Unknown,Transcriptomics,Genomics,Proteomics

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Dual-species microarray for assessing gene expression in stromal microenvironment, cancer cells and their interactions (v2 array)

ABSTRACT: Design a human-mouse dual-species microarray to provide a technology for investigation of cancer-stromal interaction in xenograft model. The 2 reference RNA were used to evaluate and identify probes with potential the cross-species hybridization, so that we can label these probes and exclude them before analysis of biological samples/data. Reference RNA from human and mouse were labeled using Cy3. Samples were hybridized on customized-commercial array with Agilent probes and user-designed species-specific probes (Human-mouse dual-species array HomoMus_v2). This array is designed and improved from hte first version GPL10714

ORGANISM(S): Mus musculus

SUBMITTER: Yong Huang

PROVIDER: E-GEOD-23364 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Intratracheal application of bleomycin is known to induce inflammatory and fibrotic reactions in the lung within a short period of time and histological features include infiltration of inflammatory cells, collagen deposition and obliteration of alveolar spaces. Because some of these features are found in patients with idiopathic pulmonary fibrosis (IPF), the bleomycin-induced lung fibrosis animal model is commonly used. However, exploratory treatments that were successfully used in this animal model and progressed to clinical trials lacked significant efficacy in humans. Here, the bleomycin-induced rat lung fibrosis model was studied using whole genome expression data that was collected at various time points and the relevance to human disease was evaluated through comparison with whole genome expression data from IPF patient-derived lung biopsies. The highest gene expression correlation between both species was observed in animals 7 days after bleomycin instillation. These gene expression signatures helped to identify a set of twelve novel disease-relevant translational gene markers that were able to separate IPF patients from controls. Furthermore, three Wnt/-catenin pathway-related genes that belong to this translational gene marker set showed, together with clinical diffusing capacity of the lung for carbon monoxide (DLCO) measurements, the potential to stratify IPF patients according to disease severity. Pirfenidone attenuated a subset of the translational gene markers in the bleomycin-induced fibrosis model, in particular those related to Wnt/-catenin-signaling. This novel translational gene marker panel offers improved possibilities to evaluate disease-modifying efficacy of novel therapeutic concepts in the bleomycin-induced rat lung fibrosis model and could be applied as a diagnostic and prognostic tool for IPF patient care. Comparison of bleomycin-treated and control rats after 3 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 6 weeks and 8 weeks; 5 animals per group

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Dual-species microarray for assessing gene expression in stromal microenvironment, cancer cells and their interactions (v2 array)

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