Identification of network-based biomarkers of cardioembolic stroke using a systems biology approach with time series data

Sirtuins: Promising Therapeutic Targets to Treat Ischemic Stroke

Stroke is a major cause of mortality and disability globally, with ischemic stroke (IS) accounting for over 80% of all stroke cases. The pathological process of IS involves numerous signal molecules, among which are the highly conserved nicotinamide adenine dinucleotide (NAD+)-dependent enzymes known as sirtuins (SIRTs). SIRTs modulate various biological processes, including cell differentiation, energy metabolism, DNA repair, inflammation, and oxidative stress. Importantly, several studies have reported a correlation between SIRTs and IS. This review introduces the general aspects of SIRTs, including their distribution, subcellular location, enzyme activity, and substrate. We also discuss their regulatory roles and potential mechanisms in IS. Finally, we describe the current therapeutic methods based on SIRTs, such as pharmacotherapy, non-pharmacological therapeutic/rehabilitative interventions, epigenetic regulators, potential molecules, and stem cell-derived exosome therapy. The data collected in this study will potentially contribute to both clinical and fundamental research on SIRTs, geared towards developing effective therapeutic candidates for future treatment of IS.

The Role of Cullin 3 in Cerebral Ischemia-Reperfusion Injury

Cullin 3 (CUL3), a member of Cullin-RING ubiquitin ligase family, regulates multiple intracellular pathways. CUL3 expression in peripheral immune cells is highly associated with the development of stroke, while little is known about the mechanism of how CUL3 participates in cerebral ischemia/reperfusion (I/R) injury. In this study, we showed that CUL3 was obviously upregulated in brain tissues of male rats received middle cerebral artery occlusion (MCAO) and reperfusion and oxygen-glucose deprivation/reoxygenation (OGD/R)-induced neurons. We firstly confirmed that CUL3 interacted with WNK3, a protein that has been proved to be associated with brain damage after ischemic stroke. CUL3 knockdown inhibited the ubiquitination of WNK3 and accelerated the phosphorylation of OSR1 in OGD/R-stimulated neurons. CUL3 silencing did not further aggravate cerebral I/R injury and played a neuroprotective role in vitro and in vivo. CUL3 knockdown attenuated the impairment of cell viability caused by OGD/R. CUL3 silencing reduced TUNEL-positive cells, down-regulated pro-apoptotic factor (Bax and Cleaved caspase 3) levels and increased the anti-apoptotic factor (Bcl-2) level in vitro and in vivo, suggesting that CUL3 repression alleviated neuronal apoptosis. Interestingly, rescue experiments revealed that WNK3 downregulation did not block the neuroprotection of CUL3 inhibition. These findings suggested that CUL3-mediated cerebral I/R injury might be not achieved through WNK3 signaling but other pathways. Furthermore, CUL3 inhibition suppressed ubiquitin-mediated degradation of Nrf2 and activated Nrf2 signaling by increasing the nuclear translocation of Nrf2 and expression levels of HO-1 and NQO-1. Taken together, CUL3 exacerbates cerebral I/R injury potentially due to its negative regulation of Nrf2 activation.

Serum Levels of VEGF-A and Its Receptors in Patients in Different Phases of Hemorrhagic and Ischemic Strokes

