Ruda, V. | bioRxiv Science

bioRxiv2025

Transcriptional changes in non-human primate tissues after intrathecal delivery of serotype 9 adeno-associated viral vector: insights into organ toxicities

Adeno associated virus (AAV)-based gene transfer has brought transformative therapeutic benefits to patients with otherwise untreatable genetic diseases. However, treatment-related organ toxicities, particularly for high doses, remain a safety concern in the clinic with some translatability in preclinical species. In the present study, we conducted an RNAseq analysis in non-human primates administered intrathecally with scAAV9-CBA-GFP, empty viral capsid particles, or a Promoterless vector. This analysis revealed a broad and long-lasting (4 weeks after dosing) transcriptional impact of the viral transduction/transgene expression on tissues. Liver and DRG, known to be primary sites of toxicity induced by AAV9, had the highest viral load and the most significant transcriptional changes. Our analysis revealed that most of the differentially expressed genes were upregulated, and common gene signatures belonged to immune pathways (innate and adaptive), demonstrating a persistent low-grade immune response up to four weeks post-dosing. Interestingly and across all tissues considered, the impact of empty capsids or of the Promoterless vector was minimal, suggesting that both the presence of the capsid and of a productive viral genome contributed to the observed changes. This study provides a unique insight into the transcriptional responses to AAV9 in key tissues primarily exposed by the vector.

molecular biology↗

bioRxiv2019

In-Depth Characterization and Validation in BRG1-Mutant Lung Cancers Define Novel Catalytic Inhibitors of SWI/SNF Chromatin Remodeling

Members of the ATP-dependent SWI/SNF chromatin remodeling complexes are among the most frequently mutated genes in cancer, suggesting their dysregulation plays a critical role. The synthetic lethality between SWI/SNF catalytic subunits BRM/SMARCA2 and BRG1/SMARCA4 has instigated great interest in targeting BRM. Here we have performed a critical and in-depth investigation of novel dual inhibitors (BRM011 and BRM014) of BRM and BRG1 in order to validate their utility as chemical probes of SWI/SNF catalytic function, while obtaining insights into the therapeutic potential of SWI/SNF inhibition. In corroboration of on-target activity, we discovered compound resistant mutations through pooled screening of BRM variants in BRG1-mut cancer cells. Strikingly, genome-wide transcriptional and chromatin profiling (ATAC-Seq) provided further evidence of pharmacological perturbation of SWI/SNF chromatin remodeling as BRM011 treatment induced specific changes in chromatin accessibility and gene expression similar to genetic depletion of BRM. Finally, these compounds have the capacity to inhibit the growth of tumor-xenografts, yielding important insights into the feasibility of developing BRM/BRG1 ATPase inhibitors for the treatment of BRG1-mut lung cancers. Overall, our studies not only establish the feasibility of inhibiting SWI/SNF catalytic function, providing a framework for SWI/SNF therapeutic targeting, but have also yielded successful elucidation of small-molecule inhibitors that will be of importance in probing SWI/SNF function in various disease contexts.

cancer biology↗