Environmental and genetic predictors of human cardiovascular ageing

Cardiovascular ageing is a process that begins early in life and leads to a progressive change in structure and decline in function due to accumulated damage across diverse cell types, tissues and organs contributing to multi-morbidity. Damaging biophysical, metabolic and immunological factors exceed endogenous repair mechanisms resulting in a pro-fibrotic state, cellular senescence and end-organ damage, however the genetic architecture of cardiovascular ageing is not known. Here we use machine learning approaches to quantify cardiovascular age from image-derived traits of vascular function, cardiac motion and myocardial fibrosis, as well as conduction traits from electrocardiograms, in 39,559 participants of UK Biobank. Cardiovascular ageing is found to be significantly associated with common or rare variants in genes regulating sarcomere homeostasis, myocardial immunomodulation, and tissue responses to biophysical stress. Ageing is accelerated by cardiometabolic risk factors and we also identify prescribed medications that are potential modifiers of ageing. Through large-scale modelling of ageing across multiple traits our results reveal insights into the mechanisms driving premature cardiovascular ageing and reveal potential molecular targets to attenuate age-related processes.

Genetic and environmental determinants of diastolic heart function

Diastole is the sequence of physiological events that occur in the heart during ventricular filling and principally depends on myocardial relaxation and chamber stiffness. Abnormal diastolic function is related to many cardiovascular disease processes and is predictive of health outcomes, but its genetic architecture is largely unknown. Here, we use machine learning cardiac motion analysis to measure diastolic functional traits in 39,559 participants of the UK Biobank and perform a genome-wide association study. We identified 9 significant, independent loci near genes that are associated with maintaining sarcomeric function under biomechanical stress and genes implicated in the development of cardiomyopathy. Age, sex and diabetes were independent predictors of diastolic function and we found a causal relationship between genetically-determined ventricular stiffness and incident heart failure. Our results provide insights into the genetic and environmental factors influencing diastolic function that are relevant for identifying causal relationships and potential tractable targets.

Arbitrage-free interpolation of call option prices

In this paper, we introduce a new interpolation method for call option prices and implied volatilities with respect to the strike, which first generates, for fixed maturity, an implied volatility curve that is smooth and free of static arbitrage. Our interpolation method is based on a distortion of the call price function of an arbitrage-free financial “reference” model of one’s choice. It reproduces the call prices of the reference model if the market data is compatible with the model. Given a set of call prices for different strikes and maturities, we can construct a call price surface by using this one-dimensional interpolation method on every input maturity and interpolating the generated curves in the maturity dimension. We obtain the algorithm of N. Kahalé [An arbitrage-free interpolation of volatilities, Risk 17 2004, 5, 102–106] as a special case, when applying the Black–Scholes model as reference model.

Abstract P1-17-10: The impact of age and adjuvant chemotherapy modifications on disease-free and overall survival among African American women with breast cancer

Background: During chemotherapy for breast cancer, African American women receive less relative dose intensity with more dose reductions and early chemotherapy cessation compared to Caucasian women. Other research has found that older breast cancer patients are most at risk for treatment modifications; however, it is unclear if this remains true for African American patients. Furthermore, the clinical implications of treatment modifications and delays on survival is uncertain, particularly in African American patients.

Purpose: The purpose of this study was to investigate whether age (diagnosis <55 vs. diagnosis ≥55) was a moderator for the association between treatment modifications (dose held, dose delayed, and early cessation) and overall survival (OS) and disease-free survival (DFS) in African American women with breast cancer.

Methods: A retrospective cohort study of early stage African American breast cancer patients treated with adjuvant chemotherapy was employed. Dose held, dose delayed and early cessation were examined as dichotomous variables: any adjustment to the initially prescribed treatment plan was considered a modification. Medical record data extraction was utilized to gather this information. The sample was divided into two groups: those diagnosed <55 years of age and those diagnosed ≥55 years of age. A Cox's proportional hazards regression model was used to examine the interaction between age group and treatment modifications for OS and DFS, while controlling for stage and ER and HER2 status.

Results: In the study of 115 participants, 58 (50.4%) were diagnosed before the age of 55, and 57 (49.6%) were diagnosed age 55 or older. Across the entire sample, 43 (37.4%) patients experienced a treatment modification. There were no significant differences in the proportions of treatment modifications between the two age groups. We found no interaction between age group and treatment modifications for OS. However, there was a significant interaction between age group and held dose for DFS (p=0.045). Specifically, those diagnosed at 55 years of age and older, who had doses of chemotherapy held, experienced worse DFS compared to those who did not (hazard ratio (HR)=3.390, 95% CI (1.013,11.34)). In contrast, there was no difference in DFS between those who did and did not have doses held in patients diagnosed below 55 years of age (HR=0.563, 95%CI (0.159, 1.986)).

Conclusions: African American women receiving adjuvant chemotherapy for treatment of early stage breast cancer have high levels of treatment modifications across all age groups. However, held doses of chemotherapy in older African American patients were associated with worse DFS. Further research is needed to elucidate the clinical implications of adjuvant chemotherapy treatment modifications, particularly in African American patients, and the subgroups of patients who are at greatest risk.

Citation Format: Nugent BD, Ren D, Bender C, Rosenzweig M. The impact of age and adjuvant chemotherapy modifications on disease-free and overall survival among African American women with breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-17-10.

