Showing papers by "Charles M. Perou published in 2005"

Breast Cancer Molecular Subtypes Respond Differently to Preoperative Chemotherapy

Abstract: Purpose: Molecular classification of breast cancer has been proposed based on gene expression profiles of human tumors. Luminal, basal-like, normal-like, and erbB2+ subgroups were identified and were shown to have different prognoses. The goal of this research was to determine if these different molecular subtypes of breast cancer also respond differently to preoperative chemotherapy. Experimental Design: Fine needle aspirations of 82 breast cancers were obtained before starting preoperative paclitaxel followed by 5-fluorouracil, doxorubicin, and cyclophosphamide chemotherapy. Gene expression profiling was done with Affymetrix U133A microarrays and the previously reported “breast intrinsic” gene set was used for hierarchical clustering and multidimensional scaling to assign molecular class. Results: The basal-like and erbB2+ subgroups were associated with the highest rates of pathologic complete response (CR), 45% [95% confidence interval (95% CI), 24-68] and 45% (95% CI, 23-68), respectively, whereas the luminal tumors had a pathologic CR rate of 6% (95% CI, 1-21). No pathologic CR was observed among the normal-like cancers (95% CI, 0-31). Molecular class was not independent of conventional cliniocopathologic predictors of response such as estrogen receptor status and nuclear grade. None of the 61 genes associated with pathologic CR in the basal-like group were associated with pathologic CR in the erbB2+ group, suggesting that the molecular mechanisms of chemotherapy sensitivity may vary between these two estrogen receptor–negative subtypes. Conclusions: The basal-like and erbB2+ subtypes of breast cancer are more sensitive to paclitaxel- and doxorubicin-containing preoperative chemotherapy than the luminal and normal-like cancers.

Standardizing global gene expression analysis between laboratories and across platforms

Abstract: Addendum: Standardizing global gene expression analysis between laboratories and across platforms

Molecular portraits and 70-gene prognosis signature are preserved throughout the metastatic process of breast cancer.

Abstract: Microarray analysis has been shown to improve risk stratification of breast cancer. Breast tumors analyzed by hierarchical clustering of expression patterns of "intrinsic" genes have been reported to subdivide into at least four molecular subtypes that are associated with distinct patient outcomes. Using a supervised method, a 70-gene expression profile has been identified that predicts the later appearance or absence of clinical metastasis in young breast cancer patients. Here, we show that distant metastases display both the same molecular breast cancer subtype as well as the 70-gene prognosis signature as their primary tumors. Our results suggest that the capacity to metastasize is an inherent feature of most breast cancers. Furthermore, our data imply that poor prognosis breast carcinomas classified either by the intrinsic gene set or the 70 prognosis genes represent distinct disease entities that seem sustained throughout the metastatic process.

αB-Crystallin is a novel oncoprotein that predicts poor clinical outcome in breast cancer

Abstract: Recent gene profiling studies have identified a new breast cancer subtype, the basal-like group, which expresses genes characteristic of basal epithelial cells and is associated with poor clinical outcomes. However, the genes responsible for the aggressive behavior observed in this group are largely unknown. Here we report that the small heat shock protein α-basic–crystallin (αB-crystallin) was commonly expressed in basal-like tumors and predicted poor survival in breast cancer patients independently of other prognostic markers. We also demonstrate that overexpression of αB-crystallin transformed immortalized human mammary epithelial cells (MECs). In 3D basement membrane culture, αB-crystallin overexpression induced luminal filling and other neoplastic-like changes in mammary acini, while silencing αB-crystallin by RNA interference inhibited these abnormalities. αB-Crystallin overexpression also induced EGF- and anchorage-independent growth, increased cell migration and invasion, and constitutively activated the MAPK kinase/ERK (MEK/ERK) pathway. Moreover, the transformed phenotype conferred by αB-crystallin was suppressed by MEK inhibitors. In addition, immortalized human MECs overexpressing αB-crystallin formed invasive mammary carcinomas in nude mice that recapitulated aspects of human basal-like breast tumors. Collectively, our results indicate that αB-crystallin is a novel oncoprotein expressed in basal-like breast carcinomas that independently predicts shorter survival. Our data also implicate the MEK/ERK pathway as a potential therapeutic target for these tumors.

High reproducibility using sodium hydroxide-stripped long oligonucleotide DNA microarrays.

Abstract: Recently, long oligonucleotide (60- to 70-mer) microarrays for two-color experiments have been developed and are gaining widespread use. In addition, when there is limited availability of mRNA from...

Housekeeping genes and methods for identifying the same

Abstract: Disclosed are compositions and methods related to housekeeping genes and methods and compositions related to detecting and classifying cancer.

