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1.  Dynamics of Short-Term Gene Expression Profiling in Liver Following Thermal Injury 
The Journal of Surgical Research  2011;176(2):549-558.
Background
Severe trauma, including burns, triggers a systemic response that significantly impacts on the liver, which plays a key role in the metabolic and immune responses aimed at restoring homeostasis. While many of these changes are likely regulated at the gene expression level, there is a need to better understand the dynamics and expression patterns of burn injury-induced genes in order to identify potential regulatory targets in the liver. Herein we characterized the response within the first 24 h in a standard animal model of burn injury using a time series of microarray gene expression data.
Methods
Rats were subjected to a full thickness dorsal scald burn injury covering 20% of their total body surface area while under general anesthesia. Animals were saline resuscitated and sacrificed at defined time points (0, 2, 4, 8, 16, and 24 h). Liver tissues were explanted and analyzed for their gene expression profiles using microarray technology. Sham controls consisted of animals handled similarly but not burned. After identifying differentially expressed probesets between sham and burn conditions over time, the concatenated data sets corresponding to these differentially expressed probesets in burn and sham groups were combined and analyzed using a “consensus clustering” approach.
Results
The clustering method of expression data identified 621 burn-responsive probesets in 4 different co-expressed clusters. Functional characterization revealed that these 4 clusters are mainly associated with pro-inflammatory response, anti-inflammatory response, lipid biosynthesis, and insulin-regulated metabolism. Cluster 1 pro-inflammatory response is rapidly up-regulated (within the first 2 h) following burn injury, while Cluster 2 anti-inflammatory response is activated later on (around 8 h post burn). Cluster 3 lipid biosynthesis is downregulated rapidly following burn, possibly indicating a shift in the utilization of energy sources to produce acute phase proteins which serve the anti-inflammatory response. Cluster 4 insulin-regulated metabolism was down-regulated late in the observation window (around 16 h postburn), which suggests a potential mechanism to explain the onset of hypermetabolism, a delayed but well-known response that is characteristic of severe burns and trauma with potential adverse outcome.
Conclusions
Simultaneous analysis and comparison of gene expression profiles for both burn and sham control groups provided a more accurate estimation of the activation time, expression patterns, and characteristics of a certain burn-induced response based on which the cause-effect relationship among responses were revealed.
doi:10.1016/j.jss.2011.09.052
PMCID: PMC3319855  PMID: 22099593
Burn; gene expression; microarray; inflammation; liver
2.  Dynamics of hepatic gene expression profile in a rat cecal ligation and puncture model 
The Journal of Surgical Research  2011;176(2):583-600.
Background
Sepsis remains a major clinical challenge in intensive care units. The difficulty in developing new and more effective treatments for sepsis exemplifies our incomplete understanding of the underlying pathophysiology of it. One of the more widely used rodent models for studying polymicrobial sepsis is cecal ligation and puncture (CLP). While a number of CLP studies investigated the ensuing systemic inflammatory response, they usually focus on a single time point post CLP and therefore fail to describe the dynamics of the response. Furthermore, previous studies mostly use surgery without infection (herein referred to as Sham CLP, SCLP) as a control for the CLP model, however SCLP represents an aseptic injurious event that also stimulates a systemic inflammatory response. Thus, there is a need to better understand the dynamics and expression patterns of both injury- and sepsis- induced gene expression alterations to identify potential regulatory targets. In this direction, we characterized the response of the liver within the first 24 h in a rat model of SCLP and CLP using a time series of microarray gene expression data.
Methods
Rats were randomly divided into three groups, sham, SCLP and CLP. Rats in SCLP group are subjected to laparotomy, cecal ligation and puncture while those in CLP group are subjected to the similar procedures without cecal ligation and puncture. Animals were saline resuscitated and sacrificed at defined time points (0, 2, 4, 8, 16, and 24 h). Liver tissues were explanted and analyzed for their gene expression profiles using microarray technology. Unoperated animals (Sham) serve as negative controls. After identifying differentially expressed probesets between sham and SCLP or CLP conditions over time, the concatenated data sets corresponding to these differentially expressed probesets in sham and SCLP or CLP groups were combined and analyzed using a “consensus clustering” approach. Promoters of genes that share common characteristics were extracted, and compared with gene batteries comprised of co expressed genes in order to identify putatative transcription factors which could be responsible for the co regulation of those genes.
Results
The SCLP/CLP genes whose expression patterns significantly changed compared to sham over time were identified, clustered, and finally analyzed for pathway enrichment. Our results indicate that both CLP and SCLP triggered the activation of a pro-inflammatory response, enhanced synthesis of acute-phase proteins, increased metabolism and tissue damage markers. Genes triggered by CLP which can be directly linked to bacteria removal functions were absent in SCLP injury. In addition, genes relevant to oxidative stress induced damage were unique to CLP injury, which may be due to the increased severity of CLP injury vs. SCLP injury. Pathway enrichment identified pathways with similar functionality but different dynamics in the two injury models, indicating that the functions controlled by those pathways are under the influence of different transcription factors and regulatory mechanisms. Putatively identified transcription factors, notably including CREB, NF-KB and STAT, were obtained through analysis of the promoter regions in the SCLP/CLP genes. Our results show that while transcription factors such as NF-KB, HOMF, and GATA were common in both injuries for the IL-6 signaling pathway, there were many other transcription factors associated with that pathway which were unique to CLP, including FKHD, HESF and IRFF. There were 17 transcription factors that were identified as important in at least 2 pathways in the CLP injury, but only 7 transcription factors with that property in the SCLP injury. This also supports the hypothesis of unique regulatory modules that govern the pathways present in both the CLP and SCLP response.
