Juan Martinez Villalobos

CRISPR screening is a powerful technique that allows researchers to systematically study gene function across entire genomes. Whether you are new to CRISPR screens or looking to strengthen your analysis skills, this workshop will guide you through the essentials of CRISPR screen analysis. We will break down complex analysis workflows into manageable steps and introduce you to MAGeCKFlute, a popular analysis pipeline used by many researchers in the field.

Small cell lung cancer (SCLC), characterized by rapid proliferation, early metastasis, and a dismal 5-year survival rate below 8%, remains the most aggressive form of lung cancer (Szczepanski, A., et al, 2024). Dissecting the mechanisms that promote the development of SCLC will result in the identification of novel therapeutic targets and strategies. Genomic analyses of human SCLC tumors have uncovered near-universal bi-allelic inactivation of the tumor suppressor genes Trp53 and Rb1, and frequent inactivating mutations in genes that encode for epigenetic regulators (ref). In line with these observations, we have identified mutations in genes that encode for subunits of the mammalian switch/sucrose non-fermentable (mSWI/SNF) complexes which exist in three main forms (BAF, PBAF and ncBAF). More specifically, we have found that the PBAF complex is mutated in 15-20% of human SCLC tumors. To study the function of PBAF in SCLC, we have employed CRISPR/Cas9 technology to systematically inactivate all specific PBAF subunits (Pbrm1, Arid2, Brd7, and Phf10) in a premalignant model of SCLC. To interrogate the transcriptional and epigenetic mechanisms underlying PBAF-deficient SCLCs, this study employs a multi-omics approach (i.e., RNA-seq, ATAC-seq, and CUT&RUN). Preliminary results demonstrate that PBAF-deficiency is associated with alterations in chromatin accessibility that correlate with gene expression changes and histone marks at key regulatory regions including the transcriptional start site (TSS) of genes involved in SCLC. This work presents the first dissection of the epigenetic and transcriptomic landscape of PBAF-deficient SCLC tumors, offering novel mechanistic insights and contributing to a deeper understanding of SCLC biology