Non-parametric quantification of protein lysate arrays.

MOTIVATION: Proteins play a crucial role in biological activity, so much can be learned from measuring protein expression and post-translational modification quantitatively. The reverse-phase protein lysate arrays allow us to quantify the relative expression levels of a protein in many different cellular samples simultaneously. Existing approaches to quantify protein arrays use parametric response curves fit to dilution series data. The results can be biased when the parametric function does not fit the data. RESULTS: We propose a non-parametric approach which adapts to any monotone response curve. The non-parametric approach is shown to be promising via both simulation and real data studies; it reduces the bias due to model misspecification and protects against outliers in the data. The non-parametric approach enables more reliable quantification of protein lysate arrays. AVAILABILITY: Code to implement the proposed method in the statistical package R is available at: http://odin.mdacc.tmc.edu/jhu/lysatearray-analysis/

Future of personalized medicine in oncology: a systems biology approach.

The development of cost-effective technologies able to comprehensively assess DNA, RNA, protein, and metabolites in patient tumors has fueled efforts to tailor medical care. Indeed validated molecular tests assessing tumor tissue or patient germline DNA already drive therapeutic decision making. However, many theoretical and regulatory challenges must still be overcome before fully realizing the promise of personalized molecular medicine. The masses of data generated by high-throughput technologies are challenging to manage, visualize, and convert to the knowledge required to improve patient outcomes. Systems biology integrates engineering, physics, and mathematical approaches with biologic and medical insights in an iterative process to visualize the interconnected events within a cell that determine how inputs from the environment and the network rewiring that occurs due to the genomic aberrations acquired by patient tumors determines cellular behavior and patient outcomes. A cross-disciplinary systems biology effort will be necessary to convert the information contained in multidimensional data sets into useful biomarkers that can classify patient tumors by prognosis and response to therapeutic modalities and to identify the drivers of tumor behavior that are optimal targets for therapy. An understanding of the effects of targeted therapeutics on signaling networks and homeostatic regulatory loops will be necessary to prevent inadvertent effects as well as to develop rational combinatorial therapies. Systems biology approaches identifying molecular drivers and biomarkers will lead to the implementation of smaller, shorter, cheaper, and individualized clinical trials that will increase the success rate and hasten the implementation of effective therapies into the clinical armamentarium.

Somatic mutations in BRCA1 and BRCA2 could expand the number of patients that benefit from poly (ADP ribose) polymerase inhibitors in ovarian cancer.

PURPOSE: The prevalence of BRCA(1/2) mutations in germline DNA from unselected ovarian cancer patients is 11% to 15.3%. It is important to determine the frequency of somatic BRCA(1/2) changes, given the sensitivity of BRCA-mutated cancers to poly (ADP ribose) polymerase-1 (PARP1) inhibitors and platinum analogs. PATIENTS AND METHODS: In 235 unselected ovarian cancers, BRCA(1/2) was sequenced in 235, assessed by copy number analysis in 95, and tiling arrays in 65. 113 tumors were sequenced for TP53. BRCA(1/2) transcript levels were assessed by quantitative polymerase chain reaction in 220. When available for tumors with BRCA(1/2) mutations, germline DNA was sequenced. RESULTS: Forty-four mutations (19%) in BRCA1 (n = 31)/BRCA2 (n = 13) were detected, including one homozygous BRCA1 intragenic deletion. BRCA(1/2) mutations were particularly common (23%) in high-grade serous cancers. In 28 patients with available germline DNA, nine (42.9%) of 21 and two (28.6%) of seven BRCA1 and BRCA2 mutations were demonstrated to be somatic, respectively. Five mutations not previously identified in germline DNA were more commonly somatic than germline (four of 11 v one of 17; P = .062). There was a positive association between BRCA1 and TP53 mutations (P = .012). BRCA(1/2) mutations were associated with improved progression-free survival (PFS) after platinum-based chemotherapy in univariate (P = .032; hazard ratio [HR] = 0.65; 95% CI, 0.43 to 0.98) and multivariate (P = .019) analyses. BRCA(1/2) deficiency, defined as BRCA(1/2) mutations or expression loss (in 24 [13.3%] BRCA(1/2)-wild-type cancers), was present in 67 ovarian cancers (30%) and was also significantly associated with PFS in univariate (P = .026; HR = 0.67; 95% CI, 0.47 to 0.96) and multivariate (P = .008) analyses. CONCLUSION: BRCA(1/2) somatic and germline mutations and expression loss are sufficiently common in ovarian cancer to warrant assessment for prediction of benefit in clinical trials of PARP1 inhibitors.

c-Jun-NH2-kinase-1 inhibition leads to antitumor activity in ovarian cancer.