Conclusions
By using microarrays to assess multiple genes in a high throughput manner, we demonstrate that an inflammatory response involving different dynamics and different genes is triggered by SCLP and CLP. From our analysis of the CLP data, the key characteristics of sepsis are a pro inflammatory response which drives hypermetabolism, immune cell activation, and damage from oxidative stress. This contrasts with SCLP, which triggers a modified inflammatory response leading to no immune cell activation, decreased detoxification potential, and hyper metabolism. Many of the identified transcription factors that drive the CLP-induced response are not found in the SCLP group, suggesting that SCLP and CLP induce different types of inflammatory responses via different regulatory pathways.
doi:10.1016/j.jss.2011.11.1031
PMCID: PMC3368040  PMID: 22381171
sepsis; trauma; gene expression; transcription factor; microarray; inflammation; liver
3.  Long-term Dynamic Profiling of Inflammatory Mediators in Double-hit Burn and Sepsis Animal Models 
Cytokine  2012;58(2):307-315.
Burn injuries together with its subsequent complications, mainly bacterial infections originating from gastrointestinal tract, activate the host immune system through stimulation of a series of local and systemic responses, including the release of inflammatory mediators. To gain a more comprehensive understanding of these complex physiological changes and to propose therapeutic approaches to combat the deleterious consequences of burn and septic shocks, it is essential to analyze animal models of burn and sepsis. In this study, we analyzed the long term profiles of cytokines and chemokines in rat models which received burn injury followed two days later by cecal ligation and puncture (CLP) to induce sepsis and were sacrificed at different time points within 10 days (0, 1, 2, 3, 4, 7 and 10 days). It was observed that MCP-1 concentrations were elevated in all animal models following the burn injury or CLP treatment. IP-10 concentration was persistently decreased after CLP or sham-CLP treatments. GRO/KC concentration was also increased following the burn injury and CLP. It was elucidated that, in more severe injury model which received both burn and CLP treatments, GMCSF and MIP-1α (chemokines), IL-1α (a pro-inflammatory cytokine) and IL-6 (exhibiting both pro- and anti-inflammatory behaviors) were upregulated on the 7th and 10th days, which might be to protect the host system from the subsequent complications caused by burn and sepsis. In order to elucidate critical regulatory interactions, putative transcription factors of the inflammatory mediators which have been significantly changed following the injuries were further identified by analyzing the conserved regions of the promoters of cytokines and chemokines. In conclusion, the long term profiles of the inflammatory mediators were profoundly characterized in this study to gain a comprehensive understanding of inflammatory mediators’ behaviors in various injury models.
doi:10.1016/j.cyto.2012.01.017
PMCID: PMC3355995  PMID: 22402033
Burn; Cecal ligation and puncture; Cytokines; Chemokines; Long term inflammatory response; Transcription Factors
4.  A semi-mechanistic integrated toxicokinetic–toxicodynamic (TK/TD) model for arsenic(III) in hepatocytes 
Journal of theoretical biology  2012;317:244-256.
Background
A systems engineering approach is presented for describing the kinetics and dynamics that are elicited upon arsenic exposure of human hepatocytes. The mathematical model proposed here tracks the cellular reaction network of inorganic and organic arsenic compounds present in the hepatocyte and analyzes the production of toxicologically potent by-products and the signaling they induce in hepatocytes.
Methods and results
The present modeling effort integrates for the first time a cellular-level semi-mechanistic toxicokinetic (TK) model of arsenic in human hepatocytes with a cellular-level toxicodynamic (TD) model describing the arsenic-induced reactive oxygen species (ROS) burst, the antioxidant response, and the oxidative DNA damage repair process. The antioxidant response mechanism is described based on the Keap1-independent Nuclear Factor-erythroid 2-related factor 2 (Nrf2) signaling cascade and accounts for the upregulation of detoxifying enzymes. The ROS-induced DNA damage is simulated by coupling the TK/TD formulation with a model describing the multistep pathway of oxidative DNA repair. The predictions of the model are assessed against experimental data of arsenite-induced genotoxic damage to human hepatocytes; thereby capturing in silico the mode of the experimental dose–response curve.
Conclusions
The integrated cellular-level TK/TD model presented here provides significant insight into the underlying regulatory mechanism of Nrf2-regulated antioxidant response due to arsenic exposure. While computational simulations are in a fair good agreement with relevant experimental data, further analysis of the system unravels the role of a dynamic interplay among the feedback loops of the system in controlling the ROS upregulation and DNA damage response. This TK/TD framework that uses arsenic as an example can be further extended to other toxic or pharmaceutical agents.
doi:10.1016/j.jtbi.2012.09.019
PMCID: PMC4026948  PMID: 23069314
Arsenic; Nrf2; Anti-oxidant response; Human hepatocytes; Indirect response modeling
5.  Modeling Physiologic Variability in Human Endotoxemia 
The control and management of inflammation is a key aspect of clinical care for critical illnesses such as sepsis. In an ideal reaction to injury, the inflammatory response provokes a strong enough response to heal the injury and then restores homeostasis. When inflammation becomes dysregulated, a persistent inflammatory state can lead to significant deleterious effects and clinical challenges. Thus, gaining a better biological understanding of the mechanisms driving the inflammatory response is of the utmost importance. In this review, we discuss our work with the late Stephen F. Lowry to investigate systemic inflammation through systems biology of human endotoxemia. We present our efforts in modeling the human endotoxemia response with a particular focus on physiologic variability. Through modeling, with a focus ultimately on translational applications, we obtain more fundamental understanding of relevant physiological processes. And by taking advantage of the information embedded in biological rhythms, ranging in time scale from high-frequency autonomic oscillations reflected in heart rate variability to circadian rhythms in inflammatory mediators, we gain insight into the underlying physiology.
