P5-13-17: Multigene Signature Assays in Patients with Early-Stage Breast Cancer (ESBC) Receiving Neoadjuvant Chemotherapy: An NCI-Funded Systematic Review and Evidence Summary of Predictive Performance

Background: A comprehensive literature search and evidence synthesis of multigene signatures predictive of response to systemic chemotherapy in patients with breast cancer was initiated as a part of an NCI-funded program on Comparative Effectiveness Research.

Methods: Validation studies were sought of multigene signatures for prediction of chemotherapy response (favorable vs unfavorable) in ESBC patient cohorts different from those used for signature development. Pooled estimates [±95% CI] of assay performance for predicting clinical outcome included sensitivity, specificity, likelihood ratio, predictive value (PV) and predictive odds ratio (POR) utilizing mixed effects models based on the method of Mantel-Haenszel. Exploratory metaregression analyses on log (POR) were also performed. Studies were classified by validation type including cell lines to patients, independent internal sample, random split sample, or external validation. Evidence for publication bias was assessed by Egger's regression intercept and Begg and Mazumdar's rank correction. Results: Dual-blind review of abstracts identified 33 studies of neoadjuvant chemotherapy response of which 29 stratified treatment response by signature classifier category. Classifier development was based on tumor response prediction in 20 studies, prognosis in 5, and molecular classification in 4. The Table shows assay performance measures overall and by study validation type. Assay performance based on the POR was positively associated with overall study quality (P=.015) and journal impact factor (P=.020). However, strong evidence for publication bias was observed based on both regression intercept (P<.001) and rank correlation (P=.005). No significant differences in assay performance were noted for assays originally developed for response prediction (POR=5.3), prognosis (POR=6.6) or molecular classification (P=6.9) (P=.770).

Implementation of genomic predictors of chemotherapy response for guiding preoperative therapy in a prospective breast cancer trial

11057

Background: Personalized approaches to breast cancer therapy depend on genomic assays. While assays based on fixed tissues offer greater convenience, the spectrum of biology interrogated is limited. Full-transcriptome assays using microarrays are more challenging, but have the advantage of providing multiple prognostic and predictive signatures in one assay. We have created a clinical infrastructure with the objective of obtaining full genome expression data on breast cancer samples as a clinical assay for use in a prospective trial. Methods: “Performance of Genomic Expression Profiles to Direct the Use of Preoperative Chemotherapy for Early Stage Breast Cancer” is a prospective trial validating genomic signatures for predicting response to doxorubicin (A) or docetaxel (T) treatment in HER2 negative cancers. Fresh-frozen cores are reviewed by the study pathologist for tumor content. RNA is then extracted and probe generated to hybrize to an Affymetrix U133Plus2.0 microarray. Microarray data quality is determined using summary metrics for U133Plus2.0 arrays and principal component analysis (PCA) plots. The data is then used for predicting A or T sensitivity. Results: Thirteen cancers have been analyzed in the context of the above trial. Histologic type was lobular for 1, and predominantly ductal for 12 (10 ER positive, 3 ER negative). Median tumor size was 3.4 cm (range, 1.8–5.7). Microarray analysis was successful on 11 tumors (84%), providing data of sufficient quality to make predictions of A and T sensitivity. One sample hybridization failed QC as detected by PCA analysis, and one sample had insufficient RNA. The median “tissue to array data” time and “study consent to initiation of treatment” time were 5 days (range, 3–8) and 14 days (range, 11–36), respectively. Conclusions: Our initial experience shows that full-genome expression analysis on frozen tumor using an Affymetrix platform is feasible as a clinical assay for breast cancer. The resulting data is being used in a prospective marker validation protocol for predicting chemosensitivity. The data can also be analyzed for a variety of other potential prognostic and predictive signatures for guiding therapy.

No significant financial relationships to disclose.

A genomic signature of chemotherapeutic multidrug resistance provides a rational approach to identify patients for targeted therapy in advanced solid tumors

