Outcomes for Patients with Residual Stage II/III Breast Cancer Following Neoadjuvant Chemotherapy (AFT-01).

INTRODUCTION: Pathologic complete response (pCR) after neoadjuvant chemotherapy has a demonstrated survival advantage; however, outcomes for non-pCR by receptor status are less understood. We sought to evaluate survival and distant recurrence by receptor status for patients with residual stage II/III breast cancer. METHODS: A stage-stratified random sample of 11,366 patients with stage II-III breast cancer in 2006-2007 was selected from 1217 facilities in the National Cancer Database for a Commission on Cancer Special Study. We identified patients with residual pathologic stage II/III cancer who received standard of care therapy based on receptor status. Distant recurrence and 5-year survival were abstracted and Kaplan-Meier curves were generated by receptor status. Multivariable Cox regression was used to estimate hazard ratios for death and distant recurrence. RESULTS: A total of 734 patients had residual disease; 58%, 28%, and 14% were ER or PR+/Her2neu-, ER and PR-/Her2neu-, and Her2neu+ (any ER/PR), respectively. ER and PR-/Her2neu- cancers had the poorest 5-year overall (52% vs. 82% for Her2neu+ and ER or PR+/Her2neu-, p < 0.0001) and distant recurrence-free survival (57% vs. 72% Her2neu+ and 77% ER or PR+/Her2neu, p < 0.0001). Cox regression models demonstrated a higher likelihood of distant recurrence and death for patients with ER and PR-/Her2neu- disease (HR 2.25, 95% CI 1.56-3.24 and HR 3.19, 95% CI 2.20-4.64 respectively) compared with ER or PR+/Her2neu-. CONCLUSIONS: Patients with residual ER and PR-/Her2neu- cancer have a significant risk of distant recurrence and mortality compared with other breast cancer types, supporting the consideration for additional adjuvant therapy and novel clinical trials in this cohort. Trial registry number ClinicalTrials.gov identifier NCT02171078.

Gene expression profile alone is inadequate in predicting complete response in multiple myeloma.

With advent of several treatment options in multiple myeloma (MM), a selection of effective regimen has become an important issue. Use of gene expression profile (GEP) is considered an important tool in predicting outcome; however, it is unclear whether such genomic analysis alone can adequately predict therapeutic response. We evaluated the ability of GEP to predict complete response (CR) in MM. GEP from pretreatment MM cells from 136 uniformly treated MM patients with response data on an IFM, France led study were analyzed. To evaluate variability in predictive power due to microarray platform or treatment types, additional data sets from three different studies (n=511) were analyzed using same methods. We used several machine learning methods to derive a prediction model using training and test subsets of the original four data sets. Among all methods employed for GEP-based CR predictive capability, we got accuracy range of 56-78% in test data sets and no significant difference with regard to GEP platforms, treatment regimens or in newly diagnosed or relapsed patients. Importantly, permuted P-value showed no statistically significant CR predictive information in GEP data. This analysis suggests that GEP-based signature has limited power to predict CR in MM, highlighting the need to develop comprehensive predictive model using integrated genomics approach.

Hierarchical model for evaluating pyrantel efficacy against strongyle parasites in horses.

Anthelmintic resistance is an increasing challenge for the control of equine parasites. The fecal egg count reduction test (FECRT) is the practical gold standard method for evaluating reduction in anthelmintic efficacy, but the interpretation is complicated due to high levels of variability. A hierarchical statistical model was described for analysis of FECRT data from multiple farms to evaluate the role of biological factors in determining the strongyle efficacy of pyrantel pamoate in a study performed in Denmark. The model was then used to describe two notions of farm efficacy, namely conditional and marginal efficacy. The median of the lower prediction limits was used to describe a robust classification rule. The performance of the methodology was evaluated using Monte Carlo simulations. The field study was performed on 64 Danish horse farms of different breeds. Of 1644 horses, 614 had egg counts ≥ 200 eggs per gram (EPG) and were treated. Individual coprocultures were performed for identification of Strongylus vulgaris from all horses pre-treatment. Thirty-one farms (48.4%) were positive for S. vulgaris, but pyrantel efficacy was unaffected by the presence of this parasite in the statistical model. Further, there were no significant effects of age, gender, or interactions between these, while the pre-treatment egg count was negatively associated with the egg count reduction. The statistical model classified 81.3%, 10.9%, and 7.8% of farms as no signs of resistance (NR), suspect resistance (SR), and resistance (RE), respectively. In comparison, arithmetic calculations classified 68.8%, 17.2%, and 14.1% in the same categories. Using 10,000 simulated data sets, the methodology provided a classification of farms into different efficacy categories with a false discovery of reduced farm efficacy rate equaling 8.74%. In addition, model-classification was unaffected by presence of single outlier horses in a separate simulation study.

