Abstract P5-11-04: Post-translational modification of the cell-fate factor Dachshund determines p53 binding and signaling modules in breast cancer

Breast cancer is a leading form of cancer in the world. Initially cloned as a dominant inhibitor of the hyperactive EGFR, Ellipse, in Drosophila, the mammalian DACH1 regulates expression of target genes in part through interacting with DNA-binding transcription factors (c-Jun, Smads, Six, ERα), and in part through intrinsic DNA-sequence specific binding to Forkhead binding sites. The Drosophila dac gene is a key member of the retinal determination gene network (RDGN), which also includes eyes absent (eya), ey, twin of eyeless (toy), teashirt (tsh) and sin oculis (so), that specifies eye tissue identity.

Several lines of evidence suggest DACH1 may function as a tumor suppressor. Clinical studies have demonstrated a correlation between poor prognosis and reduced expression of the cell-fate determination factor DACH1 in breast cancer, and loss of DACH1 expression has been observed in prostate and endometrial cancer. DACH1 inhibits breast cancer tumor metastasis and reduces breast cancer stem cell expansion via Sox2/Nanog. Although these studies suggest DACH1 may function as a tumor suppressor, the molecular mechanisms remain poorly defined. Herein, endogenous DACH1 co-localized with p53 in a nuclear, extranucleolar compartment and bound to p53 in human breast cancer cell lines, p53 and DACH1 bound common genes in ChIP-Seq. Full inhibition of breast cancer contact-independent growth by DACH1 required p53. The p53 breast cancer mutants R248Q and R273H, evaded DACH1 binding. DACH1 phosphorylation at serine residue (S439) inhibited p53 binding and phosphorylation at p53 amino-terminal sites (S15, S20) enhanced DACH1 binding. DACH1 binding to p53 was inhibited by NAD-dependent deacetylation via DACH1 K628. DACH1 repressed p21CIP1 and induced RAD51, an association found in basal breast cancer. DACH1 inhibits breast cancer cellular growth in an NAD and p53 dependent manner through direct protein-protein association.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-11-04.

Abstract P1-08-20: Increased risk of hormone therapy failure in breast cancers expressing low phospho-Stat5: Validation of quantitative immunofluorescence assay parameters

Previous analyses of three breast cancer cohorts revealed that loss of phospho-Stat5 in breast cancer is associated with significantly elevated risk of hormone therapy failure (1, 2). Nuclear localized tyrosine phosphorylated Stat5 (Nuc-pYStat5) may therefore have clinical value as a predictive marker. Analysis of two of the three previously reported anti-estrogen treated patient cohorts used pathologist scoring of diaminobenzidine (DAB) chromogen-stained Stat5. However the third cohort, analyzed by quantitative immunofluorescence analysis (QIF) on the Genoptix/HistoRx AQUA platform, revealed a greater hazard ratio than the cohorts analyzed by pathologist DAB-scoring. To extend and validate these observations, we applied the Nuc-pYStat5 cutpoint derived in our previous study (2) to an independent cohort of anti-estrogen-treated breast cancer patients using two distinct QIF software platforms, AQUA and Definiens Tissue Studio. Tissue Studio relies on supervised machine learning and multiparametric features of a high-resolution whole slide image to identify cancer cell regions, while AQUA software relies on costaining of a tumor marker to identify cancer cell regions. The two QIF platforms produced highly concordant Nuc-pYStat5 levels (R2 linear = 0.96, P<0.001, N = 344) and confirmed a significant elevated risk of failing antiestrogen therapy in patients whose tumors had lost Nuc-pYStat5 (Hazard ratio 3.6; 95% CI 1.8-7.4; P<0.02; N = 98). On both QIF platforms, Nuc-pYStat5 remained an independent marker after multivariate adjustment for standard pathology parameters, including ER/PR, HER2, age, node status and grade, with a hazard ratio of 5.8 (95% CI 1.3-22.2; P = 0.02; N = 52). High concordance between Nuc-pYStat5 levels produced by the two QIF platforms held up in a second independent dataset of more than 300 breast cancer specimens (R2 linear = 0.97, P<0.001, N = 382). Nuc-pYStat5 levels by the two QIF methods remained highly concordant across the entire dynamic range in both patient cohorts. Furthermore, high concordance was also observed between replicate QIF analyses of Nuc-pYStat5 on serial tumor microarray sections stained in the same run on an automated immunostainer (Concordance Correlation Coefficient (CCC) = 0.96; 95% CI 0.96-0.97). Modest inter-assay staining variation (CCC = 0.84; 95% CI 0.82-0.87) for Nuc-pYStat5 when serial tumor microarrays were stained on different runs several days apart could be corrected for by normalization procedures (CCC = 0.94; 95% CI 0.92-0.95). This progress supports the utility of QIF analysis of Nuc-pYStat5 levels in human breast cancer and further documents the potential value of Nuc-pYStat5 as a predictive marker of response to antiestrogen therapy. The study confirms that further retrospective and prospective validation studies are warranted.

References:

1) Yamashita et al. Stat5 expression predicts response to endocrine therapy and improves survival in estrogen receptor-positive breast cancer. Endocr Relat Cancer. 2006;13:885-93.

2) Peck et al. Loss of nuclear localized and tyrosine phosphorylated Stat5 in breast cancer predicts poor clinical outcome and increased risk of antiestrogen therapy failure. J Clin Oncol. 2011;29:2448-58.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-08-20.

