Boolean network modeling of \u03b2-cell apoptosis and insulin resistance in type 2 diabetes mellitus

Type 2 diabetes (T2D) is a metabolic disorder characterized by high levels of blood glucose resulting from defects in insulin secretion and insulin action. Of all the diagnosed cases of diabetes, T2D accounts for approximately 90% of the cases. The pathogenesis of T2D involves both biological factors as well as social factors. These factors have intricate interactions with each other, and to study the behaviour of such complex systems computational models are required. Computational models provide a framework to summarize existing knowledge, enable competing hypotheses to be compared qualitatively and quantitatively, and facilitate the interpretation of complex data. Moreover, computational models allow questions to be investigated that are difficult to approach experimentally. Theories can be tested in context, identifying the gaps in our understanding and potentially leading to new hypotheses. 
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\nIn this thesis, three computational models are proposed: a system dynamics model of the system of social norms regarding body weight perception and obesity prevalence, a Boolean network model of the insulin resistance pathway and pancreatic beta-cell apoptosis pathway, and an ordinary differential equation model of the system of signalling components involved in insulin gene expression and beta-cell identity. In addition, this thesis also includes two methods for inferring computational models from cross-sectional data.
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\nGroup‐level obesity can be seen as an emergent property of a complex system, consisting of feedback loops between individual body weight perception, individual weight‐related behaviour and group‐level social norms (a product of group‐level ‘normal' body mass index (BMI) and socio-cultural ‘ideal' BMI). As overweight becomes normal, the norm might be counteracting health awareness in shaping individual weight‐related behaviour. System dynamics modelling facilitates understanding and simulating this system's emergent behaviour. Six system dynamics models (SDMs) were constructed based on an expert‐informed causal loop diagram and data from six socio-cultural groups (Dutch, Moroccan and South‐Asian Surinamese men and women). The SDMs served to explore the effect of three scenarios on group‐level BMI: ‘what if' weight‐related behaviour were driven by (1) health awareness, (2) norms or (3) a combination of the two. Median BMI decreased approximately 50% and 30% less in scenarios 2 and 3, respectively, than in 1. In men, the drop in BMI was approximately two times larger in scenario 1 versus 3, whereas in women, the drop was approximately equal in these scenarios. This study indicates that the overweight norm in men holds group‐level BMI close to overweight despite health awareness. Since norms are counteracting health awareness less strongly in women, other drivers of obesity must be more relevant.
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\nThe SDMs were calibrated using a multi‐ethnic cohort data, which is a cross-sectional data; however, to study how the system evolves over time, longitudinal data is required. A method was developed to generate pseudo‐time series data from the available cross‐sectional data by generating a set of qualitative ‘data‐generating assumptions'. These assumptions are based on the system's temporal behaviour that is expected to exist across all groups. An example of such an assumption is that, on average, an individual can lose 2 kg/month. Here, linear dynamics was assumed for the system's short‐term behaviour. The time steps in the SDMs were assumed as months to identify an approximate timescale of the system's behaviour. However, this timescale is not exact, and therefore, the relative trends are more important to interpret than the exact timescale they occur on.
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\nAnother method was developed for inferring computational models from cross-sectional data using Langevin dynamics. This method can be applied to any system that can be described as effectively following a free energy landscape which is stable and independent of any external force. A crucial assumption in this method is that the data-points are gathered from a system in (local) equilibrium. The result is a set of stochastic differential equations which capture the temporal dynamics, by assuming that groups of data-points are subject to the same free energy landscape and amount of noise. This is a `baseline' method which initiates the development of computational models which can be iteratively enhanced through the inclusion of expert knowledge. The proposed method can only estimate directions of progression, not velocities. Hence, the timescale of the predicted dynamics remains unknown. This timescale can be estimated from the data or from known statistical properties of the rates of change in reality; for instance, the fact that the maximum sustainable rate of weight loss observed in a population is about 2 kg per month. This method showed significant predictive power when compared against two population-based longitudinal datasets. The proposed method can facilitate the use of cross-sectional datasets to obtain an estimate of the underlying dynamics of the respective processes.
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\nThe metabolic disorder of T2D is characterized by insulin resistance, beta-cell dysfunction, and apoptosis. Chronic hyperglycemia causes deterioration of beta-cell function through oxidative stress, endoplasmic reticulum (ER) stress, and cytokines. In this thesis, two computational models are proposed to study beta-cell dysfunction in T2D. The first computational model is a Boolean network model integrating the insulin resistance pathway with the beta-cell apoptosis pathway. This model has five input signals, namely, ER stress, oxidative stress, tumor necrosis factor alpha (TNF-alpha), Fas ligand (FasL), and interleukin-6 (IL-6). Simulations were performed using random order asynchronous update and with different combinations of the input signals. The model simulations were able to reproduce the expression levels of genes in T2D as reported in the literature. This model can be useful in studying the qualitative behaviour of important genes in the presence of oxidative stress, ER stress, and pro-inflammatory cytokines.
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\nCompromised beta-cell identity is emerging as an important contributor of beta-cell dysfunction in T2D. Most evidence suggests that this identity loss results from hyperglycemia-induced inactivation of transcription factors involved in mature beta-cell identity. Beta-cells with compromised identity gradually become dysfunctional with defective insulin secretion in response to glucose. An integrated mathematical model was developed to study the underlying mechanisms that regulate two important beta-cell identity transcription factors and regulators of insulin promoter activity, PDX1 and MAFA, and lead to their downregulation in the presence of chronic hyperglycemia. The aim of this work was to investigate the loss of beta-cell function through loss of beta-cell identity in the presence of chronic hyperglycemia. This model was used to study the changes in PDX1, MAFA and insulin mRNA levels under the effect of different glucose concentrations. In addition, this model was used to analyse the effect of different inhibitors of PDX1 and MAFA on these transcription factors and insulin mRNA levels. This integrated model can be a useful tool to further extend our understanding of the mechanisms leading to compromised beta-cell identity and beta-cell dysfunction in the presence of chronic hyperglycemia and identify potential intervention targets.
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\nOverall, the three studies of the social and biological factors of T2D demonstrate the importance of computational models in understanding the complex systems involved in the pathogenesis of T2D and designing effective intervention strategies. These computational models facilitate the evaluation of hypothetical scenarios in silico and simulation of the effect of interventions. This is especially advantageous for systems for which comparing counterfactual scenarios would not be possible or would be difficult in vivo.