PMCID: PMC3604977  PMID: 23140122
systems biology; inflammation; mathematical modeling
6.  An Agent-Based Model of Cellular Dynamics and Circadian Variability in Human Endotoxemia 
PLoS ONE  2013;8(1):e55550.
As cellular variability and circadian rhythmicity play critical roles in immune and inflammatory responses, we present in this study an agent-based model of human endotoxemia to examine the interplay between circadian controls, cellular variability and stochastic dynamics of inflammatory cytokines. The model is qualitatively validated by its ability to reproduce circadian dynamics of inflammatory mediators and critical inflammatory responses after endotoxin administration in vivo. Novel computational concepts are proposed to characterize the cellular variability and synchronization of inflammatory cytokines in a population of heterogeneous leukocytes. Our results suggest that there is a decrease in cell-to-cell variability of inflammatory cytokines while their synchronization is increased after endotoxin challenge. Model parameters that are responsible for IκB production stimulated by NFκB activation and for the production of anti-inflammatory cytokines have large impacts on system behaviors. Additionally, examining time-dependent systemic responses revealed that the system is least vulnerable to endotoxin in the early morning and most vulnerable around midnight. Although much remains to be explored, proposed computational concepts and the model we have pioneered will provide important insights for future investigations and extensions, especially for single-cell studies to discover how cellular variability contributes to clinical implications.
doi:10.1371/journal.pone.0055550
PMCID: PMC3559552  PMID: 23383223
7.  Impact of burn priming on immune and metabolic functions of whole Liver in a rat cecal ligation and puncture model 
Previously, we have shown that systemic insults in single injury models produced immunosuppressive effects in burn, and a strong acute phase response in sepsis through hepatic gene expression. In order to investigate the implications of these effects on a combined injury, a double hit model was explored to mimic the progression of clinical burn-sepsis. Rodents were subjected to a 20% total body surface area (TSA) full-thickness burn injury, and 48 hours later underwent cecal ligation and puncture (CLP) to induce sepsis. Pathways related to innate immune signaling through cytokines and NF-KB were co regulated with xenobiotic metabolism genes and acute phase protein genes, and that these genes were suppressed early, and then activated. Furthermore, we were able to identify that, in addition to amino acid metabolism, pyruvate metabolism, fatty acid metabolism and NRF-2 mediated oxidative stress genes were down regulated over the time course. Overall, these observed trends within the double hit burn-sepsis model represent unique immune and metabolic pathways and dynamics not found in either injury, including an early suppression followed by overreaction of pro inflammatory mediators, and an increase in amino acid metabolism at the expense of central carbon pathways.
PMCID: PMC3560487  PMID: 23386986
Sepsis; burns; microarray analysis; RT-PCR analysis; liver
8.  Time-restricted feeding and the realignment of biological rhythms: translational opportunities and challenges 
It has been argued that circadian dysregulation is not only a critical inducer and promoter of adverse health effects, exacerbating symptom burden, but also hampers recovery. Therefore understanding the health-promoting roles of regulating (i.e., restoring) circadian rhythms, thus suppressing harmful effects of circadian dysregulation, would likely improve treatment. At a critical care setting it has been argued that studies are warranted to determine whether there is any use in restoring circadian rhythms in critically ill patients, what therapeutic goals should be targeted, and how these could be achieved. Particularly interesting are interventional approaches aiming at optimizing the time of feeding in relation to individualized day–night cycles for patients receiving enteral nutrition, in an attempt to re-establish circadian patterns of molecular expression. In this short review we wish to explore the idea of transiently imposing (appropriate, but yet to be determined) circadian rhythmicity via regulation of food intake as a means of exploring rhythm-setting properties of metabolic cues in the context of improving immune response. We highlight some of the key elements associated with his complex question particularly as they relate to: a) stress and rhythmic variability; and b) metabolic entrainment of peripheral tissues as a possible intervention strategy through time-restricted feeding. Finally, we discuss the challenges and opportunities for translating these ideas to the bedside.
doi:10.1186/1479-5876-12-79
PMCID: PMC3973614  PMID: 24674294
9.  Comparison of the Cytokine and Chemokine Dynamics of the Early Inflammatory Response in Models of Burn Injury and Infection 
Cytokine  2011;55(3):362-371.
The inflammatory response, and its subsequent resolution, are the result of a very complex cascade of events originating at the site of injury or infection. When the response is severe and persistent, Systemic Inflammatory Response Syndrome can set in, which is associated with a severely debilitating systemic hypercatabolic state. This complex behavior, mediated by cytokines and chemokines, needs to be further explored to better understand its systems properties and potentially identify multiple targets that could be addressed simultaneously. In this context, short term responses of serum cytokines and chemokines were analyzed in two types of insults: rats receiving a “sterile” cutaneous dorsal burn on 20% of the total body surface area (TBSA); rats receiving a cecum ligation and puncture treatment (CLP) to induce infection. Considering the temporal variability observed in the baseline corresponding to the control group, the concept of area under the curve (AUC) was explored to assess the dynamic responses of cytokines and chemokines. MCP-1, GROK/KC, IL-12, IL-18 and IL-10 were observed in both burn and CLP groups. While IL-10 concentration was only increased in the burn group, Eotaxin was only elevated in CLP group. It was also observed that Leptin and IP-1 concentrations were decreased in both CLP and sham-CLP groups. The link between the circulating protein mediators and putative transcription factors regulating the cytokine/chemokine gene expression was explored by searching the promoter regions of cytokine/chemokine genes in order to characterize and differentiate the inflammatory responses based on the dynamic data. Integrating multiple sources together with the bioinformatics tools identified mediators sensitive to type and extent of injury, and provided putative regulatory mechanisms. This is essential to gain a better understanding for the important regulatory points that can be used to modulate the inflammatory state at molecular level.