A Robust and All-Inclusive Pipeline for Shuffling of Adeno-Associated Viruses

Adeno-associated viruses (AAV) are attractive templates for engineering of synthetic gene delivery vectors. A particularly powerful technology for breeding of novel vectors with improved properties is DNA family shuffling, i.e., generation of chimeric capsids by homology-driven DNA recombination. Here, to make AAV DNA shuffling available to a wider community, we present a robust experimental and bioinformatical pipeline comprising: (i) standardized and partially codon-optimized plasmids carrying 12 different AAV capsid genes; (ii) a scalable protocol including troubleshooting guide for viral library production; and (iii) the freely available software SALANTO for comprehensive analysis of chimeric AAV DNA and protein sequences. Moreover, we describe a set of 12 premade and ready-to-use AAV libraries. Finally, we demonstrate the usefulness of DNA barcoding technology to trace AAV capsid libraries within a complex mixture. Our protocols and resources facilitate the implementation and tailoring of AAV evolution technology in any laboratory interested in customized viral gene transfer.

New Results on Excited States in the one-particle one-hole nucleus 56Co measured with MINIBALL detectors

The non-yrast states of the odd-odd nucleus 56Co have been investigated by studying the γ-rays induced in the predominantly fusion-evaporation reaction 56Fe(p,n γ)56Co at an incident energy of 10 MeV. The γ-rays were measured in-beam with four high-resolution MINIBALL-triple germanium (Ge) detectors. The experiment provided excellent data in γ-γ coincidences. The complex level scheme of 56Co was constructed mainly based on the analysis of these γ-γ coincidences. The angular distributions of the γ-rays were also analysed and allowed us to assign spin-parity values to most of the excited states in this nucleus. Despite the extensive work previously done studying the 56Co nucleus, the analysis presented in this work has resulted in a large improvement in the knowledge of its structure.

Implementation of Plate Imaging for Demonstration of Monoclonality in Biologics Manufacturing Development

Monoclonality of mammalian cell lines used for production of biologics is a regulatory expectation and one of the attributes assessed as part of a larger process to ensure consistent quality of the biologic. Historically, monoclonality has been demonstrated through statistics generated from limiting dilution cloning or through verified flow cytometry methods. A variety of new technologies are now on the market with the potential to offer more efficient and robust approaches to generating and documenting a clonal cell line.Here we present an industry perspective on approaches for the application of imaging and integration of that information into a regulatory submission to support a monoclonality claim. These approaches represent the views of a consortium of companies within the BioPhorum Development Group and include case studies utilising imaging technology that apply scientifically sound approaches and efforts in demonstrating monoclonality. By highlighting both the utility of these alternative approaches and the advantages they bring over the traditional methods, as well as their adoption by industry leaders, we hope to encourage acceptance of their use within the biologics cell line development space and provide guidance for regulatory submission using these alternative approaches.LAY ABSTRACT: In the manufacture of biologics produced in mammalian cells, one recommendation by regulatory agencies to help ensure product consistency, safety, and efficacy is to produce the material from a monoclonal cell line derived from a single, progenitor cell. The process by which monoclonality is assured can be supplemented with single-well plate images of the progenitor cell. Here we highlight the utility of that imaging technology, describe approaches to verify the validity of those images, and discuss how to analyze that information to support a biologic filing application. This approach serves as an industry perspective to increased regulatory interest within the scope of monoclonality for mammalian cell culture-derived biologics.

Sticky Continuous Processes have Consistent Price Systems

Under proportional transaction costs, a price process is said to have a consistent price system, if there is a semimartingale with an equivalent martingale measure that evolves within the bid-ask spread. We show that a continuous, multi-asset price process has a consistent price system, under arbitrarily small proportional transaction costs, if it satisfies a natural multi-dimensional generalization of the stickiness condition introduced by Guasoni (2006).

Biophysical and Sequence-Based Methods for Identifying Monovalent and Bivalent Antibodies with High Colloidal Stability

In vitro antibody discovery and/or affinity maturation are often performed using antibody fragments (Fabs), but most monovalent Fabs are reformatted as bivalent IgGs (monoclonal antibodies, mAbs) for therapeutic applications. One problem related to reformatting antibodies is that the bivalency of mAbs can lead to increased antibody self-association and poor biophysical properties (e.g., reduced antibody solubility and increased viscosity). Therefore, it is important to identify monovalent Fabs early in the discovery and/or optimization process that will display favorable biophysical properties when reformatted as bivalent mAbs. Here we demonstrate a facile approach for evaluating Fab self-association in a multivalent assay format that is capable of identifying antibodies with low self-association and favorable colloidal properties when reformatted as bivalent mAbs. Our approach (self-interaction nanoparticle spectroscopy, SINS) involves immobilizing Fabs on gold nanoparticles in a multivalent format (multiple Fabs per nanoparticle) and evaluating their self-association behavior via shifts in the plasmon wavelength or changes in the absorbance values. Importantly, we find that SINS measurements of Fab self-association are correlated with self-interaction measurements of bivalent mAbs and are useful for identifying antibodies with favorable biophysical properties. Moreover, the significant differences in the levels of self-association detected for Fabs and mAbs with similar frameworks can be largely explained by the physicochemical properties of the complementarity-determining regions (CDRs). Comparison of the properties of the CDRs in this study relative to those of approved therapeutic antibodies reveals several key factors (net charge, fraction of charged residues, and presence of self-interaction motifs) that strongly influence antibody self-association behavior. Increased positive charge in the CDRs was observed to correlate with increased risk of high self-association for the mAbs in this study and clinical-stage antibodies. We expect that these findings will be useful for improving the development of therapeutic antibodies that are well suited for high concentration applications.