Bridges between mitochondrial oxidative stress, ER stress and mTOR signaling in pancreatic β cells

Perivascular adipose tissue (PVAT) plays a crucial role in vascular homeostasis. Recent studies in adipose tissue demonstrated that endoplasmic reticulum (ER) stress and autophagy are activated in Type 2 diabetes mellitus (T2DM), while the precise role of ER stress and autophagy in PVAT is unclear. We aimed to investigate the possible influence of pioglitazone on ER stress and autophagy response in PVAT of T2DM rats. T2DM was induced by high-fat diet/low-dose streptozotocin (HFD/STZ) in male Wistar rats (8-10 weeks), and pioglitazone (20 mg/kg/p.o.) was administered for 6 weeks. Changes in biochemical parameters (nonfasting glucose, total cholesterol, and triglyceride) were verified in blood samples. ER stress-related (ATF4, CHOP, and GRP78) and autophagy-related (MAP1LC3B/LC3-II, BECN-1/Beclin, and SQSTM1/p62) gene expression levels in thoracic PVAT were measured by RT-PCR. Pioglitazone treatment reversed the increased nonfasting glucose and triglyceride levels in T2DM. ER stress and autophagy responses were significantly increased in PVAT of T2DM rats. Pioglitazone increased ER stress-related GRP78 gene expression while decreasing autophagy-related MAP1LC3B and BECN-1 gene expression levels in T2DM. Interestingly, SQSTM1 gene expression levels were increased by pioglitazone in the control and T2DM groups. The current study provides original findings regarding the effects of pioglitazone on ER stress and autophagy response in PVAT of HFD/STZ-induced T2DM rats. Pioglitazone treatment in T2DM increased GRP78 and SQSTM1 gene expressions, which both play a crucial role in adipocyte differentiation and adipogenesis, besides ER stress and autophagy. Further studies clarifying the adipogenic effect of pioglitazone on PVAT are needed for a better understanding of its effect on the vascular system.

