Druggable epigenetic suppression of interferon-induced chemokine expression linked toMYCNamplification in neuroblastoma

Abstract

BackgroundAmplification of the MYCN oncogene is a molecular hallmark of aggressive neuroblastoma (NB), a childhood cancer of the sympathetic nervous system. There is evidence that MYCN promotes a non-inflamed and T-cell infiltration-poor (‘cold’) tumor microenvironment (TME) by suppressing interferon signaling. This may explain, at least in part, why patients with NB seem to have little benefit from single-agent immune checkpoint blockade (ICB) therapy. Targeting MYCN or its effectors could be a strategy to convert a cold TME into a ‘hot’ (inflamed) TME and improve the efficacy of ICB therapy.MethodsNB transcriptome analyses were used to identify epigenetic drivers of a T-cell infiltration-poor TME. Biological and molecular responses of NB cells to epigenetic drugs and interferon (IFN)-γ exposure were assessed by proliferation assays, immunoblotting, ELISA, qRT-PCR, RNA-seq and ChIP-qPCR as well as co-culture assays with T cells.ResultsWe identified H3K9 euchromatic histone-lysine methyltransferases EHMT2 and EHMT1, also known as G9a and GLP, as epigenetic effectors of the MYCN-driven malignant phenotype and repressors of IFN-γ transcriptional responses in NB cells. EHMT inhibitors enhanced IFN-γ-induced expression of the Th1-type chemokines CXCL9 and CXCL10, key factors of T-cell recruitment into the TME. In MYCN-amplified NB cells, co-inhibition of EZH2 (enhancer of zeste homologue 2), a H3K27 histone methyltransferase cooperating with EHMTs, was needed for strong transcriptional responses to IFN-γ, in line with histone mark changes at CXCL9 and CXCL10 chemokine gene loci. EHMT and EZH2 inhibitor response gene signatures from NB cells were established as surrogate measures and revealed high EHMT and EZH2 activity in MYCN-amplified high-risk NBs with a cold immune phenotype.ConclusionOur results delineate a strategy for targeted epigenetic immunomodulation of high-risk NBs, whereby EHMT inhibitors alone or in combination with EZH2 inhibitors (in particular, MYCN-amplified NBs) could promote a T-cell-infiltrated TME via enhanced Th1-type chemokine expression.

EHMT2/G9a as an Epigenetic Target in Pediatric and Adult Brain Tumors

“…G9a inhibition is required for transcriptional responses to IFN-γ and histone mark changes at CXCL9 and CXCL10 gene loci in MYCN-positive NB cells. These findings highlight the important role of G9a in high-risk, MYCN-expressing, NB [73].…”

Identification of methylation signatures associated with CAR T cell in B-cell acute lymphoblastic leukemia and non-hodgkin’s lymphoma

“…MYCN also downregulates DKK3 expression and activates the Wnt/β-catenin signaling pathway at the transcriptional level, boosting the development of B-ALL ( 69 ). Meanwhile, MYCN apparently decreases the interferon signaling, promoting a non-inflamed and T-cell infiltration-poor (“cool”) tumor microenvironment ( 70 ). In the classification rule based on the MCFS results, HDGF targeted by cg18593717 was an important locus, which exhibited a lower methylation level.…”

The role of histone methylase and demethylase in antitumor immunity: A new direction for immunotherapy

“…For example, G9a is inversely associated with CD8 + T cell infiltration in melanoma and colon cancer. Moreover, it can inhibit the activated of Th1 cytokines/chemokines ( 32 , 33 ). Further investigation revealed that Ga9 induces chromatin variability in chemokine-related genes, involved in homing of intratumoral effector lymphocytes and natural killer cells ( 34 ).…”