1
|
Azim N, Ahmad J, Iqbal N, Siddiqa A, Majid A, Ashraf J, Jalil F. Petri Net modelling approach for analysing the behaviour of Wnt/[inline-formula removed] -catenin and Wnt/Ca2+ signalling pathways in arrhythmogenic right ventricular cardiomyopathy. IET Syst Biol 2020; 14:350-367. [PMID: 33399099 PMCID: PMC8687399 DOI: 10.1049/iet-syb.2020.0038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/20/2020] [Accepted: 08/03/2020] [Indexed: 12/20/2022] Open
Abstract
Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart muscle disease that may result in arrhythmia, heart failure and sudden death. The hallmark pathological findings are progressive myocyte loss and fibro fatty replacement, with a predilection for the right ventricle. This study focuses on the adipose tissue formation in cardiomyocyte by considering the signal transduction pathways including Wnt/[inline-formula removed]-catenin and Wnt/Ca2+ regulation system. These pathways are modelled and analysed using stochastic petri nets (SPN) in order to increase our comprehension of ARVC and in turn its treatment regimen. The Wnt/[inline-formula removed]-catenin model predicts that the dysregulation or absence of Wnt signalling, inhibition of dishevelled and elevation of glycogen synthase kinase 3 along with casein kinase I are key cytotoxic events resulting in apoptosis. Moreover, the Wnt/Ca2+ SPN model demonstrates that the Bcl2 gene inhibited by c-Jun N-terminal kinase protein in the event of endoplasmic reticulum stress due to action potential and increased amount of intracellular Ca2+ which recovers the Ca2+ homeostasis by phospholipase C, this event positively regulates the Bcl2 to suppress the mitochondrial apoptosis which causes ARVC.
Collapse
Affiliation(s)
- Nazia Azim
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Jamil Ahmad
- Department of Computer Science and Information Technology, University of Malakand, Chakdara, Pakistan.
| | - Nadeem Iqbal
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Amnah Siddiqa
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Abdul Majid
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Javaria Ashraf
- Research Centre for modeling and Simulation, National University of Sciences and Technology, Islamabad Pakistan
| | - Fazal Jalil
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| |
Collapse
|
2
|
Siddiqa A, Ahmad J, Ali A, Khan S. Deciphering the expression dynamics of ANGPTL8 associated regulatory network in insulin resistance using formal modelling approaches. IET Syst Biol 2020; 14:47-58. [PMID: 32196463 PMCID: PMC8687251 DOI: 10.1049/iet-syb.2019.0032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
ANGPTL8 is a recently identified novel hormone which regulates both glucose and lipid metabolism. The increase in ANGPTL8 during compensatory insulin resistance has been recently reported to improve glucose tolerance and a part of cytoprotective metabolic circuit. However, the exact signalling entities and dynamics involved in this process have remained elusive. Therefore, the current study was conducted with a specific aim to model the regulation of ANGPTL8 with emphasis on its role in improving glucose tolerance during insulin resistance. The main contribution of this study is the construction of a discrete model (based on kinetic logic of René Thomas) and its equivalent Stochastic Petri Net model of ANGPTL8 associated Biological Regulatory Network (BRN) which can predict its dynamic behaviours. The predicted results of these models are in‐line with the previous experimental observations and provide comprehensive insights into the signalling dynamics of ANGPTL8 associated BRN. The authors’ results support the hypothesis that ANGPTL8 plays an important role in supplementing the insulin signalling pathway during insulin resistance and its loss can aggravate the pathogenic process by quickly leading towards Diabetes Mellitus. The results of this study have potential therapeutic implications for treatment of Diabetes Mellitus and are suggestive of its potential as a glucose‐lowering agent.
Collapse
Affiliation(s)
- Amnah Siddiqa
- Research Center for Modelling and Simulation (RCMS), National university of Sciences and Technology (NUST), Sector H-12, Islamabad 46000, Pakistan
| | - Jamil Ahmad
- Department of Computer Science and Information Technology, University of Malakand, Chakdara, Dir Lower, Khyber Pakhtunkhwa 18800, Pakistan.