Statistical and biological considerations in evaluating drug efficacy in equine strongyle parasites using fecal egg count data.

Anthelmintic resistance (AR) is a serious problem for the control of equine gastrointestinal nematodes, particularly in the cyathostomins. The fecal egg count reduction test (FECRT) is the most common method for diagnosing AR and serves as the practical gold standard. However, accurate quantification of resistance and especially accurate diagnosis of emerging resistance to avermectin/milbemycin (A/M) drugs, is hampered by a lack of accepted standards for study design, data analysis, and data interpretation. In order to develop rational evidence-based standards for diagnosis of resistance, one must first take into account the numerous sources of variability, both biological and technical, that affect the measurement of fecal egg counts (FECs). Though usually ignored, these issues can greatly impact the observed efficacy. Thus, to accurately diagnose resistance on the basis of FECRT data, it is important to reduce levels of variability through improved study design, and then deal with inherent variability that cannot be removed, by performing thorough and proper statistical analysis. In this paper we discuss these issues in detail, and provide an explanation of the statistical models and methods that are most appropriate for analyzing these types of data. We also provide several examples using data from laboratory, field, and simulation experiments illustrating the benefits of these approaches.

Nucleoprotein complex formed between herpes simplex virus UL9 protein and the origin of DNA replication: inter- and intramolecular interactions.

The UL9 gene of herpes simplex virus type 1 encodes an origin-binding protein. UL9 protein purified from baculovirus vector-infected insect cells forms a stable complex with DNA containing the herpes simplex virus origin of DNA replication, oriS. Contained within oriS are two UL9 protein-binding sites, I and II, bracketing an (A + T)-rich region. UL9 protein, visualized by electron microscopy, binds selectively at the site of the origin and covers approximately 120 base pairs. Upon formation of the nucleoprotein complex, the apparent contour length of the DNA is shortened, suggesting that this amount of DNA is wrapped or condensed by the protein. A nucleoprotein complex of similar size and structure forms on an inactive origin deleted for binding site II. Multiple intermolecular interactions occur. In particular, UL9 nucleoprotein complexes interact in trans with other UL9 nucleoprotein complexes such that dimer DNA molecules are formed with a junction at the position of protein binding. The DNA molecules in these intermolecular complexes are aligned predominantly in a parallel orientation.

Expression of a functional foreign gene in adult mammalian brain following in Vivo transfer via a herpes simplex virus type 1 defective viral vector.

We report here the first use of a herpes simplex virus defective viral vector for the transfer and expression of a foreign gene in the adult rat brain in vivo. Defective vectors offer unique advantages over other systems. Our vector genome consists of multiple copies of a plasmid-based amplicon, with a human cytomegalovirus promoter and lacZ gene as a reporter. Helper functions were provided by an HSV1 mutant incapable of replication at physiological temperatures. The resulting defective viral vector was stereotaxically microinjected into rat hippocampus and hypothalamus, and cells expressing functional beta-galactosidase were detected in both areas. Expression was confined to regions at or near the site of injection. Positive cells were identified by 18 hr following injection, and expression was still detectable after 2 weeks. All animals survived with no behavioral, gross, or microscopic anatomical evidence of a virulent neurologic infection.

Herpes simplex virus DNA synthesis at a preformed replication fork in vitro.

Proteins from herpes simplex virus (HSV)-infected cells were used to reconstitute DNA synthesis in vitro on a preformed replication fork. The preformed replication fork consisted of a nicked, double-stranded, circular DNA molecule with a 5' single-strand tail that was noncomplementary to the template. The products of DNA synthesis on this substrate were rolling-circle molecules, as demonstrated by electron microscopy and alkaline agarose gel electrophoresis. The tails contained double-stranded regions, indicating that both leading- and lagging-strand DNA syntheses occurred. Rolling-circle DNA replication was dependent upon HSV DNA polymerase and ATP and was stimulated by a crude fraction containing ICP8 (HSV DNA-binding protein). Similar protein fractions from mock-infected cells were unable to support rolling-circle DNA replication. This in vitro DNA replication system should prove useful in the identification and characterization of the enzymatic activities required at the HSV replication fork.