Characteristics of Cross-Hybridization and Cross-Alignment in Pseudo-Xenograft samples by RNA-Seq and Microarrays [Illumina HumanWG-6 v3.0]

In order to study molecular changes in the stroma from tissue samples it is recommended to separate tumor tissue from stromal tissue. This is particularly relevant to mouse tumor xenograft models where tumor, particularly metastatic tumors, can be small and difficult to separate from the host tissue. In our research we compared qualitatively the ability of high-throughput mRNA sequencing, RNA-Seq, and microarrays to detect tumor (human) and stromal (mouse) expression from mixed tumor-stromal samples in terms of the genes and pathways that are involved in cross-alignment (RNA-Seq) and cross-hybridization (microarrays). Human samples consisted of total RNA obtained from MDA-MB-231 human breast carcinoma cell line and isolated from three independent cultures of sub-confluent MDA-MB-231 cell lines in exponential phase of growth. Mouse samples were obtained from NOD scid gamma mice, and normal lung tissue was harvested from three independent age-matched mice.

为探究组织样本中基质的分子变化，需将肿瘤组织与基质组织分离。这一要求在小鼠肿瘤异种移植模型中尤为关键——此类模型中的肿瘤（尤其是转移性肿瘤）往往体积较小，难以与宿主组织分离。本研究通过定性分析，比较了高通量mRNA测序（RNA-Seq）与基因芯片（microarrays）两种技术在混合肿瘤-基质样本中检测人源肿瘤与鼠源基质基因表达的能力，分析维度涵盖涉及跨序列比对（RNA-Seq）与交叉杂交（基因芯片）的基因及信号通路。人源样本为MDA-MB-231人乳腺癌细胞系的总RNA，该RNA分别从3株处于指数生长期的亚汇合MDA-MB-231细胞独立培养物中分离获得。鼠源样本取自NOD scid gamma小鼠的正常肺组织，该组织采集自3只同年龄段的独立小鼠。