PD-1 blockade: a therapeutic option for treatment of metastatic Merkel cell carcinoma

The immune system is extremely important in the development and progression of Merkel cell carcinoma (MCC). Immune checkpoint blockade has recently been shown to enable efficacious treatment of a variety of tumours. We report the use of an anti-programmed death receptor 1 (PD-1) antibody for treatment of a patient with metastatic MCC. An 80-year-old patient with metastatic MCC received off-label treatment with the anti-PD-1 antibody pembrolizumab after the disease had progressed during therapy with oral etoposide. A positron emission tomography (PET) computed tomography scan performed after three cycles of pembrolizumab revealed responses to therapy with reduced size of the adrenal gland metastases and less PET activity in the adrenal gland and lymph node metastases. Treatment was resumed owing to disease progression after a treatment-free interval of > 4 months. During subsequent months of treatment, the size of the metastases stabilized and uptake of nuclide by all tumour sites once again decreased. These results reveal the potential efficacy of an anti-PD-1 antibody for treatment of metastatic MCC. Thus, they contribute to currently limited data on the use of anti-PD-1 antibodies for the treatment of MCC. Moreover, this is the first report of successful resumption of treatment of metastatic MCC with an anti-PD-1 antibody. Results from ongoing trials will contribute to determination of the relevance of PD-1 blockade in metastatic MCC.

CXorf61 is a target for T cell based immunotherapy of triple-negative breast cancer

Triple-negative breast cancer (TNBC) is a high medical need disease with limited treatment options. CD8+ T cell-mediated immunotherapy may represent an attractive approach to address TNBC. The objectives of this study were to assess the expression of CXorf61 in TNBCs and healthy tissues and to evaluate its capability to induce T cell responses.

We show by transcriptional profiling of a broad comprehensive set of normal human tissue that CXorf61 expression is strictly restricted to testis. 53% of TNBC patients express this antigen in at least 30% of their tumor cells. In CXorf61-negative breast cancer cell lines CXorf61 expression is activated by treatment with the hypomethylating agent 5-aza-2′-deoxycytidine.

By vaccination of HLA-A*02-transgenic mice with CXorf61 encoding RNA we obtained high frequencies of CXorf61-specific T cells. Cloning and characterization of T cell receptors (TCRs) from responding T cells resulted in the identification of the two HLA-A*0201-restricted T cell epitopes CXorf61_66–74 and CXorf61_79–87. Furthermore, by in vitro priming of human CD8+ T cells derived from a healthy donor recognizing CXorf61_66–74 we were able to induce a strong antigen-specific immune response and clone a human TCR recognizing this epitope.

In summary, our data confirms this antigen as promising target for T cell based therapies.

Integrating Volatility Clustering Into Exponential Lévy Models

We introduce a class of stock models that interpolates between exponential Lévy models based on Brownian subordination and certain stochastic volatility models with Lévy-driven volatility, such as the Barndorff-Nielsen–Shephard model. The driving process in our model is a Brownian motion subordinated to a business time which is obtained by convolution of a Lévy subordinator with a deterministic kernel. We motivate several choices of the kernel that lead to volatility clusters while maintaining the sudden extreme movements of the stock. Moreover, we discuss some statistical and path properties of the models, prove absence of arbitrage and incompleteness, and explain how to price vanilla options by simulation and fast Fourier transform methods.

An iterative method for multiple stopping: convergence and stability

We present a new iterative procedure for solving the multiple stopping problem in discrete time and discuss the stability of the algorithm. The algorithm produces monotonically increasing approximations of the Snell envelope which coincide with the Snell envelope after finitely many steps. Unlike backward dynamic programming, the algorithm allows us to calculate approximative solutions with only a few nestings of conditional expectations and is, therefore, tailor-made for a plain Monte Carlo implementation.

Reconstruction of Protein Networks Using Reverse-Phase Protein Array Data

In this chapter, we describe an approach to reconstruct cellular signaling networks based on measurements of protein activation after different stimulation experiments. As experimental platform reverse-phase protein arrays (RPPA) are used. RPPA allow the measurement of proteins and phosphoproteins across many samples in parallel with minimal sample consumption using a panel of highly target protein-specific antibodies. Functional interactions of proteins are modeled using a Boolean network. We describe the Boolean network reconstruction approach ddepn (dynamic deterministic effects propagation networks), which uses time course data to derive protein interactions based on perturbation experiments. We explain how the method works, give a practical application example, and describe how the results can be interpreted. Furthermore prior knowledge on signaling pathways is essential for network reconstruction. Here we describe the use of our software rBiopaxParser to integrate prior knowledge on protein signaling available in public databases. All applied methods are freely available as open-source R software packages. We describe the preparation of RPPA data as well as all relevant programming steps to format the RPPA data, to infer the prior knowledge, and to reconstruct and analyze the protein signaling networks.

Boolean ErbB network reconstructions and perturbation simulations reveal individual drug response in different breast cancer cell lines

Background

Despite promising progress in targeted breast cancer therapy, drug resistance remains challenging. The monoclonal antibody drugs trastuzumab and pertuzumab as well as the small molecule inhibitor erlotinib were designed to prevent ErbB-2 and ErbB-1 receptor induced deregulated protein signalling, contributing to tumour progression. The oncogenic potential of ErbB receptors unfolds in case of overexpression or mutations. Dimerisation with other receptors allows to bypass pathway blockades. Our intention is to reconstruct the ErbB network to reveal resistance mechanisms. We used longitudinal proteomic data of ErbB receptors and downstream targets in the ErbB-2 amplified breast cancer cell lines BT474, SKBR3 and HCC1954 treated with erlotinib, trastuzumab or pertuzumab, alone or combined, up to 60 minutes and 30 hours, respectively. In a Boolean modelling approach, signalling networks were reconstructed based on these data in a cell line and time course specific manner, including prior literature knowledge. Finally, we simulated network response to inhibitor combinations to detect signalling nodes reflecting growth inhibition.

