Targeting SWI/SNF ATPases in H3.3K27M diffuse intrinsic pontine gliomas

Diffuse midline gliomas (DMGs) including diffuse intrinsic pontine gliomas (DIPGs) bearing lysine-to-methionine mutations in histone H3 at lysine 27 (H3K27M) are lethal childhood brain cancers. These tumors harbor a global reduction in the transcriptional repressive mark H3K27me3 accompanied by an increase in the transcriptional activation mark H3K27ac. We postulated that H3K27M mutations, in addition to altering H3K27 modifications, reprogram the master chromatin remodeling switch/sucrose nonfermentable (SWI/SNF) complex. The SWI/SNF complex can exist in two main forms termed BAF and PBAF that play central roles in neurodevelopment and cancer. Moreover, BAF antagonizes PRC2, the main enzyme catalyzing H3K27me3. We demonstrate that H3K27M gliomas show increased protein levels of the SWI/SNF complex ATPase subunits SMARCA4 and SMARCA2, and the PBAF component PBRM1. Additionally, knockdown of mutant H3K27M lowered SMARCA4 protein levels. The proteolysis targeting chimera (PROTAC) AU-15330 that simultaneously targets SMARCA4, SMARCA2, and PBRM1 for degradation exhibits cytotoxicity in H3.3K27M but not H3 wild-type cells. AU-15330 lowered chromatin accessibility measured by ATAC-Seq at nonpromoter regions and reduced global H3K27ac levels. Integrated analysis of gene expression, proteomics, and chromatin accessibility in AU-15330-treated cells demonstrated reduction in the levels of FOXO1, a key member of the forkhead family of transcription factors. Moreover, genetic or pharmacologic targeting of FOXO1 resulted in cell death in H3K27M cells. Overall, our results suggest that H3K27M up-regulates SMARCA4 levels and combined targeting of SWI/SNF ATPases in H3.3K27M can serve as a potent therapeutic strategy for these deadly childhood brain tumors.

 

Comments:

Thank you for providing this detailed information about the research findings related to diffuse midline gliomas (DMGs), specifically diffuse intrinsic pontine gliomas (DIPGs), bearing lysine-to-methionine mutations in histone H3 at lysine 27 (H3K27M). This research highlights the molecular mechanisms underlying these lethal childhood brain cancers and proposes a potential therapeutic strategy for treating these tumors.

To summarize the key points from the provided text:

1. **Mutation and Epigenetic Changes:** H3K27M mutations in DMGs lead to alterations in histone modifications, including a reduction in the repressive mark H3K27me3 and an increase in the activation mark H3K27ac.

2. **Reprogramming of SWI/SNF Complex:** H3K27M mutations reprogram the SWI/SNF complex, a chromatin remodeling complex, by increasing the protein levels of specific subunits (SMARCA4, SMARCA2, and PBRM1). The SWI/SNF complex exists in BAF and PBAF forms, which are crucial in neurodevelopment and cancer.

3. **Targeting SWI/SNF Complex:** A proteolysis targeting chimera (PROTAC) called AU-15330 was introduced. This compound simultaneously targets SMARCA4, SMARCA2, and PBRM1 for degradation. AU-15330 exhibited cytotoxicity specifically in cells with the H3.3K27M mutation but not in H3 wild-type cells.

4. **Effects of AU-15330:** Treatment with AU-15330 reduced chromatin accessibility at nonpromoter regions and lowered global H3K27ac levels. Integrated analysis demonstrated a reduction in the levels of FOXO1, a critical transcription factor.

5. **Targeting FOXO1:** Further experiments showed that genetic or pharmacologic targeting of FOXO1 resulted in cell death in H3K27M cells.

6. **Therapeutic Implications:** The study suggests that upregulation of SMARCA4 is a characteristic feature of H3K27M gliomas. Targeting multiple ATPases within the SWI/SNF complex, particularly in H3.3K27M-mutant cells, could serve as a promising therapeutic strategy for these aggressive childhood brain tumors.

This research provides valuable insights into the molecular pathways affected by H3K27M mutations and offers a potential targeted therapy approach for treating DMGs, which are notoriously difficult to treat. Targeting specific components of the SWI/SNF complex and downstream effectors like FOXO1 may hold promise for the development of effective treatments for these cancers.

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E1103	AU-15330	AU-15330 is a proteolysis-targeting chimera (PROTAC) degrader of the SWI/SNF ATPase subunits, SMARCA2 and SMARCA4, which can induce potent inhibition of tumor growth in xenograft models of prostate cancer.

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PROTAC