Abstract

Mesenchymal tumor subpopulations secrete pro-tumorigenic cytokines and promote treatment resistance1,2,3,4. This phenomenon has been implicated in chemorefractory small cell lung cancer and resistance to targeted therapies5,6,7,8, but remains incompletely defined. Here, we identify a subclass of endogenous retroviruses (ERVs) that engages innate immune signaling in these cells. Stimulated 3 prime antisense retroviral coding sequences (SPARCS) are oriented inversely in 3′ untranslated regions of specific genes enriched for regulation by STAT1 and EZH2. Derepression of these loci results in double-stranded RNA generation following IFN-γ exposure due to bi-directional transcription from the STAT1-activated gene promoter and the 5′ long terminal repeat of the antisense ERV. Engagement of MAVS and STING activates downstream TBK1, IRF3, and STAT1 signaling, sustaining a positive feedback loop. SPARCS induction in human tumors is tightly associated with major histocompatibility complex class 1 expression, mesenchymal markers, and downregulation of chromatin modifying enzymes, including EZH2. Analysis of cell lines with high inducible SPARCS expression reveals strong association with an AXL/MET-positive mesenchymal cell state. While SPARCS-high tumors are immune infiltrated, they also exhibit multiple features of an immune-suppressed microenviroment. Together, these data unveil a subclass of ERVs whose derepression triggers pathologic innate immune signaling in cancer, with important implications for cancer immunotherapy.

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Acknowledgements

We thank J. Albanell, A. Rovira, and E. Arriola (Hospital del Mar Medical Research Institute, Barcelona, Spain) for providing human SCLC cell lines and the H69/H69M cell model. We also thank W.G. Kaelin, Jr. (Dana–Farber Cancer Institute, Boston, MA) for providing human ccRCC cell lines. This work was supported by NCI-R01 CA190394-02 and NIH-U01 CA2143A1-01 (D.A.B.), the Gloria T. Maheu, Steven J. Schaubert, and Heerwagen Family Funds for Lung Cancer Research (D.A.B.), the Rising Tide Foundation (D.A.B.), NIH-U01 CA217885 (J.W.K., P.T.), NIH/NCI P01CA120964 (K.K.W.), 5R01CA163896-04 (K.K.W.), 5R01CA140594-07 (K.K.W.), 5R01CA122794-10 (K.K.W.), 5R01CA166480-04 (K.K.W.), the Gross-Loh Family Fund for Lung Cancer Research (K.K.W., D.A.B.), and the Susan Spooner Family Lung Cancer Research Fund at Dana–Farber Cancer Institute (K.K.W.). Additional funding was provided by NIH grants P01 CA114046, P01 CA025874, P30 CA010815, and R01 CA047159 and by the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation and the Melanoma Research Foundation. The support for Shared Resources used in this study was provided by Cancer Center Support Grant CA010815 (to The Wistar Institute). Additional support from a Stand Up To Cancer–American Cancer Society Lung Cancer Dream Team Translational Research Grant (SU2CAACR-DT1715). Stand Up to Cancer is a program of the Entertainment Industry Foundation. Research grants are administered by the American Association for Cancer Research, the Scientific Partner of SU2C. R.T. is a Howard Hughes Medical Institute Medical Research Fellow.

Author information

Author notes

  1. These authors contributed equally to this work: Rohit Thummalapalli, Jong Wook Kim.

Affiliations

  1. Department of Medical Oncology, Dana–Farber Cancer Institute, Boston, MA, USA

    • Israel Cañadas
    • , Rohit Thummalapalli
    • , Jong Wook Kim
    • , Shunsuke Kitajima
    • , Russell William Jenkins
    • , Camilla Laulund Christensen
    • , Marco Campisi
    • , Yanxi Zhang
    • , Diana Miao
    • , Tran Thai
    • , Brandon Piel
    • , Hideki Terai
    • , Anika Elise Adeni
    • , Christine Anne Lydon
    • , Thanh Uyen Barbie
    • , Ravindra Uppaluri
    • , Jacob Sands
    • , Kwok Kin Wong
    •  & David Allen Barbie
  2. Broad Institute of Harvard and MIT, Cambridge, MA, USA

