Purpose Cisplatin is a chemotherapeutic agent not used routinely for breast cancer treatment. As a DNA cross-linking agent, cisplatin may be effective treatment for hereditary BRCA1-mutated breast cancers. Because sporadic triple-negative breast cancer (TNBC) and BRCA1-associated breast cancer share features suggesting common pathogenesis, we conducted a neoadjuvant trial of cisplatin in TNBC and explored specific biomarkers to identify predictors of response. Patients and Methods Twenty-eight women with stage II or III breast cancers lacking estrogen and progesterone receptors and HER2/Neu (TNBC) were enrolled and treated with four cycles of cisplatin at 75 mg/m2 every 21 days. After definitive surgery, patients received standard adjuvant chemotherapy and radiation therapy per their treating physicians. Clinical and pathologic treatment response were assessed, and pretreatment tumor samples were evaluated for selected biomarkers. Results Six (22%) of 28 patients achieved pathologic complete responses, including both patients with BRCA1 germline mutations;18 (64%) patients had a clinical complete or partial response. Fourteen (50%) patients showed good pathologic responses (Miller-Payne score of 3, 4, or 5), 10 had minor responses (Miller-Payne score of 1 or 2), and four (14%) progressed. All TNBCs clustered with reference basal-like tumors by hierarchical clustering. Factors associated with good cisplatin response include young age (P = .001), low BRCA1 mRNA expression (P = .03), BRCA1 promoter methylation (P = .04), p53 nonsense or frameshift mutations (P = .01), and a gene expression signature of E2F3 activation (P = .03). Conclusion Single-agent cisplatin induced response in a subset of patients with TNBC. Decreased BRCA1 expression may identify subsets of TNBCs that are cisplatin sensitive. Other biomarkers show promise in predicting cisplatin response.

UK Medical Research Council; Cancer Research UK; the National Institute for Health Research (UK); the Danish Council for Independent Research-Medical Sciences (FSS); Breast Cancer Research Foundation (New York); Fondation Luxembourgeoise contre le Cancer; the Fonds National de la Recherche Scientifique; Brussels Region (IRSIB-IP, Life Sciences 2007) and Walloon Region (Biowin-Keymarker); Sally Pearson Breast Cancer Fund; and the European Commission.

Chromosomal instability (CIN) is a common cause of tumour heterogeneity and poor prognosis in solid tumours and describes cell-cell variation in chromosome structure or number across a tumour population. In this article we consider evidence suggesting that CIN may be targeted and may influence response to distinct chemotherapy regimens, using HER2-positive breast cancer as an example. Pre-clinical models have indicated a role for HER2 signalling in initiating CIN and defective cell-cycle control, and evidence suggests that HER2-targeting may attenuate this process. Anthracyclines and platinum agents may target tumours with distinct patterns of karyotypic complexity, whereas taxanes may have preferential activity in tumours with relative chromosomal stability. A greater understanding of karyotypic complexity and identification of methods to directly examine and target CIN may support novel strategies to improve outcome in cancer.