Abstract P4-06-09: HER2+ and HER2- luminal B subtypes have similar overall survival and histologic grade distributions

Background There are multiple subtypes in invasive breast cancers (IBCs). Immunohistochemistry (IHC)-based assays using ER, PR, HER2, and Ki67 for subtyping has been developed. However, association between such subtypes and treatment outcomes and histology is not completely known, and are impacted by dataset-to-dataset and pathologist-to-pathologist variations. We report an analysis on these problems, as a pilot study of a project involving 5,000 patients and 250 protein biomarkers.

Methods Patients were enrolled for the Clinical Breast Care Project from a military site with data collected per IRB-approved protocols, from 2000 to 2010. Total of 215 female IBC cases were included in this study, with surgically resected tumors (SRT) assayed for ER, PR, HER2, and Ki67 by IHC in a central CLIA-certified lab following clinical guidelines where applicable. All slides were reviewed by a single experienced breast pathologist. ER and PR was positive if nuclear staining was >5%. HER2 was negative if IHC = 0 or 1+ and positive if IHC = 3+; For IHC = 2+, the FISH result determined the final call. Ki67 was positive if nuclear staining was > = 15%. For IBC subtypes, LA was ER+/HER2-/Ki67-; Two LB subtypes were defined, with LB1 being ER+/HER2-/Ki67+ and LB2 being ER+/HER2+; Her2+ was ER-/PR-/HER2+; TN was ER-/PR-/HER2-. Statistical analyses were performed using SAS, Kaplan-Meier estimate and log-rank test were used for survival analysis and the follow-up period was 10 years with a median of 4.6 years. Chi-Square test was used for categorical data analysis supplemented by Fisher's Exact test as appropriate.

Results 204 of the 215 cases were classified into subtypes of LA (n = 74, 7 deceased), LB1 (n = 53, 4 deceased), LB2 (n = 14, 1 deceased), Her2+ (n = 14, 1 deceased), and TN (n = 49, 16 deceased). Despite the low number of events in some subtypes, there was a significant difference in overall survival between the 5 subtypes of IBCs defined here (p = 0.0023), with TN cases showing the least favorable outcome. No difference was observed in outcome between LB1 and LB2 (p = 0.86). Overall, Ki67+ cases trended toward worse outcomes (p = 0.08), which was also observed in TN (p = 0.17) but not other subtypes. Histologic grades were significantly different among the 5 subtypes (p = 6.25E-20); 96% of LA cases were G1 or G2, over 80% of LB1 and LB2 cases were G2 or G3, and all Her2+ and 93% of TN cases were G2 or G3. Within the luminal subtypes, grade distribution for LA cases was significantly different from that for LB cases (p<0.0001) but there was no difference between LB1 and LB2 cases (p = 0.95).

Discussion In this cohort where all IHC and pathology slides were reviewed by a single pathologist, we used cell proliferation marker Ki67 to help classify luminal IBCs into LA, LB1 (HER2-), and LB2 (HER2+). Overall survival analysis result for all cases was consistent with the literature, Ki67+ cases trended toward worse outcomes, and no outcome difference was identified between LB1 and LB2. Histologic grade distributions in different subtypes were consistent with the literature; we further found no difference between LB1 and LB2 subtypes.

The views expressed in this abstract are those of the authors and do not reflect the official policy of the Department of Defense, or US Government.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-06-09.

Abstract S1-8: Prolactin-humanized mice: an improved animal recipient for therapy response-testing of patient-derived breast cancer xenotransplants

Eighty percent of newly diagnosed breast cancer represents estrogen receptor(ER)-positive luminal subtypes. Many patients with luminal breast cancer develop antiestrogen resistant disease. It has historically been particularly difficult to establish ER-positive breast cancer lines from primary breast cancer in the laboratory or in mice. Murine and bovine prolactins, the major lactogens in current laboratory experimental in vivo and in vitro conditions, fail to activate human prolactin receptors because of species incompatibility. In fact, murine prolactin is a potent antagonist for human prolactin receptors. Because ER-positive, luminal breast cancers also express prolactin receptors, we hypothesized that lack of human lactogenic activity under experimental conditions selected against establishment of ER-positive breast cancer in the laboratory. We therefore genetically engineered mice to express physiological levels of human prolactin in place of mouse prolactin and backcrossed the mice for ten generations into the immunodeficient NSG strain. The resulting hPRL.NSG mice have a greatly improved take rate for ER positive, luminal type of breast cancer, suggesting key tumor-promoting roles for prolactin in luminal breast cancer. A panel of novel transplantable human breast cancer lines has been established in hPrl.NSG mice, the majority of which are ER-positive. The transplantable lines maintain key histopathological characteristics and expression of major marker proteins of the primary patient tumors. Intriguingly, initial tumor establishment and growth rates of breast cancer xenografts were consistently greater in the hPrl.NSG mice than in wildtype NSG mice. Furthermore, tumors grown in hPrl.NSG were more responsive to tamoxifen than size-matched tumors grown in wildtype NSG mice. At least two new tumor lines examined so far develop spontaneous distant metastases in hPrl.NSG mice, with evidence of prolactin-dependent progression of ER-positive disease. Collectively, these observations validate the hPrl.NSG mice as an improved recipient for preclinical modeling of human breast cancer in vivo, both for therapeutic targeting of prolactin-pathways and other growth and survival pathways, as well as overcoming anti-estrogen resistance.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr S1-8.

