Super elongation complex as a targetable dependency in diffuse midline glioma

Abstract

<jats:title>Abstract</jats:title><jats:p>Mutations in the histone 3 gene (H3K27M) are the eponymous drivers in diffuse intrinsic pontine gliomas (DIPGs) and other diffuse midline gliomas (DMGs), aggressive pediatric brain cancers for which no curative therapy currently exists. The salient molecular consequence of these recurrent oncohistones is a global loss of repressive H3K27me3 residues and broad epigenetic dysregulation. In order to identify specific, therapeutically targetable epigenetic dependencies within this disease context, we performed an shRNA screen targeting 408 genes classified as epigenetic/chromatin-associated molecules in patient-derived DMG cultures. This approach identified AFF4, the scaffold protein of the super elongation complex (SEC), as a previously-undescribed dependency in DMG. Interrogation of SEC function demonstrated a key role for maintaining DMG cell viability and clonogenic potential while promoting self-renewal of DMG tumor stem cells. Small-molecule inhibition of the SEC with the highly-specific, clinically relevant CDK9 inhibitors atuveciclib and AZD4573 restores regulatory RNA polymerase II pausing, promotes cellular differentiation, and leads to potent anti-tumor effect both <jats:italic>in vitro</jats:italic> and in patient-derived xenograft models. These studies present a biologic rationale for translational exploration of CDK9 inhibition as a promising therapeutic approach in a disease which currently has no effective medical therapies.</jats:p>

Senescence Induced by BMI1 Inhibition Is a Therapeutic Vulnerability in H3K27M-Mutant DIPG

“…In H3K27M-SU-DIPG04 cells, our analysis identified shRNAs targeting 80 genes with significant loss at day 21. Several tophit genes, including AFF4, HDACs, BRDs, and JMJDs, have already been shown as crucial targets in DIPG, validating our target identification (Dahl et al, 2020;Grasso et al, 2015;Hashizume, 2017;Piunti et al, 2017). Target genes depleted in at least 3 replicates and scored in the top 25% of the depleted shRNAs for each significant gene were considered top hits.…”

Modeling by disruption and a selected‐for partner for the nude locus

“…While this explanation accounts for the data, we note that AFF4‐positive elongation complexes have been detected and studied primarily in contexts that are pathological or stressful, such as hypoxia (Galbraith et al , 2013), oncogenic protein production (Lin et al , 2010; Yokoyama et al , 2010), high temperature (Lin et al , 2010; Luo et al , 2012), growth factor starvation/stimulation procedures (Lin et al , 2011; Gardini et al , 2014), cell lines derived from cancerous (often metastatic) tumors (Liang et al , 2018; Dahl et al , 2020), or the transcription of viruses, specifically, human immunodeficiency virus‐1, herpes simplex virus‐1, or hepatitis B virus (Niedzielski et al , 2007; He et al , 2010; Sobhian et al , 2010; Alfonso‐Dunn et al , 2017; Francisco et al , 2017). This apparent association between AFF4 activity and abnormal cellular conditions suggests another unifying explanation: that AFF4 plays exclusively specific roles in cells, but one of these specific roles is to cope with a general problem, such as stress or cellular damage.…”

Pediatric high‐grade glioma: moving toward subtype‐specific multimodal therapy

“…The super elongation complex (SEC) was recently shown to be dysregulated in DMGs, resulting in aberrant positive upregulation of transcription elongation. Inhibition of CDK9, the catalytic subunit of the SEC, using AZD4573 has shown a promising effect in orthotopic models, and current use in adult clinical trials makes it a possible drug for future pediatric DMG trials [30]. Disruption of lineage-specific transcription overall has additionally been hypothesized for treatment in DMGs, leading to the investigation of bromodomain inhibitors.…”