Formalin-fixed Paraffin-embedded Breast Cancer Research Articles

Sec62 Bridges the Gap from 3q Amplification to Molecular Cell Biology in Non–Small Cell Lung Cancer

The molecular carcinogenesis of lung cancer has yet to be clearly elucidated. We investigated the possible oncogenic function of SEC62 in lung cancer, which was predicted based on our previous findings that lung and thyroid cancer tissue samples exhibited increased Sec62 protein levels. The SEC62 gene locus is at 3q26.2, and 3q amplification is reportedly the most common genomic alteration in non-small cell lung cancer. We analyzed SEC62 mRNA and protein levels in tissue samples from lung cancer patients by real-time quantitative PCR, Western blot, and IHC and found significantly increased SEC62 mRNA and protein levels in tumors compared with tumor-free tissue samples from the same patients. Correlation analyses revealed significantly higher Sec62 levels in tumors with lymph node metastases compared with nonmetastatic tumors, as well as in poorly compared with moderately differentiated tumors. On the basis of these promising results, we examined the role of Sec62 in cancer cell biology in vitro. Cell migration assays with lung and thyroid cancer cells showed distinct stimulation of migration in SEC62-overexpressing cells and inhibition of migration in Sec62-depleted cells. Moreover, we found that SEC62 silencing sensitized the cells to thapsigargin-induced endoplasmic reticulum stress. Thus, our results indicate that SEC62 represents a potential candidate oncogene in the amplified 3q region in cases of non-small cell lung cancer and harbors various functions in cancer cell biology.

P1-07-12: Assessment of Real World HER2 Status by Immunohistochemistry (IHC) and Fluorescence In Situ Hybridization (FISH) in Breast Cancers: Comparison with HERmark®, a Validated Quantitative Measure of HER2 Protein Expression.

Abstract Background: Accurate assessment of the HER2 status is critical in determining appropriate therapy for patients with invasive breast cancer. ASCO/CAP HER2 testing guidelines caution that up to 20% of routine HER2 testing by IHC/FISH may be unreliable (Wolff et al. JCO 2007;25:118). The HERmark assay is a novel quantitative HER2 protein measurement for determining HER2 status in breast cancer. Central HER2 testing showed high concordance (96-98%) with HERmark for positive and negative categories when equivocal subsets were excluded (Huang et al. Am J Clin Pathol 2010;134:303; Joensuu et al, 2008 SABCS, abstract 2071). In this study, we examined concordance between HERmark and routine HER2 testing by IHC and FISH from “real world” formalin-fixed, paraffin-embedded (FFPE) breast cancers submitted commercially for HERmark testing. Methods: 717 HERmark results on FFPE breast cancers tested from 2008 to 2010 and corresponding HER2 IHC/FISH results were reviewed. The IHC and FISH results, per pathology reports submitted at the time of HERmark testing, were compared to HERmark categorical (negative, equivocal, positive) results. Results: 590 (419) samples had IHC (FISH) and HERmark results available. Of these cases, 92% (94%) were either negative or equivocal by IHC (FISH). The HERmark testing reported 33% HERmark negative, 33% HERmark equivocal and 34% HERmark positive. Comparisons of HER2 status by IHC and FISH vs. HERmark are detailed in Table 1. 19% of cases classified as IHC 0 or 1+ were positive by HERmark; 35% classified as FISH negative were HERmark positive. Of the 158 triple negative cases by IHC/FISH (ER, PR and HER2 negative, data not shown), 38 (24%) were reclassified as HER2 positive by HERmark. Conclusions: Higher than expected discordance between HER2 IHC/FISH and the HERmark assay was observed in this study compared with central HER2 testing of prior study cohorts. Selection bias may have impacted these results as ≥ 92% of cases submitted for HERmark testing were either equivocal or negative by routine HER2 IHC/FISH. Central HER2 FISH retesting of these samples will be performed and compared with HERmark results to further evaluate the discordance observed in this analysis. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-07-12.

