Understanding endothelial cell apoptosis: what can the transcriptome, glycome and proteome reveal?

Therapy-naïve malignancy causes cardiovascular disease: a state-of-the-art cardio-oncology perspective

Cardiovascular disease (CVD) and cancer are the leading causes of mortality worldwide. Although generally thought of as distinct diseases, the intersectional overlap between CVD and cancer is increasingly evident in both causal and mechanistic relationships. The field of cardio-oncology is largely focused on the cardiotoxic effects of cancer therapies (e.g., chemotherapy, radiation). Furthermore, the cumulative effects of cardiotoxic therapy exposure and the prevalence of CVD risk factors in patients with cancer lead to long-term morbidity and poor quality of life in this patient population, even when patients are cancer-free. Evidence from patients with cancer and animal models demonstrates that the presence of malignancy itself, independent of cardiotoxic therapy exposure or CVD risk factors, negatively impacts cardiac structure and function. As such, the primary focus of this review is the cardiac pathophysiological and molecular features of therapy-naïve cancer. We also summarize the strengths and limitations of preclinical cancer models for cardio-oncology research and discuss therapeutic strategies that have been tested experimentally for the treatment of cancer-induced cardiac atrophy and dysfunction. Finally, we explore an adjacent area of interest, called "reverse cardio-oncology," where the sequelae of heart failure augment cancer progression. Here, we emphasize the cross-disease communication between malignancy and the injured heart and discuss the importance of chronic low-grade inflammation and endocrine factors in the progression of both diseases.

Defining the Cell Surface Cysteinome Using Two-Step Enrichment Proteomics

The plasma membrane proteome is a rich resource of functionally important and therapeutically relevant protein targets. Distinguished by high hydrophobicity, heavy glycosylation, disulfide-rich sequences, and low overall abundance, the cell surface proteome remains undersampled in established proteomic pipelines, including our own cysteine chemoproteomics platforms. Here, we paired cell surface glycoprotein capture with cysteine chemoproteomics to establish a two-stage enrichment method that enables chemoproteomic profiling of cell Surface Cysteinome. Our "Cys-Surf" platform captures >2,800 total membrane protein cysteines in 1,046 proteins, including 1,907 residues not previously captured by bulk proteomic analysis. By pairing Cys-Surf with an isotopic chemoproteomic readout, we uncovered 821 total ligandable cysteines, including known and novel sites. Cys-Surf also robustly delineates redox-sensitive cysteines, including cysteines prone to activation-dependent changes to cysteine oxidation state and residues sensitive to addition of exogenous reductants. Exemplifying the capacity of Cys-Surf to delineate functionally important cysteines, we identified a redox sensitive cysteine in the low-density lipoprotein receptor (LDLR) that impacts both the protein localization and uptake of low-density lipoprotein (LDL) particles. Taken together, the Cys-Surf platform, distinguished by its two-stage enrichment paradigm, represents a tailored approach to delineate the functional and therapeutic potential of the plasma membrane cysteinome.

Defining the Cell Surface Cysteinome using Two-step Enrichment Proteomics

The plasma membrane proteome is a rich resource of functional and therapeutically relevant protein targets. Distinguished by high hydrophobicity, heavy glycosylation, disulfide-rich sequences, and low overall abundance, the cell surface proteome remains undersampled in established proteomic pipelines, including our own cysteine chemoproteomics platforms. Here we paired cell surface glycoprotein capture with cysteine chemoproteomics to establish a two-stage enrichment method that enables chemoproteomic profiling of cell Surface Cysteinome. Our "Cys-Surf" platform captures >2,800 total membrane protein cysteines in 1,046 proteins, including 1,907 residues not previously captured by bulk proteomic analysis. By pairing Cys-Surf with an isotopic chemoproteomic readout, we uncovered 821 total ligandable cysteines, including known and novel sites. Cys-Surf also robustly delineates redox-sensitive cysteines, including cysteines prone to activation-dependent changes to cysteine oxidation state and residues sensitive to addition of exogenous reductants. Exemplifying the capacity of Cys-Surf to delineate functionally important cysteines, we identified a redox sensitive cysteine in the low-density lipoprotein receptor (LDLR) that impacts both the protein localization and uptake of LDL particles. Taken together, the Cys-Surf platform, distinguished by its two-stage enrichment paradigm, represents a tailored approach to delineate the functional and therapeutic potential of the plasma membrane cysteinome.