To mimic in vivo conditions during chlamydial infections, Chlamydia trachomatis serovar D and Chlamydia pneumoniae CWL029 were cultured in low-oxygen atmospheres containing 4% O 2 , with parallel controls cultured in atmospheric air. Both were enriched with 5% CO 2 . The results showed a dramatic increase in the growth of C. pneumoniae but not of C. trachomatis.The chlamydial developmental cycle is biphasic, alternating between an infectious metabolically inactive elementary body (EB) specialized for extracellular survival and a noninfectious proliferating intracellular reticulate body (RB). During the course of an infection, the EB is endocytosed by a susceptible host cell into a host-derived vacuole, the chlamydial inclusion. After internalization, the EB develops into an RB, which proliferates by binary fission. Following several rounds of proliferation lasting 48 to 72 h, RBs transform into EBs and are released by the disruption of the host cell (for a review, see reference 9).Chlamydia trachomatis is an obligate human pathogen causing ocular and genital infections. Chlamydia pneumoniae causes respiratory tract infections, often asymptomatic, but may cause bronchitis and pneumonia (5). Traditionally, both C. trachomatis and C. pneumoniae have been studied in vitro by infecting cell culture monolayers and incubating the infected cells in incubators in a humid atmosphere containing atmospheric air enriched with 5% CO 2 , resulting in an oxygen concentration of approximately 20%. However, the in vivo oxygen tension is much lower, generally in the range of 3 to 6% (Table 1), and as different tissues have different oxygen requirements, the in vivo oxygen tension may vary considerably from tissue to tissue. The oxygen requirements of Chlamydia have never been evaluated before, but it is known that the oxygen tension of host tissue is important for viral replication and the viral life cycle (3) and that many infecting microorganisms are microaerophilic. As Chlamydia proliferates in vivo where the oxygen tension varies between different tissues, it is plausible that Chlamydia is also affected by the oxygen tension and would experience enhanced growth in tissues with optimum oxygen tension.C. trachomatis and C. pneumoniae produced enlarged inclusions in 4% oxygen. To determine the visible effect of low oxygen tension on chlamydial inclusions, infected HeLa cells were cultured on coverslips at 4% and 20% O 2 . HeLa 229 cells (ATCC, Rockville, MD) cultured in 24-well trays (TPP, Trasadingen, Switzerland) were infected with either C. trachomatis serovar D/UW-3/CX (ATCC) or C. pneumoniae CWL029 (ATCC) as previously described (12, 15) and cultured in the presence of cycloheximide in either 4% or 20% oxygen atmospheres. Low-oxygen atmospheres were achieved by placing trays with infected HeLa cells in an airtight custom-made box (40 by 30 by 16 cm [width by diameter by height]). An OX-500 Clark-type oxygen sensor (UniSense, Aarhus, Denmark) was placed inside the box to measure the oxygen concentration. The box was flushed w...

BackgroundExpression of the oestrogen receptor (ER) in breast cancer predicts benefit from endocrine therapy. Minimising the frequency of false negative ER status classification is essential to identify all patients with ER positive breast cancers who should be offered endocrine therapies in order to improve clinical outcome. In routine oncological practice ER status is determined by semi-quantitative methods such as immunohistochemistry (IHC) or other immunoassays in which the ER expression level is compared to an empirical threshold[1], [2]. The clinical relevance of gene expression-based ER subtypes as compared to IHC-based determination has not been systematically evaluated. Here we attempt to reduce the frequency of false negative ER status classification using two gene expression approaches and compare these methods to IHC based ER status in terms of predictive and prognostic concordance with clinical outcome.Methodology/Principal FindingsFirstly, ER status was discriminated by fitting the bimodal expression of ESR1 to a mixed Gaussian model. The discriminative power of ESR1 suggested bimodal expression as an efficient way to stratify breast cancer; therefore we identified a set of genes whose expression was both strongly bimodal, mimicking ESR expression status, and highly expressed in breast epithelial cell lines, to derive a 23-gene ER expression signature-based classifier. We assessed our classifiers in seven published breast cancer cohorts by comparing the gene expression-based ER status to IHC-based ER status as a predictor of clinical outcome in both untreated and tamoxifen treated cohorts. In untreated breast cancer cohorts, the 23 gene signature-based ER status provided significantly improved prognostic power compared to IHC-based ER status (P = 0.006). In tamoxifen-treated cohorts, the 23 gene ER expression signature predicted clinical outcome (HR = 2.20, P = 0.00035). These complementary ER signature-based strategies estimated that between 15.1% and 21.8% patients of IHC-based negative ER status would be classified with ER positive breast cancer.Conclusion/SignificanceExpression-based ER status classification may complement IHC to minimise false negative ER status classification and optimise patient stratification for endocrine therapies.