doi:10.1016/j.cyto.2011.05.010
PMCID: PMC3148335  PMID: 21652218
Cytokines; Chemokines; Burn injury; Cecum ligation and puncture
10.  Bioinformatics analysis of transcriptional regulation of circadian genes in rat liver 
BMC Bioinformatics  2014;15:83.
Background
The circadian clock is a critical regulator of biological functions controlling behavioral, physiological and biochemical processes. Because the liver is the primary regulator of metabolites within the mammalian body and the disruption of circadian rhythms in liver is associated with severe illness, circadian regulators would play a strong role in maintaining liver function. However, the regulatory structure that governs circadian dynamics within the liver at a transcriptional level remains unknown. To explore this aspect, we analyzed hepatic transcriptional dynamics in Sprague-Dawley rats over a period of 24 hours to assess the genome-wide responses.
Results
Using an unsupervised consensus clustering method, we identified four major gene expression clusters, corresponding to central carbon and nitrogen metabolism, membrane integrity, immune function, and DNA repair, all of which have dynamics which suggest regulation in a circadian manner. With the assumption that transcription factors (TFs) that are differentially expressed and contain CLOCK:BMAL1 binding sites on their proximal promoters are likely to be clock-controlled TFs, we were able to use promoter analysis to putatively identify additional clock-controlled TFs besides PARF and RORA families. These TFs are both functionally and temporally related to the clusters they regulate. Furthermore, we also identified significant sets of clock TFs that are potentially transcriptional regulators of gene clusters.
Conclusions
All together, we were able to propose a regulatory structure for circadian regulation which represents alternative paths for circadian control of different functions within the liver. Our prediction has been affirmed by functional and temporal analyses which are able to extend for similar studies.
doi:10.1186/1471-2105-15-83
PMCID: PMC3987685  PMID: 24666587
Circadian rhythm; Microarray analysis; Gene expression; Consensus clustering; Promoter analysis; Transcription factor; Circadian regulation
11.  Tissue-Specific Gene Expression and Regulation in Liver and Muscle Following Chronic Corticosteroid Administration 
Although corticosteroids (CSs) affect gene expression in multiple tissues, the array of genes that are regulated by these catabolic steroids is diverse, highly tissue specific, and depends on their functions in the tissue. Liver has many important functions in performing and regulating diverse metabolic processes. Muscle, in addition to its mechanical role, is critical in maintaining systemic energy homeostasis and accounts for about 80% of insulin-directed glucose disposal. Consequently, a better understanding of CS pharmacogenomic effects in these tissues would provide valuable information regarding the tissue-specificity of transcriptional dynamics, and would provide insights into the underlying molecular mechanisms of action for both beneficial and detrimental effects.
We performed an integrated analysis of transcriptional data from liver and muscle in response to methylprednisolone (MPL) infusion, which included clustering and functional annotation of clustered gene groups, promoter extraction and putative transcription factor (TF) identification, and finally, regulatory closeness (RC) identification.
This analysis allowed the identification of critical transcriptional responses and CS-responsive functions in liver and muscle during chronic MPL administration, the prediction of putative transcriptional regulators relevant to transcriptional responses of CS-affected genes which are also potential secondary bio-signals altering expression levels of target-genes, and the exploration of the tissue-specificity and biological significance of gene expression patterns, CS-responsive functions, and transcriptional regulation.
The analysis provided an integrated description of the genomic and functional effects of chronic MPL infusion in liver and muscle.
doi:10.4137/GRSB.S13134
PMCID: PMC3956809  PMID: 24653645
liver; muscle; glucocorticoids; corticosteroids; gene expression; gene regulation; promoter analysis
12.  A Physiological Model for Autonomic Heart Rate Regulation in Human Endotoxemia 
Shock (Augusta, Ga.)  2011;35(3):229-239.
The systemic inflammatory response syndrome (SIRS) often accompanies critical illnesses and can be an important cause of morbidity and mortality. Marked abnormalities in cardiovascular function accompany acute illnesses manifested as sustained tachyarrhythmias which are but one component of systemic dysregulation. The realization that cardiac pacemaker activity is under control of the autonomic nervous system has promoted the analysis of heart rate variation for assessing autonomic activities. In acute illnesses, autonomic imbalance manifesting in part as parasympathetic attenuation is associated with increased morbidity in patients who manifest SIRS phenotype. Driven by the premise that biological phenotypes emerge as the outcome of the coordinated action of network elements across the host, a multiscale model of human endotoxemia, as a prototype model of systemic inflammation in humans, is developed that quantifies critical aspects of the complex relationship between inflammation and autonomic heart rate regulation. In the present study, changes in heart rate response to acute injury, phenotypically expressed as tachycardia, are simulated as a result of autonomic imbalance that reflects sympathetic activity excess and parasympathetic attenuation. The proposed model assesses both the anti-inflammatory and cardiovascular effects of antecedent stresses upon the systemic inflammatory manifestations of human endotoxemia as well as a series of non-linear inflammatory relevant scenarios. Such a modeling approach provides a comprehensive conceptual framework linking inflammation and physiological complexity via a multiscale model that may advance the translational potential of systems modeling in clinical research.
doi:10.1097/SHK.0b013e318200032b
PMCID: PMC3045969  PMID: 21063241
mathematical modeling; infection; humans; inflammation; autonomic nervous system; heart
13.  A Quantitative Model of Thermal Injury-Induced Acute Inflammation 
Mathematical biosciences  2010;229(2):135-148.