In situ hybridization and polymerase chain reaction methods for the detection of Epstein-Barr virus RNA in breast cancer specimens

The role of Epstein-Barr virus (EBV) as a cofactor in breast cancer is controversial and its association with breast cancer varies. In this study, EBV was detected by using in situhybridization technique (ISH) to detect Epstein-barr virus encoded RNA1 (EBER1) transcripts. Archival formalin-fixed paraffin embedded breast cancer tissue samples (n = 139) and normal breast tissue (n = 20) obtained from Hospital Tuanku Ja’afar were sectioned, stained and examined microscopically for nuclear staining and by DNA amplification of the same gene. By ISH, 83/139 (59.7%) and 12/20 (60%) were EBV positives in the breast cancer tissues and normal tissues, respectively. On the other hand, confirmation by polymerase chain reaction (PCR) found that additional six samples (89/139 or 64%) breast cancer tissues were positive for EBER1 gene. To further confirm the identity of these amplified products, two samples (UiTM-53 and UiTM-73) were sequenced, BLAST, analyzed phylogenetically and was found to be 100% similar to the EBV EBER1 gene sequences already deposited in the GenBank (accession numbers AB065135, FN545286, EF187853 and DQ883818). These preliminary findings suggest that there is a correlation between EBV and breast cancer but need further testing with more samples to confirm the role of EBV. Key words: Breast cancer, Epstein-Barr virus, EBER1 transcripts, in situ hybridization, polymerase chain reaction (PCR), tumour grading.

Human papillomavirus infection and increased risk of breast cancer in north of Iran.

28 Background: Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer deaths among women worldwide. Human papillomaviruses have been related to the pathogenesis of breast cancer. In this study, we have analyzed the possible relevance of HPV infection for breast cancer risk among Iranian women from north part of Iran, Mazandaran province. Methods: Polymerase chain reaction method with three different primer sets was applied for detection of HPVs in formalin-fixed paraffin-embedded breast cancer and breast fibroadema as case and control tissues, respectively. HPV genotypes were determined by phylogenetic analysis of viral genome sequences. Results: Of the 58 women with breast cancer, 25.9% (15 isolates) had positive test results for HPV DNA in breast tumor samples in contrast to 2.4% of women (1 out of 41) with non cancer status (P + 0.002). The infection of HPV had an OR of 14.247 (95% CI 1.558-130.284; P + 0.019). The HPV genotypes in samples of breast cancer patients were 26.67% for HPV-16 (4 isolates) and HPV-18 (4 isolates), 13.3% for HPV-23 (2 isolates) and HPV-6 (2 isolates), 6.67% for HPV-11 (1 isolate), HPV-15 (1 isolate) and HPV-124 (1 isolate) and one isolate could not be genotyped compared to HPV reference sequences, while the sole detected HPV in control specimens was HPV-124. Conclusions: Our study reveals that HPV infection and age are the risk factors in breast cancer development in the north part of Iran, Mazandaran province. The association between risk of breast cancer development and viral infection is open and deserves further investigation.

Let-7 MicroRNAs Induce Tamoxifen Sensitivity by Downregulation of Estrogen Receptor α Signaling in Breast Cancer

MicroRNAs (miRNAs) play an important regulatory role in breast tumorigenesis. Previously, we found that let-7 miRNAs were downregulated significantly in formalin-fixed paraffin-embedded (FFPE) breast cancer tissues. In this study, we further found that endogenous levels of let-7b and let-7i miRNAs are inversely correlated with levels of estrogen receptor (ER)-a36, a new variant of ER-α66, in the FFPE tissue set. Bioinformatic analysis suggested that ER-α36 may be another target of let-7 miRNAs. To test this hypothesis, cotransfection of let-7 mimics or inhibitors together with full-length or a fragment of ER-α36 3'UTR luciferase construct was performed, and we found that let-7b and let-7i mimics suppressed the activity of reporter gene significantly, which was enhanced remarkably by let-7b and let-7i inhibitors. Both mRNA and protein expression of ER-α36 were inhibited by let-7 mimics and enhanced by let-7 inhibitors. Furthermore, ER-α36 mediated nongenomic MAPK and Akt pathways were weakened by let-7b and let-7i mimics in triple negative breast cancer cell line MDA-MB-231. The reverse correlation between let-7 miRNAs and ER-α36 also exists in Tamoxifen (Tam)-resistant MCF7 cell line. Transfection of let-7 mimics to Tam-resistant MCF7 cells downregulated ER-α36 expression and enhanced the sensitivity of MCF7 cells to Tam in estrogen-free medium, which could be restored by overexpression of ER-α36 constructs without 3'UTR. Our results suggested a novel regulatory mechanism of let-7 miRNAs on ER-α36 mediated nongenomic estrogen signal pathways and Tam resistance.

