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
View: Text | PDF
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

×

Figure 3

Decitabine treatment activates antiviral signaling in ccRCC cells.

Options: View larger image (or click on image) Download as PowerPoint
Decitabine treatment activates antiviral signaling in ccRCC cells. 786-0...
786-0 cells were cultured for 3 days with decitabine, cells were harvested on day 5 and assayed by RNAseq. RNAseq was performed in duplicate samples (n = 2) for each experimental condition. (A) Lollipop representation of significantly enriched pathways for genes upregulated by decitabine treatment (300 nM) in 786-0 cells as compared with DMSO vehicle (RNA-Seq; Wald test, FDR < 0.05 and log2-fold > 1.5). Lollipop height and intensity color scale indicate magnitude –log10 (FDR) of the enrichment for each pathway. The number of genes enriched in that pathway is indicated inside each lollipop gene enriched in that pathway. (B) Expression levels of antiviral response genes in 786-0 cells treated with 0 nM, 100 nM, and 300 nM decitabine. Heatmap rows show mean expression of duplicate RNAseq measurements. Significance (100 nM versus 0 nM; 300 nM versus 0 nM) assessed by Wald test and corrected for multiple testing (FDR). *FDR < 0.05 and**FDR < 0.001. (C) Antiviral protein levels were assessed by immunoblot analysis. 786-0 cells were treated with 100 nM decitabine for 3 days (days 0, 1, and 2), and protein was harvested at days 1–5. Mock-treated cells were cultured with DMSO for 3 days, and protein was harvested at day 5. Protein expression levels of DNMT1, RIGI, MDA5, IRF7, ISG15, and β-actin were assessed by immunoblot. β-Actin was used as a loading control.