10613

Background: Multidrug resistance (MDR), the process by which cells resist many structurally and functionally unrelated drugs, remains a major challenge for cancer treatment. Strategies to reliably predict MDR will revolutionize cancer therapy. Methods: We made use of in vitro drug sensitivity data on 47 FDA approved chemotherapeutic agents from the NCI-60 database coupled with Affymetrix microarray data, to develop a gene expression signature of chemotherapeutic MDR, using a 'metagene’ approach to gene expression analysis (Potti et al, Nature Medicine, 2006). The capacity of the MDR signature to predict in vitro and in vivo resistance was evaluated in multiple independent cell line and patient cohorts. Results: A gene expression signature of chemotherapeutic MDR developed from cancer cell lines using a novel ‘metagene’ approach can accurately predict patients resistant to standard chemotherapeutic agents, including multi-drug regimens. This includes cohorts of patients with early stage breast cancer (n = 171; accuracy: 75.5%, sensitivity: 49.3%, specificity: 92%), patients who received neoadjuvant chemotherapy (n = 51; accuracy: 78.5%, sensitivity: 73.7%, specificity: 92.3%), and ovarian cancer (n = 105; accuracy: 83.8%, sensitivity: 71.8%, specificity: 93.7%). We further show that MDR signature expression is an independent prognostic factor in early stage breast cancer (p = 0.02, odds ratio: 3.49) and a large cohort of non-small cell lung cancer (p = 0.03, odds ratio: 5.70), in a multivariate analysis. Finally, to identify a rational therapeutic strategy in patients with the MDR phenotype, we have integrated the prediction of MDR with profiles of oncogenic pathway deregulation (Bild A, Nature, 2006) and show that targeting the Src pathway using a Src specific inhibitor (SU6656) circumvents MDR in the in vitro setting. Conclusions: The development of a gene expression signature of MDR, that can predict resistance to commonly used cytotoxic chemotherapies, provides a rational approach to developmental therapeutics, by identifying novel 'customized’ candidate drugs (e.g. targeting Src) for further clinical development.

No significant financial relationships to disclose.

Opposing effects of the D70 mutation and the shared epitope in HLA-DR4 on disease activity and certain disease phenotypes in rheumatoid arthritis

BACKGROUND

Certain sequences present in the hypervariable region of human leucocyte antigen (HLA)-DRB1 known as the shared epitope (SE) are hypothesised to increase the risk of rheumatoid arthritis (RA), whereas alleles encoding aspartic acid at position 70 (D70 alleles) may have a protective effect.

METHODS

Patient HLA-DRB1 serotypes were assessed and the genotypes encoding the SE motif or the putatively protective D70 motif identified in a large RA cohort. Logistic regression was used to analyse associations of genotype with presence of disease, comorbidities and disease severity, and association between genotype and change in disease activity over time.

RESULTS

The 689 patients enrolled had a mean (SD) age of 57.9 (13.7) years and mean (SD) disease duration of 15.3 (12.7) years. In a comparison with 482 ethnicity matched population-based controls, the D70 sequence exerted a strong protective effect (OR = 0.52, p<0.001) that remained significant when the SE at the same locus was accounted for (OR = 0.72, 95% CI 0.60 to 0.86, p<0.001). The SE assessed on all HLA-DRB1 serotypic backgrounds except DR1 was associated with RA susceptibility (additive OR = 2.43, p<0.001). Associations were found between SE and serum levels of rheumatoid factor (p<0.001, with correlation of 0.18) and anti-cyclic citrullinated peptide antibodies (p<0.001, with correlation of 0.25) but not with serum C-reactive protein.

CONCLUSION

The D70 allele has a significant protective effect that is mitigated but still significant when the risk effect of the SE at the same locus is taken into account. The presence of the SE on DR4 is associated with greater RA susceptibility and certain disease-activity measures.

A genomic strategy to combinatorial therapeutics in solid tumors

2031

Background: For most advanced solid tumors, the response rate to cytotoxic drugs is generally low, highlighting the importance of identifying those patients most likely to respond, either to single agents or combinations of cytotoxic or targeted therapies. Methods: We have made use of in vitro drug response data generated on the NCI-60 panel of cancer cell lines, coupled with Affymetrix U133 2.0 plus gene expression data, to develop genomic predictors of chemotherapy sensitivity. These models were then validated in independent cancer cell lines as well as response data from patient treatment studies. Results: Predictive models making use of gene expression data were developed for docetaxel, adriamycin, 5-flourouracil, cyclophosphamide, paclitaxel, and topotecan. These models were shown to accurately predict sensitivity to the drugs in an independent set (n = 30) of cancer cell lines. Importantly, three of the predictors (docetaxel, topotecan, paclitaxel) also accurately (> 80%) predicted response in patient studies. When evaluated in a large collection of human cancers (n = 381), these gene expression signatures of drug response identified patterns of predicted sensitivity suggesting potential opportunities for novel combinations. We also combined the predictions of chemotherapy sensitivity with predictions of pathway deregulation (Bild A, Nature 2005), to develop further opportunities for combination therapy. For instance, this analysis revealed a significant relationship between PI3 kinase pathway deregulation and docetaxel resistance (p = 0.001), and a correlation between docetaxel sensitivity and the activation of the Rb/E2F pathway (p = 0.009). Furthermore, cell lines showing an increased probability of PI3 kinase and Rb/E2F activation were also more likely to respond to a PI3 kinase (LY-294002) inhibitor (p = 0.01) or R-Roscovitine (p = 0.03), a cell cycle inhibitor, respectively. Conclusions: The development and validation of chemotherapeutic response predictors, together with oncogenic pathway signatures that can guide the use of targeted agents, provides an opportunity to develop effective combinatorial therapeutic strategies geared to the individual patient.

No significant financial relationships to disclose.