Vascular endothelial growth factors (VEGFs) are important regulators of angiogenesis, neuroprotection, and neurogenesis. Studies have indicated the association of VEGF dysregulation with the development of neurodegenerative and cerebrovascular diseases. We studied the changes in serum levels of VEGF-A, VEGFR-1, and VEGFR-2 in patients at various phases of ischemic and hemorrhagic strokes. Quantitative assessment of VEGF-A, VEGFR-1, and VEGFR-2 in serum of patients with hemorrhagic or ischemic stroke was performed by enzyme immunoassay in the hyper-acute (1−24 h from the onset), acute (up to 1−7 days), and early subacute (7 days to 3 months) phases of stroke, and then compared with the control group and each other. Results of our retrospective study demonstrated different levels of VEGF-A and its receptors at various phases of ischemic and hemorrhagic strokes. In ischemic stroke, increased VEGFR-2 level was found in the hyper-acute (p = 0.045) and acute phases (p = 0.024), while elevated VEGF-A and reduced VEGFR-1 levels were revealed in the early subacute phase (p = 0.048 and p = 0.012, respectively). In hemorrhagic stroke, no significant changes in levels of VEGF-A and its receptors were identified in the hyper-acute phase. In the acute and early subacute phases there was an increase in levels of VEGF-A (p < 0.001 and p = 0.006, respectively) and VEGFR-2 (p < 0.001 and p = 0.012, respectively). Serum levels of VEGF-A and its receptors in patients with hemorrhagic and ischemic stroke indicate different pathogenic pathways depending on the phase of the disease.

Modulation of autophagy by melatonin via sirtuins in stroke: From mechanisms to therapies

Sirtuins perform an important effect on the neural cell fate following stroke. Several mechanisms that have been correlated with stroke are oxidative stress, apoptosis, necrosis and autophagy. Autophagy is usually regarded as unitary of the neural cell survival mechanisms. Recently, the importance of the sirtuins effect on autophagy by antioxidant agents for stroke treatment mentioned in various studies. One of these agents is melatonin. Melatonin can modulate autophagy by changing on sirtuin pathways. Melatonin and its metabolites adjust various sirtuins pathways related to apoptosis, proliferation, metastases, autophagy and inflammation in case of stroke. In this review, we will discuss about the modulation of autophagy by melatonin via sirtuins in stroke.

Hybrid modelling for stroke care: Review and suggestions of new approaches for risk assessment and simulation of scenarios

Stroke is an example of a complex and multi-factorial disease involving multiple organs, timescales, and disease mechanisms. To deal with this complexity, and to realize Precision Medicine of stroke, mathematical models are needed. Such approaches include: 1) machine learning, 2) bioinformatic network models, and 3) mechanistic models. Since these three approaches have complementary strengths and weaknesses, a hybrid modelling approach combining them would be the most beneficial. However, no concrete approach ready to be implemented for a specific disease has been presented to date. In this paper, we both review the strengths and weaknesses of the three approaches, and propose a roadmap for hybrid modelling in the case of stroke care. We focus on two main tasks needed for the clinical setting: a) For stroke risk calculation, we propose a new two-step approach, where non-linear mixed effects models and bioinformatic network models yield biomarkers which are used as input to a machine learning model and b) For simulation of care scenarios, we propose a new four-step approach, which revolves around iterations between simulations of the mechanistic models and imputations of non-modelled or non-measured variables. We illustrate and discuss the different approaches in the context of Precision Medicine for stroke.

Ctnnb1 transcriptional upregulation compensates for Mdm2/p53-mediated β-catenin degradation in neutrophils following cardioembolic stroke

BACKGROUND

A better understanding of the mechanism(s) underlying cardioembolic stroke can promote recovery and reduce the risk of recurrent embolisms.

METHODS

Peripheral blood mononuclear cell (PBMC) gene expression datasets from cardioembolic patients and healthy controls were obtained from the Gene Expression Omnibus (GEO) database (GSE58294). The Limma software package was utilized to identify differentially-expressed genes (DEGs). Protein-protein interaction (PPI) analysis of the DEGs was performed using STRING. A weighted gene co-expression network analysis (WGCNA) was used to build a gene co-expression network. In vitro experiments assessed the effects on neutrophils exposed to oxygen and glucose-deprived (OGD) cortical neurons. An in vivo murine model of thromboembolic stroke was constructed through thrombin injection to examine effects on circulating neutrophils. Mechanistic in vitro studies were conducted using the proteasome inhibitor MG132, the p53-Mdm2 binding inhibitor Nutlin-3a, Mdm2 small-interfering RNA (siRNA), and Ctnnb1 siRNA.

