RNA-seq analysis of NCI-H1693 cells treated with the selective SMARCA2 degrader PRT3789

The goal of this study was to examine the transcriptional consequences of selective SMARCA2 degradation in a SMARCA4-deficient non-small cell lung cancer (NSCLC) model. NCI-H1693 cells were treated with the SMARCA2 degrader PRT3789 (50 nM) or vehicle control for 6 h, 48 h, and 72 h. RNA-seq was performed to identify changes in gene expression that could reveal pathways associated with synthetic lethality and clarify the mechanism of action of SMARCA2 degraders in the absence of SMARCA4. For each of three time points (6 h, 48 h, 72 h), NCI-H1693 cells were treated with PRT3789 (50 nM) or DMSO control in triplicate. Cell pellets were collected, flash-frozen, and shipped to GENEWIZ (now Azenta Life Sciences) for RNA extraction, library preparation, and sequencing. Poly(A)-enriched stranded mRNA libraries were prepared and sequenced on an Illumina platform to generate paired-end 150 bp reads. Downstream analysis, including quality control, read alignment to the human reference genome (GRCh38), and quantification of gene-level counts, was performed using Pluto Bio (https://pluto.bio). Briefly, paired-end FASTQ files were processed using the nf-core/rnaseq pipeline (v3.17.0) (auto strandedness). Adapter sequences were removed with Trim Galore. Reads were aligned with STAR to GRCh38 (NCBI, p.14, release 110) and quantified to gene counts using RSEM.