[Show abstract][Hide abstract] ABSTRACT: Gene set enrichment analysis (GSA) methods have been widely adopted by biological labs to analyze data and generate hypotheses for validation. Most of the existing comparison studies focus on whether the existing GSA methods can produce accurate P-values; however, practitioners are often more concerned with the correct gene-set ranking generated by the methods. The ranking performance is closely related to two critical goals associated with GSA methods: the ability to reveal biological themes and ensuring reproducibility, especially for small-sample studies. We have conducted a comprehensive simulation study focusing on the ranking performance of seven representative GSA methods. We overcome the limitation on the availability of real data sets by creating hybrid data models from existing large data sets. To build the data model, we pick a master gene from the data set to form the ground truth and artificially generate the phenotype labels. Multiple hybrid data models can be constructed from one data set and multiple data sets of smaller sizes can be generated by resampling the original data set. This approach enables us to generate a large batch of data sets to check the ranking performance of GSA methods. Our simulation study reveals that for the proposed data model, the Q2 type GSA methods have in general better performance than other GSA methods and the global test has the most robust results. The properties of a data set play a critical role in the performance. For the data sets with highly connected genes, all GSA methods suffer significantly in performance.
Cancer informatics 02/2014; 13(Suppl 1):1-16. DOI:10.4137/CIN.S13305
[Show abstract][Hide abstract] ABSTRACT: Insensitivity to standard clinical interventions, including chemotherapy, radiotherapy and tyrosine kinase inhibitor (TKI) treatment, remains a substantial hindrance towards improving the prognosis of patients with non-small cell lung cancer (NSCLC). The molecular mechanism of therapeutic resistance remains poorly understood. The TNF-like weak inducer of apoptosis (TWEAK)-FGF-inducible 14 (Fn14) signaling axis is known to promote cancer cell survival via NF-kappaB activation and the up-regulation of pro-survival Bcl-2 family members. Here, a role was determined for TWEAK-Fn14 pro-survival signaling in NSCLC through the up-regulation of myeloid cell leukemia sequence 1 (Mcl-1). Mcl-1 expression significantly correlated with Fn14 expression, advanced NSCLC tumor stage, and poor patient prognosis in human primary NSCLC tumors. TWEAK stimulation of NSCLC cells induced NF-kappaB-dependent Mcl-1 protein expression and conferred Mcl-1-dependent chemo- and radio-resistance. Depletion of Mcl-1 via siRNA or pharmacological inhibition of Mcl-1, using EU-5148, sensitized TWEAK-treated NSCLC cells to cisplatin- or radiation-mediated inhibition of cell survival. Moreover, EU-5148 inhibited cell survival across a panel of NSCLC cell lines. In contrast, inhibition of Bcl-2/Bcl-xL function had minimal effect on suppressing TWEAK-induced cell survival. Collectively, these results position TWEAK-Fn14 signaling through Mcl-1 as a significant mechanism for NSCLC tumor cell survival, and open new therapeutic avenues to abrogate the high mortality rate seen in NSCLC. Implications: The TWEAK-Fn14 signaling axis enhances lung cancer cell survival and therapeutic resistance through Mcl-1, positioning both TWEAK-Fn14 and Mcl-1 as therapeutic opportunities in lung cancer.
Molecular Cancer Research 01/2014; 12(4). DOI:10.1158/1541-7786.MCR-13-0458 · 4.50 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In this paper, a model that combining cell population and genetic regulation within a single cell by using stochastic hybrid systems is proposed. The objective is to study the response of a population of cancer cells to various drugs that targeting the proliferation and survival pathways. The proposed model captures both the dynamics of the cell population and the dynamics of gene regulations within each individual cell. We use drug Lapatinib applied to colon cancer cell line HCT-116 as an example to validate the proposed model. Simulation results demonstrate the phenomena that observed in TGen experiments.
2013 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS); 11/2013
[Show abstract][Hide abstract] ABSTRACT: Background
Identifying similarities and differences in the molecular constitutions of various types of cancer is one of the key challenges in cancer research. The appearances of a cancer depend on complex molecular interactions, including gene regulatory networks and gene-environment interactions. This complexity makes it challenging to decipher the molecular origin of the cancer. In recent years, many studies reported methods to uncover heterogeneous depictions of complex cancers, which are often categorized into different subtypes. The challenge is to identify diverse molecular contexts within a cancer, to relate them to different subtypes, and to learn underlying molecular interactions specific to molecular contexts so that we can recommend context-specific treatment to patients.