Comprehensive assessment of truncated HER2 in formalin-fixed paraffin embedded breast cancer tissue by chromogenic duplex immunohistochemistry.

e11059 Background: Truncated forms of HER2, previously described in subsets of HER2 positive breast cancer, lack the extracellular domain (ECD) but may retain intracellular domain (ICD) functionali...

Technical note on the validation of a semi-automated image analysis software application for estrogen and progesterone receptor detection in breast cancer

BackgroundThe immunohistochemical detection of estrogen (ER) and progesterone (PR) receptors in breast cancer is routinely used for prognostic and predictive testing. Whole slide digitalization supported by dedicated software tools allows quantization of the image objects (e.g. cell membrane, nuclei) and an unbiased analysis of immunostaining results. Validation studies of image analysis applications for the detection of ER and PR in breast cancer specimens provided strong concordance between the pathologist's manual assessment of slides and scoring performed using different software applications.MethodsThe effectiveness of two connected semi-automated image analysis software (NuclearQuant v. 1.13 application for Pannoramic™ Viewer v. 1.14) for determination of ER and PR status in formalin-fixed paraffin embedded breast cancer specimens immunostained with the automated Leica Bond Max system was studied. First the detection algorithm was calibrated to the scores provided an independent assessors (pathologist), using selected areas from 38 small digital slides (created from 16 cases) containing a mean number of 195 cells. Each cell was manually marked and scored according to the Allred-system combining frequency and intensity scores. The performance of the calibrated algorithm was tested on 16 cases (14 invasive ductal carcinoma, 2 invasive lobular carcinoma) against the pathologist's manual scoring of digital slides.ResultsThe detection was calibrated to 87 percent object detection agreement and almost perfect Total Score agreement (Cohen's kappa 0.859, quadratic weighted kappa 0.986) from slight or moderate agreement at the start of the study, using the un-calibrated algorithm. The performance of the application was tested against the pathologist's manual scoring of digital slides on 53 regions of interest of 16 ER and PR slides covering all positivity ranges, and the quadratic weighted kappa provided almost perfect agreement (κ = 0.981) among the two scoring schemes.ConclusionsNuclearQuant v. 1.13 application for Pannoramic™ Viewer v. 1.14 software application proved to be a reliable image analysis tool for pathologists testing ER and PR status in breast cancer.

Abstract P3-09-05: Let-7 microRNAs Regulate a Novel Variant of Estrogen Receptor Alpha, ER-≥36, Nongenomic Estrogen Signal Pathway, and Tamoxifen Resistance in Breast Cancer

