Targeting the SWI/SNF Chromatin Remodeling Complex Subunit SMARCA4 in ALL
Bibliographic record
Abstract
Background: B-cell-derived acute lymphoblastic leukemia (B-ALL) is a type of blood cancer characterized by the overproduction of immature lymphocytes and is the most common cancer in children. The current overall survival (OS) rates for children with B-ALL are nearly 90% when diagnosed with good- and intermediate-risk subtypes. However, OS rates for children diagnosed with high-risk subtypes, such as KMT2A-Rearranged (KMT2A-R) and Philadelphia-like (Ph-like), are significantly lower, highlighting the urgent need to identify critical leukemogenic pathways for targeted therapeutic interventions. SMARCA4 is part of the SWI/SNF chromatin-remodeling complex, which is crucial for regulating gene expression by altering chromatin structure. SMARCA4 is mutated in about 10% of non-small cell lung cancer patients, resulting in significantly lower OS. More recently, SMARCA4 has been identified as essential for early B cell development, identity, and growth. However, its importance in ALL has not been studied. Results: We performed single-cell DNA sequencing experiments paired with meta-analyses of whole exome and whole genome sequencing data from 1717 patients with B-ALL. We found that SMARCA4 is only mutated in 0.35% of patients with B-ALL, suggesting that, unlike in non-small cell lung cancer, SMARCA4 mutations may not benefit ALL growth. Gene expression analysis of B cells at different developmental stages demonstrated that SMARCA4 is specifically upregulated during early B cell development (early pro-B to small pre-B stages), overlapping with the stages where ALL cells are arrested. Direct comparisons of human pre-B cells, B-ALL, CD34+, and T-ALL showed that pre-B cells and B-ALL cells have the highest SMARCA4 expression levels, indicating a potential dependency of B-ALL on SMARCA4. Analysis using the DepMAP portal confirmed that B-ALL cells are highly dependent on SMARCA4, confirming that a SMARCA4 inhibitor-based therapy may be beneficial for children with B-ALL. However, survival analysis of 207 children from the COG trial P9906 indicated no impact on patient outcomes from varying SMARCA4 expression levels. When we separated the patients based on their B-ALL subtype, we found that SMARCA4 was significantly highly expressed in children with Ph-like ALL than in those with KMT2A-R B-ALL, which we confirmed via Western blotting using Ph-like and KMT2A-R ALL cell lines. A survival analysis focused on these subtypes revealed that poor outcomes correlated with higher SMARCA4 expression in Ph-like ALL, while, surprisingly, high SMARCA4 expression levels correlated with good outcomes in KMT2A-R ALL. Based on these results, we hypothesized that Ph-like ALL, but not KMT2A-R B-ALL, may depend on high SMARCA4 expression levels. Validating our hypothesis, pharmacologic SMARCA4 inhibition using two recently developed inhibitors (BRM014 and FHD-286) showed that Ph-like B-ALL was significantly more sensitive to SMARCA4 inhibition compared to KMT2A-R ALL. KMT2A-R cell lines were highly resistant to both inhibitors, while Ph-like cells were highly sensitive, with IC50s for BRM014 at 10-50nM and 1nM for FHD-286. Conclusion: Our results identify that SMARCA4 has a very low mutation frequency in B-ALL and is highly expressed in Ph-like B-ALL. Furthermore, we demonstrate a direct correlation between high SMARCA4 expression and poor patient outcomes, as well as a clear dependency of Ph-like B-ALL on SMARCA4. Based on our data, applying a SMARCA4 inhibitor-based therapy may specifically benefit patients with Ph-like B-ALL.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".