In this study, we describe a novel method to discern molecular interactions specific to certain molecular contexts. Unlike conventional approaches to build modular networks of individual genes, our focus is to identify cancer-generic and subtype-specific interactions between contextual gene sets, of which each gene set share coherent transcriptional patterns across a subset of samples, termed contextual gene set. We then apply a novel formulation for quantitating the effect of the samples from each subtype on the calculated strength of interactions observed. Two cancer data sets were analyzed to support the validity of condition-specificity of identified interactions. When compared to an existing approach, the proposed method was much more sensitive in identifying condition-specific interactions even in heterogeneous data set. The results also revealed that network components specific to different types of cancer are related to different biological functions than cancer-generic network components. We found not only the results that are consistent with previous studies, but also new hypotheses on the biological mechanisms specific to certain cancer types that warrant further investigations.
The analysis on the contextual gene sets and characterization of networks of interaction composed of these sets discovered distinct functional differences underlying various types of cancer. The results show that our method successfully reveals many subtype-specific regions in the identified maps of biological contexts, which well represent biological functions that can be connected to specific subtypes.
[Show abstract][Hide abstract] ABSTRACT: Two issues are critical to the development of effective cancer-drug combinations. First, it is necessary to determine common combinations of alterations that exert strong control over proliferation and survival regulation for the general type of cancer being considered. Second, it is necessary to have a drug testing method that allows one to assess the variety of responses that can be provoked by drugs acting at key points in the cellular processes dictating proliferation and survival. Utilizing a previously reported GFP (green fluorescent protein) reporter-based technology that provides dynamic measurements of individual reporters in individual cells, the present paper proposes a dynamical systems approach to these issues. It involves a three-state experimental design: (1) formulate an oncologic pathway model of relevant processes; (2) perturb the pathways with the test drug and drugs with known effects on components of the pathways of interest; and (3) measure process activity indicators at various points on cell populations. This design addresses the fundamental problems in the design and analysis of combinatorial drug treatments. We apply the dynamical approach to three issues in the context of colon cancer cell lines: (1) identification of cell subpopulations possessing differing degrees of drug sensitivity; (2) the consequences of different drug dosing strategies on cellular processes; and (3) assessing the consequences of combinatorial versus monotherapy. Finally, we illustrate how the dynamical systems approach leads to a mechanistic hypothesis in the colon cancer HCT116 cell line.
Journal of Biological Systems 02/2013; 20(04). DOI:10.1142/S0218339012400049 · 0.96 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: For science, theoretical or applied, to significantly advance, researchers must use the most appropriate mathematical methods. A century and a half elapsed between Newton's development of the calculus and Laplace's development of celestial mechanics. One cannot imagine the latter without the former. Today, more than three-quarters of a century has elapsed since the birth of stochastic systems theory. This article provides a perspective on the utilization of systems theory as the proper vehicle for the development of systems biology and its application to complex regulatory diseases such as cancer.
Cancer informatics 10/2012; 11:185-90. DOI:10.4137/CIN.S10630
[Show abstract][Hide abstract] ABSTRACT: Background
Molecularly targeted agents (MTAs) are increasingly used for cancer treatment, the goal being to improve the efficacy and selectivity of cancer treatment by developing agents that block the growth of cancer cells by interfering with specific targeted molecules needed for carcinogenesis and tumor growth. This approach differs from traditional cytotoxic anticancer drugs. The lack of specificity of cytotoxic drugs allows a relatively straightforward approach in preclinical and clinical studies, where the optimal dose has usually been defined as the "maximum tolerated dose" (MTD). This toxicity-based dosing approach is founded on the assumption that the therapeutic anticancer effect and toxic effects of the drug increase in parallel as the dose is escalated. On the contrary, most MTAs are expected to be more selective and less toxic than cytotoxic drugs. Consequently, the maximum therapeutic effect may be achieved at a "biologically effective dose" (BED) well below the MTD. Hence, dosing study for MTAs should be different from cytotoxic drugs. Enhanced efforts to molecularly characterize the drug efficacy for MTAs in preclinical models will be valuable for successfully designing dosing regimens for clinical trials.
A novel preclinical model combining experimental methods and theoretical analysis is proposed to investigate the mechanism of action and identify pharmacodynamic characteristics of the drug. Instead of fixed time point analysis of the drug exposure to drug effect, the time course of drug effect for different doses is quantitatively studied on cell line-based platforms using system identification, where tumor cells' responses to drugs through the use of fluorescent reporters are sampled over a time course. Results show that drug effect is time-varying and higher dosages induce faster and stronger responses as expected. However, the drug efficacy change along different dosages is not linear; on the contrary, there exist certain thresholds. This kind of preclinical study can provide valuable suggestions about dosing regimens for the in vivo experimental stage to increase productivity.
