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

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.

Bacterial immobilization by adhesion onto agave-fiber/polymer foamed composites

Adhesion of Pseudomonas putida F1 onto agave-fiber/recycled-polyethylene foamed composites was studied under different controlled conditions. The adhesion process was analyzed in batch experiments controlling factors such as pH, contact time, temperature, initial biomass concentration and ionic strength; and was verified by scanning electron microscopy (SEM). The number of adhered bacteria after the experimental time was determined by difference between concentration of suspended cells in NaCl solution contained in two different Erlenmeyer flasks, one of the flasks with composite pellets and the other one without them. The concentration of cells in each flask was obtained using the serial dilution technique. Experimental data analysis showed that adsorption follows first-order kinetics. And it was further corroborated to be an irreversible process. For the first time, an equation is proposed here to predict the correlation between adhered bacteria and aqueous pH. In addition to the obvious reuse of waste material, these results suggested that agave-fiber/polymer foamed composites could be used as support for bacterial immobilization to be applied, among others in environmental processes such as bioremediation and biofiltration of gases with almost limitless possibilities.

[Long-term outcome of lung transplantation]

Lung transplantation (LTx) nowadays is an established therapeutic option for various end-stage lung diseases in despite of an optimal medical therapy in selected patients affected with various pathologies such as emphysema/chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF) and various forms of bronchiectasis, pulmonary fibrosis and pulmonary hypertension. Progress and refinement over the last two decades in both surgical techniques and medical management including especially the introduction of cyclosporine A, have been impressive. Patient survival improved significantly over time. According to the most recent data of the International Registry of Lung Transplantation (ISHLT), actuarial survival is 79%, 63%, 52% and 29% at 1, 3, 5 and 10 years respectively, with a current overall survival half-life of 5.3 years, and more than 7 years for those who survived 1 year or more. However, survival depends on different parameters such as the underlying disease, data relative to the donor, the recipient and/or the transplant procedure. Major limitation of long-term survival is still chronic allograft dysfunction, which is histologically represented by an obliterative bronchiolitis and functionally by the bronchiolitis obliterans syndrome (BOS). In uncomplicated cases near-normalization of pulmonary function is the rule, with more than 80% of survivors at 1, 3, 5 and 10 years reporting no activity limitations. Functional results after single LTx remain lower than those of the bilateral LTx, and depend on the potential worsening of the underlying disease and complications arising on the native lung. Exercise performance usually is approximately 50% of predicted, suggesting extrapulmonary causes such as side effects of immunosuppressive drugs. Quality of life improves significantly in all domains including employment status.

Viability and functional capacity after thawing of hematopoietic progenitor cells cryopreserved at a cord blood stem cell bank in Colombia

OBJECTIVE

To evaluate the viability and functional capacity of hematopoietic progenitor cells from cord blood samples cryopreserved at the Banco de Células Stem de Colombia.

METHODS

After thawing and centrifugation of 20 samples, viable white blood cells were numbered by the trypan blue method and CD34(+)CD45(+dim) hematopoietic progenitor cells were numbered by flow cytometry. Clonogenic assays also tested the functional capacity of viable CD34(+)CD45(+dim) cells.

RESULTS

The median rates of viable CD34(+)CD45(+dim) cells were 99.6% before freezing and 73.0% after thawing (P<0.001). The 20 cultures yielded a median of 12 cells with a lineage of red cells, 17.5 cells with a lineage of white cells, and 10 cells with a mixed lineage.

CONCLUSION

Although the rate of viable CD34(+)CD45(+dim) cells was decreased by 26.6% after thawing by the method we used, the numbers of CD34(+)CD45(+dim) cells that formed colonies were similar to those obtained by other published methods.

Gene Expression Profiling of Formalin-Fixed, Pariffin-Embedded (FFPE) Tissues from Triple-Negative (TN) Breast Cancer (BC) Patients

Background: FFPE tumor samples present a technical challenge for gene expression profiling studies. Newer technologies are resulting in quality data and new insights from these archived tissues. TNBC is a sub-type of BC 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 therapeutic agents, and has different incidence among ethnic groups. A better understanding of the genetic and molecular mechanisms underlying TNBC is critical to improving clinic outcomes and developing individualized therapies.Study Objective: We demonstrate the utility of FFPE samples in obtaining consistent, reproducible data from gene expression arrays, and apply this technology to the identification of differentially expressed genes between TNBC and normal breast tissue that are common or unique among selected ethnic groups.Methods: RNA isolation and labeled cDNA preparation from freshly cut FFPE blocks (marked by a pathologist as to normal vs. tumor tissue) was performed using the NuGEN™ WT-Ovation™ FFPE RNA Amplification System. Hybridization of tumor and normal cDNAs occurred to a breast cancer focused gene expression array (Breast Cancer DSA Research Tool, Almac Diagnostics Inc). Each patient' sample served as it's own control (tumor vs. normal). In total, 75 FFPE samples were profiled. The quality of each DSA chip was assessed on parameters selected automatically from GCOS report files per chip using MATLAB script based web application developed by Almac Dx. 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 using Principal Component Analysis and Clustering Analysis in Rosetta Resolver Gene Expression Data Analysis System 7.1 to identify potential outliers, contamination, or intra-tumor heterogeneity.Results: A Sign Agreement Matrix of FFPE and fresh frozen tissue samples during validation of the Breast Cancer DSA demonstrated that 98% of the probesets showed the same direction of fold change [p Spearman(FC)=0.84]. The FFPE samples had an average present call ∼ 43%, and more than 90% of the FFPE samples had present call rates greater than 25%. QC analysis demonstrated that the Almac Breast Cancer DSA was able to clearly and consistently separate tumor samples from normal in FFPE tissues and to identify samples of quality or integrity issues. Application of this methodology to analyses of differentially expressed transcripts between cancer and normal tissue samples across ethnicities in the TNBC samples, detected 1350 differentially expressed genes in the African-American group, 1220 genes in the Caucasian group and 1226 genes in the White Hispanic group. We also observed certain subtle ethnic-specific expression patterns across these three ethnic groups.Summary: The above-described methodology can be used to reliably measure gene expression in FFPE breast samples. Our study results are being validated in a larger data set.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 6125.