Hormone receptor negative and basal-like subtypes are overrepresented in invasive breast carcinoma from women of African ancestry

Abstract: Proc Amer Assoc Cancer Res, Volume 46, 2005 2550 Purpose: Gene expression profile of breast carcinomas distinguish molecular subsets of estrogen receptor (ER)+/luminal, normal breast-like, HER2 overexpressing, and basal-like groups with clinical implications. A panel of four antibodies (ER, HER1, HER2, and cytokeratin 5/6) may identify these subsets. In this report, we surveyed a series of invasive breast tumors from Nigerian patients to ascertain the relative frequency of these subtypes as breast cancers can display distinct biological characteristics in different ethnic populations. Experimental Design: On archival breast cancer tissue diagnosed in Nigeria, immunohistochemical staining for ER and Cytokeratin 5/6 were performed using Anti-ER (clone 6F11; 1:40, Novocastra) and Anti- Cytokeratin 5/6 (1:10, Boehringer Mannheim). HER1 and HER2 were stained using the PharmDX and Herceptest kits, respectively, according to manufacturer’s instructions (DAKO). Result: Of the 148 cases, 67% were premenopausal with a mean age of 43.8±11.2 years; large tumor size (mean 4.2±1.3cm); 78% had histological grade 2 or 3. ER expression was present in only 23.0% and HER2 was overexpressed in 19%. HER1 and Cytokeratin 5/6 expression were present in 40% and 23%. The proportion of tumors in each subtype was: ER-HER2- 86/148 (58%), HER2+ 28/148 (19%) and ER+ 34/148 (23%). In the ER-HER2- subset, HER1 and anti-Cytokeratin expressions were observed in 35/86 (41%) and 12/86 (14%), respectively. Conclusion: Our results suggest that molecularly portraits of breast tumors are broadly conserved between women of African and European ancestry. However the relative frequencies of the subsets differ, with a majority of tumors from Nigeria lacking the expression of important therapeutic targets like ER, HER2 and HER1. These findings provide further evidence that breast tumor subtypes with the worse outcomes are overrepresented in women of African ancestry. Novel therapeutic targets are desperately needed to combat disparities in health outcomes associated with these tumor subtypes. * Perou CM et al. Immunohistochemical and clinical characterization of the basal-like subtype of invasive breast carcinoma. Clin Cancer Res 2004;10:5367-74. ![Figure][1] [1]: pending:yes

Identification of drug targets for the treatment of Basal-like tumors

Abstract: Genomic studies have identified at least five distinct subtypes of breast tumors [1]. These subtypes are believed to develop from different epithelial cell types and show different overall survival outcomes. Of particular interest is the estrogen receptor (ER)-negative Basal-like subtype, which accounts for 10–15% of all breast tumors and shows poor outcomes. In the breast cancer clinic, there are currently two biologically directed therapies that target either the ER or HER2 proteins. The Basal-like tumors lack both of these proteins [2], and hence the only treatment options for these patients are cytotoxic chemotherapies. A goal of ours was therefore to use primary breast tumor gene expression data and cell line models to identify and validate candidate biologically-based therapies for Basal-like tumors. To identify potential targets, the gene expression data for approximately 1500 drug targets were examined across a breast tumor data set of 150 samples. Squalene epoxidase (SQLE) was expressed in most Basal-like tumors, as well as in the Basal-like tumor-derived cell lines SUM102 and SUM149. SQLE is an attractive target because it is highly expressed, it is a rate-limiting step in the cholesterol biosynthetic pathway, and there is an available inhibitor (NB598) [3]. Recent studies using inhibitors of HMGCoA reductase (the first rate-limiting step) in epithelial cell lines suggest that inhibition of this pathway may be a potential target for therapeutic intervention [4]. Using the SUM102 and SUM149 cell lines and two more widely used luminal/ER+ lines (MCF-7 and ZR-75-1), we treated cells with NB598 and separately with lovastatin (an HMGCoA reductase inhibitor) and determined their sensitivity by identifying their 72-hour IC50 dose. Sensitivity was similar across three of the four cell lines for NB598, with the exception of SUM102, which was approximately 300 times more sensitive. Conversely, sensitivity to lovastatin was similar across three of the four cell lines except MCF-7, which was approximately five times more resistant. Since many drugs are rarely used as single agents, we also looked at the interactions between these two inhibitors and commonly used chemotherapeutics. Drug-combination sensitivities again varied across the four cell lines; however, it appears that combinations of NB598 and 5-fluorouracil were typically synergistic, while combinations with carboplatin or paclitaxel were typically antagonistic. Similar analyses are being performed for lovastatin/chemotherapy combinations. Gene expression responses of these cell lines were also assayed using DNA microarrays. The effect on the cholesterol pathway showed that, for MCF-7 and SUM102, adding either inhibitor greatly induced most genes in the cholesterol biosynthetic pathway, while SUM149 treated with lovastatin showed induction of the pathway but treatment with NB598 did not. ZR-75-1 treated with either drug showed a slight reduction in expression of the pathway. These in vitro data suggest that inhibition of SQLE activity can reduce cell line proliferation rates and, in some instances, was synergistic with chemotherapy. These data also suggest that inhibition of the cholesterol pathway by addition of HMGCoA reductase inhibitors is different from inhibition of the pathway with SQLE inhibitors.

