title: RNA-Seq Differentiates Tumour and Host mRNA Expression Changes Induced by Treatment of Human Tumour Xenografts with the VEGFR Tyrosine Kinase Inhibitor Cediranib.
abstract: Pre-clinical models of tumour biology often rely on propagating human tumour cells in a mouse. In order to gain insight into the alignment of these models to human disease segments or investigate the effects of different therapeutics, approaches such as PCR or array based expression profiling are often employed despite suffering from biased transcript coverage, and a requirement for specialist experimental protocols to separate tumour and host signals. Here, we describe a computational strategy to profile transcript expression in both the tumour and host compartments of pre-clinical xenograft models from the same RNA sample using RNA-Seq. Key to this strategy is a species-specific mapping approach that removes the need for manipulation of the RNA population, customised sequencing protocols, or prior knowledge of the species component ratio. The method demonstrates comparable performance to species-specific RT-qPCR and a standard microarray platform, and allowed us to quantify gene expression changes in both the tumour and host tissue following treatment with cediranib, a potent vascular endothelial growth factor receptor tyrosine kinase inhibitor, including the reduction of multiple murine transcripts associated with endothelium or vessels, and an increase in genes associated with the inflammatory response in response to cediranib. In the human compartment, we observed a robust induction of hypoxia genes and a reduction in cell cycle associated transcripts. In conclusion, the study establishes that RNA-Seq can be applied to pre-clinical models to gain deeper understanding of model characteristics and compound mechanism of action, and to identify both tumour and host biomarkers.
authors.affiliation: Oncology, AstraZeneca Pharmaceuticals, Alderley Park, Cheshire, United Kingdom.
authors.forename: James R
authors.initials: JR
authors.lastname: Bradford
authors.forename: Matthew
authors.initials: M
authors.lastname: Farren
authors.forename: Steve J
authors.initials: SJ
authors.lastname: Powell
authors.forename: Sarah
authors.initials: S
authors.lastname: Runswick
authors.forename: Susie L
authors.initials: SL
authors.lastname: Weston
authors.forename: Helen
authors.initials: H
authors.lastname: Brown
authors.forename: Oona
authors.initials: O
authors.lastname: Delpuech
authors.forename: Mark
authors.initials: M
authors.lastname: Wappett
authors.forename: Neil R
authors.initials: NR
authors.lastname: Smith
authors.forename: T Hedley
authors.initials: TH
authors.lastname: Carr
authors.forename: Jonathan R
authors.initials: JR
authors.lastname: Dry
authors.forename: Neil J
authors.initials: NJ
authors.lastname: Gibson
authors.forename: Simon T
authors.initials: ST
authors.lastname: Barry
mesh_terms: D000818:Animals; D002289:Carcinoma, Non-Small-Cell Lung / Q000188:drug therapy* / Q000235:genetics; D002453:Cell Cycle / Q000187:drug effects; D015687:Cell Hypoxia / Q000187:drug effects; D045744:Cell Line, Tumor; D019295:Computational Biology; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D053263:Gene Regulatory Networks / Q000187:drug effects*; D006801:Humans; D008175:Lung Neoplasms / Q000188:drug therapy* / Q000235:genetics; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D047428:Protein Kinase Inhibitors / Q000008:administration & dosage* / Q000494:pharmacology; D011799:Quinazolines / Q000008:administration & dosage* / Q000494:pharmacology; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods*; D013045:Species Specificity; D023041:Xenograft Model Antitumor Assays; D007211:Indoles
chemical_list: D047428:Protein Kinase Inhibitors; D011799:Quinazolines; C500926:cediranib; D007211:Indoles