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

Xinan Yang, Younghee Lee, Yong Huang, James L. Chen, Rosie H. Xing, Yves A Lussier

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Background: Mouse 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.Results: By 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.Conclusions: Using 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.

Original languageEnglish (US)
Article numberS11
JournalBMC Bioinformatics
Volume11
Issue numberSUPPL. 9
DOIs
StatePublished - Oct 28 2010
Externally publishedYes

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Biological Phenomena
Heterografts
Gene expression
Gene Expression
Tumors
Tumor
Mouse
Probe
Genes
Neoplasms
Microdissection
Laser Capture Microdissection
Gene
Experiment
Tumor Microenvironment
Metastasis
Sequence Alignment
Experiments
Cell
Human Genome

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics
  • Structural Biology

Cite this

Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models. / Yang, Xinan; Lee, Younghee; Huang, Yong; Chen, James L.; Xing, Rosie H.; Lussier, Yves A.

In: BMC Bioinformatics, Vol. 11, No. SUPPL. 9, S11, 28.10.2010.

Research output: Contribution to journalArticle

Yang, Xinan ; Lee, Younghee ; Huang, Yong ; Chen, James L. ; Xing, Rosie H. ; Lussier, Yves A. / Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models. In: BMC Bioinformatics. 2010 ; Vol. 11, No. SUPPL. 9.
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