Abstract P2-05-21: Molecular subtypes of invasive breast cancers show differential expression of the proliferation marker Aurora Kinase A (AURKA)

Background: Invasive breast cancer (IBC) has been classified into four major subtypes based on gene expression profiling. The luminal A subtype (LA) has the best prognosis, when compared to luminal B (LB), HER2+, and basal-like (Basal). Ki67 by gene expression or immunohistochemistry (IHC) is commonly used as a proliferation index. The function of Ki67 in proliferation remains unknown. AURKA (STK15) is known to play an important role in mitosis, and is a component of the 21-gene recurrence score of the Oncotype Dx. With multiple platforms of molecular data available from hundreds of IBC tissues in The Cancer Genome Atlas project (TCGA), we sought to study the association of AURKA with different IBC subtypes and explore its use as a proliferation marker in IBCs.

Methods: Gene expression (Agilent, log2 transformed), relative DNA copy number (CN, Affymetrix SNP 6.0), and exome sequence mutation (Illumina) data for 459 IBC cases were downloaded from the TCGA data portal. PAM50 classification results of all samples were obtained from the TCGA breast cancer AWG group and included 203 LA, 113 LB, 51 HER2+, 84 Basal-like, and 8 Normal-like which were not used in this study due to the low numbers. Kruskal-Wallis tests were used to evaluate the differences among four subtypes on AURKA expression and CN, followed by Wilcoxon Mann-Whitney test with Bonferroni adjustment for pairwise analyses. Pearson's Correlation Coefficient was used for correlation analyses. All statistical analyses were performed using SAS and R, and two-sided, p values <.05 were considered statistically significant.

Results: There was a significant difference among IBC subtypes, in gene expression as well as in CN (p values < 0.0001). AURKA mRNA levels were significantly lower in LA (mean±SD, −2.61±0.63) compared to LB (−1.45±0.78), HER2+ (−1.38±0.61), and Basal (−1.26±0.62) subtypes (p values all < 0.0001). No significant difference was detected between other subtype pairs. In CN analysis, Basal (0.09±0.22) was lower than HER2+ (0.32±0.308, p < 0.0002) and LB (0.33±0.41, p < 0.0001), and LA (0.14±0.28) is lower than HER2 (p < 0.0016) and LB (p < 0.0001), but no other significant CN difference between the subtypes were found. The means and SDs are provided for reference only. No correlation of p53 mutation status and AURKA expression were observed. However, AURKA gene expression level is correlated with MKI67 gene expression (R = 0.69, p < 2.2e−16), and its correlation with PAM50 proliferation score is even higher (R = 0.80, p < 2.2e−16).

Discussion: Using the TCGA data we observed that the mean gene expression level of AURKA is significantly lower in LA than the other IBC subtypes, by more than 50% (note the log2 transformation). This differential expression is not completely due to CN changes (especially for the Basal subtype). There is a strong association with other tumor cell proliferation markers such as the MKI67 gene and the PAM50 proliferation score. We are using computational and laboratorial studies to better understand the role of AURKA in the etiology of invasive breast cancers.

The views expressed in this article are those of the author and do not reflect the official policy of the Department of Defense, or U.S. Government.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-05-21.

Abstract P5-01-07: Fibroadenomatoid changes are more prevalent in middle-aged women and have a positive association with invasive breast cancer

Background: The role of benign breast diseases (BBDs) in the development of invasive breast cancers (IBCs) has been studied for many years. Some BBDs have been studied comprehensively (e.g., fibrocystic changes (FCC)) while less is known about other BBDs (e.g., fiboadenomatoid changes (FAC)). FAC has been considered by some researchers as a precursor of fibroadenoma (FA). Conclusions from different studies vary, partially due to different interpretation methods and diagnostic criteria when multiple hospitals and pathologists were involved. In this study, we used subjects in the Clinical Breast Care Project (CBCP) from a military medical center where pathology slides were reviewed by a single breast pathologist to study FAC, FA, and FCC in comparison to the published literature.

Methods: Subjects were enrolled in the study following IRB-approved, HIPAA-compliant protocols. All the clinicopathologic data are available from the CBCP data warehouse (DW4TR). In the CBCP, FCC is composed of 4 components: stromal fibrosis, cysts, apocrine metaplasia, and sclerosing adenosis. Two modeling studies were performed. i) For the BBDs and IBC association study, two groups of subjects were identified: 1136 subjects diagnosed with “Benign” or “Atypical” diseases, and 619 cases diagnosed with IBCs. A logistic regression model was developed for the prediction of IBCs by the 3 BBDs and 2 well-established risk factors (RF): age (younger, <=40; middle-aged, 41–60; older, >60) and race (Caucasian, African American, Asian, and other). ii) For the RF association study with the BBDs, 6 additional RFs reported to be associated with these BBDs were identified from the literature: current use of oral contraceptives, number of live births, education, body mass index, hormonal replacement therapy, and IBC family history. These 8 RFs were used to develop a logistic regression model for each of the BBDs. The analyses were performed in SAS.

