title: Comparative RNA-Seq and microarray analysis of gene expression changes in B-cell lymphomas of Canis familiaris.
abstract: Comparative oncology is a developing research discipline that is being used to assist our understanding of human neoplastic diseases. Companion canines are a preferred animal oncology model due to spontaneous tumor development and similarity to human disease at the pathophysiological level. We use a paired RNA sequencing (RNA-Seq)/microarray analysis of a set of four normal canine lymph nodes and ten canine lymphoma fine needle aspirates to identify technical biases and variation between the technologies and convergence on biological disease pathways. Surrogate Variable Analysis (SVA) provides a formal multivariate analysis of the combined RNA-Seq/microarray data set. Applying SVA to the data allows us to decompose variation into contributions associated with transcript abundance, differences between the technology, and latent variation within each technology. A substantial and highly statistically significant component of the variation reflects transcript abundance, and RNA-Seq appeared more sensitive for detection of transcripts expressed at low levels. Latent random variation among RNA-Seq samples is also distinct in character from that impacting microarray samples. In particular, we observed variation between RNA-Seq samples that reflects transcript GC content. Platform-independent variable decomposition without a priori knowledge of the sources of variation using SVA represents a generalizable method for accomplishing cross-platform data analysis. We identified genes differentially expressed between normal lymph nodes of disease free dogs and a subset of the diseased dogs diagnosed with B-cell lymphoma using each technology. There is statistically significant overlap between the RNA-Seq and microarray sets of differentially expressed genes. Analysis of overlapping genes in the context of biological systems suggests elevated expression and activity of PI3K signaling in B-cell lymphoma biopsies compared with normal biopsies, consistent with literature describing successful use of drugs targeting this pathway in lymphomas.
authors.affiliation: Laboratory of Translational Medicine, Van Andel Research Institute, Grand Rapids, Michigan, United States of America.
authors.forename: Marie
authors.initials: M
authors.lastname: Mooney
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Bond
authors.forename: Noel
authors.initials: N
authors.lastname: Monks
authors.forename: Emily
authors.initials: E
authors.lastname: Eugster
authors.forename: David
authors.initials: D
authors.lastname: Cherba
authors.forename: Pamela
authors.initials: P
authors.lastname: Berlinski
authors.forename: Steve
authors.initials: S
authors.lastname: Kamerling
authors.forename: Keith
authors.initials: K
authors.lastname: Marotti
authors.forename: Heather
authors.initials: H
authors.lastname: Simpson
authors.forename: Tony
authors.initials: T
authors.lastname: Rusk
authors.forename: Waibhav
authors.initials: W
authors.lastname: Tembe
authors.forename: Christophe
authors.initials: C
authors.lastname: Legendre
authors.forename: Hollie
authors.initials: H
authors.lastname: Benson
authors.forename: Winnie
authors.initials: W
authors.lastname: Liang
authors.forename: Craig Paul
authors.initials: CP
authors.lastname: Webb
mesh_terms: D000818:Animals; D001482:Base Composition; D016000:Cluster Analysis; D004285:Dogs; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D014644:Genetic Variation; D016393:Lymphoma, B-Cell / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D020411:Oligonucleotide Array Sequence Analysis; D015398:Signal Transduction