Trans-differentiation of trophoblast stem cells: implications in placental biology

Trophoblast invasion is a hallmark of hemochorial placentation. Invasive trophoblast cells replace the endothelial cells of uterine spiral arteries. The mechanism by which the invasive trophoblast cells acquire this phenotype is unknown. Here, we demonstrate that, during differentiation, a small population of trophoblast stem (TS) cells trans-differentiate into a hybrid cell type expressing markers of both trophoblast (TC) and endothelial (EC) cells. In addition, a compendium of EC-specific genes was found to be associated with TS cell differentiation. Using functional annotation, these genes were categorized into angiogenesis, cell adhesion molecules, and apoptosis-related genes. HES1 repressed transcription of EC genes in TS cells. Interestingly, differentiated TCs secrete TRAIL, but its receptor DR4 is expressed only in ECs and not in TCs. TRAIL induced apoptosis in EC but not in TC. Co-culture of ECs with TC induced apoptosis in ECs via extrinsic apoptotic pathway. These results highlight that (a) TS cells possess the potential to trans-differentiate into "trophendothelial" phenotype, regulated by HES1 and (b) trophoblast differentiation-induced TRAIL secretion directs preferential demise of ECs located in their vicinity.

Biphasic Effect of Pirfenidone on Angiogenesis

Pirfenidone (PFD), a synthetic arsenic compound, has been found to inhibit angiogenesis at high concentrations. However, the biphasic effects of different PFD concentrations on angiogenesis have not yet been elucidated, and the present study used an in vitro model to explore the mechanisms underlying this biphasic response. The effect of PFD on the initial angiogenesis of vascular endothelial cells was investigated through a Matrigel tube formation assay, and the impact of PFD on endothelial cell migration was evaluated through scratch and transwell migration experiments. Moreover, the expression of key migration cytokines, matrix metalloproteinase (MMP)-2 and MMP-9, was examined. Finally, the biphasic mechanism of PFD on angiogenesis was explored through cell signaling and apoptosis analyses. The results showed that 10–100 μM PFD has a significant and dose-dependent inhibitory effect on tube formation and migration, while 10 nM–1 μM PFD significantly promoted tube formation and migration, with 100 nM PFD having the strongest effect. Additionally, we found that a high concentration of PFD could significantly inhibit MMP-2 and MMP-9 expression, while low concentrations of PFD significantly promoted their expression. Finally, we found that high concentrations of PFD inhibited EA.hy926 cell tube formation by promoting apoptosis, while low concentrations of PFD promoted tube formation by increasing MMP-2 and MMP-9 protein expression predominantly via the EGFR/p-p38 pathway. Overall, PFD elicits a biphasic effect on angiogenesis through different mechanisms, could be used as a new potential drug for the treatment of vascular diseases.

SARS-CoV-2 and Plasma Hypercoagulability

Hypercoagulability has emerged as a prominent consequence of COVID-19. This presents challenges not only in the clinic, but also in thrombosis research. Health and safety considerations, the status of the blood and plasma supply, the infection status of individual donors, and the mechanisms by which SARS-CoV-2 activates coagulation are all of concern. In this review, we discuss these topics from the basic research perspective. As in other respiratory illnesses, blood and plasma from COVID-19 positive patients carries minimal to no risk of infection to practitioners or researchers. There are currently no special regulatory mandates directing individual donors (for research purposes), blood centers/services or vendors (for blood products for research) to test blood/plasma for SARS-CoV-2 or antibodies. We discuss current theories about how SARS-CoV-2 leads to hyper-coagulant state in severe cases of COVID-19. Our current understanding of the mechanisms behind COVID-19 associated thromboembolic events have centered around three different pathways: (1) direct activation of platelets, enhancing coagulation; (2) direct infection and indirect activation (e.g. cytokine storm) of endothelial cells by SARS-CoV-2, shifting endothelium from an anti-thrombotic to a pro-thrombotic state; and (3) direct activation of complement pathways, promoting thrombin generation. Further investigation on how SARS-CoV-2 affects thrombosis in COVID-19 patients may bring novel anti-thrombotic therapies to combat the disease.