Results: In the first study, age and race were confirmed as RFs for IBCs. FAC was positively associated with IBC (OR = 3.04, 95%CI=2.06 to 4.50). FA was negatively associated with IBC, and the level of the association was stronger in women without FCC (OR = 0.15, 95%CI=0.08 to 0.28), compared to women with FCC (OR = 0.40, 95%CI=0.24 to 0.65). FCC was not significantly associated with IBC. Results from the second study indicated that, age was significantly associated with FAC (p = 0.015), specifically the middle-aged women were more likely to have FAC compared to younger women (OR = 2.03, 95%CI=1.23 to 3.34), while the older women were at a non-significantly increased risk. Trends of association with FAC were also noted for the number of live birth (p = 0.095), ethnicity (p = 0.096), and current oral contraceptive pill use (p = 0.077). The FCC model results were in general consistent with the literature, and we also confirmed that age was negatively associated with the diagnosis of FA.

Discussion: Our study was consistent with FCC findings in the literature. We observed that FAC was positively associated with IBC, whereas FA was negatively associated. Also, FAC occurred more often in middle-aged women while FAs occurrence was higher in younger women. Our results suggest that FAC and FA may be two different diseases.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-01-07.

Protein dynamics and ion traffic in bacterioferritin

Bacterioferritin (Bfr) is a spherical protein composed of 24 subunits and 12 heme molecules. Bfrs contribute to regulate iron homeostasis in bacteria by capturing soluble but potentially toxic Fe(2+) and by compartmentalizing it in the form of a bioavailable ferric mineral inside the protein's hollow cavity. When iron is needed, Fe(3+) is reduced and mobilized into the cytosol as Fe(2+). Hence, key to the function of Bfr is its ability to permeate iron ions in and out of its interior cavity, which is likely imparted by a flexible protein shell. To examine the conformational flexibility of Bfrs in a native-like environment and the way in which the protein shell interacts with monovalent cations, we have performed molecular dynamics (MD) simulations of BfrB from Pseudomonas aeruginosa (Pa BfrB) in K(2)HPO(4) solutions at different ionic strengths. The results indicate the presence of coupled thermal fluctuations (dynamics) in the 4-fold pores and B-pores of the protein, which is key to allowing passage of monovalent cations through the protein shell using B-pores as conduits. The MD simulations also show that Pa BfrB ferroxidase centers are highly dynamic and permanently populated by transient cations exchanging with other cations in the interior cavity, as well as the solution bathing the protein. Taken together, the findings suggest that Fe(2+) passes across the Pa BfrB shell via B-pores and that the ferroxidase pores allow the capture and oxidation of Fe(2+), followed by translocation of Fe(3+) to the interior cavity, aided by the conformationally active H130.

Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores

Brownian dynamics (BD) based on accurate potential of mean force is an efficient and accurate method for simulating ion transport through wide ion channels. Here, a web-based graphical user interface (GUI) is presented for carrying out grand canonical Monte Carlo (GCMC) BD simulations of channel proteins: http://www.charmm-gui.org/input/gcmcbd. The webserver is designed to help users avoid most of the technical difficulties and issues encountered in setting up and simulating complex pore systems. GCMC/BD simulation results for three proteins, the voltage dependent anion channel (VDAC), α-Hemolysin (α-HL), and the protective antigen pore of the anthrax toxin (PA), are presented to illustrate the system setup, input preparation, and typical output (conductance, ion density profile, ion selectivity, and ion asymmetry). Two models for the input diffusion constants for potassium and chloride ions in the pore are compared: scaling of the bulk diffusion constants by 0.5, as deduced from previous all-atom molecular dynamics simulations of VDAC, and a hydrodynamics based model (HD) of diffusion through a tube. The HD model yields excellent agreement with experimental conductances for VDAC and α-HL, while scaling bulk diffusion constants by 0.5 leads to underestimates of 10-20%. For PA, simulated ion conduction values overestimate experimental values by a factor of 1.5-7 (depending on His protonation state and the transmembrane potential), implying that the currently available computational model of this protein requires further structural refinement.

P1-06-24: Nuclear Localization of Stat5a Predicts Response to Antiestrogen Therapy and Prognosis of Clinical Breast Cancer Outcome

Nuclear-localized and tyrosine-phosphorylated Stat5 has been reported as a favorable prognostic marker and predictor of response to antiestrogen therapy in breast cancer. Phospho-Stat5 antibodies do not distinguish between phosphorylated Stat5a and the closely related Stat5b, but Stat5a is considered more critical for normal mammary development than Stat5b. The purpose of this study was to determine whether levels of nuclear-localized Stat5a protein (Nuc-Stat5a) were prognostic of clinical outcome or predictive of antiestrogen response. Stat5a was detected by traditional diaminobenzidine-chromogen immunohistochemistry (IHC) and pathologist scoring or by quantitative immunofluorescence in five archival cohorts of breast cancer. Levels of nuclear-localized Stat5a (Nuc-Stat5a) were evaluated by pathologist scoring of whole tissue sections detected by IHC or automated quantitative analysis (AQUA) of immunofluorescently-labeled tissue microarrays. Levels of Nuc-Stat5a were reduced in invasive breast cancer tissues and lymph node metastases compared to normal tissue and ductal carcinoma in situ when quantified by AQUA (Material I; n=180). Tissues from patients not treated with adjuvant therapy or treated with antiestrogen monotherapy were analyzed according to Nuc-Stat5a status for breast cancer-specific survival (CSS) and time to recurrence (TTR) using univariate and multivariate statistical models, adjusting for clinical features including tumor grade, size, lymph node and ER, PR and Her2 status. In two prognostic cohorts of node-negative breast cancer patients, low expression of Nuc-Stat5a, detected by standard IHC (Material II; n=223) or quantitative analysis (Material III; n=198), was prognostic of poor breast cancer outcome as measured by univariate and multivariate CSS (Material II/III) and TTR (Material II). CSS and TTR analysis of two independent materials of tumors from patients treated with antiestrogen monotherapy and analyzed by standard IHC (Material IV; n=73) or quantitative immunofluorescence (Material V; n=97) indicated that patients whose tumors expressed low levels of Nuc-Stat5a were at a greater than 4-fold risk of antiestrogen therapy failure when adjusted for hormone receptor status and clinical features (multivariate CSS: Material IV HR=4.3 (1.2,15.6), p=0.03; Material V HR=5.0 (1.87,13.06), p=0.001). In conclusion, loss of Nuc-Stat5a is a promising independent marker of poor breast cancer prognosis in node-negative, non-adjuvant treated breast cancer patients. Additionally, Nuc-Stat5a may be a useful clinical tool to predict tumor response to antiestrogen therapy.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-06-24.