Progress in adolescent mental health

This chapter reviews the status of emotional and behavioral problems in adolescents and current issues in their assessment and treatment. The authors emphasize the need for the development of mental health programs for adolescents in natural settings such as schools, and present a conceptual framework for intervention based on provider knowledge of risk and protective factors.

Hypertensive heart disease syndrome in women in a cardiology practice

The authors hypothesized that a population of female patients exist whose historical and clinical findings are typical regarding hypertensive heart disease syndrome, so they can be readily identified in a clinical practice and benefit from specific therapy.

rZIP, a RING-leucine zipper protein that regulates cell fate determination during Dictyostelium development

rZIP is an approx. 32 kDa, multi-domain protein of Dictyostelium discoideum whose structural motifs include a RING (zinc-binding) domain, a leucine zipper, a glutamine repeat, an SH3-binding region and a consensus phosphorylation site for MAP kinase. In vitro, rZIP forms homodimers and interacts specifically with the SH3 domain(s) of the Nck adaptor protein. rZIP is expressed maximally during cell differentiation at approximately equivalent levels in all cells. Disruption of the rZIP gene rzpA results in altered cellular aggregation, impaired slug migration, and aberrant patterning of prespore and prestalk cells, the major progenitor classes. In rzpA- strains, prespore-specific genes are overexpressed and prestalk expression zones are reduced. Conversely, constitutive overexpression of rzpA markedly decreases prespore-specific gene expression and significantly increases the expression of prestalk-specific genes. Further, induced transdifferentiation of prespore cells into prestalk cells is inhibited in rzpA-slugs. In light of these patterning defects, we suggest that the RING/zipper protein rZIP plays an important role in early cell fate decisions in Dictyostelium, acting as a positive regulator of prestalk differentiation and an inhibitor of prespore differentiation.

Diarrhoeal disease in children in Gaza

A 1-year prospective study in Gaza of diarrhoeal disease in children aged < 5 years demonstrated that Salmonella spp. (18.5% of cases), Cryptosporidium (14.6%), Campylobacter spp. (8.3%) and rotavirus (6.8%) were the major pathogens. However, when compared with non-diarrhoeic controls, only Cryptosporidium and rotavirus were significantly associated with diarrhoea. Cryptosporidiosis was found only in children aged < 2 years and significantly more children with cryptosporidiosis were malnourished. This malnutrition may have been due to the infection, since children with cryptosporidiosis tended to have had diarrhoea for relatively long periods prior to admission. It was not possible to distinguish between the different enteropathogens on clinical grounds. However, more children with rotavirus infection vomited and cryptosporidial diarrhoea lasted significantly longer (14.9 days) than rotavirus diarrhoea (5.9 days). Overcrowding was linked with an increased risk of cryptosporidiosis and breast feeding was associated with some protection. Twenty-one of the 29 children who died during the study died with diarrhoea and Cryptosporidium was detected in eight (38%) of these 21 children.

[The "Ashkelon" hypertension detection and follow-up program]

The program described aims at enhancing awareness of high blood pressure and other risk factors for cardiovascular disease (CVD) and promoting a healthy lifestyle. The study population consisted of 11,000 workers at worksites and visitors to community centers, aged 25-65 years. The program was carried out in cooperation with primary care clinics and non-pharmacological control of high blood pressure was by a community center for prevention of CVD. In 1980, 56.0% of hypertensives were unaware of their condition, while by 1988 this was reduced to 6.1%. Body weight reduction resulted in lowering of blood pressure which enabled cessation of all antihypertensive treatment in 25%. Deep muscle relaxation enabled cessation in 47%. The savings effected in terms of antihypertensive treatment outweight the total cost of the program 3-fold.

Inositol trisphosphate and diacylglycerol can differentially modulate gene expression in Dictyostelium

We have previously shown that several genes expressed during Dictyostelium development could be induced in shaking culture by exogenous cAMP, even though the accumulation of intracellular cAMP was inhibited. The use of selected cAMP analogs indicated that the exogenous cAMP functioned by activating the cell surface cAMP receptor and not by interacting with the regulatory subunit of the intracellular cAMP-dependent protein kinase. Although some genes in Dictyostelium appear to be regulated by intracellular cAMP, these data suggest that this is not the case for all genes regulated by cAMP. Intracellular second messengers other than cAMP may, therefore, promote the expression of these other genes. Here, we have examined inositol trisphosphate and diacylglycerol as candidates for such mediators of signal transduction. We have studied three genes that exhibit disparate modes of temporal and spatial expression during development of Dictyostelium. In shaking cultures, maximal levels of expression of each are dependent on the accumulation of or exposure to extracellular cAMP. We show that the addition of inositol trisphosphate and/or diacylglycerol to cells in shaking culture has distinct effects on the expression of each gene and, under specific conditions, can bypass the requirement for extracellular cAMP. These data suggest that extracellular cAMP interacting with its cell surface receptor may promote synthesis of inositol trisphosphate and diacylglycerol to regulate gene expression and aspects of differentiation in Dictyostelium.