Severe burns are among the most common causes of death from unintentional injury. The induction and resolution of the burn-induced systemic inflammatory response are mediated by a network of factors and regulatory proteins. Numerous mechanisms operate simultaneously, thus requiring a systems level approach to characterize their overall impact. Towards this goal, we propose an in silico semi-mechanistic model of burn-induced systemic inflammation using liver specific gene expression from a rat burn model. Transcriptional responses are coupled with extracellular signals through a receptor mediated indirect response (IDR) and transit compartment model. The activation of the innate immune system in response to the burn stimulus involves the interaction between extracellular signals and critical receptors which triggers downstream signal transduction cascades leading to transcriptional changes. The resulting model consists of fifteen (15) coupled ordinary differential equations capturing key aspects of inflammation such as pro-inflammation, anti-inflammation and hypermetabolism. The model was then evaluated through a series of biologically relevant scenarios aiming at revealing the non-linear behavior of acute inflammation including: investigating the implication of effect of different severity of thermal injury; examining possible mechanistic dysregulation of IKK-NFκB system which may reflect secondary effects that lead to potential malfunction of the response; and exploring the outcome of administration of receptor antagonist or anti-body to significant cytokines.
doi:10.1016/j.mbs.2010.08.003
PMCID: PMC3239409  PMID: 20708022
thermal injury; trauma; inflammation; hypermetabolism; modeling; liver; rat
14.  Pharmacokinetics and Pharmacodynamics of Phase II Drug Metabolizing/Antioxidant Enzymes Gene Response by Anti-cancer Agent Sulforaphane in Rat Lymphocytes 
Molecular pharmaceutics  2012;9(10):2819-2827.
PURPOSE
This study assesses the pharmacokinetics (PK) and pharmacodynamics (PD) of Nrf2-mediated increased expression of Phase II drug metabolizing enzyme (DME) and antioxidant enzymes which represents an important component of cancer chemoprevention in rat lymphocytes following intravenous (i.v.) administration of an anti-cancer phytochemical sulforaphane (SFN)
METHODS
SFN was administered intravenously to four groups of male Sprague-Dawley JVC rats each group comprising four animals. Blood samples were drawn at selected time points. Plasma were obtained from half of the blood samples and analyzed using a validated LC-MS/MS method. Lymphocytes were collected from the remaining blood samples using Ficoll-Paque™ Plus centrifuge medium. Lymphocyte RNAs were extracted, converted to cDNA, and quantitative real-time PCR analyses were performed and fold changes were calculated against those at time zero for the relative expression of Nrf2-target genes of phase II DME/antioxidant enzymes. PK-PD modeling was conducted based on Jusko’s indirect response model (IDR) using GastroPlus™ and Bootstrap Method.
RESULTS
SFN plasma concentration declined biexponentially and the pharmacokinetic parameters were generated. Rat lymphocyte mRNA expression levels showed no change for GSTM1, SOD, NF-κB, UGT1A1, or UGT1A6. Moderate increases (2-5 folds) over the time zero were seen for HO-1, Nrf2, and NQO1, and significant increase (> 5 folds) for GSTT1, GPx1, and Maf. PK-PD analyses using GastroPlus™ and Bootstrap method provided reasonable fitting for the PK and PD profiles and parameter estimates.
CONCLUSION
Our present study shows that SFN could induce Nrf2-mediated phase II DME/antioxidant mRNA expression for NQO1, GSTT1, Nrf2, GPx, Maf, and HO-1 in rat lymphocytes after i.v. administration, suggesting that Nrf2-mediated mRNA expression in lymphocytes may serve as surrogate biomarkers. The PK-PD IDR model simultaneously linking the plasma concentrations of SFN and the PD response of lymphocyte mRNA expression is valuable for quantitating Nrf2 mediated effects of SFN. This study may provide a conceptual framework for future clinical PK-PD studies of dietary cancer chemopreventive agents in human.
doi:10.1021/mp300130k
PMCID: PMC3580178  PMID: 22931102
sulforaphane; pharmacokinetics; pharmacodynamics; lymphocyte; phase II genes; Nrf2
15.  Sepsis: Something Old, Something New, and a Systems View 
Journal of Critical Care  2011;27(3):314.e1-314.e11.