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad 46000, Pakistan
| | - Sharifullah Khan
- School of Electrical Engineering and Computer Science (SEECS), National University of Sciences and Technology (NUST), Pakistan
| |
Collapse
|
3
|
Bae SA, Fang MZ, Rustgi V, Zarbl H, Androulakis IP. At the Interface of Lifestyle, Behavior, and Circadian Rhythms: Metabolic Implications. Front Nutr 2019; 6:132. [PMID: 31555652 PMCID: PMC6722208 DOI: 10.3389/fnut.2019.00132] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/06/2019] [Indexed: 12/29/2022] Open
Abstract
Nutrient metabolism is under circadian regulation. Disruption of circadian rhythms by lifestyle and behavioral choices such as work schedules, eating patterns, and social jetlag, seriously impacts metabolic homeostasis. Metabolic dysfunction due to chronic misalignment of an organism's endogenous rhythms is detrimental to health, increasing the risk of obesity, metabolic and cardiovascular disease, diabetes, and cancer. In this paper, we review literature on recent findings on the mechanisms that communicate metabolic signals to circadian clocks and vice versa, and how human behavioral changes imposed by societal and occupational demands affect the physiological networks integrating peripheral clocks and metabolism. Finally, we discuss factors possibly contributing to inter-individual variability in response to circadian changes in the context of metabolic (dys)function.
Collapse
Affiliation(s)
- Seul-A Bae
- Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ, United States
| | - Ming Zhu Fang
- Department of Environmental and Occupational Medicine, Robert Wood Johnson Medical School, Piscataway, NJ, United States.,National Institute for Environmental Health Sciences (NIEHS) Center for Environmental Exposures and Disease, Environmental and Occupational Health Sciences Institute, Piscataway, NJ, United States.,Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Vinod Rustgi
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Helmut Zarbl
- Department of Environmental and Occupational Medicine, Robert Wood Johnson Medical School, Piscataway, NJ, United States.,National Institute for Environmental Health Sciences (NIEHS) Center for Environmental Exposures and Disease, Environmental and Occupational Health Sciences Institute, Piscataway, NJ, United States.,Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Ioannis P Androulakis
- Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ, United States.,Biomedical Engineering Department, Rutgers University, Piscataway, NJ, United States.,Department of Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| |
Collapse
|
4
|
Androulakis IP. The quest for digital health: From diseases to patients. Comput Chem Eng 2019. [DOI: 10.1016/j.compchemeng.2019.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
5
|
Ashraf H, Ahmad J, Hassan A, Ali A. Computational modeling and analysis of the impacts of sleep deprivation on glucose stimulated insulin secretion. Biosystems 2019; 179:1-14. [PMID: 30790613 DOI: 10.1016/j.biosystems.2019.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 01/02/2019] [Accepted: 02/13/2019] [Indexed: 01/12/2023]
Abstract
Circadian clock is an exquisite internal biological clock functioning in all living organisms. Lifestyle changes such as shift work or frequent travelling might result in malfunctioning of the central and consequently the peripheral clocks leading to different metabolic disorders. Disruptions in β cell clock have been found to be a potential reason behind β cell failure that makes a person prone towards developing type 2 diabetes (T2DM). In this study, a Petri net model for β cell circadian clock has been developed, followed by analysis of the negative impacts of sleep deprivation conditions on the process of glucose stimulated insulin secretion (GSIS) through misalignment of circadian clock. The analysis of structural properties of the Petri net model reveals robustness of the circadian system. The simulation results predict that sleep loss negatively affects the expression of circadian genes which eventually leads to impaired GSIS and β cell failure. These results suggest that sleep/wake cycle is a vital contributor for the entrainment of the circadian clock and normal functioning of β cell.
Collapse
Affiliation(s)
- Hufsah Ashraf
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Jamil Ahmad
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan; Department of Computer Science and Information Technology, University of Malakand, Chakdara, Pakistan.
| | - Azka Hassan
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Amjad Ali
- Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| |
Collapse
|
6
|
Hassan A, Ahmad J, Ashraf H, Ali A. Modeling and analysis of the impacts of jet lag on circadian rhythm and its role in tumor growth. PeerJ 2018; 6:e4877. [PMID: 29892500 PMCID: PMC5994163 DOI: 10.7717/peerj.4877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 05/10/2018] [Indexed: 12/31/2022] Open
Abstract
Circadian rhythms maintain a 24 h oscillation pattern in metabolic, physiological and behavioral processes in all living organisms. Circadian rhythms are organized as biochemical networks located in hypothalamus and peripheral tissues. Rhythmicity in the expression of circadian clock genes plays a vital role in regulating the process of cell division and DNA damage control. The oncogenic protein, MYC and the tumor suppressor, p53 are directly influenced by the circadian clock. Jet lag and altered sleep/wake schedules prominently affect the expression of molecular clock genes. This study is focused on developing a Petri net model to analyze the impacts of long term jet lag on the circadian clock and its probable role in tumor progression. The results depict that jet lag disrupts the normal rhythmic behavior and expression of the circadian clock proteins. This disruption leads to persistent expression of MYC and suppressed expression of p53. Thus, it is inferred that jet lag altered circadian clock negatively affects the expressions of cell cycle regulatory genes and contribute in uncontrolled proliferation of tumor cells.
