Project description:While Chronic Myelogenous Leukemia (CML) is generally well controlled with Imatinib and other kinase inhibitors, blast crisis CML (bcCML) continues to be resistant to current therapies and remains highly lethal. Here we report a genome-wide in vivo CRISPR screen to better define the biological determinants of bcCML establishment and propagation in a physiologic context. This screen identified a large number of new genes and programs critically required for bcCML including those essential for chromatin remodeling, spliceosomal assembly, PLK1 and Myc signaling.
Project description:Here we report the genomic impact on murine bcCML by Sdc1 loss. We compare bcCML derived from a wildtype cell source to bcCML derived from a Sdc1 knockout mouse. This RNA-seq identifies a number of potential critical regulators of growth, migration, and adhesion.
Project description:Genome-wide CRISPR-Cas9 knockout screen using TKOv1 sgRNA library was performed in isogenic RBM10-proficient and RBM10-deficient HCC827 cells.
Project description:CRISPR-based loss-of-function screens have been proven powerful to identify genetic regulators in mammalian cells, but current approaches for single guide RNA (sgRNA) library construction are expensive and difficult to be adapted in most laboratories. Here, we present a Molecular Chipper technology for inexpensive and easily customizable sgRNA library generation, and a proof-of-principle screen that identifies novel cis-regulatory regions for miR-142 biogenesis. This method will be useful for functional interrogation of non-coding elements in mammalian genomes
Project description:While Chronic Myelogenous Leukemia (CML) is generally well controlled with Imatinib and other kinase inhibitors, blast crisis CML (bcCML) continues to be resistant to current therapies and remains highly lethal. In this study, we identify the double stranded RNA binding protein Stau2 as a as key new dependency of bcCML. To define the impact of Staufen2 in myeloid leukemia, we developed a germline knockout with targeted loss of its RNA binding domains. Genetic deletion of Staufen2 led to a profound decrease in bcCML growth and propagation, and markedly improved overall survival in mouse models. Further, Staufen2 was also expressed and required for growth of primary bcCML as well as de novo AML patient samples, indicating a conserved utilization across human disease. Finally, an integrated computational analysis of eCLIP, RNA-Seq analysis and the functional genomic CRISPR screen identified Staufen2 as a regulator of a remarkable network of broad acting chromatin modifiers, resulting in changes in global histone methylation patterns.
Project description:We performed a CRISPR-based functional genetic screen targeting CTCF binding elements (CBEs) located in the vicinity of ERα-bound enhancers. The screen identified four functional CBEs whose targeting resulted in a marked negative effect on the proliferation of MCF-7 cells (ERα-positive cells) but no significant effect on MDA-MB-231 (ERα-negative cells) cells. Here, we carried out GRO-seq analysis on MCF-7 cells induced with an sgRNA vector targeting one of the hits detected by the screen: sgRNA_1118, as well as non-targeting sgRNA and sg1830 as control.
Project description:Genome-wide CRISPR-Cas9 knockout screen using TKOv1 sgRNA library performed in isogenic RBM10-proficient and RBM10-deficient HCC827 cells.