Apoptosis in diabetes

Diabetes mellitus comprises a cohort of genetic and metabolic diseases which are characterized by the hallmark symptom of hyperglycemia. Diabetic subtypes are based on their pathogenetic origins: the most prevalent subtypes are the autoimmune-mediated type 1 diabetes mellitus (T1DM) and the metabolic disease of type 2 diabetes mellitus (T2DM). Genetic factors are major contributory aspects to diabetes development, particularly in T2DM where there is close to 80% concordance rates between monozygotic twins. However, the functional state of the pancreatic β cell is of paramount importance to the development of diabetes. Perturbations that lead to β cell dysfunction impair insulin production and secretion and precede diabetes onset. The endoplasmic reticulum (ER) is a subcellular organelle network of tubes and cisternae with multifaceted roles in cellular metabolism. Alterations to ER function such as those begotten by the accumulation of misfolded and unfolded ER client proteins upset the ER homeostatic balance, leading to a condition termed ER stress. Subsequent sensing of ER stress by three ER transmembrane proteins, initiates an adaptive reaction to alleviate ER stress: this is known as the unfolded protein response (UPR). Divergent cascades of the UPR attempt to mitigate ER stress and restore ER homeostasis: Failing that, the UPR initiates pro-apoptotic pathways. The demand of insulin production on the β cell necessitates the presence of a highly functional ER. However, the consequence of dependence on the ER for insulin synthesis and secretion portends disaster for the functional state of the β cell. Disturbances to the ER that elicit ER stress and UPR activation causes β cell dysfunction and may lead to apoptosis. There are numerous well-characterized models of ER stress-mediated diabetes, including genetic mutations in UPR transducers and insulin. Recently, polymorphisms in Wolfram syndrome 1 (WFS1), an ER transmembrane protein involved in the UPR, were suggested to contribute to T2DM risk. In this thesis, one of the highlighted WFS1 polymorphism, H611R, was examined to identify its contribution to β cell function and viability, and hence, diabetes risk. It was revealed that augmentation of WFS1 expression increased insulin secretion and cellular content. In addition, WFS1 protected β cells against ER stress-mediated dysfunction, with a more pronounced effect in the WFS1-R611 protective allele. Subsequent gene expression analysis identified netrin-1 as a WFS1-induced survival factor. As a contributory factor to diabetes progression, ER stress and UPR are potential drug and biomarker targets. In this dissertation, a novel UPR-regulating microRNA (miRNA) family was uncovered in ER stressed, WFS1-deficient islets. These miRNAs, the miR-29 family, are induced in WFS1 -/- islets as a possible adaptive alteration to chronic ER stress conditions, and indirectly decreases the expression of UPR transducers, while directly targeting downstream ER stress-related pro-apoptotic factors.…

From Fat to Inflammation

ObjectiveIncreasing evidence suggested that endoplasmic reticulum (ER) stress contributes to insulin resistance, which plays an important role in the development of type 2 diabetes mellitus (T2DM). Accumulation of endogenous nitric oxide synthase (NOS) inhibitor, asymmetric dimethylarginine (ADMA), is associated with insulin resistance, T2DM, and diabetic cardiovascular complications, although the mechanisms have not been elucidated. This study was to determine whether elevated endogenous ADMA is involved in hepatic ER stress of type 2 diabetic rats, verify their causal relationship, and elucidate the potential mechanism underlying ADMA induced ER stress in rat hepatocytes.MethodsImmunoglobulin binding protein (Bip) transcription, eukaryotic initiation factor 2α kinase (eIF2α) phosphorylation, X box-binding protein-1 (XBP-1) mRNA splicing and C/EBP homologues protein (CHOP) expression were measured to reflect ER stress. Contents of ADMA and nitrite/nitrate as well as activities or expression of NOS and dimethylarginine dimethylaminohydrolase (DDAH) were detected to show the changes in DDAH/ADMA/NOS/NO pathway. The lipid peroxidation product malondialdehyde content and antioxidant enzyme superoxide dismutase activity were analyzed to evaluate oxidative stress.ResultsER stress was provoked in the liver of type 2 diabetic rats, as expressed by increases of Bip transcription, eIF2α phosphorylation, XBP-1 splicing and CHOP expression, all of which were in parallel with the elevation of serum ADMA, suppression of NO generation, NOS and DDAH activities in the liver. Exposure of hepatocytes to ADMA or hydrogen peroxide also induced ER stress, which was associated with the inhibition of NO production and increase of oxidative stress. Treatment of hepatocytes with antioxidant pyrrolidine dithiocarbamate not only decreased ADMA-induced oxidative stress and inhibition of NO production but also reduced ADMA-triggered ER stress.ConclusionsThese results indicate that increased endogenous ADMA contributes to hepatic ER stress in type 2 diabetic rats, and the mechanism underlying ADMA-induced ER stress may relate to oxidative stress via NOS uncoupling.

