American Association for Cancer Research
crc-23-0382_fig1.png (478.09 kB)

FIGURE 1 from The ncBAF Complex Regulates Transcription in AML Through H3K27ac Sensing by BRD9

Download (478.09 kB)
posted on 2024-01-30, 14:21 authored by David C. Klein, Santana M. Lardo, Sarah J. Hainer

Inhibition of the BRD9 bromodomain selectively kills AML cells but not HEK293T cells. A, Growth assays depicting difference in ratio of cells remaining after indicated hours of growth in medium containing 1% DMSO (vehicle), 10 µmol/L I-BRD9, 2 µmol/L cytarabine (AraC), or a combination. n = 4 replicates per drug condition and cell line (HEK293T, n = 3). Y-axis indicates ratio of cells counted to those originally plated, compared with vehicle. Points are shown ± SEM. B, Averaged results of growth assays across all cell lines (left) and HEK293T cells (right). Error bars indicate SEM. (n = 20 per drug condition, analyzed via two-way ANOVA. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001; ns, P > 0.05).


HHS | NIH | National Institute of General Medical Sciences (NIGMS)



The non-canonical BAF complex (ncBAF) subunit BRD9 is essential for acute myeloid leukemia (AML) cell viability but has an unclear role in leukemogenesis. Because BRD9 is required for ncBAF complex assembly through its DUF3512 domain, precise bromodomain inhibition is necessary to parse the role of BRD9 as a transcriptional regulator from that of a scaffolding protein. To understand the role of BRD9 bromodomain function in regulating AML, we selected a panel of five AML cell lines with distinct driver mutations, disease classifications, and genomic aberrations and subjected these cells to short-term BRD9 bromodomain inhibition. We examined the bromodomain-dependent growth of these cell lines, identifying a dependency in AML cell lines but not HEK293T cells. To define a mechanism through which BRD9 maintains AML cell survival, we examined nascent transcription, chromatin accessibility, and ncBAF complex binding genome-wide after bromodomain inhibition. We identified extensive regulation of transcription by BRD9 bromodomain activity, including repression of myeloid maturation factors and tumor suppressor genes, while standard AML chemotherapy targets were repressed by inhibition of the BRD9 bromodomain. BRD9 bromodomain activity maintained accessible chromatin at both gene promoters and gene-distal putative enhancer regions, in a manner that qualitatively correlated with enrichment of BRD9 binding. Furthermore, we identified reduced chromatin accessibility at GATA, ETS, and AP-1 motifs and increased chromatin accessibility at SNAIL-, HIC-, and TP53-recognized motifs after BRD9 inhibition. These data suggest a role for BRD9 in regulating AML cell differentiation through modulation of accessibility at hematopoietic transcription factor binding sites. The bromodomain-containing protein BRD9 is essential for AML cell viability, but it is unclear whether this requirement is due to the protein's role as an epigenetic reader. We inhibited this activity and identified altered gene-distal chromatin regulation and transcription consistent with a more mature myeloid cell state.

Usage metrics

    Cancer Research Communications



    Ref. manager