Abstract Background: MicroRNAs (miRNAs) have important regulatory functions in breast cancer tumorigenesis. We previously found that let-7 miRNAs were significantly downregulated in formalin-fixed paraffin-embedded (FFPE) breast cancer tissues. Material and Methods: QRT-PCR was used to check let-7 family miRNAs in FFPE tissues and breast cancer cell lines as well as expression of estrogen receptor (ER)-≥36, a variant of ER-≥66, after let-7 miRNA transfecton. Immunoblot analysis was employed to check protein expression in FFPE tissue and breast cancer cell lines. Luciferase reporter assay was used to detect direct regulation of let-7 miRNA on ER-α expression. MTT assay was applied for cell proliferation after transfection of let-7 miRNAs. Results: We found that there was an inverse correlation between the expression of ER-≥36 and several members of let-7 family miRNAs in the FFPE tissue set. Let-7 miRNA sequences match sequence in the 3’ untranslated region (3’ UTR) of ER-≥36, indicating ER-≥36 may be a target of let-7. Cotransfection of let-7 mimics with ER-≥36 3’ UTR luciferase construct decreased the activity of reporter gene. Conversely, let-7 inhibitors enhanced the reporter gene activity. Transfection of let-7 mimics inhibited both the mRNA and protein levels of ER-≥36 and further inhibited the non-genomic estrogen pathway mediated by ER-≥36 in MDA-MB-231 cells. On the contrary, transfection of let-7 inhibitors enhanced the ER-≥36 expression at both mRNA and protein levels in 184A1 cells. The high expression of ER-≥36 in tamoxifen resistant MCF7 cells can be inhibited by transfection of let-7 mimics and sensitivity toward tamoxifen is enhanced. Conclusion: Let-7 miRNAs regulate the expression of ER-≥36, which is involved in non-genomic estrogen pathway and tamoxifen resistance. Let-7 could be therapeutic target for breast cancer treatment. Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-09-05.

Abstract P4-08-12: Gene Expression Profiling of Formalin-Fixed, Paraffin-Embedded (FFPE) Breast Cancer Samples and Analysis of Intrinsic Subtypes

Abstract Background: The advent of microarray technology has enabled robust, high throughput analysis of breast cancer (BC) transcriptomes. Indeed, molecular classification of BC has been revolutionized by the advent of Gene Expression Profiling (GEP). FFPE tumor samples have presented a technical challenge for GEP studies due to degradation of extracted RNA. Newer technologies have overcome this challenge, and have lead to generation of quality GEP data and thus, new insights using archived tissues. Of particular interest to our group has been application of these techniques to the study of triple negative breast cancer (TNBC). TNBC is a BC sub-type characterized by a lack of erbB2 gene amplification and estrogen and progesterone receptor expression. This clinically-defined BC sub-type carries a poor prognosis, is insensitive to hormonal or HER-2 targeted therapies, and displays different incidences among ethnic groups. A better understanding of the genetic and molecular mechanisms underlying TNBC is critical to improving clinic outcomes and developing tailorized therapies. Study Objective: We demonstrate utility of FFPE BC samples in obtaining consistent, reproducible GEP data, and apply this technology to validate the ability to identify intrinsic BC subtypes in unselected specimens, as well to identify differentially expressed genes in TNBC. Methods: RNA isolation and labelled cDNA preparation were performed from freshly cut FFPE sections. Samples were hybridized to a breast cancer focused gene expression array (Breast Cancer DSA Research Tool, Almac Diagnostics Inc). DSA chip quality was assessed on parameters selected automatically from GCOS report files per chip using MATLAB script based web application developed by Almac. Data pre-processing used the Resolver Error Model. All parameters including Raw Q, Background, Scaling Factor and all controls met quality criteria set by Affymetrix and Almac Dx SOPs. Hybridization results were assessed with Principal Component Analysis and Cluster Analysis in a Rosetta Resolver Gene Expression Data Analysis System to identify potential outliers, contamination, or intra-tumor heterogeneity. In total, 47 FFPE breast cancer samples covering a range of hormonal receptor status and sub-types were profiled, as were 28 TNBC FFPE tumor samples. Results: Cluster analysis demonstrated that the Almac Breast Cancer DSA was able to clearly separate the 47 tumor samples of the mixed subtype group into the previously described intrinsic subgroups. Moreover, the DSA array contains 167 probesets which correspond to the 40 of the PAM-50 gene set used as a subtype predictor (Parker et al 2009). Analysis of the TNBC samples using the 167 probeset (based on mean intensity for probes representing each of the 40 genes) showed 100% consistency with published results demonstrating a basal-like gene expression signature. Summary: We have shown that our study methodology used can reliably measure gene expression in FFPE BC samples, and that the Breast Cancer DSA can be used to evaluate intrinsic subtypes of BC specimens. Analysis of the TNBC cases showed complete concordance between the PAM-50 gene set and the corresponding genes in the DSA. These study results are being validated in a larger data set. Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P4-08-12.