P5-14-12: Bayesian Belief Network Mortality Analysis of a Breast Cancer Registry Data Set

Introduction: Bayesian Belief Networks have been used in medicine to evaluate clinical data and develop predictive and prognostic models. As classification models, they allow us to represent pattern complexity beyond what can be accomplished with traditional Kaplan-Meier or regression models. We sought to evaluate the use of machine-learned Bayesian Belief Networks (ml-BBNs) to develop mortality models in breast cancer and to evaluate classification performance for this method.

Methods: A set of 2,300 breast bancer cases from a tumor registry at Thomas Jefferson University were used to train ml-BBNs. The registry set was broken into cohorts for modeling by follow-up times of 1 (n=2,202), 2 (n=2,183), 3 (n=2,157), and 5 (n=2,027) years. Each cohort was then used to train a ***m1-BBN and each model was evaluated for structure. Variables were recoded into categories: biomarkers (ER, PR, Ki67, HER2, p53) as positive or negative; grading, staging, and size were broken in categories; while race was recoded into Caucasian or African-American. Income and poverty level by census tract were also included. Models were evaluated for ability to classify mortality (yes/no) within the follow-up period using 10-fold cross-validation and Receiver Operating Characteristic curves.

Results: Area Under the Curve (AUC), Positive Predictive Value (PPV), and Negative Predictive Value (NPV) were calculated for each set of cohort training models and mean values and 95% confidence intervals were calculated for mortality (yes/no) within the follow-up period. AUCs (and CIs) for 1, 2, 3, and 5 years were: 0.81 (0.70 — 0.91), 0.74 (0.69 — 0.79), 0.81 (0.77 — 0.86), 0.77 (0.74 — 0.80). PPVs for 1, 2, 3, and 5 years were: 12.3% (7.5% — 17.1%), 18.8% (15.4% — 22.1%), 18.0% (15.1% — 20.9%), 28.2% (24.7% — 31.7%). NPVs for 1, 2, 3, and 5 years were: 99.2% (98.8% — 99.7%), 97.4% (96.9% — 97.8%), 96.4% (95.1% — 97.7%), 91.7% (89.1% — 94.3%). Predictors of mortality at 1 year were Tumor Stage, at 2 years were Estrogen Receptor and Tumor Stage, and at 3 and 5 years were Diagnosis Age, Tumor Stage, Estrogen Receptor status, and Ki-67 receptor status. Discussion / Conclusion: We were able to successfully train ***m1-BBNs to estimate mortality using breast cancer registry cohorts. Cross-validation showed the models to be robust. The structure of the models can inform us how different data elements contribute to the estimate of mortality. These models can be used to calculate individual probabilities for prognostic guidance given age, staging criteria, and biomarkers. Overall 5-year mortality in the study set is 15.2%, however we can derive subject-specific mortality estimates. For example, a 43-year old Stage 3, ER-Negative, Ki-67 Negative subject has a 19.9% probability of 5-year mortality, while the same subject with positive Ki-67 has a 37.8% probability of mortality. Meanwhile, the same probabilities for a 70 year old woman are 67.0% and 59.0%, respectively.

Membrane tension, lipid adaptation, conformational changes, and energetics in MscL gating

This study aims to explore gating mechanisms of mechanosensitive channels in terms of membrane tension, membrane adaptation, protein conformation, and energetics. The large conductance mechanosensitive channel from Mycobacterium tuberculosis (Tb-MscL) is used as a model system; Tb-MscL acts as a safety valve by releasing small osmolytes through the channel opening under extreme hypoosmotic conditions. Based on the assumption that the channel gating involves tilting of the transmembrane (TM) helices, we have performed free energy simulations of Tb-MscL as a function of TM helix tilt angle in a dimyristoylphosphatidylcholine bilayer. Based on the change in system dimensions, TM helix tilting is shown to be essentially equivalent to applying an excess surface tension to the membrane, causing channel expansion, lipid adaptation, and membrane thinning. Such equivalence is further corroborated by the observation that the free energy cost of Tb-MscL channel expansion is comparable to the work done by the excess surface tension. Tb-MscL TM helix tilting results in an expanded water-conducting channel of an outer dimension similar to the proposed fully open MscL structure. The free energy decomposition indicates a possible expansion mechanism in which tilting and expanding of TM2 facilitates the iris-like motion of TM1, producing an expanded Tb-MscL.

