A systems biology approach for the study of cumulative oncogenes with applications to the MAPK signal transduction pathway

NF-kB in Signaling Patterns and Its Temporal Dynamics Encode/Decode Human Diseases

Defects in signaling pathways are the root cause of many disorders. These malformations come in a wide variety of types, and their causes are also very diverse. Some of these flaws can be brought on by pathogenic organisms and viruses, many of which can obstruct signaling processes. Other illnesses are linked to malfunctions in the way that cell signaling pathways work. When thinking about how errors in signaling pathways might cause disease, the idea of signalosome remodeling is helpful. The signalosome may be conveniently divided into two types of defects: phenotypic remodeling and genotypic remodeling. The majority of significant illnesses that affect people, including high blood pressure, heart disease, diabetes, and many types of mental illness, appear to be caused by minute phenotypic changes in signaling pathways. Such phenotypic remodeling modifies cell behavior and subverts normal cellular processes, resulting in illness. There has not been much progress in creating efficient therapies since it has been challenging to definitively confirm this connection between signalosome remodeling and illness. The considerable redundancy included into cell signaling systems presents several potential for developing novel treatments for various disease conditions. One of the most important pathways, NF-κB, controls several aspects of innate and adaptive immune responses, is a key modulator of inflammatory reactions, and has been widely studied both from experimental and theoretical perspectives. NF-κB contributes to the control of inflammasomes and stimulates the expression of a number of pro-inflammatory genes, including those that produce cytokines and chemokines. Additionally, NF-κB is essential for controlling innate immune cells and inflammatory T cells' survival, activation, and differentiation. As a result, aberrant NF-κB activation plays a role in the pathogenesis of several inflammatory illnesses. The activation and function of NF-κB in relation to inflammatory illnesses was covered here, and the advancement of treatment approaches based on NF-κB inhibition will be highlighted. This review presents the temporal behavior of NF-κB and its potential relevance in different human diseases which will be helpful not only for theoretical but also for experimental perspectives.

Impact of accumulated alterations in driver and passenger genes on response to radiation therapy

OBJECTIVE

Although various single genetic factors have been shown to affect radiosensitivity, high-throughput DNA sequencing analyses have revealed complex genomic landscapes in many cancer types. The aim of this study is to elucidate the association between accumulated alterations in driver and passenger genes and radiation therapy response.

METHODS

We used 59 human solid cancer cell lines derived from 11 organ sites. Radiation-induced cell death was measured using a standard colony-forming assay delivered as a single dose ranging from 0 to 12 Gy. Comprehensive genomic data for the cell lines were acquired from the Catalogue Of Somatic Mutations In Cancer v. 80. Random forest classifiers were constructed to predict radioresistant phenotypes using genomic features. The Cancer Genome Atlas data sets were used to evaluate the clinical impact of the genomic feature following radiotherapy.

RESULTS

The 59 cancer cell lines harbored either nucleotide variations or copy number variations in a median of 157 genes per cell. Radiosensitivity of the cancer cells was correlated with neither the number of driver gene mutations nor the number of passenger gene mutations. However, the proportion of driver gene alterations to total gene alterations in gene sets selected from the Kyoto Encyclopedia Genes and Genomes predicted radioresistant cells with sensitivity of 85% and specificity of 73%. High probability of radioresistance predicted by the model was associated with worse overall survival following definitive radiotherapy in patients of The Cancer Genome Atlas data sets.

CONCLUSION

Cellular radiosensitivity was associated with the proportion of driver to total gene alterations in the selected oncogenic pathways, which may be a biomarker candidate for response to radiation therapy.

ADVANCES IN KNOWLEDGE

These findings suggest that accumulated alterations in not only driver genes but also passenger genes affect radiosensitivity.

Identification of Critical Molecular Components in a Multiscale Cancer Model Based on the Integration of Monte Carlo, Resampling, and ANOVA

To date, parameters defining biological properties in multiscale disease models are commonly obtained from a variety of sources. It is thus important to examine the influence of parameter perturbations on system behavior, rather than to limit the model to a specific set of parameters. Such sensitivity analysis can be used to investigate how changes in input parameters affect model outputs. However, multiscale cancer models require special attention because they generally take longer to run than does a series of signaling pathway analysis tasks. In this article, we propose a global sensitivity analysis method based on the integration of Monte Carlo, resampling, and analysis of variance. This method provides solutions to (1) how to render the large number of parameter variation combinations computationally manageable, and (2) how to effectively quantify the sampling distribution of the sensitivity index to address the inherent computational intensity issue. We exemplify the feasibility of this method using a two-dimensional molecular-microscopic agent-based model previously developed for simulating non-small cell lung cancer; in this model, an epidermal growth factor (EGF)-induced, EGF receptor-mediated signaling pathway was implemented at the molecular level. Here, the cross-scale effects of molecular parameters on two tumor growth evaluation measures, i.e., tumor volume and expansion rate, at the microscopic level are assessed. Analysis finds that ERK, a downstream molecule of the EGF receptor signaling pathway, has the most important impact on regulating both measures. The potential to apply this method to therapeutic target discovery is discussed.

Protein phosphatase 2A subunit gene haplotypes and proliferative breast disease modify breast cancer risk

BACKGROUND

Protein phosphatase 2A (PP2A) is a major cellular phosphatase and plays key regulatory roles in growth, differentiation, and apoptosis. Women who are diagnosed with benign proliferative breast disease are at increased risk for the subsequent development of breast cancer.

