Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions

<p>Abstract</p> <p>Background</p> <p>Modern gene perturbation techniques, like RNA interference (RNAi), enable us to study effects of targeted interventions in cells efficiently. In combination with mRNA or protein expression data this allows to gain insights into the behavior of complex biological systems.</p> <p>Results</p> <p>In this paper, we propose Deterministic Effects Propagation Networks (DEPNs) as a special Bayesian Network approach to reverse engineer signaling networks from a combination of protein expression and perturbation data. DEPNs allow to reconstruct protein networks based on combinatorial intervention effects, which are monitored via changes of the protein expression or activation over one or a few time points. Our implementation of DEPNs allows for latent network nodes (i.e. proteins without measurements) and has a built in mechanism to impute missing data. The robustness of our approach was tested on simulated data. We applied DEPNs to reconstruct the <it>ERBB </it>signaling network in <it>de novo </it>trastuzumab resistant human breast cancer cells, where protein expression was monitored on Reverse Phase Protein Arrays (RPPAs) after knockdown of network proteins using RNAi.</p> <p>Conclusion</p> <p>DEPNs offer a robust, efficient and simple approach to infer protein signaling networks from multiple interventions. The method as well as the data have been made part of the latest version of the R package "nem" available as a supplement to this paper and via the Bioconductor repository.</p

A new analysis approach of epidermal growth factor receptor pathway activation patterns provides insights into cetuximab resistance mechanisms in head and neck cancer

The pathways downstream of the epidermal growth factor receptor (EGFR) have often been implicated to play crucial roles in the development and progression of various cancer types. Different authors have proposed models in cell lines in which they study the modes of pathway activities after perturbation experiments. It is prudent to believe that a better understanding of these pathway activation patterns might lead to novel treatment concepts for cancer patients or at least allow a better stratification of patient collectives into different risk groups or into groups that might respond to different treatments. Traditionally, such analyses focused on the individual players of the pathways. More recently in the field of systems biology, a plethora of approaches that take a more holistic view on the signaling pathways and their downstream transcriptional targets has been developed. Fertig et al. have recently developed a new method to identify patterns and biological process activity from transcriptomics data, and they demonstrate the utility of this methodology to analyze gene expression activity downstream of the EGFR in head and neck squamous cell carcinoma to study cetuximab resistance. Please see related article: http://www.biomedcentral.com/1471-2164/13/16

Boolean Modeling of Biochemical Networks

The use of modeling to observe and analyze the mechanisms of complex biochemical network function is becoming an important methodological tool in the systems biology era. Number of different approaches to model these networks have been utilized-- they range from analysis of static connection graphs to dynamical models based on kinetic interaction data. Dynamical models have a distinct appeal in that they make it possible to observe these networks in action, but they also pose a distinct challenge in that they require detailed information describing how the individual components of these networks interact in living cells. Because this level of detail is generally not known, dynamic modeling requires simplifying assumptions in order to make it practical. In this review Boolean modeling will be discussed, a modeling method that depends on the simplifying assumption that all elements of a network exist only in one of two states

Study of Anti-proliferative Activity of Cucurbitacins Inspired Estrone Analogs on Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is considered the third leading cause of death from cancer. Overall survival rate is significantly low, due to the emerging resistance to chemotherapeutic agents and lack of selectivity. Recent studies have demonstrated that epidermal growth factor receptor (EGFR) is a promising molecular target for cancer therapy, especially HCC. Current studies showed that cucurbitacins are potent anticancer compounds which target EGFR. This prompted us to investigate the antiproliferative activity of novel cucurbitacins inspired estrone analogs (CIEA) against sensitive and resistant HepG2 cell lines. Anti-proliferation activity of 20 CIEA analogs were examined against HepG2 using MTT assay and showed that antiproliferative activity of analogs MMA132, and MMA102 IC50 are 2μM, and 3 μM respectively in comparison to Erlotinib 25 μM. Study of the mechanism of anti-proliferation effects of these novel analogs was elucidated. Western blot analysis showed that MMA132, and MMA102 significantly inhibit EGFR/pEGFR, RAF/pRAF, MEK/pMEK, and ERK/PERK. Cell cycle analysis on HepG2 cell line revealed that MMA132 and MMA102 arrested the cells at G1 phase and inhibited the HepG2 cell migration after 24 hr. MMA132 induced apoptosis through activation of caspase 3,9 and inhibition of PARP. Treatment of HepG2-R (Erlotinib resistant) with MMA132 and MMA102 showed that these two novel drug candidates still possessing potent anti-proliferation activities against HepG2-R. Further characterization of the anti-proliferation of these lead compounds was demonstrated through mapping the change in EGFR signaling pathway (ERK, pERK, RAS, AKT and MEK) by western blot, cell cycle analysis, demonstrated that MMA132 and MMA102 stop the cell cycle of HepG2-R at G2 phase and inhibited cell migration after 48hrs. HepG2-R cell line significantly expressed MRP2 in comparing to sensitive cells. Moreover, MK571(MRP2 inhibitor) showed an inhibitory effect on resistant HepG2-R cancer cell lines. Combination of MMA132 with MK571 (13 μM and 15 μM respectively) showed a significant increase in the cytotoxicity of MK571 from 18.5 μM to 10 μM. In conclusion, our study documented the discovery of novel estrone analogs as potential drug candidates for treatment of HCC and promising chemotherapeutic agent toward HepG2 resistant to erlotinib