Results

The networks pointed to cell line specific activation patterns of the MAPK and PI3K pathway. In BT474, the PI3K signal route was favoured, while in SKBR3, novel edges highlighted MAPK signalling. In HCC1954, the inferred edges stimulated both pathways. For example, we uncovered feedback loops amplifying PI3K signalling, in line with the known trastuzumab resistance of this cell line. In the perturbation simulations on the short-term networks, we analysed ERK1/2, AKT and p70S6K. The results indicated a pathway specific drug response, driven by the type of growth factor stimulus. HCC1954 revealed an edgetic type of PIK3CA-mutation, contributing to trastuzumab inefficacy. Drug impact on the AKT and ERK1/2 signalling axes is mirrored by effects on RB and RPS6, relating to phenotypic events like cell growth or proliferation. Therefore, we additionally analysed RB and RPS6 in the long-term networks.

Conclusions

We derived protein interaction models for three breast cancer cell lines. Changes compared to the common reference network hint towards individual characteristics and potential drug resistance mechanisms. Simulation of perturbations were consistent with the experimental data, confirming our combined reverse and forward engineering approach as valuable for drug discovery and personalised medicine.

Synthese und Kristallstruktur des Bromdifluormethyl-triphenyl- phosphoniumbromids, [(C6H5)3PCF2Br]+ Br- / Synthesis and Crystal Structure of Bromodifluoromethyl-triphenylphosphonium Bromide, [(C6H5)3PCF2Br]+ Br-

Difluorobromomethyl-triphenylphosphonium bromide [(C6H5)3PCF2Br]+ Br- (1) has been prepared by the reaction of triphenylphosphine with dibromodifluoro-methane in acetonitrile or methylene chloride. The colorless crystals are monoclinic, space group P 21/n, Z=4, a = 1067.1(2), b = 1488,5(2), c = 1178,2(2) pm, β = 95,67(3)°. The lattice contains Br- anions and [(C6H5)3PCF2Br]+ cations with a Br-Br distance of 322,33(11) pm.. For the title compound the results of AM 1, PM 3 ,and MNDO calculations are in good agreement with corresponding values determined by the X-ray analysis only in the case of PM 3.

The yellow-red [(C6H5)3PCF2Br]+ Br3 - (2) has been obtained by treating 1 with equimolar quantities of elemental bromine in methylene chloride solution.

Immunomic, genomic and transcriptomic characterization of CT26 colorectal carcinoma

Background

Tumor models are critical for our understanding of cancer and the development of cancer therapeutics. Here, we present an integrated map of the genome, transcriptome and immunome of an epithelial mouse tumor, the CT26 colon carcinoma cell line.

Results

We found that Kras is homozygously mutated at p.G12D, Apc and Tp53 are not mutated, and Cdkn2a is homozygously deleted. Proliferation and stem-cell markers, including Top2a, Birc5 (Survivin), Cldn6 and Mki67, are highly expressed while differentiation and top-crypt markers Muc2, Ms4a8a (MS4A8B) and Epcam are not. Myc, Trp53 (tp53), Mdm2, Hif1a, and Nras are highly expressed while Egfr and Flt1 are not. MHC class I but not MHC class II is expressed. Several known cancer-testis antigens are expressed, including Atad2, Cep55, and Pbk. The highest expressed gene is a mutated form of the mouse tumor antigen gp70. Of the 1,688 non-synonymous point variations, 154 are both in expressed genes and in peptides predicted to bind MHC and thus potential targets for immunotherapy development. Based on its molecular signature, we predicted that CT26 is refractory to anti-EGFR mAbs and sensitive to MEK and MET inhibitors, as have been previously reported.

Conclusions

CT26 cells share molecular features with aggressive, undifferentiated, refractory human colorectal carcinoma cells. As CT26 is one of the most extensively used syngeneic mouse tumor models, our data provide a map for the rationale design of mode-of-action studies for pre-clinical evaluation of targeted- and immunotherapies.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-190) contains supplementary material, which is available to authorized users.

Efficacy of different carrier gases for barrier discharge plasma generation compared to chlorhexidine on the survival of Pseudomonas aeruginosa embedded in biofilm in vitro

Because of its antimicrobial properties, nonthermal plasma could serve as an alternative to chemical antisepsis in wound treatment. Therefore, this study investigated the inactivation of biofilm-embedded Pseudomonas aeruginosa SG81 by a surface barrier-discharged (SBD) plasma for 30, 60, 150 and 300 s. In order to optimize the efficacy of the plasma, different carrier gases (argon, argon admixed with 1% oxygen, and argon with increased humidity up to approx. 80%) were tested and compared against 0.1% chlorhexidine digluconate (CHG) exposure for 600 s. The antimicrobial efficacy was determined by calculating the difference between the numbers of colony-forming units (CFU) of treated and untreated biofilms. Living bacteria were distinguished from dead by fluorescent staining and confocal laser scanning microscopy. Both SBD plasmas and CHG showed significant antimicrobial effects compared to the untreated control. However, plasma treatment led to a higher antimicrobial reduction (argon plasma 4.9 log10 CFU/cm(2), argon with admixed oxygen 3 log10 CFU/cm(2), and with increased gas humidity 2.7 log10 CFU/cm(2) after 300 s) compared to CHG. In conclusion, SBD plasma is suitable as an alternative to CHG for inactivation of Pseudomonas aeruginosa embedded in biofilm. Further development of SBD plasma sources and research on the role of carrier gases and humidity may allow their clinical application for wound management in the future.