Collapse
Affiliation(s)
- Azka Hassan
- Research Center for Modeling and Simulation (RCMS), National University of Scinces and Technology (NUST), Islamabad, Pakistan
| | - Jamil Ahmad
- Research Center for Modeling and Simulation (RCMS), National University of Scinces and Technology (NUST), Islamabad, Pakistan
| | - Hufsah Ashraf
- Research Center for Modeling and Simulation (RCMS), National University of Scinces and Technology (NUST), Islamabad, Pakistan
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Science and Technology, Islamabad, Pakistan
| |
Collapse
|
7
|
Bae SA, Androulakis IP. Mathematical analysis of circadian disruption and metabolic re-entrainment of hepatic gluconeogenesis: the intertwining entraining roles of light and feeding. Am J Physiol Endocrinol Metab 2018; 314:E531-E542. [PMID: 29351477 PMCID: PMC6032066 DOI: 10.1152/ajpendo.00271.2017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The circadian rhythms influence the metabolic activity from molecular level to tissue, organ, and host level. Disruption of the circadian rhythms manifests to the host's health as metabolic syndromes, including obesity, diabetes, and elevated plasma glucose, eventually leading to cardiovascular diseases. Therefore, it is imperative to understand the mechanism behind the relationship between circadian rhythms and metabolism. To start answering this question, we propose a semimechanistic mathematical model to study the effect of circadian disruption on hepatic gluconeogenesis in humans. Our model takes the light-dark cycle and feeding-fasting cycle as two environmental inputs that entrain the metabolic activity in the liver. The model was validated by comparison with data from mice and rat experimental studies. Formal sensitivity and uncertainty analyses were conducted to elaborate on the driving forces for hepatic gluconeogenesis. Furthermore, simulating the impact of Clock gene knockout suggests that modification to the local pathways tied most closely to the feeding-fasting rhythms may be the most efficient way to restore the disrupted glucose metabolism in liver.
Collapse
Affiliation(s)
- Seul-A Bae
- Chemical & Biochemical Engineering Department, Rutgers University , Piscataway, New Jersey
| | - Ioannis P Androulakis
- Chemical & Biochemical Engineering Department, Rutgers University , Piscataway, New Jersey
- Biomedical Engineering Department, Rutgers University , Piscataway, New Jersey
- Department of Surgery, Rutgers-Robert Wood Johnson Medical School , New Brunswick, New Jersey
| |
Collapse
|
8
|
Ashraf J, Ahmad J, Ali A, Ul-Haq Z. Analyzing the Behavior of Neuronal Pathways in Alzheimer's Disease Using Petri Net Modeling Approach. Front Neuroinform 2018; 12:26. [PMID: 29875647 PMCID: PMC5974338 DOI: 10.3389/fninf.2018.00026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/30/2018] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's Disease (AD) is the most common neuro-degenerative disorder in the elderly that leads to dementia. The hallmark of AD is senile lesions made by abnormal aggregation of amyloid beta in extracellular space of brain. One of the challenges in AD treatment is to better understand the mechanism of action of key proteins and their related pathways involved in neuronal cell death in order to identify adequate therapeutic targets. This study focuses on the phenomenon of aggregation of amyloid beta into plaques by considering the signal transduction pathways of Calpain-Calpastatin (CAST) regulation system and Amyloid Precursor Protein (APP) processing pathways along with Ca2+ channels. These pathways are modeled and analyzed individually as well as collectively through Stochastic Petri Nets for comprehensive analysis and thorough understating of AD. The model predicts that the deregulation of Calpain activity, disruption of Calcium homeostasis, inhibition of CAST and elevation of abnormal APP processing are key cytotoxic events resulting in an early AD onset and progression. Interestingly, the model also reveals that plaques accumulation start early (at the age of 40) in life but symptoms appear late. These results suggest that the process of neuro-degeneration can be slowed down or paused by slowing down the degradation rate of Calpain-CAST Complex. In the light of this study, the suggestive therapeutic strategy might be the prevention of the degradation of Calpain-CAST complexes and the inhibition of Calpain for the treatment of neurodegenerative diseases such as AD.