    • Jong Wook Kim
    •  & Diana Miao
  3. Division of Medical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA

    • Russell William Jenkins
  4. Belfer Institute for Applied Cancer Science, Dana–Farber Cancer Institute, Boston, MA, USA

    • Yanan Kuang
    • , Amir Reza Aref
    •  & Cloud Peter Paweletz
  5. Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA

    • Evisa Gjini
    • , Lynnette Marie Sholl
    •  & Scott Rodig
  6. Melanoma Research Center and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA

    • Gao Zhang
    •  & Meenhard Herlyn
  7. Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA

    • Tian Tian
    •  & Zhi Wei
  8. Department of Pediatric Oncology, Dana–Farber Cancer Institute, Boston, MA, USA

    • Debattama Rai. Sen
  9. Gastroenterological Surgery, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan

    • Yu Imamura
    •  & Masayuki Watanabe
  10. Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan

    • Yu Imamura
    •  & Hideo Baba
  11. Department of Oncologic Pathology, Dana–Farber Cancer Institute, Boston, MA, USA

    • Timothy Hagan
    •  & Ewa Sicinska
  12. Department of Respiratory Medicine, Allergy and Rheumatic Diseases, Osaka University Graduate School of Medicine, Osaka, Japan

    • Shohei Koyama
  13. Moores Cancer Center and School of Medicine, University of California San Diego, La Jolla, CA, USA

    • Pablo Tamayo
  14. Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA

    • Thanh Uyen Barbie
    •  & Ravindra Uppaluri
  15. Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA

    • Kwok Kin Wong
  16. Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA

    • Hideo Watanabe
  17. Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA

    • Hideo Watanabe

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Contributions

I.C. and D.A.B. designed the research and wrote the manuscript. J.W.K., G.Z., T.Ti., D.M., P.T., Z.W., M.H., and H.W. performed and supervised computational analyses. I.C., R.T., S.Ki., R.W.J., M.C., T.Th., B.P., H.T., A.R.A., S.Ko., T.U.B., R.U., K.K.W., and D.A.B. performed and supervised biological and cellular studies. C.L.C., Y.I., T.H., M.W., H.B., A.E.A., C.A.L., L.M.S., E.S., and J.S. obtained samples and performed or supervised immunohistochemistry. E.G. and S.R. performed and supervised multiplexed immunofluorescence. D.R.S. and H.W. performed ATAC sequencing and analysis. C.L.C. and Y.Z. performed in vivo experiments. C.P.P. and Y.K. performed ddPCR experiments.

Competing interests

D.A.B. is a consultant for N-of-One.

Corresponding author

Correspondence to David Allen Barbie.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1–15 and Supplementary Table 1

  2. Reporting Summary

  3. Supplementary Dataset 1

    List of 3(UTR repeat elements from RefSeq and list of 452 top genes upregulated/downregulated in H69M versus H69

  4. Supplementary Dataset 2

    List of gene sets and genes coexpressed with the SPARCS signature across cancers in the TCGA and CCLE datasets

  5. Supplementary Dataset 3

    List of gene sets coexpressed with control 3(UTR antisense ERVs from H69M downregulated genes across the TCGA dataset

  6. Supplementary Dataset 4

    List of chromosomal alterations associated with the SPARCS signature across the TCGA and CCLE datasets

  7. Supplementary Dataset 5

    List of the top 200 genes that overlap after intersecting the top 1,000 genes co-regulated with SPARCS from the TCGA and CCLE datasets

  8. Supplementary Dataset 6

    List of cell lines from CCLE or tumors from TCGA ranked based on SPARCS score and RPKM gene expression values of indicated genes

  9. Supplementary Dataset 7

    Sequences used in this study

  10. Supplementary Dataset 8

    List of genes tested in the OncoPanel Assay

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DOI

https://doi.org/10.1038/s41591-018-0116-5