Automated Scale-up and Maintenance of Stem Cell-Induced Neurons for Long-Term Culture and High-Throughput Screening

Successful drug screens benefit from testing large compound libraries in biologically relevant models. Recent advancements in the reprogramming of somatic cells to pluripotent stem (iPS) cells and the methods to differentiate such cells into tissue-specific cell types have allowed for increased reliability and scale-up of more relevant cell models. Specifically, the method of inducing iPSC and ESCs to cortical excitatory neurons by expression of NGN2 has made scale-up for HTS possible, but challenges such as increased risk of contamination, stability of growth media, plate coatings, and frequent media changes remain. Here we present a method for expanding and differentiating iPSC and ESCs into induced neurons (iNs) using a CompacT SelecT for up to 48 days and the subsequent plating and maintaining of the cells in 1536 well plates using a GNF Systems automated screening system for up to 14 days. We were able to demonstrate that cells cultured using these methods maintained the phenotype of NGN2-induced neurons through expression profiling with single-cell qPCR and protein expression and localization by immuno-fluorescence. We were further able to show that iN cells frozen after a 48 hour induction can be re-plated into 1536 well plates and maintain the same gene expression profiles, allowing for batched cell banking. These methods allow for the successful scale-up and long-term culture of iN cells to enable HTS

Exquisite Sensitivity to Dual BRG1/BRM ATPase Inhibitors Reveals Broad SWI/SNF Dependencies in Acute Myeloid Leukemia

Various subunits of mammalian SWI/SNF chromatin remodeling complexes display loss-of- function mutations characteristic of tumor suppressors in different cancers, but an additional role for SWI/SNF supporting cell survival in distinct cancer contexts is emerging. In particular, dependence on the catalytic subunit BRG1/SMARCA4 has been observed in acute myeloid leukemia (AML), yet the feasibility of direct therapeutic targeting of SWI/SNF catalytic activity in leukemia remains unknown. Here, we evaluated the activity of BRG1/BRM ATPase inhibitors across a genetically diverse panel of cancer cell lines and observed that hematopoietic cancer cell lines were among the most sensitive compared to other lineages. This result was striking in comparison to data from pooled short hairpin RNA screens, which showed that only a subset of leukemia cell lines display sensitivity to BRG1 knockdown. We demonstrate that combined genetic knockdown of BRG1 and BRM is required to recapitulate the effects of dual inhibitors, suggesting that SWI/SNF dependency in human leukemia extends beyond a predominantly BRG1-driven mechanism. Through gene expression and chromatin accessibility studies, we show that the dual inhibitors act at genomic loci associated with oncogenic transcription factors, and observe a downregulation of leukemic pathway genes including MYC, a well-established target of BRG1 activity in AML. Overall, small molecule inhibition of BRG1/BRM induced common transcriptional responses across leukemia models resulting in a spectrum of cellular phenotypes. Our studies reveal the breadth of SWI/SNF dependency and support targeting SWI/SNF catalytic function as a potential therapeutic strategy in AML

LXH254, a Potent and Selective ARAF-Sparing Inhibitor of BRAF and CRAF for the Treatment of MAPK-Driven Tumors

Purpose: Targeting RAF for anti-tumor therapy in RAS-mutant tumors holds promise. Herein we describe in detail novel properties of the type II RAF inhibitor LXH254. Experimental Design: LXH254 was profiled in biochemical, in vitro, and in vivo assays including examining the activities of the drug in a large panel of cancer-derived cell lines, and a comprehensive set of in vivo models. In addition, activity of LXH254 was assessed in cells where different sets of RAF paralogs were ablated, or that expressed kinase-impaired and dimer-deficient variants of ARAF. Results: We describe an unexpected paralog selectivity of LXH254, which is able to potently inhibit BRAF and CRAF, but has less activity against ARAF. LXH254 was active in models harboring BRAF alterations, including atypical BRAF alterations co-expressed with mutant K/NRAS, and NRAS mutants, but had only modest activity in KRAS mutants. In RAS mutant lines loss of ARAF, but not BRAF or CRAF, sensitized cells to LXH254. ARAF-mediated resistance to LXH254 required both kinase function and dimerization. Higher concentrations of LXH254 were required to inhibit signaling in RAS-mutant cells expressing only ARAF relative to BRAF or CRAF. Moreover, specifically in cells expressing only ARAF, LXH254 caused paradoxical activation of MAPK signaling in a manner similar to dabrafenib. Lastly, in vivo, LXH254 drove complete regressions of isogenic variants of RAS mutant cells lacking ARAF expression, while parental lines were only modestly sensitive. Conclusions: LXH254 is a novel RAF-inhibitor able to inhibit dimerized BRAF and CRAF as well as monomeric BRAF while largely sparing ARAF

CYP27A1 dependent anti-melanoma activity of limonoid natural products targets mitochondrial metabolism

Three limonoid natural products with selective anti-proliferative activity against BRAF(V600E) and NRAS(Q61K)-mutation dependent melanoma cell lines were identified. Differential transcriptome analysis revealed dependency of compound activity on expression of the mitochondrial cytochrome P450 oxidase CYP27A1, a transcriptional target of MITF. We determined that CYP27A1 activity is necessary for the generation of a reactive metabolite that proceeds to inhibit cellular proliferation. A genome-wide siRNA screen in combination with chemical proteomics experiments revealed genedrug functional epistasis, suggesting that these compounds target mitochondrial biogenesis and inhibit tumor bioenergetics. Our work suggests a strategy for melanoma specific targeting by exploiting the expression of MITF target gene CYP27A1 and inhibiting mitochondrial oxidative phosphorylation in BRAF mutant melanomas