METHODS

The authors evaluated genetic variation of PP2A holoenzyme subunits for their potential contribution to breast cancer risk. A nested case-control investigation was performed on a cohort of women who had a history of benign breast disease. The women were followed for an average of 18 years, and DNA prepared from the original archival benign breast biopsy (1954-1995) was available for 450 women who were diagnosed with breast cancer on follow-up and for 890 of 900 women in a control group who were matched on race, age, and year of entry biopsy.

RESULTS

Single allele-based and haplotype-based tests of association were conducted with assessment of significance by permutation testing. Significant risk and protective haplotypes of the PP2A structural/regulatory subunit A alpha isoform (PPP2R1A) were identified and had odds ratios of 1.63 (95% confidence interval [CI], 1.3-2.1) and 0.55 (95% CI, 0.41-0.76), respectively. These odds ratios remained significant after the analysis was adjusted for multiple comparisons. Women who had both the PPP2R1A risk haplotype and a history of proliferative breast disease had an odds ratio of 2.44 (95% CI, 1.7-3.5) for the subsequent development of breast cancer. The effects of haplotypes for 2 PP2A regulatory subunit genes, PP2 regulatory subunit B alpha isoform (PPP2R2A) and PP2A regulatory subunit B' epsilon isoform (PPP2R5E) on breast cancer risk were nominally significant but did not remain significant after the analysis was adjusted for multiple comparisons.

CONCLUSIONS

The current findings supported the previously hypothesized role of PP2A as a tumor suppressor gene in breast cancer.

Signaling perturbations induced by invading H. pylori proteins in the host epithelial cells: a mathematical modeling approach

Helicobacter pylori (H. pylori), a gram-negative bacterium, infects the stomach of approximately 50% of the world population. H. pylori infection is a risk factor for developing chronic gastric ulcers and gastric cancer. The bacteria produce two main cytotoxic proteins: Vacuolating cytotoxin A (VacA) and Cytotoxin-Associated gene A (CagA). When these proteins enter the host cell they interfere with the host MAP Kinase and Apoptosis signaling pathways leading to aberrant cell growth and premature apoptosis. The present study expanded existing quantitative models of the MAP Kinase and Apoptosis signaling pathways to take into account the protein interactions across species using the CellDesigner tool. The resulting network contained hundreds of differential equations in which the coefficients for the biochemical rate constants were estimated from previously published studies. The effect of VacA and CagA on the function of this network were simulated by increasing levels of bacterial load. Simulations showed that increasing bacterial load affected the MAP Kinase signaling in a dose dependant manner. The introduction of CagA decreased the activation time of mapK signaling and extended activation indefinitely despite normal cellular activity to deactivate the protein. Introduction of VacA produced a similar response in the apoptosis pathway. Bacterial load activated both pathways even in the absence of external stimulation. Time course of emergence of transcription factors associated with cell division and cell death predicted by our simulation showed close agreement with that determined from a publicly accessible microarray data set of H. pylori infected stomach epithelium. The quantitative model presented in this study lays the foundation for investigating the affects of single nucleotide polymorphisms (SNPs) on the efficiency of drug treatment.

Novel targeted therapies in epithelial ovarian cancer: from basic research to the clinic

The development of new molecularly targeted therapies represents a high priority for the treatment of epithelial ovarian cancer. P-glycoprotein overexpression has been associated with multidrug resistance, and the use of multidrug resistance modulators, such as valspodar, is being explored in combination with chemotherapy. Human epidermal receptor (HER) family members are attractive targets for biological therapies. The addition of erlotinib or cetuximab to first-line paclitaxel- plus carboplatin-based chemotherapy is feasible and well tolerated. Gefitinib is able to inhibit the proliferation of ovarian clear-cell carcinoma in in vitro and in vivo experimental models. Single-agent trastuzumab has a limited value for recurrent epithelial ovarian cancer owing to the low frequency of HER2 overexpression and the low rate of objective responses among HER2-overexpressing patients. A Gynecologic Oncology Group Phase II trial of the proteasome inhibitor bortezomib in recurrent epithelial ovarian cancer is currently ongoing, and the combination of bortezomib and chemotherapeutic agents should be assessed. The mammalian target of rapamycin (mTOR) plays an important role in stimulating the translation of mRNAs encoding key proteins for cell growth and angiogenesis, and mTOR inhibitors, such as AP-23573 (ARIAD), deserve to be tested in selected epithelial ovarian cancer patients. The addition of intraperitoneal treatment with adenovirus containing human wild-type p53 to standard paclitaxel- plus carboplatin-based chemotherapy failed to improve the clinical outcome of patients with mutated p53 epithelial ovarian cancer. The Gynecologic Oncology Group is conducting a Phase II trial of single-agent bevacizumab (antivascular endothelial growth factor monoclonal antibody) in platinum-resistant disease. In conclusion, emerging drugs for epithelial ovarian cancer include agents designed to overcome chemoresistance, HER-targeting agents, proteasome inhibitors, mTOR inhibitors and angiogenesis inhibitors. A new paradigm of treatment could consist of chemotherapy combined with a biological agent for six cycles, and followed by chronic maintenance therapy with the biological agent alone. Advances in genomics and proteomics will elucidate the molecular mechanisms of ovarian carcinogenesis, which will hopefully lead to individualized molecular medicine in the next years.