Selective inhibition of HDAC3 targets synthetic vulnerabilities and activates immune surveillance in lymphoma

Abstract

45 46CREBBP mutations are highly recurrent in B-cell lymphomas and either inactivate its 47 histone acetyltransferase (HAT) domain or truncate the protein. Herein, we show that 48 these two classes of mutations yield different degrees of disruption of the epigenome, 49 with HAT mutations being more severe and associated with inferior clinical outcome. 50 Genes perturbed by CREBBP mutation are direct targets of the BCL6/HDAC3 onco-51 repressor complex. Accordingly, we show that HDAC3 selective inhibitors fully reverse 52 CREBBP mutant aberrant epigenetic programming resulting in: a) growth inhibition of 53 lymphoma cells through induction of BCL6 target genes such as CDKN1A and b) 54 restoration of immune surveillance due to induction of BCL6 repressed IFN pathway and 55 antigen presentation genes. By reactivating these genes, exposure to HDAC3-i restored 56 the ability of tumor infiltrating lymphocytes to kill DLBCL cells in an MHC II and MHC I 57 dependent manner. Hence HDAC3-i represent a novel mechanism-based immune-58 epigenetic therapy for CREBBP mutant lymphomas. 59 60 61 62 We have leveraged the molecular characterization of different types of CREBBP 63 mutations to define a rational approach for targeting these mutations through selective 64 inhibition of HDAC3. This represents an attractive therapeutic avenue for targeting 65 synthetic vulnerabilities in CREBBP mutant cells in tandem with promoting anti-tumor 66 immunity. 67 68 69 70 Diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL) are the two most 71 frequent subtypes of non-Hodgkin lymphoma. These diseases originate from germinal 72 center B (GCB)-cells; a stage of development that naturally allows for the proliferation 73 and affinity maturation of antigen-experienced B-cells to produce terminally-differentiated 74 memory B-cells or plasma cells. The germinal center (GC) reaction is regulated by B-cell-75 intrinsic activation and suppression of large sets of genes by master regulators such as 76 the BCL6 transcription factor 1 , and extrinsically via the interaction of GCB-cells with 77 follicular helper T (TFH)-cells and other immune cells within the GC 2 . The BCL6 78 transcription factor is critical for GCB-cell development and coordinately suppresses the 79 expression of large sets of genes by recruiting SMRT and NCOR co-repressor complexes 80 containing HDAC3 3 and tethering a non-canonical polycomb repressor 1-like complex in 81 cooperation with EZH2 4 . These genes are normally reactivated to drive GC exit and 82 terminal differentiation, but the epigenetic control of these dynamically-regulated GC 83 transcriptional programs is perturbed in DLBCL and FL via the downstream effects of 84 somatic mutation of chromatin modifying genes 5 (CMG). 85 86 STATEMENT OF SIGNIFICANCEThe second most frequently mutated CMG in both DLBCL and FL is the CREBBP gene, 87 which encodes a histone acetyltransferase that activates transcription via acetylation of 88 histone H3 lysine 27 (H3K27Ac) and other residues. We have previously fo...

Germinal center‐derived lymphomas: The darkest side of humoral immunity

“…87 HDAC3 selective inhibitors yield transcriptional signatures in DLBCL cells consisting almost entirely of gene activation, consistent with their effects being truly epigenetic 165. HDAC3 is mostly contained in SMRT and NCOR corepressor complexes, which in GC B cells are almost uniquely associated with BCL6.…”

“…81,150 By genetic DLBCL subtypes, SP1R2 and GNA13 are disrupted in 38% of EZB cases, 81 GNA13 is frequently altered in C3, and both GNA13 and its downstream mediators RHOA and SGK1 are disrupted in C4. 165 Somatic mutation of EZH2 is associated with profound silencing of both MHC I and MHC II genes, and EZH2-mutant lymphomas in both mouse and humans manifest reduced expression of these genes and a reduction in lymphoma infiltrating CD4 and CD8 T cells. MHC class II-dependent manner.…”

“…165,186 Perhaps a more precise approach for targeting the epigenome is provided by specific EZH2 inhibitors, which are particularly effective in suppressing EZH2 mutant lymphoma cells and EZH2 mutant lymphomas in humans. 165,186 Perhaps a more precise approach for targeting the epigenome is provided by specific EZH2 inhibitors, which are particularly effective in suppressing EZH2 mutant lymphoma cells and EZH2 mutant lymphomas in humans.…”

“…HDAC3 selective inhibitors are of interest for precision therapy of patients with CREBBP-mutant lymphomas. The major benefits of these compounds is expected to be in restoring anti-lymphoma immunity through induction of MHC I/II, with potential synergy in combination with checkpoint inhibitors, and in their ability to achieve full target suppression without invoking the toxicity associated with pan-HDAC inhibitors 165. 87 HDAC3 selective inhibitors yield transcriptional signatures in DLBCL cells consisting almost entirely of gene activation, consistent with their effects being truly epigenetic 165.…”

“…IL-10 receptor is a therapeutic target in DLBCL171 and an IL-10 receptor-neutralizing antibody prevented STAT3 activation (phosphorylation) and induction of PD-L1 protein expression 170. Therefore, BTK inhibition, NFAT targeting, or IL-10 blocking could potentially be used to improve the efficacy of T cell-directed therapies.Finally, PD-L1 is co-regulated with MHC I/II through IFNγ response pathways, which are suppressed by BCL6 in GC B cells, an effect that is again reinforced by CREBBP mutation 165. Therefore, BTK inhibition, NFAT targeting, or IL-10 blocking could potentially be used to improve the efficacy of T cell-directed therapies.Finally, PD-L1 is co-regulated with MHC I/II through IFNγ response pathways, which are suppressed by BCL6 in GC B cells, an effect that is again reinforced by CREBBP mutation 165.…”