Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of human breast tumors and their paired normal tissues

ABSTRACT: Microarray is widely used to monitor gene expression changes in breast cancer. The transcriptomic changes in breast cancer is commonly occured during the transition of normal cells to cancerous cells. This is the first study on gene expression profiling of multi ethnic of Malaysian breast cancer patients (Malays, Chinese and Indian). We aim to identify differentially expressed genes between tumors and normal tissues. We have identified a set of 33 significant differentially expressed genes in the tumor vs. normal group at p<0.001. We study the gene expression patterns of 43 breast tumors and their paired normal control by using Affymetrix genechip U133A. We have identified a set of 33 significant differentially expressed genes in the tumor vs. normal group at p<0.001. Experiment Overall Design: Total RNAs were extracted from breast cancer and normal tissues. Samples were processed and hybridized on the chip for 16 hours. At the end of the study, we obtained a total of 86 set of gene expression data, which were from 43 tumors and 43 normal tissues. The gene expression were then compared between the tumor and normal groups.

ORGANISM(S): Homo sapiens

SUBMITTER: Ivyna PN Bong

PROVIDER: E-GEOD-15852 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The tissue stroma plays a major role in tumors natural history. Important programs for tumor progression such as epithelial mesenchymal transition are not activated as cell-autonomous processes but under the conditions of cross-talk between tumor and stroma. Adipose tissue is a major component of the stroma and, because of their extended half-life, adipocytes are witnesses of tissue exposures. This study compares breast fat in women with breast tumors to those in healthy women to try to define a signature that could be translated into biomarkers for cancer and / or cancer risk. In the tumor-bearing breasts, we sampled adipose tissues adjacent to or distant from the tumor. Parameters studied include: adipocytes size and density; immune cells infiltration, vascularization, functional excretion and gene expression. Adipose tissues from tumor-bearing breasts whether adjacent to or distant from the tumor, did not differ from each other by any of these parameters. By contrast, when compared to adipose tissues from tumor-free breasts, tissues from tumor-bearing breasts displayed functional characteristics pointing to some sort of \\"activation\\". They have the capacity to excrete twice as much of interleukin 8 (p=0.001) and they differentially express a set of around 200 genes, at a threshold of p-value 0.001, of which many belong to inflammation mediated by chemokine and cytokine signaling and integrin signaling pathways. The presence of mast cells appears as a strong predictor of IL-8 secretion capacity (Log2 scale p = 0.002). Therefore, breast fat tissues from breast cancer patients have distinct functional and expression profiles. Although a dialogue effect with the tumor cannot be ruled out, it is also possible that this status is individually defined thus determining the constitutive permissiveness of the tissue for the development of cancer. The activation of pathways that was observed could potentially be translated into biomarkers or therapeutic targets. This transcriptomic analysis has been performed on two types of samples at short and long distances from the tumour in comparison with samples from normal tissues on Illumina beadarrays.

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Transcription profiling of human breast tumors and their paired normal tissues

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