DNA hypomethylation promotes transposable element expression and activation of immune signaling in renal cell cancer
Aguirre A. de Cubas, William Dunker, Andrew Zaninovich, Rachel A. Hongo, Anuj Bhatia, Anshuman Panda, Kathryn E. Beckermann, Gyan Bhanot, Shridar Ganesan, John Karijolich, W. Kimryn Rathmell
Aguirre A. de Cubas, William Dunker, Andrew Zaninovich, Rachel A. Hongo, Anuj Bhatia, Anshuman Panda, Kathryn E. Beckermann, Gyan Bhanot, Shridar Ganesan, John Karijolich, W. Kimryn Rathmell
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Research Article Immunology Oncology

DNA hypomethylation promotes transposable element expression and activation of immune signaling in renal cell cancer

Abstract

Recently, we reported that expression of endogenous retroviruses (ERVs) is associated with response to immune checkpoint blockade (ICB) in renal cell carcinoma (RCC). We show that decitabine, a DNA hypomethylating agent, activates transposable element (TE) expression (LINE1 and ERVs ERV3-2 and ERV4700) and antiviral signaling to potentially enhance response to ICB in kidney cancer cell lines and primary cells. KO of RIGI and MDA5 dsRNA sensors attenuated activation of antiviral signaling associated with DNA hypomethylation, and RIGI and MDA5 IPs showed increased ERV binding with decitabine treatment. Bioinformatic analyses showed the decitabine-induced signature could be associated with increased immune infiltration and response to ICB. Cytokine secretion induced by decitabine could modestly improve T cell activation and robustly enhanced T cell migration. In a small retrospective cohort of metastatic clear cell RCC (ccRCC) patients treated with anti-PD1/PDL1 blockade, activation of some antiviral genes was significantly higher in responders. Thus, we identified a potential strategy to induce TE expression through inhibition of DNA methylation in modulating T cell action via regulation of the innate antiviral pathway.

Authors

Aguirre A. de Cubas, William Dunker, Andrew Zaninovich, Rachel A. Hongo, Anuj Bhatia, Anshuman Panda, Kathryn E. Beckermann, Gyan Bhanot, Shridar Ganesan, John Karijolich, W. Kimryn Rathmell

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Figure 9

ccRCC cells treated with decitabine secrete IFNs and inflammatory cytokines and can activate antiviral signaling in naive T cells.

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ccRCC cells treated with decitabine secrete IFNs and inflammatory cytoki...
(A–D) HKC and 786-0 cells were treated with indicated doses of decitabine (or DMSO) for 3 days, fresh media was add 24 hours before harvest (day 4), and conditioned media was harvested on day 5. Dot plots show levels of indicated cytokines — IFN-β1, or IFNB1 (A); IFN-λ1, or IL29 (B); CXCL10 (C); and CCL5 (D) — were measured by ELISA in culture media on day 5. Dot plot colors indicate decitabine dose. Blue dot and line indicate mean ± SD (n = 3). Significance (100 nM versus 0 nM; 300 nM versus 0 nM) assessed by 2-tailed t test, and P values were adjusted via Holm-Bonferroni correction. *P < 0.05. (E–J) 786-0 cells were treated with decitabine or DMSO for 3 consecutive days; fresh media was added and harvested 24 hours later to obtain conditioned media. T cells isolated from healthy donor blood were cultured in conditioned media for 2, 4, 6, and 24 hours. Antiviral signaling was assessed measuring expression of DDX58 (E), IFIH1 (F), IRF7 (G), ISG15 (H), MX1 (I), and OAS3 (J) by qPCR.