Macrophage apoptosis is an important feature of atherosclerotic plaque development. Research directed at understanding the functional consequences of macrophage death in atherosclerosis has revealed opposing roles for apoptosis in atherosclerotic plaque progression. In early lesions, macrophage apoptosis limits lesion cellularity and suppresses plaque progression. In advanced lesions, macrophages apoptosis promotes the development of the necrotic core, a key factor in rendering plaques vulnerable to disruption and in acute lumenal thrombosis. The first section of this review will examine the role of phagocytic clearance of apoptotic macrophages, a process known as efferocytosis, in the dichotomous roles of macrophage apoptosis in early vs. advanced lesions. The second section will focus on the molecular and cellular mechanisms that are thought to govern macrophage death during atherosclerosis. Of particular interest is the complex and coordinated role that the endoplasmic reticulum (ER) stress pathway and pattern recognition receptors (PRRs) may play in triggering macrophage apoptosis.

Obese individuals are both insulin resistant and have high levels of circulating free fatty acids (FFAs). In cell culture, saturated but not unsaturated fatty acids induce endoplasmic reticulum (ER) stress. We hypothesized that chronic exposure to low dose fatty acids would significantly attenuate the acute stress response to a saturated fatty acid challenge and that unsaturated fatty acids (oleate) would be more protective than saturated fatty acids (palmitate). The ER stress response to palmitate was reduced after low dose fatty acid exposure in human hepatoma cells. Palmitate and oleate gave distinctive transcript responses, both acutely and after chronic low dose exposure. Differentially regulated pathways included lipid, cholesterol, fatty acid, and triglyceride metabolism, and IkappaB kinase and nuclear factor kappaB kinase inflammatory cascades. Oleate reduced palmitate-induced changes significantly more than low dose palmitate and completely blocked palmitate-induced phosphoinositide 3 kinase inhibitor (PIK3IP1) as well as induction of GADD45A and B. These changes are predicted to alter the PI3 kinase pathway and the pro-apoptotic p38 MAPK pathway. We recapitulated the oleate response by small interfering RNA-mediated block of PIK3IP1 stimulation with palmitate and significantly protected cells from palmitate-mediated ER stress. We show that transcriptional responses to oleate and palmitate are distinct, broad, and often discordant. We identified several potential candidates that may direct the transcriptional networks and demonstrate that PIK3IP1 partially accounts for the protective effects of oleate.

Endoplasmic reticulum (ER) stress is characterized by the accumulation of unfolded and misfolded proteins in the ER lumen. Unfolded and misfolded protein accumulation interferes with the ER function and triggers ER stress response. Thus, ER stress response, also called unfolded protein response (UPR), is an adaptive process that controls the protein amount in the ER lumen and the downstream protein demand. In normal conditions, the role of ER stress is to maintain ER homeostasis, restore ER function, and protect stressed cells from apoptosis, by coordinating gene expression, protein synthesis, and accelerating protein degradation through several molecular pathways. However, prolonged ER stress response plays a paradoxical role, which leads to cell damage, apoptosis, and concomitant tissue injuries. A number of tissue alterations are involved with diabetes mellitus progress and its comorbidities via ER stress. However, certain pharmacological agents affecting ER stress have been identified. In this review, we summarized the relationship between ER stress and insulin resistance development. Moreover, we aim to explain how ER stress influences type 2 diabetes mellitus (T2DM) development. In addition, we reviewed the literature on ER stress and UPR in three kinds of tissue injuries induced by T2DM. Finally, a retrospective analysis of the effects of anti-diabetes medications on ER stress is presented.

Vitamin D receptor (VDR)-dependent mechanisms regulate human cathelicidin antimicrobial peptide (CAMP)/LL-37 in various cell types, but CAMP expression also increases after external perturbations (such as infection, injuries, UV irradiation, and permeability barrier disruption) in parallel with induction of endoplasmic reticulum (ER) stress. We demonstrate that CAMP mRNA and protein expression increase in epithelial cells (human primary keratinocytes, HaCaT keratinocytes, and HeLa cells), but not in myeloid (U937 and HL-60) cells, following ER stress generated by two mechanistically different, pharmacological stressors, thapsigargin or tunicamycin. The mechanism for increased CAMP following exposure to ER stress involves NF-κB activation leading to CCAAT/enhancer-binding protein α (C/EBPα) activation via MAP kinase-mediated phosphorylation. Furthermore, both increased CAMP secretion and its proteolytic processing to LL-37 are required for antimicrobial activities occur following ER stress. In addition, topical thapsigargin also increases production of the murine homologue of CAMP in mouse epidermis. Finally and paradoxically, ER stress instead suppresses the 1,25(OH)(2) vitamin D(3)-induced activation of VDR, but blockade of VDR activity does not alter ER stress-induced CAMP up-regulation. Hence, ER stress increases CAMP expression via NF-κB-C/EBPα activation, independent of VDR, illuminating a novel VDR-independent role for ER stress in stimulating innate immunity.