RESULTS

DEG analysis identified 44 upregulated and 66 downregulated genes in cardioembolic stroke PBMCs. PPI analysis of these DEGs yielded one eight-node protein module with β-catenin (CTNNB1) as the central hub protein. Integration of the DEGs with WGCNA-derived hub genes revealed the key hub DEGs CTNNB1 and mouse double minute 2 (MDM2). Follow-up experiments revealed Mdm2, p53, and phospho-β-catenin upregulation in neutrophils exposed to OGD neurons in vitro and following thromboembolic stroke in vivo. Mechanistic studies revealed that neutrophils transcriptionally upregulate Ctnnb1 expression to compensate for Mdm2/p53-mediated β-catenin degradation induced by exposure to OGD neurons, thereby promoting neutrophil survival.

CONCLUSION

Compensatory Ctnnb1 transcriptional upregulation in neutrophils induced by ischemic neuron exposure may be involved in promoting neutrophil survival following cardioembolic stroke.

Involvement of Epigenetic Mechanisms and Non-coding RNAs in Blood-Brain Barrier and Neurovascular Unit Injury and Recovery After Stroke

Cessation of blood flow leads to a complex cascade of pathophysiological events at the blood-vascular-parenchymal interface which evolves over time and space, and results in damage to neural cells and edema formation. Cerebral ischemic injury evokes a profound and deleterious upregulation in inflammation and triggers multiple cell death pathways, but it also induces a series of the events associated with regenerative responses, including vascular remodeling, angiogenesis, and neurogenesis. Emerging evidence suggests that epigenetic reprograming could play a pivotal role in ongoing post-stroke neurovascular unit (NVU) changes and recovery. This review summarizes current knowledge about post-stroke recovery processes at the NVU, as well as epigenetic mechanisms and modifiers (e.g., DNA methylation, histone modifying enzymes and microRNAs) associated with stroke injury, and NVU repair. It also discusses novel drug targets and therapeutic strategies for enhancing post-stroke recovery.

The NAD+-Dependent Family of Sirtuins in Cerebral Ischemia and Preconditioning

SIGNIFICANCE

Sirtuins are an evolutionarily conserved family of NAD+-dependent lysine deacylases and ADP ribosylases. Their requirement for NAD+ as a cosubstrate allows them to act as metabolic sensors that couple changes in the energy status of the cell to changes in cellular physiological processes. NAD+ levels are affected by several NAD+-producing and NAD+-consuming pathways as well as by cellular respiration. Thus their intracellular levels are highly dynamic and are misregulated in a spectrum of metabolic disorders including cerebral ischemia. This, in turn, compromises several NAD+-dependent processes that may ultimately lead to cell death. Recent Advances: A number of efforts have been made to replenish NAD+ in cerebral ischemic injuries as well as to understand the functions of one its important mediators, the sirtuin family of proteins through the use of pharmacological modulators or genetic manipulation approaches either before or after the insult. Critical Issues and Future Directions: The results of these studies have regarded the sirtuins as promising therapeutic targets for cerebral ischemia. Yet, additional efforts are needed to understand the role of some of the less characterized members and to address the sex-specific effects observed with some members. Sirtuins also exhibit cell-type-specific expression in the brain as well as distinct subcellular and regional localizations. As such, they are involved in diverse and sometimes opposing cellular processes that can either promote neuroprotection or further contribute to the injury; which also stresses the need for the development and use of sirtuin-specific pharmacological modulators. Antioxid. Redox Signal. 28, 691-710.