Neoadjuvant platinum-based chemotherapy (CT) for triple-negative locally advanced breast cancer (LABC): Retrospective analysis of 125 patients

625

Background: Triple-negative breast cancer (TNBC), defined by lack of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2, accounts for 15–20% of all breast cancers and is associated with poor prognosis. There is no consensus regarding optimal CT for treatment of such patients. Preclinical data suggests TNBC may be sensitive to platinums because of deficiencies in BRCA-associated DNA repair. The aim of this study was to evaluate pathologic complete response (pCR) and overall survival (OS) in patients with TNBC treated with neoadjuvant platinum-based CT. Methods: We identified 674 patients with LABC who received neoadjuvant CT between January 1999 and June 2008 at University of Miami. Of these, 125 (18.5%) had histopathologic confirmation of TNBC. All patients received neoadjuvant platinum salts + docetaxel. 76 (61%) also received neoadjuvant AC, while 42 (34%) received adjuvant AC. pCR was defined as no residual invasive disease in breast and axilla. OS was calculated according to Kaplan-Meier. Results: Demographics: median age 50 (28–86 years). 60% premenopausal. TNM stage distribution: T1 0.9%, T2 5.2%, T3 53.4%, T4 40.5%, N0 25.0%, N1 36.2%, N2 35.4%, N3 3.4%, M0 100%, inflammatory 11%, median tumor size = 9.5 cm. Follow up duration ranged from 0.3 to 8.9 years. pCR was observed in 42 of 125 patients (34%; 95% CI 26–43%). Among patients receiving neoadjuvant AC, 30 of 76 (40%; 95% CI 28–51%) had pCR, while amongst those receiving adjuvant AC, 12 of 42 (29%, 95% CI 16–45%) had pCR at the time of definitive surgery. Patients achieving pCR had significantly higher OS (5-yr rate = 73% in pCR, vs. 49% in non-pCR; p < 0.001). OS in TNBC patients receiving cisplatin/docetaxel was significantly superior to those receiving carboplatin/docetaxel (11 mortality events out of 78 patients receiving cisplatin based CT vs 24 out of 47 receiving carboplatin based CT logrank p = 0.001). Conclusions: To date, this is the largest single institution cohort of locally advanced TNBC uniformly treated with platinum+docetaxel-based CT regimens. Platinum/docetaxel-based neoadjuvant CT provided high rates of pCR and excellent OS for women with locally advanced TNBC.

No significant financial relationships to disclose.

Distinct multiethnic genome-wide alterations in breast cancer using paraffin embedded samples: preliminary analysis

Abstract #2024

Background and Rational: Ethnic-specific disparities in breast cancer (BC) stage of presentation and survival rates are well documented. To further investigate possible ethnic-specific genetic contributions to these disparities, we are completing gene expression profiling studies in a multi-ethnic cohort consisting of thirty “Triple Negative” BC patients [10 each African-American (AA), Hispanic (His) and non-Hispanic white (Cauc) women] matched for age of diagnosis and hormone receptor status. The overall study aim is an increased understanding of the biological basis of ethnic-specific BC disparities, leading ultimately to individualized, ethnic-specific diagnostic and therapeutic approaches. Two immediate study goals are to demonstrate the utility of FFPE samples in obtaining consistent, reproducible data from gene expression arrays, and secondly, to identify differentially expressed genes between tumor and normal tissue that are common or unique among the three ethnic groups. Methods: Pathology specimens were freshly cut from FFPE blocks and marked by a pathologist as to normal vs. tumor tissue. RNA isolation, labeled cDNA preparation, and hybridization of tumor and normal cDNAs to a breast cancer focused gene expression microarray (Breast Cancer DSA Research Tool) was performed by Almac Diagnostics. Each patient was self-matched (tumor vs. normal tissue) for gene expression studies. Results: Using 36 matched tumor and normal FFPE samples from 18 patients, approximately 17516 transcripts were detected on the Breast Cancer DSA with intensity significantly greater than background. For normal and tumor tissue samples, 9399 and 10,296 transcripts respectively, were detected in all three ethnic groups. Importantly, a subset of transcripts (hundreds to one thousand) was detected in only one or two ethnic groups. Using two-way ANOVA (disease state and ethnicity), a subset of 6479 transcripts was identified with p-value less than 0.01 in the statistical test and was selected and further used in data quality control. Data QC indicated that patient samples clustered well with respect to both ethnicity and normal versus tumor tissue. Additional analytical methods included K-means 2-Dimensional clustering and Principal Component Analysis. From these analyses, we identified ethnic-specific expression patterns in the matched normal and tumor tissue samples. We are completing these studies by increasing sample size and matching for stage of diagnosis, mapping clusters of differentially-expressed genes in pathway analysis, and validation by real-time PCR. In the longer term, DNA copy number variation (CNV) and chromosomal alterations will be investigated by high density arrays. Summary: These preliminary analyses shows that high quality gene expression data can be generated from FFPE samples, and that ethnic specific gene expression differences can be detected in tumor and matched normal breast tissue samples across ethnic groups.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2024.