Xenotransplantation of surgical specimens of human breast cancer directly into genetically engineered prolactin-humanized immunodeficient mice

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Background: Prolactin is an important hormone in mammary gland biology and is indispensible for lobulo-alveolar development during pregnancy and homeostasis during lactation. Prolactin has also been implicated in promoting proliferation, survival, and/ or differentiation of breast cancer. Importantly, murine and bovine prolactin, which are the major lactogens in current laboratory experimental conditions in vivo and in vitro, fail to effectively activate human prolactin receptors because of species incompatibility. Therefore, current established human breast cancer cell lines have been selected in the absence of human prolactin and do not represent the potential subgroup of cancers that depends on prolactin for survival or growth.

Methods: In an effort to improve in vivo preclinical modeling of human breast cancer and to establish new human breast cancer lines that are prolactin-dependent or prolactin-sensitive, we used genetic-engineering to generate a human prolactin knock-in mouse line, which expresses physiological levels of human prolactin in place of mouse prolactin. We have crossed the prolactin-humanized mouse line into the immunodeficient NSG strain for effective xenotransplantation studies. Fresh surgical specimens from breast cancer patients were directly transplanted orthotopically into female mice within 2 hours of surgery. We then followed the growth of the xenograft tumors over time and retransplanted the tumors if they engrafted.

Results: Our initial data suggested about a take rate of ~35% for the xenografted tumors. Estrogen receptor-positive luminal tumors usually have a very low engraftment rate in immunodeficient mice. However, we observed a relatively high rate of engraftment for luminal tumors.

Conclusions: This new prolactin-humanized mouse model is highly relevant for in vivo exploration of tumor biology and drug response testing of breast cancer, especially for luminal subtypes.

Molecular dynamics studies of ion permeation in VDAC

The voltage-dependent anion channel (VDAC) in the outer membrane of mitochondria serves an essential role in the transport of metabolites and electrolytes between the cell matrix and mitochondria. To examine its structure, dynamics, and the mechanisms underlying its electrophysiological properties, we performed a total of 1.77 μs molecular dynamics simulations of human VDAC isoform 1 in DOPE/DOPC mixed bilayers in 1 M KCl solution with transmembrane potentials of 0, ±25, ±50, ±75, and ±100 mV. The calculated conductance and ion selectivity are in good agreement with the experimental measurements. In addition, ion density distributions inside the channel reveal possible pathways for different ion species. Based on these observations, a mechanism underlying the anion selectivity is proposed; both ion species are transported across the channel, but the rate for K(+) is smaller than that for Cl(-) because of the attractive interactions between K(+) and residues on the channel wall. This difference leads to the anion selectivity of VDAC.

Brownian dynamics simulations of ion transport through the VDAC

It is important to gain a physical understanding of ion transport through the voltage-dependent anion channel (VDAC) because this channel provides primary permeation pathways for metabolites and electrolytes between the cytosol and mitochondria. We performed grand canonical Monte Carlo/Brownian dynamics (GCMC/BD) simulations to explore the ion transport properties of human VDAC isoform 1 (hVDAC1; PDB:2K4T) embedded in an implicit membrane. When the MD-derived, space-dependent diffusion constant was used in the GCMC/BD simulations, the current-voltage characteristics and ion number profiles inside the pore showed excellent agreement with those calculated from all-atom molecular-dynamics (MD) simulations, thereby validating the GCMC/BD approach. Of the 20 NMR models of hVDAC1 currently available, the third one (NMR03) best reproduces both experimental single-channel conductance and ion selectivity (i.e., the reversal potential). In addition, detailed analyses of the ion trajectories, one-dimensional multi-ion potential of mean force, and protein charge distribution reveal that electrostatic interactions play an important role in the channel structure and ion transport relationship. Finally, the GCMC/BD simulations of various mutants based on NMR03 show good agreement with experimental ion selectivity. The difference in ion selectivity between the wild-type and the mutants is the result of altered potential of mean force profiles that are dominated by the electrostatic interactions.

Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations

Protegrin-1 (PG-1) belongs to the family of antimicrobial peptides. It interacts specifically with the membrane of a pathogen and kills the pathogen by releasing its cellular contents. To fully understand the energetics governing the orientation of PG-1 in different membrane environments and its effects on the physicochemical properties of the peptide and membrane bilayers, we have performed the potential of mean force (PMF) calculations as a function of its tilt angle at four distinct rotation angles in explicit membranes composed of either DLPC (1,2-dilauroylphosphatidylcholine) or POPC (1-palmitoyl-2-oleoylphosphatidylcholine) lipid molecules. The resulting PMFs in explicit lipid bilayers were then used to search for the optimal hydrophobic thickness of the EEF1/IMM1 implicit membrane model in which a two-dimensional PMF in the tilt and rotation space was calculated. The PMFs in explicit membrane systems clearly reveal that the energetically favorable tilt angle is affected by both the membrane hydrophobic thickness and the PG-1 rotation angle. Local thinning of the membrane around PG-1 is observed upon PG-1 tilting. The thinning is caused by both hydrophobic mismatch and arginine-lipid head group interactions. The two-dimensional PMF in the implicit membrane is in good accordance with those from the explicit membrane simulations. The ensemble-averaged Val16 (15)N and (13)CO chemical shifts weighted by the two-dimensional PMF agree fairly well with the experimental values, suggesting the importance of peptide dynamics in calculating such ensemble properties for direct comparison with experimental observables.