Synergism between Hedgehog-GLI and EGFR signaling in Hedgehog-responsive human medulloblastoma cells induces downregulation of canonical Hedgehog-target genes and stabilized expression of GLI1

Aberrant activation of Hedgehog (HH) signaling has been identified as a key etiologic factor in many human malignancies. Signal strength, target gene specificity, and oncogenic activity of HH signaling depend profoundly on interactions with other pathways, such as epidermal growth factor receptor-mediated signaling, which has been shown to cooperate with HH/GLI in basal cell carcinoma and pancreatic cancer. Our experimental data demonstrated that the Daoy human medulloblastoma cell line possesses a fully inducible endogenous HH pathway. Treatment of Daoy cells with Sonic HH or Smoothened agonist induced expression of GLI1 protein and simultaneously prevented the processing of GLI3 to its repressor form. To study interactions between HH- and EGF-induced signaling in greater detail, time-resolved measurements were carried out and analyzed at the transcriptomic and proteomic levels. The Daoy cells responded to the HH/EGF co-treatment by downregulating GLI1, PTCH, and HHIP at the transcript level; this was also observed when Amphiregulin (AREG) was used instead of EGF. We identified a novel crosstalk mechanism whereby EGFR signaling silences proteins acting as negative regulators of HH signaling, as AKT- and ERK-signaling independent process. EGFR/HH signaling maintained high GLI1 protein levels which contrasted the GLI1 downregulation on the transcript level. Conversely, a high-level synergism was also observed, due to a strong and significant upregulation of numerous canonical EGF-targets with putative tumor-promoting properties such as MMP7, VEGFA, and IL-8. In conclusion, synergistic effects between EGFR and HH signaling can selectively induce a switch from a canonical HH/GLI profile to a modulated specific target gene profile. This suggests that there are more wide-spread, yet context-dependent interactions, between HH/GLI and growth factor receptor signaling in human malignancies.

MicroRNA-31 sensitizes human breast cells to apoptosis by direct targeting of protein kinase C epsilon (PKCepsilon)

MicroRNAs post-transcriptionally regulate gene expression and thereby contribute to the modulation of numerous complex and disease-relevant cellular phenotypes, including cell proliferation, cell motility, apoptosis, and stress response. In breast cancer cell systems, miR-31 has been shown to inhibit cell migration, invasion, and metastasis. Here, we link enhanced expression of miR-31 to the inhibition of the oncogenic NF-κB pathway, thus supporting the tumor-suppressive function of this microRNA. We identified protein kinase C epsilon (PKCε encoded by the PRKCE gene) as a novel direct target of miR-31 and show that down-regulation of PKCε results in impaired NF-κB signaling, enhanced apoptosis, and increased sensitivity of MCF10A breast epithelial and MDA-MB-231 triple-negative breast cancer cells toward ionizing radiation as well as treatment with chemotherapeutics. Mechanistically, we attribute this sensitization to anti-cancer treatments to the PRKCE-mediated down-regulation of the anti-apoptotic factor BCL2. In clinical breast cancer samples, high BCL2 expression was associated with poor prognosis. Furthermore, we found an inverse correlation between miR-31 and BCL2 expression, highlighting the functional relevance of the indirect down-regulation of BCL2 via direct targeting of PRKCE by miR-31.

Selective unilateral lung ventilation in preterm infants with acquired bullous emphysema: a series of nine cases

BACKGROUND AND AIMS

Immature lungs of preterm infants are particularly prone to overdistension from mechanical ventilation or continuous positive airway pressure. In these infants a localized pulmonary emphysema (PE) can develop. Conventional therapy regimens to resolve this process sometimes fail and especially in the case of bullous emphysema (BE) invasive procedures such as surgical resection of the affected lobe ultimately may be required. In the past few years we have applied selective one-sided lung ventilation, a nearly forgotten therapeutic option, in these infants with acquired BE.

METHODS

Medical charts of preterm infants in two Divisions of Neonatology, born between 1993 and 2010 with acquired BE treated with selective one-sided ventilation were reviewed. Gestational age, clinical presentation, course of disease, associated treatment, duration of ventilation and outcome of one-sided lung ventilation are recorded. Therapy was deemed successful if thereafter chest X-ray showed a permanent resolution of the BE and, in case of BPD, lung appearance was comparable to a grade < III according to Weinstein [Weinstein et al. Pediatr Pulmonol 1994; 18: 284-289].

RESULTS

Overall, nine preterm infants with a gestational age between 24 and 35 weeks and a birth weight between 500 and 3,170 g underwent one-sided lung ventilation. This intervention was started between day 12 and day 35 after birth and was continued for 24 hr to 7 days. In three cases selective intubation was performed on the left side. Two patients needed a second course of one-sided ventilation and one had three courses. Therapy was successful in seven patients, who had no recurrence of BE.

CONCLUSIONS

Selective one-sided intubation is technically challenging, in particular for the left bronchus, but seems to be feasible and helpful. If during selective intubation the affected lung lobe shows complete atelectasis for more than 48 hr the overdistension of airways probably will permanently resolve.