Collapse
Affiliation(s)
- Javaria Ashraf
- Research Center for Modeling and Simulation, National University of Sciences and Technology, Islamabad, Pakistan
| | - Jamil Ahmad
- Research Center for Modeling and Simulation, National University of Sciences and Technology, Islamabad, Pakistan
| | - Amjad Ali
- Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical Sciences, University of Karachi, Karachi, Pakistan
| |
Collapse
|
9
|
Bae SA, Androulakis IP. The Synergistic Role of Light-Feeding Phase Relations on Entraining Robust Circadian Rhythms in the Periphery. GENE REGULATION AND SYSTEMS BIOLOGY 2017; 11:1177625017702393. [PMID: 28469414 PMCID: PMC5404903 DOI: 10.1177/1177625017702393] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/02/2017] [Indexed: 01/05/2023]
Abstract
The feeding and fasting cycles are strong behavioral signals that entrain biological rhythms of the periphery. The feeding rhythms synchronize the activities of the metabolic organs, such as liver, synergistically with the light/dark cycle primarily entraining the suprachiasmatic nucleus. The likely phase misalignment between the feeding rhythms and the light/dark cycles appears to induce circadian disruptions leading to multiple physiological abnormalities motivating the need to investigate the mechanisms behind joint light-feeding circadian entrainment of peripheral tissues. To address this question, we propose a semimechanistic mathematical model describing the circadian dynamics of peripheral clock genes in human hepatocyte under the control of metabolic and light rhythmic signals. The model takes the synergistically acting light/dark cycles and feeding rhythms as inputs and incorporates the activity of sirtuin 1, a cellular energy sensor and a metabolic enzyme activated by nicotinamide adenine dinucleotide. The clock gene dynamics was simulated under various light-feeding phase relations and intensities, to explore the feeding entrainment mechanism as well as the convolution of light and feeding signals in the periphery. Our model predicts that the peripheral clock genes in hepatocyte can be completely entrained to the feeding rhythms, independent of the light/dark cycle. Furthermore, it predicts that light-feeding phase relationship is a critical factor in robust circadian oscillations.
Collapse
Affiliation(s)
- Seul-A Bae
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Ioannis P Androulakis
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Surgery, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| |
Collapse
|
10
|
Abstract
This review summarizes various mathematical models of cell-autonomous mammalian circadian clock. We present the basics necessary for understanding of the cell-autonomous mammalian circadian oscillator, modern experimental data essential for its reconstruction and some special problems related to the validation of mathematical circadian oscillator models. This work compares existing mathematical models of circadian oscillator and the results of the computational studies of the oscillating systems. Finally, we discuss applications of the mathematical models of mammalian circadian oscillator for solving specific problems in circadian rhythm biology.
Collapse
|
11
|
Liu F, Heiner M, Yang M. Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters. PLoS One 2016; 11:e0149674. [PMID: 26910830 PMCID: PMC4766190 DOI: 10.1371/journal.pone.0149674] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/29/2016] [Indexed: 12/27/2022] Open
Abstract
Stochastic Petri nets (SPNs) have been widely used to model randomness which is an inherent feature of biological systems. However, for many biological systems, some kinetic parameters may be uncertain due to incomplete, vague or missing kinetic data (often called fuzzy uncertainty), or naturally vary, e.g., between different individuals, experimental conditions, etc. (often called variability), which has prevented a wider application of SPNs that require accurate parameters. Considering the strength of fuzzy sets to deal with uncertain information, we apply a specific type of stochastic Petri nets, fuzzy stochastic Petri nets (FSPNs), to model and analyze biological systems with uncertain kinetic parameters. FSPNs combine SPNs and fuzzy sets, thereby taking into account both randomness and fuzziness of biological systems. For a biological system, SPNs model the randomness, while fuzzy sets model kinetic parameters with fuzzy uncertainty or variability by associating each parameter with a fuzzy number instead of a crisp real value. We introduce a simulation-based analysis method for FSPNs to explore the uncertainties of outputs resulting from the uncertainties associated with input parameters, which works equally well for bounded and unbounded models. We illustrate our approach using a yeast polarization model having an infinite state space, which shows the appropriateness of FSPNs in combination with simulation-based analysis for modeling and analyzing biological systems with uncertain information.
Collapse
Affiliation(s)
- Fei Liu
- Control and Simulation Center, Harbin Institute of Technology, Harbin, 150080 China
- * E-mail: (FL); (MY)
| | - Monika Heiner
- Department of Computer Science, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, 03013 Germany
| | - Ming Yang
- Control and Simulation Center, Harbin Institute of Technology, Harbin, 150080 China
- * E-mail: (FL); (MY)
| |
Collapse
|