Serum Neuroinflammatory Disease-Induced Central Nervous System Proteins Predict Clinical Onset of Experimental Autoimmune Encephalomyelitis

There is an urgent need in multiple sclerosis (MS) patients to develop biomarkers and laboratory tests to improve early diagnosis, predict clinical relapses, and optimize treatment responses. In healthy individuals, the transport of proteins across the blood–brain barrier (BBB) is tightly regulated, whereas, in MS, central nervous system (CNS) inflammation results in damage to neuronal tissues, disruption of BBB integrity, and potential release of neuroinflammatory disease-induced CNS proteins (NDICPs) into CSF and serum. Therefore, changes in serum NDICP abundance could serve as biomarkers of MS. Here, we sought to determine if changes in serum NDICPs are detectable prior to clinical onset of experimental autoimmune encephalomyelitis (EAE) and, therefore, enable prediction of disease onset. Importantly, we show in longitudinal serum specimens from individual mice with EAE that pre-onset expression waves of synapsin-2, glutamine synthetase, enolase-2, and synaptotagmin-1 enable the prediction of clinical disease with high sensitivity and specificity. Moreover, we observed differences in serum NDICPs between active and passive immunization in EAE, suggesting hitherto not appreciated differences for disease induction mechanisms. Our studies provide the first evidence for enabling the prediction of clinical disease using serum NDICPs. The results provide proof-of-concept for the development of high-confidence serum NDICP expression waves and protein biomarker candidates for MS.

Emerging Roles of Sirtuins in Ischemic Stroke

Ischemic stroke is one of the leading causes of death worldwide. It is characterized by a sudden disruption of blood flow to the brain causing cell death and damage, which will lead to neurological impairments. In the current state, only one drug is approved to be used in clinical setting and new therapies that confer ischemic neuroprotection are desperately needed. Several targets and pathways have been indicated to be neuroprotective in ischemic stroke, among which the sirtuin family of nicotinamide adenine dinucleotide (NAD+)-dependent deacetylases has emerged as important modulators of several processes in the normal physiology and pathological conditions such as stroke. Recent studies have identified some members of the sirtuin family are able to ameliorate the devastating consequences of ischemic stroke by conferring neuroprotection by means of reducing neuronal cell death, oxidative stress, and neuroinflammation whereas some sirtuins are found to be detrimental in the pathophysiology of ischemic stroke. This review summarizes implications of sirtuins in ischemic stroke and the experimental evidences that demonstrate the potential of sirtuin modulators as neuroprotective therapy for ischemic stroke.

Personalized Analysis by Validation of Monte Carlo for Application of Pathways in Cardioembolic Stroke

BACKGROUND Cardioembolic stroke (CES), which causes 20% cause of all ischemic strokes, is associated with high mortality. Previous studies suggest that pathways play a critical role in the identification and pathogenesis of diseases. We aimed to develop an integrated approach that is able to construct individual networks of pathway cross-talk to quantify differences between patients with CES and controls. MATERIAL AND METHODS One biological data set E-GEOD-58294 was used, including 23 normal controls and 59 CES samples. We used individualized pathway aberrance score (iPAS) to assess pathway statistics of 589 Ingenuity Pathways Analysis (IPA) pathways. Random Forest (RF) classification was implemented to calculate the AUC of every network. These procedures were tested by Monte Carlo Cross-Validation for 50 bootstraps. RESULTS A total of 28 networks with AUC >0.9 were found between CES and controls. Among them, 3 networks with AUC=1.0 had the best performance for classification in 50 bootstraps. The 3 pathway networks were able to significantly identify CES versus controls, which showed as biomarkers in the regulation and development of CES. CONCLUSIONS This novel approach could identify 3 networks able to accurately classify CES and normal samples in individuals. This integrated application needs to be validated in other diseases.

Profiling of Signaling Proteins in Penumbra After Focal Photothrombotic Infarct in the Rat Brain Cortex