Quantitation of p95HER2 in Paraffin Sections by Using a p95-Specific Antibody and Correlation with Outcome in a Cohort of Trastuzumab-Treated Breast Cancer Patients

p95HER2 is an NH(2)-terminally truncated form of HER2 that lacks the trastuzumab binding site and is therefore thought to confer resistance to trastuzumab treatment. In this report, we introduce a new antibody that has enabled the first direct quantitative measurement of p95HER2 in formalin-fixed paraffin-embedded (FFPE) breast cancer tissues. We sought to show that quantitative p95HER2 levels would correlate with outcome in trastuzumab-treated HER2-positive metastatic breast cancer. The novel p95HER2 antibody used here was characterized for sensitivity, specificity, and selectivity over full-length HER2. Quantitative p95HER2 levels were measured in 93 metastatic breast tumors using a VeraTag FFPE assay to determine the correlation of p95HER2 levels with outcomes. Within a cohort of trastuzumab-treated metastatic breast cancer patients, high levels of p95HER2 were found to correlate with shorter progression-free survival [hazard ratio (HR), 1.9; P = 0.017] and overall survival (HR, 2.2; P = 0.012) in patients with tumors selected to be HER2 positive by the VeraTag HER2 assay. For those with tumors found to be fluorescence in situ hybridization positive, elevated p95HER2 correlated similarly with shorter progression-free survival (HR, 1.8; P = 0.022) and overall survival (HR, 2.2; P = 0.009). We have successfully generated an antibody that can specifically detect p95HER2, and developed an assay to quantify expression in FFPE tumor specimens. Using this novel assay, we have identified a group of HER2-positive patients expressing p95HER2 that have a worse outcome while on trastuzumab. As p95HER2 retains sensitivity to kinase inhibitors, measurement of p95HER2 in breast tumor sections may be useful in guiding treatment for patients with HER2-positive breast cancer.

Estrogen receptor alpha phosphorylated at tyrosine 537 is associated with poor clinical outcome in breast cancer patients treated with tamoxifen.

A phospho-tyrosine 537-ERα (p-Y537-ERα) antibody was validated for immunohistochemistry of formalin-fixed paraffin-embedded human breast cancer biopsies and used to interrogate multiple ER positive breast cancer cases present on tissue microarrays already constructed by the Manitoba Breast Tumor Bank. Nuclear p-Y537-ERα protein expression was positively associated with positive nodes (Spearman r = 0.20, P = 0.0002) and large tumor size (r = 0.13, P = 0.02). On univariate analysis, high levels of p-Y537 were associated with poor overall survival (HR = 1.65, 95% CI 1.08-2.52, P = 0.02) but not relapse free survival from breast cancer. The association with overall survival was not significant on multivariate analysis. These data support the relevance of phosphorylation at p-Y537-ERα in human breast cancers and add further support to the presence of a phosphorylation code for ERα in human breast cancer in vivo.

Comparative validation of the SP6 antibody to Ki67 in breast cancer

AimTo compare SP6 and MIB1 antibodies for Ki67 staining in breast cancer.BackgroundImmunohistochemical detection of Ki67 has been widely used to assess the proliferative fraction in breast cancer. Ki67 is used...