Structural, NMR spectroscopic, and computational investigation of hemin loading in the hemophore HasAp from Pseudomonas aeruginosa

When challenged by low-iron conditions several Gram-negative pathogens secrete a hemophore (HasA) to scavenge hemin from its host and deliver it to a receptor (HasR) on their outer membrane for internalization. Here we report results from studies aimed at probing the structural and dynamic processes at play in the loading of the apo-hemophore secreted by P. aeruginosa (apo-HasAp) with hemin. The structure of apo-HasAp shows a large conformational change in the loop harboring axial ligand His32 relative to the structure of holo-HasAp, whereas the loop bearing the other axial ligand, Tyr75, remains intact. To investigate the role played by the axial ligand-bearing loops in the process of hemin capture we investigated the H32A mutant, which was found to exist as a monomer in its apo-form and as a mixture of monomers and dimers in its holo-form. We obtained an X-ray structure of dimeric H32A holo-HasAp, which revealed that the two subunits are linked by cofacial interactions of two hemin molecules and that the conformation of the Ala32 loop in the dimer is identical to that exhibited by the His32 loop in wild type apo-HasAp. Additional data suggest that the conformation of the Ala32 loop in the dimer is mainly a consequence of dimerization. Hence, to investigate the effect of hemin loading on the topology of the His32 loop we also obtained the crystal structure of monomeric H32A holo-HasAp coordinated by imidazole (H32A-imidazole) and investigated the monomeric H32A HasAp and H32A-imidazole species in solution by NMR spectroscopy. The structure of H32A-imidazole revealed that the Ala32 loop attains a "closed" conformation nearly identical to that observed in wild type holo-HasAp, and the NMR investigations indicated that this conformation is maintained in solution. The NMR studies also highlighted conformational heterogeneity at the H32 loop hinges and in other key sections of the structure. Targeted molecular dynamics simulations allowed us to propose a possible path for the closing of the His32 loop upon hemin binding and identified molecular motions that are likely important in transmitting the presence of hemin in the Tyr75 loop to the His32 loop to initiate its closing. Importantly, residues implicated as undergoing motions in the computations are also observed as being dynamic by NMR. Taken together, these observations provide direct experimental evidence indicating that hemin loads onto the Tyr75 loop of apo-HasAp, which triggers the closing of the His32 loop.

Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function

Understanding the delicate balance of forces governing helix or beta-hairpin interactions in transmembrane (TM) proteins is central to understanding membrane structure and function. These membrane constituent interactions play an essential role in determining the structure and function of membrane proteins, and protein interactions in membranes, and thus form the basis for many vital processes, including TM signaling, transport of ions and small molecules, energy transduction, and cell-cell recognition. "Why does a single-pass TM helix or beta-hairpin have specific orientations in membranes?" "What are the roles of hydrogen bonds, close packing, and helix-lipid or beta-hairpin-lipid interactions in helix or beta-hairpin associations in membranes?" "How do these interactions change the membrane structures?" "How do TM domains transmit signals across membranes?" These are important membrane biophysical questions that can be addressed by understanding the delicate balance of forces governing helix or beta-hairpin interactions with/in membranes. In this work, we summarize a series of helix/beta-hairpin restraint potentials that we have developed, and illustrate their applications that begin to address the complicated energetics and molecular mechanisms of these interactions at the atomic level by calculating the potentials of mean force (PMFs) along reaction coordinates relevant to helix/beta-hairpin motions in membranes and dissecting the total PMF into the contributions arising from physically important microscopic forces.

LuxO controls extracellular protease, haemolytic activities and siderophore production in fish pathogen Vibrio alginolyticus

AIMS

To characterize the luxO gene in fish pathogen Vibrio alginolyticus MVP01 and investigate its roles in regulation of extracellular products (ECP) and siderophore production.

METHODS AND RESULTS

The luxO gene was cloned from V. alginolyticus MVP01. Genetic analysis revealed that it encoded a protein with high similarity to other LuxO homologues. The luxO in-frame deletion mutant and rpoN null mutant were constructed with suicide plasmids. We demonstrated that sole deletion in LuxO increased the secretion of extracellular protease and haemolytic products, but decreased siderophore production for V. alginolyticus MVP01. Mutants with null rpoN displayed significantly enhanced protease level and siderophore production while notable reduction in haemolytic activities of ECP.

CONCLUSIONS

Vibrio alginolyticus harbours functional luxO gene that regulates the secretion of extracellular protease and haemolytic materials as well as siderophore production in either sigma(54) dependent or independent manners.

SIGNIFICANCE AND IMPACT OF THE STUDY

The current study demonstrated that V. alginolyticus MVP01 produces extracellular protease and haemolytic activity material as well as siderophore, which may be characteristics of the virulence of the strain. Revelations that secretion of these products is under the regulation of LuxO and sigma(54) as well as the potential quorum sensing systems in V. alginolyticus MVP01 will expedite the understanding of vibriosis pathogenesis.