Establishment and comparative characterization of novel squamous cell non-small cell lung cancer cell lines and their corresponding tumor tissue

BACKGROUND

Cell lines play an important role for studying tumor biology and novel therapeutic agents. Particularly in pulmonary squamous cell carcinoma (SCC) the availability of cell lines is limited and knowledge about their representativeness for corresponding tumor tissue is scanty.

MATERIALS AND METHODS

We established three novel SCC cell lines from fresh tumor tissue of 28 donors, including 8 SCC. Two cell lines were derived from different localizations of the same donor, i.e. primary tumor and lymph node metastasis. This represents a so far unique combination in lung cancer. The genotypes, gene expression profiles and mutational status of epidermal growth factor receptor (EGF-R) and Kirsten rat sarcoma (k-ras) of the cell lines and their corresponding tumor tissue were analyzed and compared. Moreover, the molecular characteristics were related to functional properties of the cell lines. Those comprised proliferation, motility and chemosensitivity. The cell lines were authenticated by single tandem repeat DNA typing. Tumorigenicity was analyzed in a murine xenograft model.

RESULTS

Comparative genomic hybridization and multiplex fluorescence in situ hybridization revealed essential genetic similarities between the cell lines and their corresponding tumor tissue, but indicated also some genetic evolution and clonal selection. EGF-R or k-ras mutations were not detected. Gene expression profiling showed various differences between tumor tissue and cell lines affecting gene clusters associated with immune response, adhesion, proliferation, differentiation and angiogenesis. However, there were also common gene expression patterns reflecting the relationship between cell lines and their corresponding tumor tissue. Moreover, the molecular characteristics of the tumor tissue and the descendent cell line were associated with functional properties of the latter. All cell lines showed a unique, heterozygous human DNA profile and one cell line displayed rapid tumor formation in mice.

CONCLUSIONS

Here, we demonstrate that cell lines represent a useful in vitro system for studying basic mechanisms in lung cancer, but cover only distinct molecular characteristics of the original tumor. Moreover, we present three novel, comprehensively characterized SCC cell lines.

Triplex DNA-binding proteins are associated with clinical outcomes revealed by proteomic measurements in patients with colorectal cancer

Background

Tri- and tetra-nucleotide repeats in mammalian genomes can induce formation of alternative non-B DNA structures such as triplexes and guanine (G)-quadruplexes. These structures can induce mutagenesis, chromosomal translocations and genomic instability. We wanted to determine if proteins that bind triplex DNA structures are quantitatively or qualitatively different between colorectal tumor and adjacent normal tissue and if this binding activity correlates with patient clinical characteristics.

Methods

Extracts from 63 human colorectal tumor and adjacent normal tissues were examined by gel shifts (EMSA) for triplex DNA-binding proteins, which were correlated with clinicopathological tumor characteristics using the Mann-Whitney U, Spearman’s rho, Kaplan-Meier and Mantel-Cox log-rank tests. Biotinylated triplex DNA and streptavidin agarose affinity binding were used to purify triplex-binding proteins in RKO cells. Western blotting and reverse-phase protein array were used to measure protein expression in tissue extracts.

Results

Increased triplex DNA-binding activity in tumor extracts correlated significantly with lymphatic disease, metastasis, and reduced overall survival. We identified three multifunctional splicing factors with biotinylated triplex DNA affinity: U2AF65 in cytoplasmic extracts, and PSF and p54nrb in nuclear extracts. Super-shift EMSA with anti-U2AF65 antibodies produced a shifted band of the major EMSA H3 complex, identifying U2AF65 as the protein present in the major EMSA band. U2AF65 expression correlated significantly with EMSA H3 values in all extracts and was higher in extracts from Stage III/IV vs. Stage I/II colon tumors (p = 0.024). EMSA H3 values and U2AF65 expression also correlated significantly with GSK3 beta, beta-catenin, and NF- B p65 expression, whereas p54nrb and PSF expression correlated with c-Myc, cyclin D1, and CDK4. EMSA values and expression of all three splicing factors correlated with ErbB1, mTOR, PTEN, and Stat5. Western blots confirmed that full-length and truncated beta-catenin expression correlated with U2AF65 expression in tumor extracts.

Conclusions

Increased triplex DNA-binding activity in vitro correlates with lymph node disease, metastasis, and reduced overall survival in colorectal cancer, and increased U2AF65 expression is associated with total and truncated beta-catenin expression in high-stage colorectal tumors.

Abstract A185: Identification of drug-associated proteins in NSCLC xenograft models by reverse-phase-protein-arrays

At present, most non-small cell lung cancer (NSCLC) treatments are not adapted to the individual response of a patient. The stratification of patients for the most efficient response to conventional chemotherapeutics and targeted therapies will improve established therapy schemes and patient's perspectives. Our project aims at unraveling the influence of specific signaling molecules on the response to common NSCLC drugs. We searched for predictive markers for the response of NSCLC tumors to certain drugs and novel combinations of treatments, which may be useful for therapy decisions towards a more efficient personalized treatment.

