Epigenetic Modifiers: Anti-Neoplastic Drugs With Immunomodulating Potential

Abstract

Cancer cells are under the surveillance of the host immune system. Nevertheless, a number of immunosuppressive mechanisms allow tumors to escape protective responses and impose immune tolerance. Epigenetic alterations are central to cancer cell biology and cancer immune evasion. Accordingly, epigenetic modulating agents (EMAs) are being exploited as anti-neoplastic and immunomodulatory agents to restore immunological fitness. By simultaneously acting on cancer cells, e.g. by changing expression of tumor antigens, immune checkpoints, chemokines or innate defense pathways, and on immune cells, e.g. by remodeling the tumor stroma or enhancing effector cell functionality, EMAs can indeed overcome peripheral tolerance to transformed cells. Therefore, combinations of EMAs with chemo- or immunotherapy have become interesting strategies to fight cancer. Here we review several examples of epigenetic changes critical for immune cell functions and tumor-immune evasion and of the use of EMAs in promoting anti-tumor immunity. Finally, we provide our perspective on how EMAs could represent a game changer for combinatorial therapies and the clinical management of cancer.

Keywords: cancer; epigenetics; immune evasion; immunotherapy; tumor microenvironment.

Figure 1

TAM polarization and its epigenetic regulatory networks. The activity of epigenetic regulators has been correlated to the phenotype and function of TAM. PRMT1, SMYD3, G9a (HMT) KDM3A (HDM) and HDAC1 promote TAM with an M2-like phenotype (CD206) and function (IL10 and arg-1), while CBP/p300 (HAT), HDAC2, 3, 4, 6, 9, 11 and DNMT1 promote TAM with an M1-like phenotype (MHC-II) and function (IL12, NOS). DNMT3B and KDM6B (HDM) seem to act as gatekeepers and can in certain conditions promote M1- or M2-like behavior. PRMT1, SMYD3, G9a, KDM3A and HDAC1 represent potential targets to improve increase the M1/M2 balance. HMT, histone methyltransferase; HDM, histone demethylases; HAT, histone deacetylase; HDAC, histone deacetylases.

Figure 2

Epigenetic factors that regulate TADC activity. Epigenetic enzymes that foster DC-activation include MLL complex (HMT); KDM6B and KDM4D (HDM); HDAC1 and 2 as well as TET2. Collectively these enzymes regulate the expression of genes involved in antigen presentation and stimulation of CTL-responses, such as CIITA, CD40, CD80, CD86, IL12 and IFNA/B. In contrast, enzymes such as the G9a (HMT), HDAC2, and the DNMT1, DNMT3A and DNMT3B rather inhibit DC-activity by acting on genes such as IL6, IFNA/B, CCL2, SOCS3 and IL1R. G9a, DOTL1, HDAC2 and DNMT represent potential targets to improve DC mediated anti-tumor immunity. iDC, immature dendritic cell; mDC, mature dendritic cell; HMT, histone methyltransferase; HDM, histone demethylases; HDAC, histone deacetylases.

Figure 3

The epigenetic landscape of MDSC. EZH2 and HDAC11 serve as negative regulators of MDSC differentiation from immature myeloid. In MDSC, the bromodomain (BRD) of CBP/p300 acts as a critical regulator of H3K27Ac across promoters and enhancers of pro-tumorigenic target genes such as Arg-1 and NOS2. Also, increased DNMT3A levels have been shown in MDSC and have been linked to repression of immunity-related genes such RUNX1, S1PR4, FAS and AQP9. CBP/p300 and its bromodomain or DNMT3A represent potential targets to inhibit MDSC. MDSC, myeloid derived suppressor cell; HDAC, histone deacetylase.

Figure 4

Epigenetic regulation of CD4⁺ T cell differentiation. CD4⁺ T cell memory formation: During memory formation, remodeling of H3K4 methylation (green) marks takes place together with the removal of repressive H3K27me3 (red) marks in genes of the JAK-STAT pathway. Moreover, permissive H3K4me3 (green) and H3K27Ac (purple) marks are present in genes related to CD4⁺ T cell function. CD4⁺ T cell polarization: T_H1 polarization is controlled by EZH2 that silences T_H2-related genes and vice versa. KDM6B favors T_H1 polarization by positive regulation of T_H1-related genes while KMT1E negatively regulates IFNG and Tbx21 (T-bet) gene expression. HDAC1 and 11 are general inhibitors of CD4⁺ T cell function through silencing of cytokine production, Eomes and Tbx21 (T-bet). Epigenetic regulation of FOXP3 expression in Treg: FOXP3 expression is regulated by epigenetic processes in Treg including (i) exchange of repressive HDAC5 and SIRT 1 for a permissive CPB/p300 (HAT) complex, (ii) permissive H3K4me3 (green) and H3 lysine acetylation (purple) in a TGFβ response element (CNS1), (iii) TET2 dependent DNA demethylation of a 5’UTR region (CNS2), and (iii) H3K4me1/2 poised state of CNS3 needed for Foxp3 expression. HDAC1, 11 and DNMT3A represent potential targets to improve CD4⁺ T cell anti-tumor immunity.

Figure 5

Epigenetic regulation of CD8⁺ T cell differentiation. Naive CD8⁺T cells are characterized by a bivalent state of permissive (green) and repressive (red) histone marks in genes related to differentiation and proliferation while effector genes are not decorated by permissive marks or repressive marks. Effector CD8⁺T cells show permissive (green) marks in effector genes while the transcription factor Tcf1 and memory and effector genes contain repressive (red) marks. Memory CD8⁺T cells show permissive (green, purple) marks in effector, memory and survival genes while Tcf1 is not DNA methylated, supporting their multipotent state. EZH2 and DNMT3A represent potential targets to increase CD8⁺ T memory formation.

Figure 6

Epigenetics and T cell exhaustion. T cell exhaustion is characterized by reduced T cell proliferation, effector functions and increased expression of inhibitory receptors such as PD-1, CTLA-4 and TIM-3. The expression of these inhibitory receptors in CD8⁺ tumor-infiltrating cells is enabled altered chromatin accessibility and binding of transcription factors such as NFAT, TOX, NR4A, T-bet, Sox1 and Rara in genes exerting a negative role for T function. In addition, DNMT3A mediates DNA methylation and silencing of effector genes, hence serving as a potential target to reverse T cell exhaustion. IR, inhibitory receptor.

Figure 7

Examples of increased tumor immunogenicity and modulation of the immune cell constitution in the TME upon treatment with epigenetic compounds. (A) EZH2 inhibition results in increased antigen presentation and T cell activity. (B) HDAC or DNMT inhibition increases antigen presentation and T cell activity while reducing MDSC and M2 macrophages. (C) Bromodomain inhibitors (JQ1) increase antigen presentation and T cell activity while it reduces tumoral PDL1 expression and IDO in the TME. JQ1 also induces a more complete picture of ICD with a type I IFN response, ecto-calreticulin, HMGB1 and ATP release. JQ1 moreover reduces CD47 expression in tumor cells (D) G9a inhibitors and CM-272 induce a type I IFN response due to viral mimicry in tumor cells. CM-272 induces a more complete picture of ICD with a type I IFN response, ecto-calreticulin, HMGB1 and ATP release. IDO, Indoleamine 2,3-dioxygenase.