The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers
<p>Abstract</p> <p>Background</p> <p>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 cons...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2008-09-01
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| Series: | BMC Cancer |
| Online Access: | http://www.biomedcentral.com/1471-2407/8/277 |
| _version_ | 1811275914433003520 |
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| author | Done Susan Boerner Scott Kulkarni Supriya Warren Keisha Wang Dong-Yu Wong Vietty Leong Wey |
| author_facet | Done Susan Boerner Scott Kulkarni Supriya Warren Keisha Wang Dong-Yu Wong Vietty Leong Wey |
| author_sort | Done Susan |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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 <it>in vivo </it>and <it>ex vivo</it>.</p> <p>Methods</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-04-12T23:45:58Z |
| format | Article |
| id | doaj.art-9ddcc305e19f4a798bae5bcf30db231e |
| institution | Directory Open Access Journal |
| issn | 1471-2407 |
| language | English |
| last_indexed | 2024-04-12T23:45:58Z |
| publishDate | 2008-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Cancer |
| spelling | doaj.art-9ddcc305e19f4a798bae5bcf30db231e2022-12-22T03:11:51ZengBMCBMC Cancer1471-24072008-09-018127710.1186/1471-2407-8-277The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancersDone SusanBoerner ScottKulkarni SupriyaWarren KeishaWang Dong-YuWong ViettyLeong Wey<p>Abstract</p> <p>Background</p> <p>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 <it>in vivo </it>and <it>ex vivo</it>.</p> <p>Methods</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2407/8/277 |
| spellingShingle | Done Susan Boerner Scott Kulkarni Supriya Warren Keisha Wang Dong-Yu Wong Vietty Leong Wey The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers BMC Cancer |
| title | The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers |
| title_full | The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers |
| title_fullStr | The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers |
| title_full_unstemmed | The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers |
| title_short | The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers |
| title_sort | effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers |
| url | http://www.biomedcentral.com/1471-2407/8/277 |
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