A SAGA Complex-Specific Dependency in Multiple Myeloma Orchestrates Oncogenic Transcriptional Programs

Multiple myeloma (MM) is a malignancy of antibody-producing plasma cells that reside within the bone marrow. Epigenetic factors contribute to the initiation, progression, relapse and clonal heterogeneity in MM, but our knowledge of epigenetic regulators involved in MM development is far from complete. Results from the Cancer Dependency Map (DepMap) Project revealed that several components of the SAGA complex are particularly important for MM cell growth and survival. The SAGA complex serves as a coactivator in transcription and also catalyzes histone acetylation and deubiquitination via its lysine acetyltransferase (KAT) and deubiquitinase (DUB) modules, respectively. Our analysis showed that each SAGA complex component is overexpressed in at least 50% of MM patients. To investigate SAGA-specific functions, we centered on ADA2B, a subunit in the KAT module that specifically functions in the SAGA complex.

We observed reduced cell viability upon ADA2B knockdown and CRISPR/Cas9-mediated knockout in MM cell lines. To identify the underlying transcriptional pathways that ADA2B regulate, we performed transcriptome sequencing using MM cell lines with and without ADA2B depletion. Our results showed several oncogenic pathways, including MYC, E2F and MM-specific MAF oncogenic programs, are tightly regulated by ADA2B. We also discovered that the protein but not transcript levels of MAF and the KATs in SAGA, GCN5 and PCAF, as well as the global level of histone H3 lysine 9 acetylation (H3K9ac) are all prominently decreased upon ADA2B depletion. To investigate whether the global reduction in H3K9ac would alter chromatin accessibility, we performed assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and found decreased accessibility at many cancer marker and cancer-promoting genes.

To decipher the protein domains that are essential for ADA2B function in MM, we generated and expressed mutated versions of ADA2B in MM cell lines. Excitingly, mutations of core hydrophobic amino acid residues in the SANT domain disrupt interactions with GCN5 and PCAF and negatively affect protein stability of ADA2B. Hence, drug inhibitors that target the SANT domain could achieve suppression of ADA2B and MM cell growth.

Our findings uncover novel epigenetic and transcriptional mechanisms controlling MM development, and suggest potential for new epigenetic inhibitors targeting SAGA-specific ADA2B as future treatment modalities for MM.