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

ABSTRACT: Paired fine needle aspiration biopsies (FNABs) of breast cancers were taken before (PRE) and after (POST) surgeries from 16 patients and compared the cDNA microarray data to determine the genes that were differentially expressed between the FNABs taken at the two time points. The timing of fine needle aspiration biopsies can be a confounding factor in microarray data analyses in breast cancer. 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. Keywords: Breast cancer, fine needle, biopsy timing, microarray standardization, early hypoxic genes Dye-swap technical replicates were included both in PRE and POST FNABs for every patient, then the two replicated array data were combined for analysis.

ORGANISM(S): Homo sapiens

SUBMITTER: Wong V

PROVIDER: S-ECPF-GEOD-12072 | biostudies-other | 2008

REPOSITORIES: biostudies-other

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

Project description:BackgroundDNA 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.MethodsFrom 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.ResultsUsing 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.ConclusionOur 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.

| S-EPMC2567989 | biostudies-literature

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

Project description:Paired fine needle aspiration biopsies (FNABs) of breast cancers were taken before (PRE) and after (POST) surgeries from 16 patients and compared the cDNA microarray data to determine the genes that were differentially expressed between the FNABs taken at the two time points. The timing of fine needle aspiration biopsies can be a confounding factor in microarray data analyses in breast cancer. 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. Keywords: Breast cancer, fine needle, biopsy timing, microarray standardization, early hypoxic genes

2008-09-09 | GSE12072 | GEO

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

2008-09-09 | E-GEOD-12072 | biostudies-arrayexpress

Expression data from Fine Needle Aspiration (FNA) biopsies from breast cancer patients

Project description:This is a stage-matched case control study. Cases with clinical diagnosis of Inflammatory Breast Cancer (IBC) were selected after reviewing all medical records of the 440 FNA samples. IBC was defined as signs of erythema and edema (peau d’orange) involving at least one third of the skin and rapid clinical presentation. Presence of tumor emboli in the dermal lymphatics of the involved skin in the pathology report was not required for inclusion as IBC. Controls were selected to match for T stage, all T4a-c tumors in the data set were included as controls. IBC breast cancer are all T4d breast cancer. We examined if gene expression differences exist between IBC and stage-matched Non-IBC stratified according to hormone receptor and HER2 status. Pre-treatment FNA from primary tumors were obtained and RNA extracted and hybridized to Affymetrix microarrays according to manufacturer protocol.

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Expression data from Fine Needle Aspiration (FNA) biopsies from breast cancer patients

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Expression data from paired matched breast cancer Fine needle aspiration (FNA) or Core needle biopsies (CBX)

Project description:Paired FNA and CBX specimens were prospectively collected from 37 breast cancers before any systemic therapy during a biomarker discovery study at The University of Texas M. D. Anderson Cancer Center. We identified 293 probe sets overexpressed in core biopsies; these included five highly coexpressed gene clusters (metagenes) corresponding to immune functions and extracellular matrix components. We compared gene expression profiles of pairs of fine-needle (stroma-poor) and core-needle (stroma-rich) biopsies from 37 cancers to identify stroma-associated genes Pre-treatment paird matched FNA and CBX from primary tumors were obtained and RNA extracted and hybridized to afymetrix microarrays according to manufacturer protocol.

| S-ECPF-GEOD-32518 | biostudies-other

Expression data from paired matched breast cancer Fine needle aspiration (FNA) or Core needle biopsies (CBX)

2011-10-31 | GSE32518 | GEO

Expression data from Fine Needle Aspiration (FNA) biopsies from breast cancer patients

2011-07-01 | E-GEOD-22597 | biostudies-arrayexpress

Expression data from fine-needle aspiration biopsies of breast cancer metastases from different anatomical sites

Project description:Breast cancer molecular subtypes preferentially metastasize to specific organs and the anatomical location of the metastasis is associated with the length of survival post-recurrence. We used microarrays to provide a detailed characterization of breast cancer site-specific metastases with particular focus on identifying genes predictive of breast cancer liver metastatic proprnsity We performed global gene expression profiling on fine-needle aspirates of metastatic lesions from different anatomical sites obtained from breast cancer patients treated within the Swedish randomized trial (TEX) of first-line chemotherapy for locally advanced or metastatic breast cancer. Samples were collected before commencement of treatment.

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Expression data from fine-needle aspiration biopsies of breast cancer metastases from different anatomical sites

Project description:To determine whether breast cancer molecular subtypes and tumor characteristics with demonstrated significance in a primary tumor setting can also confer clinically relevant information in breast cancer metastases. We assessed previously published gene expression modules of seven biological processes and the intrinsic subtypes (PAM50). The translational aspect of the Swedish randomized TEX trial included 112 patients with at least one biopsy from morphologically confirmed loco-regional or distant breast cancer metastasis diagnosed from December 2002 until June 2007. All patients had detailed clinical information, complete follow-up and metastasis gene expression information (Affymetrix array GPL10379). We performed global gene expression profiling on fine-needle aspirates of metastatic lesions from different anatomical sites obtained from breast cancer patients treated within the Swedish randomized trial (TEX) of first-line chemotherapy for locally advanced or metastatic breast cancer. Samples were collected before commencement of treatment.

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