Gene expression profiling has yielded important insights about tumor biology that may improve treatment decisions in patients. However, it is difficult to collect a specimen of pure tumor cells, and thus microarray measurements usually reflect the contribution of tumor cells as well as stromal and other normal cells. We applied unsupervised matrix factorization methods to gene expression data to derive several sets of co-expressed genes, or signatures, that together comprise a set of independent descriptors of breast tumors. Some of these signatures correspond to specific cell types (adipocytes, lymphocytes, fibroblasts), while others reflect well-known tumor-intrinsic expression programs (ER, ERBB2, proliferation). We confirmed the specificity of the signatures using expression data from purified normal cells and tumor cell lines, microdissected tumors, and bulk tumors with corresponding histological cellularity estimates. In several data sets, cell-type signatures were highly variable and anticorrelated with tumor-intrinsic signatures, confirming that variation in normal cell content is a potential source of measurement bias.Overall, these results provide an intuitive framework for the interpetation of tumor expression profiles and may lead to an improved understanding of the physiological mechanisms involved in tumor development. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 1166.

Cisplatin-based chemotherapy promotes DNA inter- and intra-strand cross-links and is effective treatment in multiple cancer types, yet it is rarely used for first-line therapy of breast cancer. Cisplatin is an effective cytotoxic in BRCA1 mutant cancer cell lines and in breast and ovarian cancers with BRCA1 mutations, prompting speculation that defective DNA double-strand break repair is associated with cisplatin sensitivity. Furthermore, tumors with BRCA1 mutation are presumed to be defective in various aspects of DNA repair and also display increased levels of chromosomal instability. Thus, we hypothesized that the total number of chromosomal breakpoints in a specific tumor may reflect defective DNA repair and/or chromosomal instability, and may therefore be used as a predictor of cisplatin sensitivity. Supporting this relationship, we identified a correlation (r = 0.8, P = 0.08) between the total number of chromosomal breakpoints, estimated by the number of genomic regions showing allelic imbalance, and cisplatin sensitivity in five triple negative breast cancer cell lines. To validate this relationship in a clinical setting we compared the total number of chromosomal breakpoints to therapy response in a cisplatin treated breast cancer cohort. A total of 28 women with stage II or III ER-/PR-/HER2- breast cancer were treated with cisplatin in the neo-adjuvant setting followed by surgery and standard adjuvant chemotherapy. A core biopsy was obtained before treatment commenced, tumor cells were enriched by needle microdissection, and DNA was extracted for genotyping. As only limited amounts of DNA were available, we used a Molecular Inversion Probe assay (in collaboration with Affymetrix), which allowed us to genotype 42,000 SNPs with only 40 ng of starting DNA. We then estimated the total number of putative genomic breakpoints in 21 samples containing at least 75% tumor cells. We compared this summary genomic measure to the response rate as quantitated by the Miller-Payne score determined on the pathological specimen obtained at surgery. This genomic measure showed a remarkably accurate separation of patients by degree of response, correctly classifying 20 out of 21 patients (P < 0.001).These results suggest that the total number of DNA breakpoints may be an accurate biomarker of breast cancers which may be sensitive to cisplatin treatment. The molecular explanations for these findings await further work. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 111.

The genome of the obligate intracellular bacteria Chlamydia pneumoniae contains 21 genes encoding polymorphic membrane proteins (Pmp). While no function has yet been attributed to the Pmps, they may be involved in an antigenic variation of the Chlamydia surface. It has previously been demonstrated that Pmp10 is differentially expressed in the C. pneumoniae CWL029 isolate. To evaluate whether the absence of Pmp10 in the outer membrane causes further changes to the C. pneumoniae protein profile, we subcloned the CWL029 isolate and selected a clone with minimal Pmp10 expression. Subsequently, we compared the proteome of the CWL029 isolate with the proteome of the subcloned strain and identified a specific cleavage of the C-terminal part of the major outer membrane protein (MOMP), which occurred only in the absence of Pmp10. In contrast, when Pmp10 was expressed we predominantly observed full-length MOMP. No other proteins appeared to be regulated according to the presence or absence of Pmp10. These results suggest a close association between MOMP and Pmp10, where Pmp10 may protect the C-terminal part of MOMP from proteolytic cleavage.