Sepsisis a clinical syndrome characterized by a multi-system response to a microbial pathogenic insult consisting of a mosaic of interconnected biochemical, cellular, and organ-organ interaction networks. A central thread that connects these responses is inflammation, which, while attempting to defend the body and prevent further harm, causes further damage through the feed-forward, pro-inflammatory effects of damage-associated molecular pattern molecules. In this review, we address the epidemiology and current definitions of sepsis, and focus specifically on the biological cascades that comprise the inflammatory response to sepsis. We suggest that attempts to improve clinical outcomes by targeting specific components of this network have been unsuccessful due to the lack of an integrative, predictive, and individualized systems-based approach to define the time-varying, multi-dimensional state of the patient. We highlight the translational impact of computational modeling and other complex systems approaches as applied to sepsis, including in silico clinical trials, patient-specific models, and complexity-based assessments of physiology.
doi:10.1016/j.jcrc.2011.05.025
PMCID: PMC3206132  PMID: 21798705
Sepsis; Inflammatory Response; Physiologic Variability; Mathematical Model
16.  Advanced Stoichiometric Analysis of Metabolic Networks of Mammalian Systems 
Metabolic engineering tools have been widely applied to living organisms to gain a comprehensive understanding about cellular networks and to improve cellular properties. Metabolic flux analysis (MFA), flux balance analysis (FBA), and metabolic pathway analysis (MPA) are among the most popular tools in stoichiometric network analysis. Although application of these tools into well-known microbial systems is extensive in the literature, various barriers prevent them from being utilized in mammalian cells. Limited experimental data, complex regulatory mechanisms, and the requirement of more complex nutrient media are some major obstacles in mammalian cell systems. However, mammalian cells have been used to produce therapeutic proteins, to characterize disease states or related abnormal metabolic conditions, and to analyze the toxicological effects of some medicinally important drugs. Therefore, there is a growing need for extending metabolic engineering principles to mammalian cells in order to understand their underlying metabolic functions. In this review article, advanced metabolic engineering tools developed for stoichiometric analysis including MFA, FBA, and MPA are described. Applications of these tools in mammalian cells are discussed in detail, and the challenges and opportunities are highlighted.
PMCID: PMC3634616  PMID: 22196224
Metabolic flux analysis; flux balance analysis; metabolic pathway analysis; mammalian cells
17.  Effect of Fasting on the Metabolic Response of Liver to Experimental Burn Injury 
PLoS ONE  2013;8(2):e54825.
Liver metabolism is altered after systemic injuries such as burns and trauma. These changes have been elucidated in rat models of experimental burn injury where the liver was isolated and perfused ex vivo. Because these studies were performed in fasted animals to deplete glycogen stores, thus simplifying quantification of gluconeogenesis, these observations reflect the combined impact of fasting and injury on liver metabolism. Herein we asked whether the metabolic response to experimental burn injury is different in fed vs. fasted animals. Rats were subjected to a cutaneous burn covering 20% of the total body surface area, or to similar procedures without administering the burn, hence a sham-burn. Half of the animals in the burn and sham-burn groups were fasted starting on postburn day 3, and the others allowed to continue ad libitum. On postburn day 4, livers were isolated and perfused for 1 hour in physiological medium supplemented with 10% hematocrit red blood cells. The uptake/release rates of major carbon and nitrogen sources, oxygen, and carbon dioxide were measured during the perfusion and the data fed into a mass balance model to estimate intracellular fluxes. The data show that in fed animals, injury increased glucose output mainly from glycogen breakdown and minimally impacted amino acid metabolism. In fasted animals, injury did not increase glucose output but increased urea production and the uptake of several amino acids, namely glutamine, arginine, glycine, and methionine. Furthermore, sham-burn animals responded to fasting by triggering gluconeogenesis from lactate; however, in burned animals the preferred gluconeogenic substrate was amino acids. Taken together, these results suggest that the fed state prevents the burn-induced increase in hepatic amino acid utilization for gluconeogenesis. The role of glycogen stores and means to increase and/or maintain internal sources of glucose to prevent increased hepatic amino acid utilization warrant further studies.
doi:10.1371/journal.pone.0054825
PMCID: PMC3564862  PMID: 23393558
18.  Metabolic Response of Perfused Livers to Various Oxygenation Conditions 
Biotechnology and bioengineering  2011;108(12):2947-2957.
Isolated liver perfusion systems have been used to characterize intrinsic metabolic changes in liver as a result of various perturbations, including systemic injury, hepatotoxin exposure, and warm ischemia. Most of these studies were done using hyperoxic conditions (95% O2) but without the use of oxygen carriers in the perfusate. Prior literature data do not clearly establish the impact of oxygenation, and in particular that of adding oxygen carriers to the perfusate, on the metabolic functions of the liver. Therefore, herein the effects of oxygen delivery in the perfusion system on liver metabolism were investigated by comparing three modes of oxygenation. Rat livers were perfused via the portal and hepatic veins at a constant flow rate of 3 mL/min/g liver in a recirculating perfusion system. In the first group, the perfusate was equilibrated in a membrane oxygenator with room air (21% O2) before entering the liver. In the second group, the perfusate was equilibrated with a 95% O2/5% CO2 gas mixture. In the third group, the perfusate was supplemented with washed bovine red blood cells (RBCs) at 10% hematocrit and also equilibrated with the 95% O2/5% CO2 gas mixture. Oxygen and CO2 gradients across the liver were measured periodically with a blood gas analyzer. The rate of change in the concentration of major metabolites in the perfusate was measured over time. Net extracellular fluxes were calculated from these measurements and applied to a stoichiometric-based optimization problem to determine the intracellular fluxes and active pathways in the perfused livers. Livers perfused with RBCs consumed oxygen at twice the rate observed using hyperoxic (95% O2) perfusate without RBCs, and also produced more urea and ketone bodies. At the flow rate used, the oxygen supply in perfusate without RBCs was just sufficient to meet the average oxygen demand of the liver but would be insufficient if it increased above baseline, as is often the case in response to environmental perturbations. Metabolic pathway analysis suggests that significant anaerobic glycolysis occurred in the absence of RBCs even using hyperoxic perfusate. Conversely, when RBCs were used, glucose production from lactate and glutamate, as well as pathways related to energy metabolism were upregulated. RBCs also reversed an increase in PPP fluxes induced by the use of hyperoxic perfusate alone. In conclusion, the use of oxygen carriers is required to investigate the effect of various perturbations on liver metabolism.
doi:10.1002/bit.23261
PMCID: PMC3193557  PMID: 21755498
liver; perfusion; oxygenation; metabolism; flux balance analysis
19.  The Dynamics of the Early Inflammatory Response in Double-hit Burn and Sepsis Animal Models 
Cytokine  2011;56(2):494-502.