Functional Genomics for Identifying Surrogate Endpoint Biomarkers in Breast Cancer Chemoprevention

Abstract: Human tumors have great diversity in morphology and natural history; this is reflected in variations in clinical outcome. Assessment of morphology and a few immunohistochemical markers in tumors have guided treatment of most cancers. By studying gene expression patterns for a large number of genes, morphologically similar tumors can be further subdivided into distinct categories of clinical relevance. Recent studies have applied DNA microarrays to the study of many types of cancer, including breast (1–6), brain (7,8), ovary (9–11), lung (12–14), colon (15–17), kidney (18), prostate (19–22), gastric (23), leukemia (24–26), and lymphoma (27–29). Most of these studies identified clinically relevant tumor subtypes that were believed to represent more homogenous clinical entities. Thus, using cDNA microarrays to characterize variation in tumors could add value to the standard battery of clinical tests. Invasive breast carcinomas are a particularly heterogeneous category of human tumors where advances in classification, risk assessment, and outcome predictions are needed. Recent studies using DNA microarrays identified new and clinically important subtypes of breast cancer that correspond to differences in clinical outcome (1–3). The genomic “profiling” approach has led to a rapid increase in the number of candidate risk and response biomarkers for invasive human breast tumors; therefore, it is likely that gene expression profiles of early breast lesions will also be valuable. Studying gene expression profiles of early lesions of the breast, such as atypical ductal hyperplasia, lobular carcinoma in situ, and ductal carcinoma in situ, can identify new biomarkers of risk and response for chemoprevention studies and treatment. In this chapter, we present a model for using genomic profiling to identify targets for chemoprevention in Phase II trials. The basic methodology described here for breast lesions could also be applied to other tissues to identify tissuespecific risk and response biomarkers.

Microarray profiling is feasible using archived tissue from a Cooperative Group Clinical Trial: Results from a pilot study in CALGB 9342

Abstract: 545 Background: CALGB 9342 was designed to test the efficacy of paclitaxel in women with advanced breast cancer. Tissue blocks were collected to retrospectively assess single gene markers (Lin et a...

Gènes domestiques et méthodes d'identification desdits gènes

Abstract: Compositions et methodes relatives a des genes domestiques et methodes et compositions permettant la detection et la classification des cancers.

Tailored therapies based upon tumor subtype biology

Abstract: Breast cancer is a spectrum of diseases comprised of different tumor subtypes, each with a distinct biology and clinical behavior. To capture this diversify, we characterized the variation in gene expression across human breast tumors using DNA microarrays and identified at least five distinct tumor subtypes that are statistically significant predictors of patient overall survival [1]. Recently, we further validated these findings using a training set of 102 tumors, which was used to derive a new 'intrinsic gene set'. This gene set was then validated using a true test set of 311 tumors compiled from three different microarray studies. Our analyses demonstrate that common patterns of gene expression can be identified across different microarray platforms, that the breast tumor 'intrinsic' subtypes are reproducible across different datasets, and that this classification was a significant predictor of outcomes after correcting for standard clinical parameters such as estrogen receptor (ER), grade and node status [2]. The biology of the 'intrinsic' subtypes is rich and extensive, and many of these expression features suggest distinct therapies. The 'intrinsic' subtypes include at least two types of ER-negative tumors (Basal-like and HER2+/ER-) and at least two types of ER-positive tumors (Luminal A and Luminal B). Basal-like tumors typically show low expression of HER2 and ER, and these tumors exhibit high expression of genes characteristic of the basal epithelial cell layer, including expression of keratin 5, keratin 6, keratin 17 and four Kallikrein genes (KLK5-KLK8). The Basal-like tumors pose a challenge from the treatment perspective because they lack ER and HER2. However, we have recently shown that most are HER1-positive and/or c-KIT-positive [3], and we have initiated a clinical trial to evaluate the efficacy of HER1-inhibitors in preselected Basal-like tumor patients. HER2-positive (i.e. gene amplified) tumors fall into at least two distinct expression groups: those that are ER-negative and typically cluster near the Basal-like tumors (HER2+/ER-), and those that are ER-positive and cluster with tumors of luminal cell origin. These findings suggest that both types of HER2+ patients should receive transtuzumab, but that the ER+/HER2+ may gain a benefit from hormone therapy. Finally, the Luminal subtype A and Luminal subtype B tumors express ER, GATA3, and genes regulated by both ER and GATA3. Compared with Luminal B tumors, Luminal A tumors express higher levels of ER, BCL2 and GATA3, and they show more favorable patient outcomes. Luminal B tumors more often express HER1, HER2 and/or cyclin E1, and they show worse outcomes. Our data, when coupled with data from others [4], suggests that Luminal A patients are likely to benefit from hormone therapy and are not likely to benefit from chemotherapy, while the opposite may be true of Luminal B patients. Experiments to answer these questions in Luminal patients are underway and will be discussed.