ABSTRACT
Functional genomics approaches can overcome limitations-such as the lack of identification of robust targets and poor clinical efficacy-that hamper cancer drug development. Here we performed genome-scale CRISPR-Cas9 screens in 324 human cancer cell lines from 30 cancer types and developed a data-driven framework to prioritize candidates for cancer therapeutics. We integrated cell fitness effects with genomic biomarkers and target tractability for drug development to systematically prioritize new targets in defined tissues and genotypes. We verified one of our most promising dependencies, the Werner syndrome ATP-dependent helicase, as a synthetic lethal target in tumours from multiple cancer types with microsatellite instability. Our analysis provides a resource of cancer dependencies, generates a framework to prioritize cancer drug targets and suggests specific new targets. The principles described in this study can inform the initial stages of drug development by contributing to a new, diverse and more effective portfolio of cancer drug targets.
Subject(s)
CRISPR-Cas Systems/genetics , Drug Discovery/methods , Gene Editing , Molecular Targeted Therapy/methods , Neoplasms/genetics , Neoplasms/therapy , Animals , Biomarkers, Tumor/genetics , Cell Line, Tumor , Female , Genome, Human/genetics , Humans , Mice , Microsatellite Instability , Neoplasm Transplantation , Neoplasms/classification , Neoplasms/pathology , Organ Specificity , Reproducibility of Results , Synthetic Lethal Mutations/genetics , Werner Syndrome/genetics , Werner Syndrome Helicase/geneticsSubject(s)
Biomedical Research/methods , Information Dissemination/ethics , Molecular Probes/chemistry , Small Molecule Libraries/chemistry , Biomedical Research/instrumentation , Humans , Intellectual Property , Internet , Molecular Probes/pharmacology , Molecular Weight , Sensitivity and Specificity , Small Molecule Libraries/pharmacologyABSTRACT
The poly-(ADP-ribose) polymerase (PARP) inhibitor, MK-4827, is a novel potent, orally bioavailable PARP-1 and PARP-2 inhibitor currently in phase I clinical trials for cancer treatment. No preclinical data currently exist on the combination of MK-4827 with radiotherapy. The current study examined combined treatment efficacy of MK-4827 and fractionated radiotherapy using a variety of human tumor xenografts of differing p53 status: Calu-6 (p53 null), A549 (p53 wild-type [wt]) and H-460 (p53 wt) lung cancers and triple negative MDA-MB-231 human breast carcinoma. To mimic clinical application of radiotherapy, fractionated radiation (2 Gy per fraction) schedules given once or twice daily for 1 to 2 weeks combined with MK-4827, 50 mg/kg once daily or 25 mg/kg twice daily, were used. MK-4827 was found to be highly and similarly effective in both radiation schedules but maximum radiation enhancement was observed when MK-4827 was given at a dose of 50 mg/kg once daily (EF = 2.2). MK-4827 radiosensitized all four tumors studied regardless of their p53 status. MK-4827 reduced PAR levels in tumors by 1 h after administration which persisted for up to 24 h. This long period of PARP inhibition potentially adds to the flexibility of design of future clinical trials. Thus, MK-4827 shows high potential to improve the efficacy of radiotherapy.
Subject(s)
Antineoplastic Agents/administration & dosage , Breast Neoplasms/therapy , Indazoles/administration & dosage , Lung Neoplasms/therapy , Piperidines/administration & dosage , Poly(ADP-ribose) Polymerase Inhibitors , Animals , Breast Neoplasms/metabolism , Breast Neoplasms/pathology , Chemoradiotherapy , Female , Humans , Lung Neoplasms/metabolism , Lung Neoplasms/pathology , Mice , Mice, Nude , Poly(ADP-ribose) Polymerases/metabolism , Tumor Burden , Xenograft Model Antitumor AssaysABSTRACT
BACKGROUND: In hepatocellular carcinoma (HCC) genes predictive of survival have been found in both adjacent normal (AN) and tumor (TU) tissues. The relationships between these two sets of predictive genes and the general process of tumorigenesis and disease progression remains unclear. METHODOLOGY/PRINCIPAL FINDINGS: Here we have investigated HCC tumorigenesis by comparing gene expression, DNA copy number variation and survival using â¼250 AN and TU samples representing, respectively, the pre-cancer state, and the result of tumorigenesis. Genes that participate in tumorigenesis were defined using a gene-gene correlation meta-analysis procedure that compared AN versus TU tissues. Genes predictive of survival in AN (AN-survival genes) were found to be enriched in the differential gene-gene correlation gene set indicating that they directly participate in the process of tumorigenesis. Additionally the AN-survival genes were mostly not predictive after tumorigenesis in TU tissue and this transition was associated with and could largely be explained by the effect of somatic DNA copy number variation (sCNV) in cis and in trans. The data was consistent with the variance of AN-survival genes being rate-limiting steps in tumorigenesis and this was confirmed using a treatment that promotes HCC tumorigenesis that selectively altered AN-survival genes and genes differentially correlated between AN and TU. CONCLUSIONS/SIGNIFICANCE: This suggests that the process of tumor evolution involves rate-limiting steps related to the background from which the tumor evolved where these were frequently predictive of clinical outcome. Additionally treatments that alter the likelihood of tumorigenesis occurring may act by altering AN-survival genes, suggesting that the process can be manipulated. Further sCNV explains a substantial fraction of tumor specific expression and may therefore be a causal driver of tumor evolution in HCC and perhaps many solid tumor types.
Subject(s)
Carcinoma, Hepatocellular/genetics , DNA Copy Number Variations , Gene Expression Profiling , Liver Neoplasms/genetics , Liver/metabolism , Adult , Aged , Animals , Cell Line, Tumor , Chromosomes, Human, Pair 1/genetics , Female , Gene Regulatory Networks , Humans , Liver/pathology , Male , Mice , Mice, Transgenic , Middle Aged , Models, Genetic , Oligonucleotide Array Sequence Analysis , Proto-Oncogene Proteins c-met/genetics , Regression AnalysisABSTRACT
A series of N-(1,3-thiazol-2-yl)pyridin-2-amine KDR kinase inhibitors have been developed that possess optimal properties. Compounds have been discovered that exhibit excellent in vivo potency. The particular challenges of overcoming hERG binding activity and QTc increases in vivo in addition to achieving good pharmacokinetics have been acomplished by discovering a unique class of amine substituents. These compounds have a favorable kinase selectivity profile that can be accentuated with appropriate substitution.