In Situ Identification of Putative Cancer Stem Cells by Multiplexing ALDH1, CD44, and Cytokeratin Identifies Breast Cancer Patients with Poor Prognosis

A subset of cells, tentatively called cancer stem cells (CSCs), in breast cancer have been associated with tumor initiation, drug resistance, and tumor persistence or aggressiveness. They are characterized by CD44 positivity, CD24 negativity, and/or ALDH1 positivity in flow cytometric studies. We hypothesized that the frequency or density of these cells may be associated with more aggressive tumor behavior. We borrowed these multiplexed, flow-based methods to develop an in situ method to define CSCs in formalin-fixed paraffin-embedded breast cancer tissue, with the goal of assessing the prognostic value of the presence of CSCs in breast cancer. Using a retrospective collection of 321 node-negative and 318 node-positive patients with a mean follow-up time of 12.6 years, we assessed TMAs using the AQUA method for quantitative immunofluorescence. Using a multiplexed assay for ALDH1, CD44, and cytokeratin to measure the coexpression of these proteins, putative CSCs appear in variable sized clusters and in 27 cases (of 490), which showed significantly worse outcome (log rank P = 0.0003). Multivariate analysis showed that this marker combination is independent of tumor size, histological grade, nodal status, ER-, PR,- and HER2-status. In this cohort, ALDH1 expression alone does not significantly predict outcome. We conclude that the multiplexed method of in situ identification of putative CSCs identifies high risk patients in breast cancer.

Abstract 327: Genomic profiling of sentinel lymph node breast cancer metastasis

Abstract The sentinel lymph node (SLN) is the first node in the axilla to harbor malignant cells in breast tumors with metastasis, and its positivity is an indication for axillary lymph node dissection. Despite significant improvement in the methods for detection of tumor cells at this site, there are a still significant number of false negative cases and the inability to detect malignant cells in lower abundance, such as in the case of micrometastasis. We propose to use methods based on the genomic alterations, which present higher sensitivity and accuracy, and can be used to augment the current methods to identify the epithelial malignant cells at the SLN. In this study, we performed CGH and array-CGH analysis in microdissected tumors cells from the SLN metastatic lesions to identify DNA copy number changes. We compared the changes observed in the SLN lesion to the ones present in the corresponding primary tumors (PT) from the same patients. Here we present the results from the initial analysis of 10 FFPE (formalin-fixed paraffin-embedded) breast cancer samples (5 pairs of SLN and PT). DNA copy number changes were detected by both methods in all the cases analyzed. A remarkable similarity in the DNA profiles between the SLN metastatic lesions and the corresponding PT were observed, despite the high level of heterogeneity observed among the cases. CGH analysis revealed most frequently gains of chromosomal regions (at both lesions) involving 1p, 1q, 6q, 9q, 11p, 11q, 13q, 16p, 17q, 19p, 19q and Xq. Array-CGH analysis detected both amplifications and deletions, affecting mostly the chromosome regions 1p (genes affected KLHL17, NOC2L, PPIAL4), 9q (ANKRD20A, COL5A), 11p (PSMD13, SIRT3), 15q (MAN2C1), 19p (MUC16, AZU1) and 20q regions (PSMA7). In addition, several genes of the HIST, FLJ, SLC and TRIM family as well as the homeobox families HOX and NK were involved in the alterations. FISH analysis is being conducted to confirm the array-CGH findings as well as the analysis of additional matching samples. The assessment of copy number changes in the SLN metastasis (and in its correspondent PT) using genomic profiling is a very sensitive method and will lead to the identification of genomic alterations that can reliably characterize breast tumor cells at the SLN lesions. Once these alterations are validated in larger series of patients, they can be used as molecular markers that can improve the predictive value of the current established methods of SLN evaluation in the identification of patients at higher risk of developing axillary lymph node metastasis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 327.

Abstract 2999: Assessment of microRNA expression in two-dimensional histopathological fields of breast cancer