Biomarker analysis by breast cancer phenotype in African-American versus Caucasian patients: Correlates with survival

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Background: Breast carcinomas in African-American (AA) patients (pts) have poorer prognosis and higher likelihood of aggressive basal phenotype (triple negative for ER, PR, HER2) than those in Caucasian (C) patients (Carey et al, JAMA 2006, 295(21):2492; Morris et al, Breast Cancer Res Treat 2006, abstr 3055). We have additionally examined biomarker expression by phenotype in AA pts in our registry to further explain more aggressive behavior in this population. Methods: Stage, grade, ER, PR, Ki-67, HER2, and p53 expressions were compiled for breast carcinomas in 2,230 AA and C pts diagnosed between 1995–2004. Immunohistochemical markers were assayed using antibodies to the above proteins on paraffin-embedded formalin-fixed tissue. Differences in expression were analyzed by Chi- squared and Wilcoxon tests, and survival by Kaplan-Meier estimates. Results: AA pts have higher propensity for basal phenotype breast cancers (20.8% vs 10.4%, p<0.001) and lower propensity for Luminal A/B (ER+/PR+-/HER2-) phenotype (44.2% vs. 54.1%, p<0.001) as compared with C pts. Higher ki-67 proliferation index was found in AA pts (86.4% vs 78.8% in basal, p=0.3423; 37.1% vs. 26.7% in Luminal A/B p=0.0233) as compared with C pts. p53-positivity was higher in AA and C pts in all cases (p=0.0158), higher in AA pts with basal phenotype (p=0.2597), but identical in AA and C pts with luminal phenotypes (p=0.881). Survival was similar in basal phenotypes between races in all cases stage for stage, and controlled for ki-67 and p53 status, with a trend toward poorer survival among luminal phenotypes between races. Conclusions: AA pts have higher propensity for basal phenotype breast cancers than C pts, with higher ki-67 expression in both basal and luminal phenotypes, and higher p53 expression in basal phenotype, but these do not correlate with significant differences in survival by phenotype between races. As neither ki-67 index nor p53 expression can therefore solely explain differences in survival rates seen between races, molecular array studies between races and matched by phenotype are proposed.

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In vivo response-based identification of direct hormone target cell populations using high-density tissue arrays

To identify cell populations directly responsive to prolactin (PRL), GH, erythropoietin, or granulocyte-colony stimulating factor within the physiological setting of an intact mammal, we combined in situ detection of hormone-activated signal transducer and activator of transcription (Stat)-5 in rats with high-throughput tissue array analysis using cutting-edge matrix assembly (CEMA). Inducible activation of Stat5a/b, as judged by levels of nuclear-localized, phosphoTyr694/699-Stat5a/b, served as an immediate and sensitive in situ marker of receptor signaling in rat tissues after injection into male and female rats of a single, receptor-saturating dose of hormone for maximal receptor activation. CEMA tissue arrays facilitated analysis of most tissues, including architecturally complex, thin-walled, and stratified tissues such as gut and skin. In 40 tissues analyzed, 35 PRL-responsive and 32 GH-responsive cell types were detected, of which 22 cell types were responsive to both hormones. Interestingly, PRL but not GH activated Stat5 in nearly all of the endocrine glands. In mammary glands, PRL activated Stat5 in a majority of luminal epithelial cells but not myoepithelial cells, stromal fibroblasts, or adipocytes, whereas GH activated Stat5 in a significant fraction of myoepithelial cells, fibroblasts, and adipocytes but only in a minority of luminal cells. Finally, the organism-wide screening revealed a yet-to-be identified erythropoietin-responsive cell type in connective tissue. CEMA tissue arrays provide cost-effective in situ analysis of large numbers of tissues. Biomarker-based identification of cell populations responsive to individual hormones may shed new light on endocrine disease as well as improve understanding of effects and side effects of hormones and drugs.

Human prolactin receptors are insensitive to mouse prolactin: implications for xenotransplant modeling of human breast cancer in mice

Experimental testing of growth, metastatic progression and drug responsiveness of human breast cancer in vivo is performed in immunodeficient mice. Drug candidates need to show promise against human breast cancer in mice before being allowed into clinical trials. Breast cancer growth is under endocrine control by ovarian steroids and the pituitary peptide hormone prolactin. While it is recognized that the most relevant biologic effects of prolactin are achieved with prolactin from the matching species, the biologic efficacy of mouse prolactin for human prolactin receptors has not been recorded. Thus, it is unclear whether the mouse endocrine environment adequately reflects the hormonal environment in breast cancer patients with regard to prolactin. We now show both recombinant and natural pituitary-derived mouse prolactin to be a poor agonist for human prolactin receptors. Mouse prolactin failed to induce human prolactin receptor-mediated biologic responses of cell clustering, proliferation, gene induction and signal transduction, including activation of Stat5, Stat3, Erk1/2 and Akt pathways. Consistent data were derived from human breast cancer lines T-47D, MCF-7 and ZR-75.1, as well as human prolactin receptor-transfected COS-7 and 32D cells. Failure of mouse prolactin to activate human prolactin receptors uncovers a key deficiency of the mouse endocrine environment for human xenotransplant studies. Since most human breast cancers express prolactin receptors, human breast cancer transferred into mice is unnaturally selected for growth in the absence of circulating prolactin. The new insight raises concerns about the validity of analyzing biology and drug responsiveness of human breast cancer in existing mouse xenotransplant models.