Severe burn trauma is generally associated with bacterial infections, which causes a more persistent inflammatory response with an ongoing hypermetabolic and catabolic state. This complex biological response, mediated by chemokines and cytokines, can be more severe when excessive interactions between the mediators take place. In this study, the early inflammatory response following the cecum ligation and puncture (CLP) or its corresponding control treatment (sham-CLP or SCLP) in burn (B) male rats was analyzed by measuring 23 different cytokines and chemokines. Cytokines and chemokines, including MCP-1, IP-10, Leptin, TNF-α, MIP-1α, IL-18, GMCSF, RANTES and GCSF were significantly altered in both B+CLP and B+SCLP groups. IL-10 and IL-6 were significantly up-regulated in the B+CLP group when compared to the B+SCLP group. Down regulation of Leptin and IP-10 concentrations were found to be related to surgery and/or infection. IL-18 and MCP-1 were elevated in all groups including previously published single injury models receiving similar treatments. In this study, insult-specific mediators with their characteristic temporal patterns were elucidated in double hit models.
doi:10.1016/j.cyto.2011.07.001
PMCID: PMC3185215  PMID: 21824784
Cytokines; Chemokines; Double-hit injury models; Burn injury; Cecum ligation and puncture
20.  Linking Inflammation, Cardiorespiratory Variability, and Neural Control in Acute Inflammation via Computational Modeling 
Acute inflammation leads to organ failure by engaging catastrophic feedback loops in which stressed tissue evokes an inflammatory response and, in turn, inflammation damages tissue. Manifestations of this maladaptive inflammatory response include cardio-respiratory dysfunction that may be reflected in reduced heart rate and ventilatory pattern variabilities. We have developed signal-processing algorithms that quantify non-linear deterministic characteristics of variability in biologic signals. Now, coalescing under the aegis of the NIH Computational Biology Program and the Society for Complexity in Acute Illness, two research teams performed iterative experiments and computational modeling on inflammation and cardio-pulmonary dysfunction in sepsis as well as on neural control of respiration and ventilatory pattern variability. These teams, with additional collaborators, have recently formed a multi-institutional, interdisciplinary consortium, whose goal is to delineate the fundamental interrelationship between the inflammatory response and physiologic variability. Multi-scale mathematical modeling and complementary physiological experiments will provide insight into autonomic neural mechanisms that may modulate the inflammatory response to sepsis and simultaneously reduce heart rate and ventilatory pattern variabilities associated with sepsis. This approach integrates computational models of neural control of breathing and cardio-respiratory coupling with models that combine inflammation, cardiovascular function, and heart rate variability. The resulting integrated model will provide mechanistic explanations for the phenomena of respiratory sinus-arrhythmia and cardio-ventilatory coupling observed under normal conditions, and the loss of these properties during sepsis. This approach holds the potential of modeling cross-scale physiological interactions to improve both basic knowledge and clinical management of acute inflammatory diseases such as sepsis and trauma.
doi:10.3389/fphys.2012.00222
PMCID: PMC3387781  PMID: 22783197
mathematical model; inflammation; physiologic variability; heart rate variability; neural control
21.  Assessment of Pharmacologic Area Under the Curve When Baselines are Variable 
Pharmaceutical research  2011;28(5):1081-1089.
Purpose
The area under the curve (AUC) is commonly used to assess the extent of exposure of a drug. The same concept can be applied to generally assess pharmacodynamic responses and the deviation of a signal from its baseline value. When the initial condition for the response of interest is not zero, there is uncertainty in the true value of the baseline measurement. This necessitates the consideration of the AUC relative to baseline to account for this inherent uncertainty and variability in baseline measurements.
Methods
An algorithm to calculate the AUC with respect to a variable baseline is developed by comparing the AUC of the response curve with the AUC of the baseline while taking into account uncertainty in both measurements. Furthermore, positive and negative components of AUC (above and below baseline) are calculated separately to allow for the identification of biphasic responses.
Results
This algorithm is applied to gene expression data to illustrate its ability to capture transcriptional responses to a drug that deviate from baseline and to synthetic data to quantitatively test its performance.
Conclusions
The variable nature of the baseline is an important aspect to consider when calculating the AUC.
doi:10.1007/s11095-010-0363-8
PMCID: PMC3152796  PMID: 21234658
AUC; baseline; bioinformatics; microarrays; pharmacogenomics
22.  Pathway Analysis of Liver Metabolism under Stressed Condition 
Journal of theoretical biology  2010;272(1):131-140.
