in maintenance of mouse colonies; T. Gutschner for discussion; and D. Spring for editing. This study was supported by the Cancer Prevention Research Institute (R120501 to P.A.F.) and the Welch Foundation’s Robert A. Welch Distinguished University Chair Award (G-0040 to P.A.F.). F.M. is supported by ACS grant RSG1514501CDD and CPRIT grant RP140612. The results shown here are in part based upon data generated by the TCGA Research Network: http://cancergenome.nih.gov/.

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Affiliations

  1. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

    • Yonathan Lissanu Deribe
    • , Christopher Terranova
    • , Fatima Khan
    • , Juan Martinez-Ledesma
    • , Chia-Chin Wu
    • , Claudia Reyes
    • , Qian Peng
    • , Akira Inoue
    • , Kunal Rai
    •  & P. Andrew Futreal
  2. Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

    • Yuting Sun
    • , Jason Gay
    • , Guang Gao
    • , Robert A. Mullinax
    • , Tin Khor
    • , Ningping Feng
    • , Frederick Robinson
    •  & Joseph Marszalek
  3. Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

    • Yu-Hsi Lin
    •  & Florian Muller
  4. Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

    • Veena Kochat
  5. Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

    • Chang-Gong Liu
  6. Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA

    • John M. Asara
  7. Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

    • Cesar Moran
  8. Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

    • Jing Wang
  9. Department of Thoracic, Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

    • Bingliang Fang
    •  & Vali Papadimitrakopoulou
  10. Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

    • Ignacio I. Wistuba

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Contributions

Y.L.D. designed the studies, performed experiments, interpreted the data and wrote the manuscript. P.A.F. provided intellectual input and wrote the manuscript. Y.S. performed the Seahorse experiments and analysis. F.K. performed the in vitro experiments and mouse genotyping. B.F. generated the PDX model. R.A.M., T.K., J.G. and N.F. conducted the in vivo pharmacology experiments. J.M.-L. and C.-C.W. performed the bioinformatics analysis. C.-G.L. performed the microarray profiling. C.T.,V.K. and K.R. performed the ChIP-seq analysis. Y.-H.L., F.M. and J.M.A. conducted the metabolomics experiment. I.I.W., J.W. and V.P. provided the BATTLE trial expression data. C.M. performed the pathology evaluation of the GEM model tumors. J.M. provided intellectual input. A.I., G.G., C.R., Q.P. and F.R. provided technical support.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Yonathan Lissanu Deribe or P. Andrew Futreal.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1–11

  2. Reporting Summary

  3. Supplementary Table 1

    Gene expression data for SMARCA4 and select OXPHOS genes from the BATTLE-2 lung cancer trial dataset

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https://doi.org/10.1038/s41591-018-0019-5

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