[Show abstract][Hide abstract] ABSTRACT: In early drug development, it would be beneficial to be able to identify those dynamic patterns of gene response that indicate that drugs targeting a particular gene will be likely or not to elicit the desired response. One approach would be to quantitate the degree of similarity between the responses that cells show when exposed to drugs, so that consistencies in the regulation of cellular response processes that produce success or failure can be more readily identified.
We track drug response using fluorescent proteins as transcription activity reporters. Our basic assumption is that drugs inducing very similar alteration in transcriptional regulation will produce similar temporal trajectories on many of the reporter proteins and hence be identified as having similarities in their mechanisms of action (MOA). The main body of this work is devoted to characterizing similarity in temporal trajectories/signals. To do so, we must first identify the key points that determine mechanistic similarity between two drug responses. Directly comparing points on the two signals is unrealistic, as it cannot handle delays and speed variations on the time axis. Hence, to capture the similarities between reporter responses, we develop an alignment algorithm that is robust to noise, time delays and is able to find all the contiguous parts of signals centered about a core alignment (reflecting a core mechanism in drug response). Applying the proposed algorithm to a range of real drug experiments shows that the result agrees well with the prior drug MOA knowledge.
The R code for the RLCSS algorithm is available at http://gsp.tamu.edu/Publications/supplementary/zhao12a.
[Show abstract][Hide abstract] ABSTRACT: Learning or inferring networks of genomic regulation specific to a cellular state, such as a subtype of tumor, can yield insight above and beyond that resulting from networklearning techniques which do not acknowledge the adaptive nature of the cellular system. In this study we show that Cellular Context Mining, which is based on a mathematical model of contextual genomic regulation, produces gene regulatory networks (GRNs) from steady-state expression microarray data which are specific to the varying cellular contexts hidden in the data; we show that these GRNs not only model gene interactions, but that they are also readily annotated with context-specific genomic information. We propose that these context-specific GRNs provide advantages over other techniques, such as clustering and Bayesian networks, when applied to gene expression data of cancer patients. 1.
[Show abstract][Hide abstract] ABSTRACT: High-content cell imaging based on fluorescent protein reporters has recently been used to track the transcriptional activities of multiple genes under different external stimuli for extended periods. This technology enhances our ability to discover treatment-induced regulatory mechanisms, temporally order their onsets and recognize their relationships. To fully realize these possibilities and explore their potential in biological and pharmaceutical applications, we introduce a new data processing procedure to extract information about the dynamics of cell processes based on this technology. The proposed procedure contains two parts: (1) image processing, where the fluorescent images are processed to identify individual cells and allow their transcriptional activity levels to be quantified; and (2) data representation, where the extracted time course data are summarized and represented in a way that facilitates efficient evaluation. Experiments show that the proposed procedure achieves fast and robust image segmentation with sufficient accuracy. The extracted cellular dynamics are highly reproducible and sensitive enough to detect subtle activity differences and identify mechanisms responding to selected perturbations. This method should be able to help biologists identify the alterations of cellular mechanisms that allow drug candidates to change cell behavior and thereby improve the efficiency of drug discovery and treatment design.
[Show abstract][Hide abstract] ABSTRACT: To effectively intervene when cells are trapped in pathological modes of operation it is necessary to build models that capture relevant network structure and include char-acterization of dynamical changes within the system. The model must be of sufficient detail that it facilitates the selection of intervention points where pathological cell behav-ior arising from improper regulation can be stopped. What is known about this type of cellular decision-making is consistent with the general expectations associated with any kind of decision-making operation. If the result of a decision at one node is seri-ally transmitted to other nodes, resetting their states, then the process may suffer from mechanistic inefficiencies of transmission or from blockage or activation of transmission through the action of other nodes acting on the same node. A standard signal-processing network model, Bayesian networks, can model these properties. This paper employs a Bayesian tree model to characterize conditional pathway logic and quantify the effects of different branching patterns, signal transmission efficiencies and levels of alternate or redundant inputs. In particular, it characterizes master genes and canalizing genes within the quantitative framework. The model is also used to examine what inferences about the network structure can be made when perturbations are applied to various points in the network.