PURPOSE: To show the functional, clinical, and biological significance of c-Jun-NH(2)-kinase (JNK)-1 in ovarian carcinoma. EXPERIMENTAL DESIGN: Analysis of the impact of JNK on 116 epithelial ovarian cancers was conducted. The role of JNK in vitro and in experimental models of ovarian cancer was assessed. We studied the role of N-5-[4-(4-methyl piperazine methyl)-benzoylamido]-2-methylphenyl-4-[3-(4-methyl)-pyridyl]-2-pyrimidine amine (WBZ_4), a novel JNK inhibitor redesigned from imatinib based on targeting wrapping defects, in cell lines and in experimental models of ovarian cancer. RESULTS: We found a significant association of pJNK with progression-free survival in the 116 epithelial ovarian cancers obtained at primary debulking therapy. WBZ_4 led to cell growth inhibition and increased apoptosis in a dose-dependent fashion in four ovarian cancer cell lines. In vivo, whereas imatinib had no effect on tumor growth, WBZ_4 inhibited tumor growth in orthotopic murine models of ovarian cancer. The antitumor effect was further increased in combination with docetaxel. Silencing of JNK-1 with systemically administered siRNA led to significantly reduced tumor weights compared with nonsilencing siRNA controls, indicating that indeed the antitumor effects observed were due to JNK-1 inhibition. CONCLUSIONS: These studies identify JNK-1 as an attractive therapeutic target in ovarian carcinoma and that the redesigned WBZ_4 compound should be considered for further clinical development.

Triple receptor-negative breast cancer: the effect of race on response to primary systemic treatment and survival outcomes.

PURPOSE: The goal of this study was to describe the effect of race on pathologic complete response (pCR) rates and survival outcomes in women with triple receptor-negative (TN) breast cancers. PATIENTS AND METHODS: Four hundred seventy-one patients with TN breast cancer diagnosed between 1996 and 2005 and treated with primary systemic chemotherapy were included. pCR was defined as no residual invasive cancer in the breast and axillary lymph nodes. Overall survival (OS) and recurrence-free survival (RFS) were estimated using the Kaplan-Meier product-limit method and compared between groups using the log-rank test. Cox proportional hazards models were fitted for each survival outcome to determine the relationship of patient and tumor variables with outcome. RESULTS: Median follow-up time was 24.5 months. One hundred patients (21.2%) were black, and 371 patients (78.8%) were white/other race. Seventeen percent of black patients (n = 17) and 25.1% of white/other patients (n = 93) achieved a pCR (P = .091). Three-year RFS rates were 68% (95% CI, 56% to 76%) and 62% (95% CI, 57% to 67%) for black and white/other patients, respectively, with no significant difference observed between the two groups (P = .302). Three-year OS was similar for the two racial groups. After controlling for patient and tumor characteristics, race was not significantly associated with RFS (hazard ratio [HR] = 1.08; 95% CI, 0.69 to 1.68; P = .747) or OS (HR = 1.08; 95% CI, 0.69 to 1.68; P = .735) when white/other patients were compared with black patients. CONCLUSION: Race does not significantly affect pCR rates or survival outcomes in women with TN breast cancer treated in a single institution under the same treatment conditions.

Mammary angiosarcomas: imaging findings in 24 patients.

PURPOSE: To retrospectively evaluate the clinical, imaging, and pathologic findings of mammary angiosarcomas in 24 patients. MATERIALS AND METHODS: The institutional review board approved this HIPAA-compliant study and waived informed consent. Twenty-four patients with records in the surgical pathology database who had a diagnosis of mammary angiosarcoma (n = 26) and who underwent preoperative imaging with mammography, ultrasonography (US), or magnetic resonance (MR) imaging were included. Mean and median ages at time of diagnosis were 40 and 38 years, respectively (range, 15-77 years). Images were reviewed in consensus by two radiologists with the American College of Radiology Breast Imaging Reporting and Data System lexicon and were compared with pathologic findings. Total length of follow-up (in months) was determined by the interval from the time of diagnosis to the time of last follow-up. Information on overall and disease-free survival was also obtained. RESULTS: Mean tumor size at time of diagnosis was 5.9 cm (range, 1-12 cm). Nineteen tumors manifested as a palpable mass, four manifested with progressive breast swelling, and three were asymptomatic. Mammograms of 16 tumors showed a noncalcified mass in eight, focal asymmetry in five, and no abnormality in three. All three mammographically occult tumors were visible at US and MR imaging. US images of 21 tumors showed a solid, frequently oval-shaped, and hyperechoic mass in 13 tumors and random mixed hyper- and hypoechogenicity with associated architectural distortion in eight tumors. Dynamic contrast material-enhanced MR imaging of nine tumors showed large, lobular, and intensely and heterogeneously enhancing masses with rapid enhancement and the washout characteristics of a malignant lesion. CONCLUSION: A mass that shows homogeneous or heterogeneous hyperechogenicity at US (with associated architectural distortion) and has a hypervascular, hemorrhagic, and heterogeneous appearance and typical malignant enhancement characteristics at MR imaging should alert the radiologist to a possible diagnosis of angiosarcoma.