RNA-seq of isogenic panel of HAP1 cell lines knockout for chromatin remodeling encoding genes

Epigenetic dysregulation is a major cancer hallmark. Notably, deleterious mutations in genes encoding subunits of SWI/SNF (SWItch Sucrose Non-Fermentable), a major chromatin remodeling complex, occur in approximately 20% of human solid tumors. SWI/SNF mutations have been linked to poor patient outcome and no targeted therapy is currently available to treat patients with SWI/SNF-deficient tumors. SWI/SNF is a modular complex composed of 12-15 subunits encoded by 29 genes, which exist in three forms: canonical BRG1/BRM associated factor (cBAF), polybromo-associated BAF (PBAF) and non-canonical (ncBAF/GBAF), which have variable compositions, targets and effects on chromatin remodeling. Each complex includes core subunits (SMARCC1, SMARCC2, and SMARCD1-3) and one of the two mutually exclusive ATPase subunits (SMARCA2 or SMARCA4). Multiple variant subunits then define each complex's specificity: ARID1A/B and DPF1-3 for cBAF; ARID2, PBRM1, BRD7 and PHF10 for PBAF; GLTSCR1/1L and BRD9 for ncBAF2. SWI/SNF orchestrates multiple cellular functions, such as transcription regulation, differentiation, proliferation, DNA repair, and immunogenicity. Still, subunit-specific oncogenic mechanisms or targetable dependencies remain poorly understood. To identify intracellular alterations and genetic vulnerabilities induced by SWI/SNF defects at the complex or subunit level, we molecularly and functionally profiled an isogenic panel of HAP1 cell lines knockout (KO) for chromatin remodeling encoding genes, including seven SWI/SNF subunits mutants (SMARCB1-, SMARCA4-, SMARCA2-, ARID1A-, ARID1B-, ARID2- and PBRM1-KO), and six non-SWI/SNF mutants (CREBBP-, BAP1-, EED-, KMT2C-, KMT2D- and SETD2-KO). 70-80% confluent cells were harvested, and total RNA was extracted using Rneasy Mini Kit (Qiagen, 74104) with DNAse treatment, according to the manufacturer's instructions. Every RNA sample was quantified with a Qubit Fluorometer and evaluated for quality controls using Agilent 2100 Bioanalyzer Instrument (RRID:SCR_018043). After RNA Integrity Number (RIN) quality control, cDNA libraries were generated using the NEBNext Ultra II RNA Library Prep Kit (NEB #E7775) on Bravo Automated Liquid Handling Platform (RRID:SCR_026137). Subsequent indexed RNA sequencing of cDNA libraries with paired-end reads was performed according to the standard Illumina protocol using Illumina NovaSeq 6000 S2 Sequencing System (RRID:SCR_016387), with a target of 100Gb per sample.