Abstract Breast cancer is the second most common type of cancer among women with an expected ∼192,000 newly diagnosed cases in the United States this year alone. Early detection methods are becoming increasingly important for guiding treatment options and decisions. Currently, standard molecular diagnostic tests of breast cancer characterize patient cases by estrogen receptor (ER), progesterone receptor (PR) and Her2neu status. The recently discovered biomolecule, microRNA (miRNA), is being assessed as a novel diagnostic tool; however, since miRNA is a regulatory molecule it is likely that expression is cell-type and location specific, thus studies that don't specifically study malignant and normal cells may mask miRNA patterns within tissue. The goal of our study was to evaluate miRNA expression within sub-regions of formalin-fixed paraffin-embedded breast cancer tissue. Utilizing a combination of laser-based and manual microdissection techniques, we evaluated the expression of several breast cancer associated miRNA via TaqMan chemistry. We dissected selected areas of tumor and normal cells, as well as a grid-like pattern over entire tissue sections to separately evaluate each histopathological region. The data suggest there is heterogeneity of miRNA expression within the tumor and the surrounding normal tissue. In order study this phenomenon in more detail, we are now adapting a new two-dimensional amplification (2D-PCR) device to measure miRNA levels across tissue specimens with fine resolution. This approach to examining miRNA profiles in tissue sections may lead to novel findings with diagnostic or prognostic implications for breast cancer patients. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2999.

Toll‐like receptor 9 expression in breast and ovarian cancer is associated with poorly differentiated tumors

Toll-like receptor 9 (TLR9) activates the innate immune response when exposed to non-methylated CpG-DNA. TLR9 was recently shown to be expressed by cancer cells which have been previously characterized by global hypomethylation. We set out to examine the expression and molecular activity of TLR9 in breast and ovarian cancer cells. Firstly, we confirmed higher levels of hypomethylated DNA in the serum of patients with metastatic breast cancer (n = 18) versus age-matched tumor-free women (n = 18). In breast cancer cell lines and tissues, TLR9 mRNA expression was associated with estrogen-receptor (ER) status (n = 124, P = 0.005). Expression also correlated with increasing tumor grade in both breast (P = 0.03) and ovarian cancer specimens (n = 138, P = 0.04). Immunohistochemical analysis of formalin-fixed paraffin-embedded (FFPE) breast cancer tissues revealed higher TLR9 protein expression in hormone-receptor (HR)-negative specimens (n = 116, P < 0.001). Using an in vitro scratch assay, we observed that cell lines transfected to overexpress TLR9 demonstrated increased cellular migration when stimulated with CpG-DNA. When assessing the molecular activity of TLR9 in breast cancer, we found a strong positive correlation of nuclear factor-kappa B (NF-kappaB) activity with TLR9 mRNA expression (correlation coefficient r = 0.7, P < 0.001). Finally, immunofluorescence analysis of BT-20 and Hs578T breast cancer cell lines showed partial colocalizations of CpG-DNA with TLR9, which diminished when the cells were exposed to methylated CpG-DNA (mCpG-DNA) or control GpC-DNA. In summary we demonstrate that TLR9 expression is associated with poor differentiation in breast and ovarian cancer specimens, and that TLR9 overexpression and stimulation with hypomethylated DNA augments the migratory capacity of cancer cell lines.

Analytical Validation of a Highly Quantitative, Sensitive, Accurate, and Reproducible Assay (HERmark®) for the Measurement of HER2 Total Protein and HER2 Homodimers in FFPE Breast Cancer Tumor Specimens

We report here the results of the analytical validation of assays that measure HER2 total protein (H2T) and HER2 homodimer (H2D) expression in Formalin Fixed Paraffin Embedded (FFPE) breast cancer tumors as well as cell line controls. The assays are based on the VeraTag technology platform and are commercially available through a central CAP-accredited clinical reference laboratory. The accuracy of H2T measurements spans a broad dynamic range (2-3 logs) as evaluated by comparison with cross-validating technologies. The measurement of H2T expression demonstrates a sensitivity that is approximately 7–10 times greater than conventional immunohistochemistry (IHC) (HercepTest). The HERmark assay is a quantitative assay that sensitively and reproducibly measures continuous H2T and H2D protein expression levels and therefore may have the potential to stratify patients more accurately with respect to response to HER2-targeted therapies than current methods which rely on semiquantitative protein measurements (IHC) or on indirect assessments of gene amplification (FISH).

