Characteristics of cross-hybridization and cross-alignment of expression in pseudo-xenograft samples by RNA-Seq and microarrays

Camilo Valdes, Pearl Seo, Nicholas Tsinoremas, Jennifer Clarke

Exploring stromal changes associated with tumor growth and development is a growing area of oncologic research. In order to study molecular changes in the stroma it is recommended to separate tumor tissue from stromal tissue. This is relevant to xenograft models where tumors can be small and difficult to separate from host tissue. We introduce a novel definition of cross-alignment/cross-hybridization to compare qualitatively the ability of high-throughput mRNA sequencing, RNA-Seq, and microarrays to detect tumor and stromal expression from mixed 'pseudo-xenograft' samples vis-à-vis genes and pathways in cross-alignment (RNA-Seq) and cross-hybridization (microarrays). Samples consisted of normal mouse lung and human breast cancer cells; these were combined in fixed proportions to create a titration series of 25% steps. Our definition identifies genes in a given species (human or mouse) with undetectable expression in same-species RNA but detectable expression in cross-species RNA. We demonstrate the comparative value of this method and discuss its potential contribution in cancer research.