Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models

BMC Bioinformatics

Proceedings

Rosie H Xing¹  James L Chen²  Yong Huang³  Younghee Lee³  Xinan Yang³  Yves A Lussier⁴ 

[1] Dept. of Pathology and of Radiation and Cellular Oncology, University of Chicago, IL, USA;UC Comprehensive Cancer Centre; Ludwig Centre for Metastasis Research, University of Chicago, IL, USA;Sect. of Hematology/Oncology, Dept. of Medicine, University of Chicago, IL, USA;Section of Genetic Medicine, Dept. of Medicine, University of Chicago, IL, USA;Section of Genetic Medicine, Dept. of Medicine, University of Chicago, IL, USA;UC Comprehensive Cancer Centre; Ludwig Centre for Metastasis Research, University of Chicago, IL, USA;Institute of Genomics and Systems Biology, Institute for Translational Medicine; Computational Institute, University of Chicago, IL, USA;

关键词: Gene Ontology;    Xenograft Model;    Laser Capture Microdissection;    Mouse Homolog;    Stromal Microenvironment;   

DOI  :  10.1186/1471-2105-11-S9-S11

来源: Springer

【 摘 要 】

BackgroundMouse xenograft models, in which human cancer cells are implanted in immune-suppressed mice, have been popular for studying the mechanisms of novel therapeutic targets, tumor progression and metastasis. We hypothesized that we could exploit the interspecies genetic differences in these experiments. Our purpose is to elucidate stromal microenvironment signals from probes on human arrays unintentionally cross-hybridizing with mouse homologous genes in xenograft tumor models.ResultsBy identifying cross-species hybridizing probes from sequence alignment and cross-species hybridization experiment for the human whole-genome arrays, deregulated stromal genes can be identified and then their biological significance were predicted from enrichment studies. Comparing these results with those found by the laser capture microdissection of stromal cells from tumor specimens resulted in the discovery of significantly enriched stromal biological processes.ConclusionsUsing this method, in addition to their primary endpoints, researchers can leverage xenograft experiments to better characterize the tumor microenvironment without additional costs. The Xhyb probes and R script are available at http://www.lussierlab.org/publications/Stroma

【 授权许可】

Unknown   
© Yang et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.