Expression of 77 proteins described to be involved in EGFR signaling (e.g. MAPK, JAK/STAT, PI3K/AKT pathways) and NSCLC disease in general were quantified in 53 patient derived NSCLC xenograft models using the reverse-phase protein array technology (RPPA). The tumor models are characterized by different response rates upon treatment with different chemotherapeutics and EGFR-targeted therapies. The response rates were obtained directly in the xenograft models. After RPPA analysis we associated the protein expression with the response to established chemotherapeutics (e.g. Vinorelbine, Paclitaxel, Carboplatin) and EGFR-targeted therapies (Cetuximab, Erlotinib). Another goal is to analyze the protein expression changes after treatment in dependence on the response rate. Therefore, protein profiles were raised in NSCLC xenograft models before and after treatment with Cetuximab, a chimeric (mouse/human) monoclonal antibody that inhibits EGFR. The major goal in this experimental subset is to find links between the activities of specific proteins and the response to Cetuximab treatment. A similar experiment with Erlotinib (an EGFR inhibitor) treated samples is ongoing.

Statistical analysis indicated significant associations between the expression of distinct proteins and the response rate to certain drugs. Proteins of the ErbB signaling pathway were differentially expressed in Carboplatin responders and non-responders. MEK1 upregulation was observed upon Cetuximab treatment in responders. We revealed an association between higher P-SRC expression and increased Gemcitabine response rates. This result fits to observations that describe coherence between SRC inhibition and reduced suppression of cell growth and survival in the presence of Gemcitabine in cancer cell lines.

We are now strengthening our results in various validation experiments. First, we selected seven target proteins based on RPPA analysis. Predictive targets for drug sensitivity are being analyzed to investigate the dependency between target protein activity, downstream signaling and response to distinct drugs in tumor cell lines in a pharmacogenomic approach. Therefore, we knocked down target genes in several NSCLC cell lines and unraveled changes in the drug sensitivity. Microarray and protein analyzes were carried out to study the mechanisms of target-drug association by investigating the downstream signaling upon target knockdown.

In summary, our study suggests predictive markers for the response of NSCLC tumors to certain drugs, which may be useful for therapy decisions towards a more efficient personalized treatment.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr A185.

Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn'

BACKGROUND

Network inference from high-throughput data has become an important means of current analysis of biological systems. For instance, in cancer research, the functional relationships of cancer related proteins, summarised into signalling networks are of central interest for the identification of pathways that influence tumour development. Cancer cell lines can be used as model systems to study the cellular response to drug treatments in a time-resolved way. Based on these kind of data, modelling approaches for the signalling relationships are needed, that allow to generate hypotheses on potential interference points in the networks.

RESULTS

We present the R-package 'ddepn' that implements our recent approach on network reconstruction from longitudinal data generated after external perturbation of network components. We extend our approach by two novel methods: a Markov Chain Monte Carlo method for sampling network structures with two edge types (activation and inhibition) and an extension of a prior model that penalises deviances from a given reference network while incorporating these two types of edges. Further, as alternative prior we include a model that learns signalling networks with the scale-free property.

CONCLUSIONS

The package 'ddepn' is freely available on R-Forge and CRAN http://ddepn.r-forge.r-project.org, http://cran.r-project.org. It allows to conveniently perform network inference from longitudinal high-throughput data using two different sampling based network structure search algorithms.

Time-resolved human kinome RNAi screen identifies a network regulating mitotic-events as early regulators of cell proliferation

Analysis of biological processes is frequently performed with the help of phenotypic assays where data is mostly acquired in single end-point analysis. Alternative phenotypic profiling techniques are desired where time-series information is essential to the biological question, for instance to differentiate early and late regulators of cell proliferation in loss-of-function studies. So far there is no study addressing this question despite of high unmet interests, mostly due to the limitation of conventional end-point assaying technologies. We present the first human kinome screen with a real-time cell analysis system (RTCA) to capture dynamic RNAi phenotypes, employing time-resolved monitoring of cell proliferation via electrical impedance. RTCA allowed us to investigate the dynamics of phenotypes of cell proliferation instead of using conventional end-point analysis. By introducing data transformation with first-order derivative, i.e. the cell-index growth rate, we demonstrate this system suitable for high-throughput screenings (HTS). The screen validated previously identified inhibitor genes and, additionally, identified activators of cell proliferation. With the information of time kinetics available, we could establish a network of mitotic-event related genes to be among the first displaying inhibiting effects after RNAi knockdown. The time-resolved screen captured kinetics of cell proliferation caused by RNAi targeting human kinome, serving as a resource for researchers. Our work establishes RTCA technology as a novel robust tool with biological and pharmacological relevance amenable for high-throughput screening.

Alcohol-induced neuronal death in central extended amygdala and pyriform cortex during the postnatal period of the rat

Mothers who consume alcohol during pregnancy may cause a neurotoxic syndrome defined as fetal alcohol spectrum disorder (FASD) in their offspring. This disorder is characterized by reduction in brain size, cognitive deficits and emotional/social disturbances. These alterations are thought to be caused by an alcohol-induced increase in apoptosis during neurodevelopment. Little is known about neuroapoptosis in the central extended amygdala and the pyriform cortex, which are key structures in emotional/social behaviors. The goal of this study was to determine the vulnerability of neuroapoptotic alcohol effects in those areas. Rats were administered alcohol (2.5g/kg s.c. at 0 and 2h) or saline on postnatal day (PND) 7, 15 and 20. The Amino-cupric-silver technique was used to evaluate neurodegeneration and immunohistochemistry to detect activated caspases 3-8 and 9 at 2h, 4, 6, 8, 12 and 24h after drug administration. We measured blood alcohol levels each hour, from 2 to 8h post second administration of alcohol in each of the ages studied. Results showed alcohol induced apoptotic neurodegeneration in the central extended amygdala on PND 7 and 15, and pyriform cortex on PND 7, 15 and 20. These structures showed activation of caspase 3 and 9 but not of caspase 8 suggesting that alcohol-induced apoptosis could occur by the intrinsic pathway. The pharmacokinetic differences between ages did not associate with the neurodegeneration age dependence. In conclusion, these limbic areas are damaged by alcohol, and each one has their own window of vulnerability during the postnatal period. The possible implications in emotional/social features in FASD are discussed.

