Tumor innate immunity primed by specific interferon-stimulated endogenous retroviruses

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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Fig. 1: Discovery of an IFN-inducible subclass of ERVs.
Fig. 2: SPARCS expression is inducible and triggers positive feedback amplification.
Fig. 3: Expression of SPARCS-containing genes across cancers.
Fig. 4: SPARCS-containing gene expression is associated with adaptive and immune-suppressive signatures.

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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.

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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.

Corresponding author

Correspondence to David Allen Barbie.

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

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–15 and Supplementary Table 1

Reporting Summary

Supplementary Dataset 1

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

Supplementary Dataset 2

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

Supplementary Dataset 3

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

Supplementary Dataset 4

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

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

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

Supplementary Dataset 7

Sequences used in this study

Supplementary Dataset 8

List of genes tested in the OncoPanel Assay

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Cañadas, I., Thummalapalli, R., Kim, J.W. et al. Tumor innate immunity primed by specific interferon-stimulated endogenous retroviruses. Nat Med 24, 1143–1150 (2018). https://doi.org/10.1038/s41591-018-0116-5

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