In ischemic stroke, cell damage propagates from infarct core to surrounding tissue. To reveal proteins involved in neurodegeneration and neuroprotection, we explored the protein profile in penumbra surrounding the photothrombotic infarct core induced in rat cerebral cortex by local laser irradiation after Bengal Rose administration. Using antibody microarrays, we studied changes in expression of 224 signaling proteins 1, 4, or 24 h after photothrombotic infarct compared with untreated contralateral cortex. Changes in protein expression were greatest at 4 h after photothrombotic impact. These included over-expression of proteins initiating, regulating, or executing various apoptosis stages (caspases, SMAC/DIABLO, Bcl-10, phosphatidylserine receptor (PSR), prostate apoptosis response 4 (Par4), E2F1, p75, p38, JNK, p53, growth arrest and DNA damage inducible protein 153 (GADD153), glutamate decarboxylases (GAD65/67), NMDAR2a, c-myc) and antiapoptotic proteins (Bcl-x, p63, MDM2, p21WAF-1, ERK1/2, ERK5, MAP kinase-activated protein kinase-2 (MAKAPK2), PKCα, PKCβ, PKCμ, RAF1, protein phosphatases 1α and MAP kinase phosphatase-1 (MKP-1), neural precursor cell expressed, developmentally down-regulated 8 (NEDD8), estrogen and EGF receptors, calmodulin, CaMKIIα, CaMKIV, amyloid precursor protein (APP), nicastrin). Phospholipase Cγ1, S-100, and S-100β were down-regulated. Bidirectional changes in levels of adhesion and cytoskeleton proteins were related to destruction and/or remodeling of penumbra. Following proteins regulating actin cytoskeleton were over-expressed: cofilin, actopaxin, p120CTN, α-catenin, p35, myosin Va, and pFAK were up-regulated, whereas ezrin, tropomyosin, spectrin (α + β), β_IV-tubulin and polyglutamated β-tubulin, and cytokeratins 7 and 19 were down-regulated. Down-regulation of syntaxin, AP2β/γ, and adaptin β1/2 indicated impairment of vesicular transport and synaptic processes. Down-regulation of cyclin-dependent kinase 6 (Cdk6), cell division cycle 7-related protein kinase (Cdc7 kinase), telomeric repeat-binding factor 1 (Trf1), and topoisomerase-1 showed proliferation suppression. Cytoprotection proteins AOP-1 and chaperons Hsp70 and Hsp90 were down-regulated. These data provide the integral view on penumbra response to photothrombotic infarct. Some of these proteins may be potential targets for antistroke therapy.

Temporal Genetic Modifications after Controlled Cortical Impact--Understanding Traumatic Brain Injury through a Systematic Network Approach

Traumatic brain injury (TBI) is a primary injury caused by external physical force and also a secondary injury caused by biological processes such as metabolic, cellular, and other molecular events that eventually lead to brain cell death, tissue and nerve damage, and atrophy. It is a common disease process (as opposed to an event) that causes disabilities and high death rates. In order to treat all the repercussions of this injury, treatment becomes increasingly complex and difficult throughout the evolution of a TBI. Using high-throughput microarray data, we developed a systems biology approach to explore potential molecular mechanisms at four time points post-TBI (4, 8, 24, and 72 h), using a controlled cortical impact (CCI) model. We identified 27, 50, 48, and 59 significant proteins as network biomarkers at these four time points, respectively. We present their network structures to illustrate the protein–protein interactions (PPIs). We also identified UBC (Ubiquitin C), SUMO1, CDKN1A (cyclindependent kinase inhibitor 1A), and MYC as the core network biomarkers at the four time points, respectively. Using the functional analytical tool MetaCore™, we explored regulatory mechanisms and biological processes and conducted a statistical analysis of the four networks. The analytical results support some recent findings regarding TBI and provide additional guidance and directions for future research.

GIW and InCoB are advancing bioinformatics in the Asia-Pacific

GIW/InCoB2015 the joint 26th International Conference on Genome Informatics (GIW) and 14th International Conference on Bioinformatics (InCoB) held in Tokyo, September 9-11, 2015 was attended by over 200 delegates. Fifty-one out of 89 oral presentations were based on research articles accepted for publication in four BMC journal supplements and three other journals. Sixteen articles in this supplement and six articles in the BMC Systems Biology GIW/InCoB2015 Supplement are covered by this introduction. The topics range from genome informatics, protein structure informatics, image analysis to biological networks and biomarker discovery.