Loss of aquaporin-4 expression and putative function in non-small cell lung cancer

Background

Aquaporins (AQPs) have been recognized to promote tumor progression, invasion, and metastasis and are therefore recognized as promising targets for novel anti-cancer therapies. Potentially relevant AQPs in distinct cancer entities can be determined by a comprehensive expression analysis of the 13 human AQPs.

Methods

We analyzed the presence of all AQP transcripts in 576 different normal lung and non-small cell lung cancer (NSCLC) samples using microarray data and validated our findings by qRT-PCR and immunohistochemistry.

Results

Variable expression of several AQPs (AQP1, -3, -4, and -5) was found in NSCLC and normal lung tissues. Furthermore, we identified remarkable differences between NSCLC subtypes in regard to AQP1, -3 and -4 expression. Higher transcript and protein levels of AQP4 in well-differentiated lung adenocarcinomas suggested an association with a more favourable prognosis. Beyond water transport, data mining of co-expressed genes indicated an involvement of AQP4 in cell-cell signalling, cellular movement and lipid metabolism, and underlined the association of AQP4 to important physiological functions in benign lung tissue.

Conclusions

Our findings accentuate the need to identify functional differences and redundancies of active AQPs in normal and tumor cells in order to assess their value as promising drug targets.

Dynamic deterministic effects propagation networks: learning signalling pathways from longitudinal protein array data

Motivation: Network modelling in systems biology has become an important tool to study molecular interactions in cancer research, because understanding the interplay of proteins is necessary for developing novel drugs and therapies. De novo reconstruction of signalling pathways from data allows to unravel interactions between proteins and make qualitative statements on possible aberrations of the cellular regulatory program. We present a new method for reconstructing signalling networks from time course experiments after external perturbation and show an application of the method to data measuring abundance of phosphorylated proteins in a human breast cancer cell line, generated on reverse phase protein arrays.

Results: Signalling dynamics is modelled using active and passive states for each protein at each timepoint. A fixed signal propagation scheme generates a set of possible state transitions on a discrete timescale for a given network hypothesis, reducing the number of theoretically reachable states. A likelihood score is proposed, describing the probability of measurements given the states of the proteins over time. The optimal sequence of state transitions is found via a hidden Markov model and network structure search is performed using a genetic algorithm that optimizes the overall likelihood of a population of candidate networks. Our method shows increased performance compared with two different dynamical Bayesian network approaches. For our real data, we were able to find several known signalling cascades from the ERBB signalling pathway.

Availability: Dynamic deterministic effects propagation networks is implemented in the R programming language and available at http://www.dkfz.de/mga2/ddepn/

Contact:c.bender@dkfz.de

Explicit memory bias for positively valenced body-related cues in women with binge eating disorder

Overweight women with and without binge eating disorder (BED) are characterized by a marked body dissatisfaction, which may in part be due to the negative comments about their weight. Weight-related teasing and discrimination is reported both by healthy overweight women and women with BED, whereas body dissatisfaction is markedly increased among women with BED. Therefore, a memory bias for negatively valenced body-related cues is suspected to occur as a mediating factor in women with BED. In an experimental study, 18 women with BED were compared to 18 overweight healthy female controls (HC) on a free recall task containing four word categories: positively valenced with and without body-related content and negatively valenced with and without body-related content. While both groups showed a bias towards negatively valenced shape-/weight-related words, women with BED retrieved positively valenced shape-/weight-related words significantly less often compared to overweight HC. Findings suggest that it may be the reduced ability to attend to positively valenced shape-/weight-related information, rather than the activation of negative body schemata that differentiates overweight women with BED from overweight women without BED. Results are discussed in the context of cognitive biases in the maintenance of body dissatisfaction.

Antiseptic efficacy and tolerance of tissue-tolerable plasma compared with two wound antiseptics on artificially bacterially contaminated eyes from commercially slaughtered pigs

AIM

To compare the tissue tolerance and efficacy of two wound antiseptics with tissue-tolerable plasma (TTP) on enucleated contaminated eyes from slaughtered pigs in order to draw consequences for the use of TTP on wounds.

METHOD

The corneas of extracted eyes were contaminated with Staphylococcus aureus or Pseudomonas aeruginosa. One and 10 min after application of 10% povidone (PVP)-iodine and 0.04% polyhexanide, respectively, the eyes were rinsed with inactivating solution. To test TTP, the plasma pen meandered over the eyes at a speed of 30 mm/s and a distance of 5 mm; the eyes were then rinsed with balanced salt solution. The reduction factor was calculated by the difference between the logarithm of colony-forming units in the rinse before and after antisepsis or TTP application.

RESULTS

The efficacy of TTP (reduction factor 2.4-2.9) was significantly higher (p < 0.001) than that of PVP-iodine and polyhexanide (reduction factor 1.7-2.1).

CONCLUSION

TTP is more effective than the tested wound antiseptics. The lack of histological damage to the eyes of slaughtered pigs would seem to make its use as a wound antiseptic a viable alternative. In contrast to antiseptics, it supplies additional energy in the form of heat, electric fields and radicals by TTP.