Viral mimicry describes an antiviral response triggered by the activation of endogenous retroviruses (ERVs) or other endogenous nucleic acids. This mechanism has been proposed to underlie the immunogenic effects of multiple cancer therapies including CDK4/6 inhibitors (CDK4/6i), where immunotherapies are being trialed to exploit the resulting increase in tumour immunogenicity. ERVs are remnants of ancient viral integration events that comprise ~10% of the human genome. Although typically epigenetically silenced, ERVs can be reactivated in cancer or during cellular stress. However, analysing repetitive elements remains challenging, with poor mapability compounded by limited functional annotation and incomplete understanding of their regulation and transcript structure. HiC is a powerful methodology which captures chromosomal interactions surrounding ERVs without the need of directly mapping repetitive regions.
In this study, we developed patient-derived xenograft (PDX) models of CDK4/6i resistant breast cancer, applying HiC to interrogate 3D genome structure. We identified altered chromatin interactions surrounding ERV loci, particularly within the major histocompatibility complex (MHC) region which is essential for T-cell recruitment. Complementary ATACseq revealed activated regulatory elements at ERV loci, and long-read methylation profiling (Oxford Nanopore) demonstrated ERV hypomethylation. Developing a bioinformatic workflow tailored to quantitation of repeat elements, we detected abundant transcription of specific endogenous retroviral (ERV) sequences. De novo transcriptome assembly further enabled annotation of novel ERV-derived long non-coding RNAs (lncRNAs), featuring distinct promoter and enhancer elements. Consistent with previous findings, CDK4/6 inhibition induced a robust immunostimulatory response, which we note is exacerbated with longer-term treatment and therapy resistance. This included strong upregulation of interferon signaling and double-stranded RNA sensor genes (MDA5, RIG-1).
Together, we provide mechanistic insight into the source of cancer immunogenicity supporting ongoing efforts to enhance immunotherapy responsiveness in breast cancer.