Pathway analysis is a useful tool which reveals important metabolic network properties. However, the big challenge is to propose an objective function for estimating active pathways which represent the actual state of network. In order to provide weight values for all possible pathways within the metabolic network, this study presents different approaches, considering the structural and physiological properties of metabolic network, aiming at a unique decomposition of the flux vector into pathways. These methods were used to analyze the hepatic metabolism considering available data sets obtained from perfused livers of fasted rats receiving burn injury. Utilizing unique decomposition techniques and different fluxes revealed that higher weights were always attributed to short pathways. Specific pathways including pyruvate, glutamate and oxaloacetate pools, and urea production from arginine were found to be important or essential in all methods and experimental conditions. Moreover, the pathways including serine production from glycine and conversion between acetoacetate and B-OH-butyrate were assigned higher weights. Pathway analysis was also used to identify the main sources for the production of certain products in the hepatic metabolic network to gain a better understanding of the effects of burn injury on liver metabolism.
doi:10.1016/j.jtbi.2010.11.042
PMCID: PMC3038651  PMID: 21163266
Pathway analysis; Liver metabolism; Burn injury
23.  Stoichiometry Based Steady-State Hepatic Flux Analysis: Computational and Experimental Aspects 
Metabolites  2012;2(1):268-291.
: The liver has many complex physiological functions, including lipid, protein and carbohydrate metabolism, as well as bile and urea production. It detoxifies toxic substances and medicinal products. It also plays a key role in the onset and maintenance of abnormal metabolic patterns associated with various disease states, such as burns, infections and major traumas. Liver cells have been commonly used in in vitro experiments to elucidate the toxic effects of drugs and metabolic changes caused by aberrant metabolic conditions, and to improve the functions of existing systems, such as bioartificial liver. More recently, isolated liver perfusion systems have been increasingly used to characterize intrinsic metabolic changes in the liver caused by various perturbations, including systemic injury, hepatotoxin exposure and warm ischemia. Metabolic engineering tools have been widely applied to these systems to identify metabolic flux distributions using metabolic flux analysis or flux balance analysis and to characterize the topology of the networks using metabolic pathway analysis. In this context, hepatic metabolic models, together with experimental methodologies where hepatocytes or perfused livers are mainly investigated, are described in detail in this review. The challenges and opportunities are also discussed extensively.
doi:10.3390/metabo2010268
PMCID: PMC3901202  PMID: 24957379
hepatocytes; perfused livers; metabolic flux analysis; flux balance analysis; metabolic pathway analysis
24.  Agent-Based Modeling of Endotoxin-Induced Acute Inflammatory Response in Human Blood Leukocytes 
PLoS ONE  2010;5(2):e9249.
Background
Inflammation is a highly complex biological response evoked by many stimuli. A persistent challenge in modeling this dynamic process has been the (nonlinear) nature of the response that precludes the single-variable assumption. Systems-based approaches offer a promising possibility for understanding inflammation in its homeostatic context. In order to study the underlying complexity of the acute inflammatory response, an agent-based framework is developed that models the emerging host response as the outcome of orchestrated interactions associated with intricate signaling cascades and intercellular immune system interactions.
Methodology/Principal Findings
An agent-based modeling (ABM) framework is proposed to study the nonlinear dynamics of acute human inflammation. The model is implemented using NetLogo software. Interacting agents involve either inflammation-specific molecules or cells essential for the propagation of the inflammatory reaction across the system. Spatial orientation of molecule interactions involved in signaling cascades coupled with the cellular heterogeneity are further taken into account. The proposed in silico model is evaluated through its ability to successfully reproduce a self-limited inflammatory response as well as a series of scenarios indicative of the nonlinear dynamics of the response. Such scenarios involve either a persistent (non)infectious response or innate immune tolerance and potentiation effects followed by perturbations in intracellular signaling molecules and cascades.
Conclusions/Significance
The ABM framework developed in this study provides insight on the stochastic interactions of the mediators involved in the propagation of endotoxin signaling at the cellular response level. The simulation results are in accordance with our prior research effort associated with the development of deterministic human inflammation models that include transcriptional dynamics, signaling, and physiological components. The hypothetical scenarios explored in this study would potentially improve our understanding of how manipulating the behavior of the molecular species could manifest into emergent behavior of the overall system.
doi:10.1371/journal.pone.0009249
PMCID: PMC2823776  PMID: 20174629
25.  Identification of Global Transcriptional Dynamics 
PLoS ONE  2009;4(7):e5992.
Background
One of the challenges in exploiting high throughput measurement techniques such as microarrays is the conversion of the vast amounts of data obtained into relevant knowledge. Of particular importance is the identification of the intrinsic response of a transcriptional experiment and the characterization of the underlying dynamics.
Methodology and Findings
The proposed algorithm seeks to provide the researcher a summary as to various aspects relating to the dynamic progression of a biological system, rather than that of individual genes. The approach is based on the identification of smaller number of expression motifs that define the transcriptional state of the system which quantifies the deviation of the cellular response from a control state in the presence of an external perturbation. The approach is demonstrated with a number of data sets including a synthetic base case and four animal studies. The synthetic dataset will be used to establish the response of the algorithm on a “null” dataset, whereas the four different experimental datasets represent a spectrum of possible time course experiments in terms of the degree of perturbation associated with the experiment as well as representing a wide range of temporal sampling strategies. This wide range of experimental datasets will thus allow us to explore the performance of the proposed algorithm and determine its ability identify relevant information.
Conclusions and Significance
In this work, we present a computational approach which operates on high throughput temporal gene expression data to assess the information content of the experiment, identify dynamic markers of important processes associated with the experimental perturbation, and summarize in a concise manner the evolution of the system over time with respect to the experimental perturbation.
doi:10.1371/journal.pone.0005992
PMCID: PMC2705787  PMID: 19593450

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