Paper Details

ABSTRACT

Introduction: Multiple myeloma (MM) remains incurable despite therapeutic advances, highlighting the need for approaches targeting the transcriptional dependencies sustaining malignant plasma cells. Analysis of the DepMap Cancer Dependency Portal CRISPR screens identified multiple components of the Spt-Ada-Gcn5 acetyltransferase (SAGA) complex, EP300, and lineage-defining transcription factors (e.g. IRF4 and MYC) as strong genetic dependencies in MM. The SAGA complex contains the histone acetyltransferases KAT2A and KAT2B, which regulate chromatin through histone acetylation. MM cells rely on super-enhancer networks that maintain expression of oncogenic transcriptional programs. SAGA cooperates with transcription factors to reinforce super-enhancer-driven transcription, while p300 maintains enhancer activity through H3K27 acetylation. Therefore, simultaneous disruption of p300 and SAGA represents a rational strategy to collapse oncogenic transcriptional programs across genetically diverse MM subtypes. 

Methods: Twelve MM cell lines representing four cytogenetic subgroups were treated with the p300 inhibitor Inobrodib, the p300/BRD4 inhibitor EP31670, and the KAT2A/B PROTAC degrader GSK-699. Genetic dependency was assessed through siRNA-mediated depletion of p300 and SAGA components, followed by viability assays. Drug sensitivity was determined by growth inhibition (GI50) analysis, transcriptional responses were evaluated by RT-qPCR, and combination effects were assessed using Synergy Finder. 

Results: Drug sensitivity differed across cytogenetic subgroups. The t(14;16) subgroup showed the greatest drug sensitivity (median GI₅₀: Inobrodib 41.76 nM, EP31670 12.79 nM and GSK-699 4.90 nM). In contrast, t(11;14) models displayed reduced sensitivity to Inobrodib (median GI₅₀ = 170.10 nM) while remaining highly sensitive to EP31670 (9.72 nM) and GSK-699 (13.70 nM). The t(4;14)+t(8;14) models displayed intermediate sensitivity, with median GI₅₀ values of 79.24 nM (Inobrodib), 31.93 nM (EP31670), and 25.18 nM (GSK-699). Genetic depletion of p300 by siRNA triggered 30% of cell viability reduction and SAGA components reduced up to 40% cell viability reduction in the cell line KMS-11. 

Transcriptional profiling revealed distinct but complementary responses to p300 and KAT2A/B inhibition. At GI₅₀ concentrations, Inobrodib induce significant IRF4 downregulation in 8 of 12 cell lines, particularly within the t(11;14) and t(14;16) subgroups (0.3–0.5-fold of control). In contrast, GSK-699 reduced IRF4 expression only in U-266 and ARP-1 (0.4–0.5-fold). MYC expression was significantly reduced by Inobrodib in t(4;14)+t(8;14) and t(14;16) models (0.03–0.4-fold) but remained unchanged in t(11;14). Conversely, GSK-699 suppressed MYC in KMS-12PE (0.5-fold). 

Subtype-associated oncogenes exhibited differential sensitivity to chromatin-targeting agents. FGFR3 was reduced by both compounds in t(4;14) models (0.2–0.4-fold), whereas NSD2 suppression was observed selectively following GSK-699 treatment (0.5–0.6-fold). Similarly, MAF expression was reduced by GSK-699 in t(14;16) models (0.4–0.7-fold), whereas Inobrodib had minimal effects on MAF-associated cell lines. These findings demonstrate that p300 and SAGA inhibition regulate overlapping yet distinct oncogenic transcriptional programs. 

Combination treatment with Inobrodib and GSK-699 was evaluated across MM cell lines with distinct single-agent response profiles. In KMS-12PE, a model resistant to Inobrodib but sensitive to GSK-699, the combination demonstrated strong Bliss synergy (score 31.6). Synergistic activity was also observed in KMS-28BM, a cell line resistant to both single agents (score 15). Additionally, KMS-11, which exhibits intermediate sensitivity to both agents, showed synergy at concentrations near the individual GI₅₀ values (score 20.3). 

Conclusions: These findings identify p300 and the SAGA complex as complementary epigenetic dependencies in MM. While p300 inhibition broadly suppresses the IRF4-centered transcriptional network, SAGA inhibition disrupts distinct subtype-associated oncogenic programs, including MYC, NSD2, and MAF, in the context where p300 inhibition is insufficient. The complementary transcriptional effects of these agents translate into synergistic activity in resistant MM models, supporting combined targeting of p300 and SAGA as a strategy to overcome transcriptional plasticity and disrupt super-enhancer-driven oncogenic programs in genetically diverse MM.