Journal of Biological Systems 12/2011; 19(04). DOI:10.1142/S0218339011004123 · 0.96 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: MOTIVATION: Cancer encompasses various diseases associated with loss of cell cycle control, leading to uncontrolled cell proliferation and/or reduced apoptosis. Cancer is usually caused by malfunction(s) in the cellular signaling pathways. Malfunctions occur in different ways and at different locations in a pathway. Consequently, therapy design should first identify the location and type of malfunction to arrive at a suitable drug combination. RESULTS: We consider the growth factor (GF) signaling pathways, widely studied in the context of cancer. Interactions between different pathway components are modeled using Boolean logic gates. All possible single malfunctions in the resulting circuit are enumerated and responses of the different malfunctioning circuits to a 'test' input are used to group the malfunctions into classes. Effects of different drugs, targeting different parts of the Boolean circuit, are taken into account in deciding drug efficacy, thereby mapping each malfunction to an appropriate set of drugs.
[Show abstract][Hide abstract] ABSTRACT: Combination chemotherapies play an important role in clinical cancer treatment. We have previously developed a microfluidic high-throughput drug screening platform and used it for the screening of prostate cancer sensitizing agents. We have further developed the system into a fully automated live cell array platform with uniform cell seeding for better control, and used the platform to investigate the gene expression regulation of colorectal cancer cells in response to combination cancer drug treatment. The results showed significant drug effects on the proliferation of the HCT116 colorectal cancer cells, demonstrating the potential of this microfluidic device as a high-throughput combination chemotherapeutic drug-screening platform.
[Show abstract][Hide abstract] ABSTRACT: A novel preclinical model combining experimental methods and theoretical analysis is proposed to investigate the mechanism of action and identify pharmacodynamic characteristic of a drug. Instead of fixed time point analysis of the drug exposure to drug effect, the time course of drug effect for different doses are quantitatively studied on cell line-based platforms using Kalman filter, where tumor cells' responses to drugs through the use of fluorescent reporters are sampled frequently over a time-course. It is expected that such preclinical study will provide valuable suggestions about dosing regimens for in vivo experimental stage to increase productivity.
[Show abstract][Hide abstract] ABSTRACT: Cancer encompasses various diseases associated with loss of cell-cycle control, leading to uncontrolled cell proliferation and/or reduced apoptosis. Cancer is usually caused by malfunction(s) in the cellular signaling pathways. Malfunctions occur in different ways and at different locations in a pathway. Consequently, therapy design should first identify the location and type of malfunction and then arrive at a suitable drug combination. We consider the growth factor (GF) signaling pathways, widely studied in the context of cancer. Interactions between different pathway components are modeled using Boolean logic gates. All possible single malfunctions in the resulting circuit are enumerated and responses of the different malfunctioning circuits to a ‘test’ input are used to group the malfunctions into classes. Effects of different drugs, targeting different parts of the Boolean circuit, are taken into account in deciding drug efficacy, thereby mapping each malfunction to an appropriate set of drugs.
[Show abstract][Hide abstract] ABSTRACT: We utilize a tree-structured Bayesian network to characterize and detect master and canalizing genes via the coefficient of determination (CoD). Master genes possess strong regulation over groups of genes, whereas canalizing genes take over the regulation of large cohorts under certain cell conditions. While related, the two concepts are not the same and the analytic measures we employ reveal that difference. We also consider hypothesis testing for successful drug intervention in the framework of the Bayesian model.
Genomic Signal Processing and Statistics (GENSIPS), 2011 IEEE International Workshop on; 01/2011
[Show abstract][Hide abstract] ABSTRACT: This paper proposes a framework to study the drug effect at the molecular level in order to address the following question of current interest in the drug community: Given a fixed total delivered drug, which is better, frequent small or infrequent large drug dosages? A hybrid system model is proposed to link the drug's pharmacokinetic and pharmacodynamic information, and allows the drug effects for different dosages and treatment schedules to be compared. A hybrid model facilitates the modeling of continuous quantitative changes that leads to discrete transitions. An optimal dosage-frequency regimen and the necessary and sufficient conditions for the drug to be effective are obtained analytically when the drug is designed to control a target gene. Then, we extend the analysis to the case where the target gene is part of a genetic regulatory network. A crucial observation is that there exists a "sweet spot," defined as the "drug efficacy region (DER)" in this paper, for certain dosage and frequency arrangements given the total delivered drug. This paper quantifies the therapeutic benefits of dosage regimen lying within the DER. Simulations are performed using MATLAB/SIMULINK to validate the analytical results.