15-Hydroxyprostaglandin dehydrogenase inhibitor SW033291 ameliorates hepatic abnormal lipid metabolism, ER stress, and inflammation through PGE2/EP4 in T2DM mice

Type 2 diabetes mellitus (T2DM) is a globally prevalent metabolic disorder characterized by insulin resistance and dysfunction of islet cells. Endoplasmic reticulum (ER) stress plays a crucial role in the pathogenesis and progression of T2DM, especially in the function and survival of β-cells. β-cells are particularly sensitive to ER stress because they require substantial insulin synthesis and secretion energy. In the early stages of T2DM, the increased demand for insulin exacerbates β-cell ER stress. Although the unfolded protein response (UPR) can temporarily alleviate this stress, prolonged or excessive stress leads to pancreatic cell dysfunction and apoptosis, resulting in insufficient insulin secretion. This review explores the mechanisms of ER stress in T2DM, particularly its impact on islet cells. We discuss how ER stress activates UPR signaling pathways to regulate protein folding and degradation, but when stress becomes excessive, these pathways may contribute to β-cell death. A deeper understanding of how ER stress impacts islet cells could lead to the development of novel T2DM treatment strategies aimed at improving islet function and slowing disease progression.

Type 2 diabetes mellitus (T2DM) is characterized by impaired glucose-stimulated insulin secretion and increased peripheral insulin resistance. Unremitting endoplasmic reticulum (ER) stress can lead to beta-cell apoptosis and has been linked to type 2 diabetes. Although many studies have attempted to link ER stress and T2DM, the specific effects of ER stress on beta-cell function remain incompletely understood. To determine the interrelationship between ER stress and beta-cell function, here we treated insulin-secreting INS-1(832/13) cells or isolated mouse islets with the ER stress-inducer tunicamycin (TM). TM induced ER stress as expected, as evidenced by activation of the unfolded protein response. Beta cells treated with TM also exhibited concomitant alterations in their electrical activity and cytosolic free Ca2+ oscillations. As ER stress is known to reduce ER Ca2+ levels, we tested the hypothesis that the observed increase in Ca2+ oscillations occurred because of reduced ER Ca2+ levels and, in turn, increased store-operated Ca2+ entry. TM-induced cytosolic Ca2+ and membrane electrical oscillations were acutely inhibited by YM58483, which blocks store-operated Ca2+ channels. Significantly, TM-treated cells secreted increased insulin under conditions normally associated with only minimal release, e.g. 5 mm glucose, and YM58483 blocked this secretion. Taken together, these results support a critical role for ER Ca2+ depletion-activated Ca2+ current in mediating Ca2+-induced insulin secretion in response to ER stress.

Fenugreek seed and some of its phytoconstituents are known to possess hypoglycemic and hypolipidemic properties but their mode of action in insulin target tissues remains to be elucidated. As hepatic insulin resistance contributes to the development of type 2 diabetes mellitus (T2DM), the protective effects of fenugreek seed extract (FSE) and two of its phytoconstituents-trigonelline and diosgenin were evaluated in T2DM rats with special focus on changes in endoplasmic reticulum (ER) stress and oxidative stress markers in liver. Trigonelline and diosgenin content in FSE were quantified by HPTLC. T2DM was induced in male Sprague–Dawley rats by feeding high-fat diet and administration of low-dose streptozotocin. T2DM rats exhibited hyperglycemia and significantly reduced serum C-peptide levels. Liver damage in T2DM rats was marked by significantly elevated levels of liver marker enzymes in serum, liver triglycerides (TGs), and reduced liver glycogen and was further confirmed by histological analysis. T2DM rats also displayed twofold–threefold increase in the levels of ER chaperones Bip, protein disulfide isomerase (PDI) as well as ER stress associated proapoptotic markers CHOP, Caspase12 and Caspase3 in liver along with elevated lipid peroxidation (LPO) and reduced antioxidant levels. Promisingly, FSE, trigonelline, and diosgenin were found to exhibit protective effects individually and brought about significant reduction in serum enzymes, liver TGs, LPO, expression of liver ER stress marker proteins, and significant increase in liver glycogen content and antioxidants. Histological analysis also supported their protective effects suggesting that FSE and its phytoconstituents alleviate T2DM associated liver damage by normalizing ER stress and oxidative stress.