Epigenetic reprogramming of tumor cell–intrinsic STING function sculpts antigenicity and T cell recognition of melanoma

Abstract

Lack or loss of tumor antigenicity represents one of the key mechanisms of immune escape and resistance to T cell–based immunotherapies. Evidence suggests that activation of stimulator of interferon genes (STING) signaling in tumor cells can augment their antigenicity by triggering a type I IFN-mediated sequence of autocrine and paracrine events. Although suppression of this pathway in melanoma and other tumor types has been consistently reported, the mechanistic basis remains unclear. In this study, we asked whether this suppression is, in part, epigenetically regulated and whether it is indeed a driver of melanoma resistance to T cell–based immunotherapies. Using genome-wide DNA methylation profiling, we show that promoter hypermethylation of cGAS and STING genes mediates their coordinated transcriptional silencing and contributes to the widespread impairment of the STING signaling function in clinically-relevant human melanomas and melanoma cell lines. This suppression is reversible through pharmacologic inhibition of DNA methylation, which can reinstate functional STING signaling in at least half of the examined cell lines. Using a series of T cell recognition assays with HLA-matched human melanoma tumor-infiltrating lymphocytes (TIL), we further show that demethylation-mediated restoration of STING signaling in STING-defective melanoma cell lines can improve their antigenicity through the up-regulation of MHC class I molecules and thereby enhance their recognition and killing by cytotoxic T cells. These findings not only elucidate the contribution of epigenetic processes and specifically DNA methylation in melanoma-intrinsic STING signaling impairment but also highlight their functional significance in mediating tumor-immune evasion and resistance to T cell–based immunotherapies.

MHC Class I Deficiency in Solid Tumors and Therapeutic Strategies to Overcome It

“…PD-1 blockade delivered together with intratumoral BO-112 achieved partial responses in some patients with primary resistance to anti-PD-1 alone [217]. However, innate interferon sensing is often epigenetically inactivated in immunogenic tumors, via hypermethylation of the promoters of cyclic GMP-AMP synthase (CGAS) and stimulator of interferon genes (STING1) genes [218]. Impaired tumor STING signaling results in impaired immunogenicity and poor response to immunotherapies [219,220].…”

“…Impaired tumor STING signaling results in impaired immunogenicity and poor response to immunotherapies [219,220]. The cGAS-STING pathway sensitivity and MHC-I expression in tumor cells, as well as the resulting T-cell reactivity, could be restored by the DNMT inhibitors such as azacytidine [218]. Treatment with another DNMT inhibitor (guadecitabine) improved T-cell responses in the animal model of breast cancer via upregulation of tumor MHC-I expression and increased T-cell recruitment to the tumor [221].…”

Oncolytic HSV: Underpinnings of Tumor Susceptibility

“…This is in line with previous studies indicating a majority of the melanoma and colorectal cancer cell lines analyzed have intact IFN production in response to poly IC dsRNA stimulation [ 76 , 77 ]. Recently, it has been identified that the use of demethylating agents can enhance cGAS/STING expression in silenced melanoma cell lines [ 78 ]. This reversal results in improved T lymphocyte recognition and increased IFN-γ production in an in vitro co-culture system [ 78 ].…”

“…Recently, it has been identified that the use of demethylating agents can enhance cGAS/STING expression in silenced melanoma cell lines [ 78 ]. This reversal results in improved T lymphocyte recognition and increased IFN-γ production in an in vitro co-culture system [ 78 ]. Although much less prevalent (< 1% of tumors within TCGA database), it should be noted that several missense mutants of cGAS and STING were identified in the TCGA database [ 33 ].…”

“…To establish an immune-suppressed environment, the γ 1 34.5 protein can inhibit DC maturation through the abrogation of TBK-1 and IKK activation of IFN and NF-κB, impairing antigen presentation and T lymphocyte activation during HSV infection [ 18 , 129 ]. Similarly, the malignant inhibition of cGAS/STING signaling through epigenetic silencing, mutant p53, or HER2 results in the simultaneous suppression of T lymphocyte infiltration in in vivo tumor models [ 34 , 35 , 78 ]. The activation of tumor endogenous STING has been identified as an important component for inducing antitumor immune responses [ 130 ].…”