Precision oncology probe set for nomination of biomarker driven intervention opportunities in lung cancer

Diversity in the genetic lesions that drive cancer initiation and progression is extreme. In consequence, a pressing challenge is the development of pharmaceuticals that selectively target disease mechanisms within the appropriate cancer patients. To help delineate the landscape of opportunities that can address this challenge, we have employed a chemistry-first discovery paradigm for de novo identification of druggable targets linked to robust patient selection hypotheses. To do this, a 200,000 compound diversity-oriented chemical library was profiled across a heavily annotated test-bed of >100 cell models representative of the somatic lesions detected in lung cancer. 171 distinct chemical/genetic associations, exploiting disease-selective mechanistic vulnerabilities within a diverse array of biological systems, were discovered. These corresponded to both novel and known oncogenotypes detectable within significant patient populations that lack effective therapy. Chemically addressab le addictions to ciliogenesis in TTC21B mutants and GLUT8-dependent serine biosynthesis in KRAS/KEAP1 double mutants are prominent examples. These observations indicate a wealth of actionable opportunities within the complex molecular etiology of cancer. One chemical in the screen corrected with high expression levels of the positive regulator of the TLR pathway, PELI2, and high expression of PELI2 was predictive of chemical sensitivities outside the training set. SW151511 was thus selected for delineation of global changes in gene expression pattern in response to chemical perturbation. In this experiment, two SW151511-sensitive cells (H596 and H2122) and two SW151511-resistant cells (H661, HCC366) were treated for 24 hours with 10 uM of either chemical or DMSO. After which, microarray expression profiles were determined using Illumina BeadArray V4 and normalized with lumi in R bioconductor. All cells were seeded in 6-well plates at 300,000 cells/well in 2 mL standard culture media (RPMI, 5%FBS, penicillin/streptomycin) and allowed to adhere overnight. The media was discarded and replaced with 1.5 mL treatment media containing either 0.1% DMSO vehicle control, or 10 uM of SW compound. After 24 hrs of treatment, total RNA was harvested using the miRNeasy Qiagen kit according to the manufacturer's instructions.