Pharmacologic inhibition of BAF chromatin remodeling complexes as a therapeutic approach to transcription factor-dependent cancers

Reviewer #1 (Public review):

Summary:

The presented study by Centore and colleagues investigates the inhibition of BAF chromatin remodeling complexes. The study is well written and includes comprehensive datasets, including compound screens, gene expression analysis, epigenetics, as well as animal studies. This is an important piece of work for the uveal melanoma research field, and sheds light on a new inhibitor class, as well as a mechanism that might be exploited to target this deadly cancer for which no good treatment options exist.

Strengths:

This is a comprehensive and well-written study.

Reviewer #2 (Public review):

Summary:

The authors generate an optimized small molecule inhibitor of SMARCA2/4 and test it in a panel of cell lines. All uveal melanoma (UM) cell lines in the panel are growth inhibited by the inhibitor making the focus of the paper. This inhibition is correlated with loss of promoter occupancy of key melanocyte transcription factors e.g. SOX10. SOX10 overexpression and a point mutation in SMARCA4 can rescue growth inhibition exerted by the SMARCA2/4 inhibitor. Treatment of a UM xenograft model results in growth inhibition and regression which correlates with reduced expression of SOX10 but not discernible toxicity in the mice. Collectively, the data suggest a novel treatment of uveal melanoma.

Strengths:

There are many strengths of the study, including the strong challenge of the on-target effect, the assays used and the mechanistic data. The results are compelling as are the effects of the inhibitor. The in vivo data is dose-dependent and doses are low enough to be meaningful and associated with evidence of target engagement.

Reviewer #3 (Public review):

Summary:

This manuscript reports the discovery of new compounds that selectively inhibit SMARCA4/SMARCA2 ATPase activity and have pronounced effects on uveal melanoma cell proliferation. They induce apoptosis and suppress tumor growth, with no toxicity in vivo. The report provides biological significance by demonstrating that the drugs alter chromatin accessibility at lineage specific gene enhancer regions and decrease expression of lineage specific genes, including SOX10 and SOX10 target genes.

Strengths:

The study provides compelling evidence for the therapeutic use of these compounds and does a thorough job at elucidating the mechanisms by which the drugs work. The study will likely have a high impact on the chromatin remodeling and cancer fields. The datasets will be highly useful to these communities.

[Editors' note: The authors have addressed all of the outstanding issues.]

Author response:

The following is the authors’ response to the previous reviews

Reviewer #1 (Public review):

Summary:

The presented study by Centore and colleagues investigates the inhibition of BAF chromatin remodeling complexes. The study is well written and includes comprehensive datasets, including compound screens, gene expression analysis, epigenetics, as well as animal studies. This is an important piece of work for the uveal melanoma research field, and sheds light on a new inhibitor class, as well as a mechanism that might be exploited to target this deadly cancer for which no good treatment options exist.

Strengths:

This is a comprehensive and well-written study.

Weaknesses:

There are minimal weaknesses.

Reviewer #2 (Public review):

Summary:

The authors generate an optimized small molecule inhibitor of SMARCA2/4 and test it in a panel of cell lines. All uveal melanoma (UM) cell lines in the panel are growth inhibited by the inhibitor making the focus of the paper. This inhibition is correlated with loss of promoter occupancy of key melanocyte transcription factors e.g. SOX10. SOX10 overexpression and a point mutation in SMARCA4 can rescue growth inhibition exerted by the SMARCA2/4 inhibitor. Treatment of a UM xenograft model results in growth inhibition and regression which correlates with reduced expression of SOX10 but not discernible toxicity in the mice. Collectively, the data suggest a novel treatment of uveal melanoma.

Strengths:

There are many strengths of the study, including the strong challenge of the on-target effect, the assays used and the mechanistic data. The results are compelling as are the effects of the inhibitor. The in vivo data is dose-dependent and doses are low enough to be meaningful and associated with evidence of target engagement.

Weaknesses:

The authors have addressed weaknesses in the revised version.

Reviewer #3 (Public review):

Summary:

This manuscript reports the discovery of new compounds that selectively inhibit SMARCA4/SMARCA2 ATPase activity and have pronounced effects on uveal melanoma cell proliferation. They induce apoptosis and suppress tumor growth, with no toxicity in vivo. The report provides biological significance by demonstrating that the drugs alter chromatin accessibility at lineage specific gene enhancer regions and decrease expression of lineage specific genes, including SOX10 and SOX10 target genes.

Strengths:

The study provides compelling evidence for the therapeutic use of these compounds and does a thorough job at elucidating the mechanisms by which the drugs work. The study will likely have a high impact on the chromatin remodeling and cancer fields. The datasets will be highly useful to these communities.

Weaknesses:

The authors have addressed all my concerns.

Recommendations for the authors:

We would, however, like to draw the authors attention to 2 comments by the referees.

Referee 1 comments: While BAP1 mutant UM cell lines were included for some of the experiments, it seems the in-vivo data mentioned in the response to the reviewers comment is missing? The authors stated that "MP46 (Supplementary Fig. 3a) is BAP1null uveal melanoma cell line with no detectable protein expression (AmiroucheneAngelozzi et al., Mol Oncol 2014), and we have observed strong tumor growth inhibition in this CDX model with our BAF ATPase inhibitor." But the CDX model data shown in Figure 4 is from 92.1 cells. If this data is available, then the manuscript would benefit from its addition.

We thank the reviewer for bringing this to our attention. As the reviewer mentioned, we show 92-1 CDX model in our manuscript. Additionally, strong tumor growth inhibition was observed in MP-46 CDX model treated with our BAF ATPase inhibitor and can be found in Vaswani et al., 2025 (PMID:39801091, https://pubmed.ncbi.nlm.nih.gov/39801091/).

Referee 3 comments:

Supplementary Figure 2C

Is the T910M mutation in the parental MP41 cells heterozygous? If so, the authors should indicate this in the figure legend. If this is a homozygous mutation, the authors should explain how the inhibitors suppress SMARCA4 activity in cells that have a LOF mutation.

Could the authors please comment on these issues before a final version is posted online?

We thank the reviewer for bringing this to our attention. T910M mutation is heterozygous and the variant allele frequency for that mutation is 0.5. We updated the figure legend accordingly to reflect the genotype of the mutations highlighted in the table.

Reviewer #1 (Recommendations for the authors):

The authors have addressed most of the questions in their review.

While BAP1 mutant UM cell lines were included for some of the experiments, it seems the in-vivo data mentioned in the response to the reviewers comment is missing? The authors stated that "MP46 (Supplementary Fig. 3a) is BAP1-null uveal melanoma cell line with no detectable protein expression (Amirouchene-Angelozzi et al., Mol Oncol 2014), and we have observed strong tumor growth inhibition in this CDX model with our BAF ATPase inhibitor." But the CDX model data shown in Figure 4 is from 92.1 cells. If this data is available, then the manuscript would benefit from its addition.

Reviewer #3 (Recommendations for the authors):

Supplementary Figure 2C

Is the T910M mutation in the parental MP41 cells heterozygous? If so, the authors should indicate this in the figure legend. If this is a homozygous mutation, the authors should explain how the inhibitors suppress SMARCA4 activity in cells that have a LOF mutation.