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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

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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 10

Conditioned media from ccRCC cells treated with decitabine can enhance T cell function.

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Conditioned media from ccRCC cells treated with decitabine can enhance T...
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. Conditioned media from 786-0 cells transfected with poly-IC was used as a positive control. Healthy donor T cells (n = 5) were cultured in conditioned media, and T cell function was assessed by flow cytometry. (A–D) T cells were stimulated with IL7, anti-CD3 antibody, and anti-CD3/CD28 antibodies and cultured for 5 days. Cell size, CD4, CD8, CD25, and CD71 was measured by flow cytometry to evaluate T cell activation. Surface expression of CD25 and CD71 (as median fluorescence intensity; MFI) was measured in CD8+ (A and B) and CD4+ (C and D) T cell subsets. (E and F) Migration of healthy donor T cells (n = 5) activated using anti-CD3/CD28 antibodies was assessed by Transwell assay. (E) Migration of activated T cells toward indicated conditioned medias. (F) Migration of activated T cells toward the indicated conditioned medias treated with either IGG isotype antibody, CXCL10 antibody, or CCL5 antibody (n = 5). Box-and-whisker plots show expression antiviral signaling genes in primary ccRCC cell lines (n = 5) treated with indicated doses of decitabine (or DMSO vehicle) as indicated by box color in key. Box ends represent the first and third quartiles, and the horizontal line inside the box corresponds to the median. The whiskers span from minimum or maximum values, and data points outside this range correspond to outliers. Significance assessed by paired t test, and P values were adjusted via Holm-Bonferroni correction. *P < 0.05.

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