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.

Pollen-Specific Activation of Arabidopsis Retrogenes Is Associated with Global Transcriptional Reprogramming

“…The only exception was a higher transcription of parents in pollen relative to seedlings in RNA sequencing (mean and quantile 1 samples; absent in the quantile 4 sample), while the opposite results were obtained using microarrays ( Figures 3A and 3F). This difference is due to the higher sensitivity of RNA sequencing technology to quantify transcripts from lowly transcribed genes (Mooney et al, 2013;Zhao et al, 2014). This partially applies also to retrogenes, as the upregulation in pollen versus seedling is more pronounced in RNA sequencing compared with microarrays ( Figure 3F).…”

The Transcriptional Landscape of Campylobacter jejuni under Iron Replete and Iron Limited Growth Conditions

“…However while microarray studies are instructive, they are being increasingly eclipsed by the utility of next generation high throughput sequencing (HTS) technologies [11]. Several studies have indicated that HTS technologies can determine gene expression level more accurately than microarrays [12,13], and also offer exciting insight into the transcript structures present under each condition studied [11,14,15]. The RpoN regulon of C. jejuni has been characterized by profiling the transcriptome of an rpoN mutant using HTS and compared to results previously obtained using microarray technologies [16].…”

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

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