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The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers.

Wong V, Wang DY, Warren K, Kulkarni S, Boerner S, Done SJ, Leong WL - BMC Cancer (2008)

Bottom Line: To examine effects of longer exposure to hypoxia on gene expression, we also compared the gene expression profiles of 10 breast cancers from clinical tissue bank.Using hierarchical clustering analysis, 12 genes were found to be differentially expressed between the FNABs taken before and after surgical removal.Therefore, it is important that future studies take timing of tissue acquisition into account.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Applied Molecular Oncology, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Canada. viettyw@uhnresearch.ca

ABSTRACT

Background: DNA microarray analysis has great potential to become an important clinical tool to individualize prognostication and treatment for breast cancer patients. However, with any emerging technology, there are many variables one must consider before bringing the technology to the bedside. There are already concerted efforts to standardize protocols and to improve reproducibility of DNA microarray. Our study examines one variable that is often overlooked, the timing of tissue acquisition, which may have a significant impact on the outcomes of DNA microarray analyses especially in studies that compare microarray data based on biospecimens taken in vivo and ex vivo.

Methods: From 16 patients, we obtained paired fine needle aspiration biopsies (FNABs) of breast cancers taken before (PRE) and after (POST) their surgeries and compared the microarray data to determine the genes that were differentially expressed between the FNABs taken at the two time points. qRT-PCR was used to validate our findings. To examine effects of longer exposure to hypoxia on gene expression, we also compared the gene expression profiles of 10 breast cancers from clinical tissue bank.

Results: Using hierarchical clustering analysis, 12 genes were found to be differentially expressed between the FNABs taken before and after surgical removal. Remarkably, most of the genes were linked to FOS in an early hypoxia pathway. The gene expression of FOS also increased with longer exposure to hypoxia.

Conclusion: Our study demonstrated that the timing of fine needle aspiration biopsies can be a confounding factor in microarray data analyses in breast cancer. We have shown that FOS-related genes, which have been implicated in early hypoxia as well as the development of breast cancers, were differentially expressed before and after surgery. Therefore, it is important that future studies take timing of tissue acquisition into account.

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Pathway linkage analysis of the differentially expressed genes between PRE and POST FNABs. Nine genes (blue halo), out of 11 differentially expressed genes, including FOS were linked in the analysis (PathwayAssist 3.0) and formed a network. The layout of cellular location for the proteins is graphically presented.
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Figure 2: Pathway linkage analysis of the differentially expressed genes between PRE and POST FNABs. Nine genes (blue halo), out of 11 differentially expressed genes, including FOS were linked in the analysis (PathwayAssist 3.0) and formed a network. The layout of cellular location for the proteins is graphically presented.

Mentions: The biological relationships of the 12 genes differentiating PRE and POST GPs were further investigated using PathwayAssist 3.0 software (Stratagene). We searched using the shortest paths between the genes to make up their biological interaction network. The software recognized 11 of the 12 genes. Nine out of the 11 genes formed a network and they were linked directly or indirectly to FOS (Fig. 2). qRT-PCR was used to validate the expression level of FOS in each of the FNAB specimens (Fig. 1B).


The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers.

Wong V, Wang DY, Warren K, Kulkarni S, Boerner S, Done SJ, Leong WL - BMC Cancer (2008)

Pathway linkage analysis of the differentially expressed genes between PRE and POST FNABs. Nine genes (blue halo), out of 11 differentially expressed genes, including FOS were linked in the analysis (PathwayAssist 3.0) and formed a network. The layout of cellular location for the proteins is graphically presented.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2567989&req=5

Figure 2: Pathway linkage analysis of the differentially expressed genes between PRE and POST FNABs. Nine genes (blue halo), out of 11 differentially expressed genes, including FOS were linked in the analysis (PathwayAssist 3.0) and formed a network. The layout of cellular location for the proteins is graphically presented.
Mentions: The biological relationships of the 12 genes differentiating PRE and POST GPs were further investigated using PathwayAssist 3.0 software (Stratagene). We searched using the shortest paths between the genes to make up their biological interaction network. The software recognized 11 of the 12 genes. Nine out of the 11 genes formed a network and they were linked directly or indirectly to FOS (Fig. 2). qRT-PCR was used to validate the expression level of FOS in each of the FNAB specimens (Fig. 1B).

Bottom Line: To examine effects of longer exposure to hypoxia on gene expression, we also compared the gene expression profiles of 10 breast cancers from clinical tissue bank.Using hierarchical clustering analysis, 12 genes were found to be differentially expressed between the FNABs taken before and after surgical removal.Therefore, it is important that future studies take timing of tissue acquisition into account.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Applied Molecular Oncology, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Canada. viettyw@uhnresearch.ca

ABSTRACT

Background: DNA microarray analysis has great potential to become an important clinical tool to individualize prognostication and treatment for breast cancer patients. However, with any emerging technology, there are many variables one must consider before bringing the technology to the bedside. There are already concerted efforts to standardize protocols and to improve reproducibility of DNA microarray. Our study examines one variable that is often overlooked, the timing of tissue acquisition, which may have a significant impact on the outcomes of DNA microarray analyses especially in studies that compare microarray data based on biospecimens taken in vivo and ex vivo.

Methods: From 16 patients, we obtained paired fine needle aspiration biopsies (FNABs) of breast cancers taken before (PRE) and after (POST) their surgeries and compared the microarray data to determine the genes that were differentially expressed between the FNABs taken at the two time points. qRT-PCR was used to validate our findings. To examine effects of longer exposure to hypoxia on gene expression, we also compared the gene expression profiles of 10 breast cancers from clinical tissue bank.

Results: Using hierarchical clustering analysis, 12 genes were found to be differentially expressed between the FNABs taken before and after surgical removal. Remarkably, most of the genes were linked to FOS in an early hypoxia pathway. The gene expression of FOS also increased with longer exposure to hypoxia.

Conclusion: Our study demonstrated that the timing of fine needle aspiration biopsies can be a confounding factor in microarray data analyses in breast cancer. We have shown that FOS-related genes, which have been implicated in early hypoxia as well as the development of breast cancers, were differentially expressed before and after surgery. Therefore, it is important that future studies take timing of tissue acquisition into account.

Show MeSH
Related in: MedlinePlus