Microenvironmental Stiffness Enhances Glioma Cell Proliferation by Stimulating Epidermal Growth Factor Receptor Signaling

The aggressive and rapidly lethal brain tumor glioblastoma (GBM) is associated with profound tissue stiffening and genomic lesions in key members of the epidermal growth factor receptor (EGFR) pathway. Previous studies from our laboratory have shown that increasing microenvironmental stiffness in culture can strongly enhance glioma cell behaviors relevant to tumor progression, including proliferation, yet it has remained unclear whether stiffness and EGFR regulate proliferation through common or independent signaling mechanisms. Here we test the hypothesis that microenvironmental stiffness regulates cell cycle progression and proliferation in GBM tumor cells by altering EGFR-dependent signaling. We began by performing an unbiased reverse phase protein array screen, which revealed that stiffness modulates expression and phosphorylation of a broad range of signals relevant to proliferation, including members of the EGFR pathway. We subsequently found that culturing human GBM tumor cells on progressively stiffer culture substrates both dramatically increases proliferation and facilitates passage through the G1/S checkpoint of the cell cycle, consistent with an EGFR-dependent process. Western Blots showed that increasing microenvironmental stiffness enhances the expression and phosphorylation of EGFR and its downstream effector Akt. Pharmacological loss-of-function studies revealed that the stiffness-sensitivity of proliferation is strongly blunted by inhibition of EGFR, Akt, or PI3 kinase. Finally, we observed that stiffness strongly regulates EGFR clustering, with phosphorylated EGFR condensing into vinculin-positive focal adhesions on stiff substrates and dispersing as microenvironmental stiffness falls to physiological levels. Our findings collectively support a model in which tissue stiffening promotes GBM proliferation by spatially and biochemically amplifying EGFR signaling.National Institutes of Health (U.S.) (grant 1DP2OD004213)National Institutes of Health (U.S.) (grant 1U54CA143836)National Science Foundation (U.S.) (Grant CMMI PESO 1105539)National Institutes of Health (U.S.) (NRSA postdoctoral fellowship (1F32CA174361))National Cancer Institute (U.S.) (MD Anderson RPPA Core facility grant (2P30CA016672)

Triple-negative breast cancer: Present challenges and new perspectives

Contains fulltext : 83751.pdf (publisher's version ) (Open Access)21 p

Novel monoclonal antibodies targeting conformational ERBB2 epitopes

Ankara : The Department of Molecular Biology and Genetics and the Graduate School of Engineering and Science of Bilkent University, 2012.Thesis (Ph. D.) -- Bilkent University, 2012.Includes bibliographical references leaves 169-198.ERBB2 is a tyrosine kinase receptor which can act as homodimers or heterodimers with other members of the ERBB family. Nearly 30% of breast cancers overexpress ERBB2, which can be effectively targeted by anti-ERBB2 monoclonal antibodies. Trastuzumab directed against an epitope on subdomain IV of the extracellular domain (ECD) of ERBB2 is a clinically used therapeutics but the response rate is poor and acquired resistance is frequent. Pertuzumab that binds to subdomain II and inhibits receptor dimerization is another promising therapeutics under clinical trials. Anti-ERBB2 antibodies directed to novel epitopes are potentially useful tools for replacement and combinatorial therapies. We produced five new anti-ERBB2 antibodies, all directed against epitope(s) present only on the native ECD. They performed selective growth inhibitory effects depending on the level of ERBB2 expression and cellular background. When used alone, novel anti-ERBB2 antibodies displayed modest but significant growth inhibition on SK-BR-3, BT-474 and MDA-MB-361 cells with ERBB2 overexpression; while no detectable inhibition was observed on MCF-7 and T47D cells lacking ERBB2 amplification. When the antibodies were tested in combination with TNF-α, they acted synergistically on SK-BR-3 cells, producing upto 80% growth inhibition; but performed antagonistically on BT-474 cells. Detailed investigation of a representative antibody indicated G1-arrest as the main mechanism of the anti-proliferative effects exerted on SK-BR-3 cells. Antibody treatment induced permanent inhibition of DNA synthesis, leading to accumulation of cells at G1-phase; an effect which was accelerated in the presence of TNF-α. In addition, treated SK-BR-3 cells displayed inhibition of Akt and ERK1/2 phosphorylation leading to cyclin D1 accumulation and growth arrest, independently from TNF-α. Novel antibodies against conformational epitopes present on the extracellular domain of ERBB2 receptor may serve as new analytical and diagnostic tools, in addition to being potent anti-cancer bioactive molecules. Cell-dependent synergy and antagonism between anti-ERBB2 antibodies and TNF-α provide evidence for a complex interplay between ERBB2 and TNF-α signaling pathways. Such complexity may drastically affect the outcome of ERBB2-directed therapeutic interventions.Ceran, CeyhanPh.D