Discrimination between healthy and tumor tissues on formalin-fixed paraffin-embedded breast cancer samples using IR imaging

This work presents a pilot study to illustrate the potential of Fourier transform infrared (FT-IR) imaging in breast cancer research. Using this technique, we have acquired infrared (IR) microspectroscopic images from healthy and cancerous breast tissue section from one patient. First of all, a Student t-test was applied, showing DNA/RNA spectral region (1400–1000 cm−1) as the most discriminant for the differentiation between healthy and tumor samples. Afterwards, a supervised pattern recognition method, Partial Least Squares (PLS) was used to develop an automated classifier to discriminate the two classes of data. Infrared spectra of independent IR measurements were used to test the classifier. The class identity was correlated with information obtained by histopathologic gold standard. The results showed that more than 95% of the training and validation spectra were correctly identified. We demonstrate that combination between IR microspectroscopic imaging and multivariate data analysis can be used as a complement to present diagnostic tools for breast cancer.

Discrimination between healthy and tumor tissues on formalin-fixed paraffin-embedded breast cancer samples using IR imaging

This work presents a pilot study to illustrate the potential of Fourier transform infrared (FT-IR) imaging in breast cancer research. Using this technique, we have acquired infrared (IR) microspectroscopic images from healthy and cancerous breast tissue section from one patient. First of all, a Studentt-test was applied, showing DNA/RNA spectral region (1400–1000 cm−1) as the most discriminant for the differentiation between healthy and tumor samples. Afterwards, a supervised pattern recognition method, Partial Least Squares (PLS) was used to develop an automated classifier to discriminate the two classes of data. Infrared spectra of independent IR measurements were used to test the classifier. The class identity was correlated with information obtained by histopathologic gold standard. The results showed that more than 95% of the training and validation spectra were correctly identified. We demonstrate that combination between IR microspectroscopic imaging and multivariate data analysis can be used as a complement to present diagnostic tools for breast cancer.

Amplification of mRNA from Formalin-Fixed Paraffin-Embedded (FFPE) Breast Cancer Tissues without 3' Bias and Multiplex Expression Analysis on Flow-Through Microarrays.

Abstract Background: FFPE samples are an abundant sample resource for validation of expression-based assays and are will suited for routine clinical testing. Analysis on microarrays enables the analysis of many transcripts from small samples. However, mRNA in FFPE sections is degraded and cross-linked, with RNA fragment sizes of a few hundred bases or less, and consequently standard methods of microarray sample preparation are not reliable unless probes are very strongly biased to the 3' end. It is not always possible to design high quality probes within this restricted region of mRNAs. Amplification of target sequences any place within transcripts would permit greater flexibility in probe design and optimization of probe sets for reliable multiplex analysis.Material and Methods: Total RNA extracted from FFPE samples was subjected to two rounds of amplification with the ExpressArt TRinucleotide kit (AmpTec), which preferentially primes cDNA synthesis near the 3'-ends of mRNAs (rather than at poly-A sites) and selects for mRNAs against ribosomal RNAs. Biotin-labeled anti-sense RNA (aRNA) was prepared from the second round cDNA with the Illumina® TotalPrep™ RNA kit (Applied Biosystems). The labeled aRNA was hybridized to probes immobilized in singlet on flow-through microarrays on the Ziplex Automated Workstation (Xceed Molecular). Performance was assessed by the analysis of titration mixtures prepared from mRNA from breast cancer and colon cancer FFPE tissue blocks.Results: Median CVs of technical replicates were less than 25%. Linear responses were observed in the analysis of the titration mixtures, and all correlations between predicted and observed expression values of the titration mixtures had R2 values greater than 0.8. The data indicated that the minimum detectable expression difference was less than two-fold. Similar signal intensities were observed for 3'-biased probes and probes several hundred bases from the 3'end, confirming the lack of 3' bias in the amplification.Discussion: The results demonstrate the feasibility of amplifying and quantifying sequences at any position within transcripts in degraded mRNA from FFPE samples. Expression differences of less than two-fold may be analyzed with tens or hundreds of probes for translational research and clinical assay development on the Ziplex Workstation. Many probes may be tested in parallel to optimize probe sets for specific tests. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3052.