Identification of hub molecules of FUS-ALS by Bayesian gene regulatory network analysis of iPSC model: iBRN

Fused in sarcoma/translated in liposarcoma (FUS) is a causative gene of amyotrophic lateral sclerosis (ALS). Mutated FUS causes accumulation of DNA damage and cytosolic stress granule (SG) formation, thereby motor neuron (MN) death. However, key molecular aetiology remains unclear. Here, we applied a novel platform technology, iBRN, "Non- biased" Bayesian gene regulatory network analysis based on induced pluripotent stem cell (iPSC)-derived cell model, to elucidate the molecular aetiology using transcriptome of iPSC-derived MNs harboring FUS^H517D. iBRN revealed "hub molecules", which strongly influenced transcriptome network, such as miR-125b-5p-TIMELESS axis and PRKDC for the molecular aetiology. Next, we confirmed miR-125b-5p-TIMELESS axis in FUS^H517D MNs such that miR-125b-5p regulated several DNA repair-related genes including TIMELESS. In addition, we validated both introduction of miR-125b-5p and knocking down of TIMELESS caused DNA damage in the cell culture model. Furthermore, PRKDC was strongly associated with FUS mis-localization into SGs by DNA damage under impaired DNA-PK activity. Collectively, our iBRN strategy provides the first compelling evidence to elucidate molecular aetiology in neurodegenerative diseases.

Regulation of docosahexaenoic acid-induced apoptosis of confluent endothelial cells: Contributions of MAPKs and caspases

Endothelial cells, which help to maintain vascular homeostasis, can be functionally modulated by polyunsaturated fatty acids. Previously, we reported that docosahexaenoic acid (DHA) reduced the viability of confluent EA.hy926 endothelial cells with caspase-3 activation. This study therefore examined the molecular mechanism by which DHA affects the viability of confluent cells, with a focus on the interaction between caspase-9, caspase-8, caspase-3, p38 mitogen-activated protein kinase (MAPK) and c-Jun N-terminal kinase (JNK) by Western blotting. Our results revealed that DHA induces apoptosis of confluent cells through both intrinsic and extrinsic pathways, which requires activation of p38 MAPK, and involves activation of JNK, caspase-9, caspase-8 and caspase-3 with the exception that cleavage of caspase-8 was incomplete and truncated BID was not detected at the maximum time (8 h) examined. Apoptosis induced by high levels of DHA in healthy endothelial cells is achieved through positive feedback loops linking these MAPKs to multiple caspases, as well as negative feedback from p38 MAPK to JNK. However, only p38 MAPK is crucial in apoptosis induction in comparison with JNK or any other caspase examined. This study has expanded the knowledge on the molecular mechanism of DHA-induced apoptosis in human endothelial cells and has also implied the differential roles of MAP kinases and caspases in apoptosis.

Apolipoprotein M/sphingosine-1-phosphate: novel effects on lipids, inflammation and kidney biology

PURPOSE OF REVIEW

In 2011, the crystal structure of apolipoprotein M (apoM) and its capacity to bind sphingosine-1-phosphate (S1P) was characterized. Since then, a variety of studies has increased our knowledge on apoM biology and functionality. From being an unknown and hardly significant player in overall metabolism, apoM has gained significant interest.

RECENT FINDINGS

Key discoveries in the last 2 years have indicated that the apoM/S1P complex has important roles in lipid metabolism (affecting triglyceride turnover), inflammation (a marker of severe sepsis and potentially providing anti-inflammatory signaling) and kidney biology (potential to protect against immunoglobulin A nephropathy).

SUMMARY

Several studies suggest a potential for apoM/S1P as biomarkers for inflammation, sepsis and nephropathy. Also, a novel chaperone is characterized and could have potential as a drug for treatment in inflammation and nephropathy.

The Effect of Vitamin E and Metallothionein on the Antioxidant Capacities of Cadmium-Damaged Liver in Grass Carp Ctenopharyngodon idellus

Cadmium (Cd) causes a broad spectrum of toxicological effects to animals. Aquatic animals were more likely to accumulate Cd than terrestrial animals because of the living environment. Clearance of Cd in aquatic animals has become an important part of aquatic food safety. The present study was focused on the oxidative damage induced by Cd in the liver of grass carp Ctenopharyngodon idellus and the protective effect of vitamin E (VE) and metallothionein (MT). Grass carp were divided into four groups: the control group, Cd+phosphate-buffered saline (PBS) group, Cd+VE group, and Cd+MT group. All fish were injected with CdCl₂ on the first day and then VE, MT, and PBS were given 4 days after injection, respectively. The liver function and antioxidant capacity of grass carp were evaluated. Cd administration resulted in damage of liver function and morphology in liver, which was expressed as the increased content of AST and ALT, rupture of organelles, and decrease of CAT, SOD, and GSH-Px activity. However, VE and MT treatments protected against Cd-induced damage of liver in grass carp by decreasing AST and ALT content, repairing organelles, and maintained the antioxidant system by elevating CAT, SOD, and GSH-Px activity and regulating related mRNA transcript expression. The results revealed that VE and MT might play an important role in the treatment of heavy metal poisoning through their antioxidative effects.

Extracellular vesicles from oral squamous carcinoma cells display pro- and anti-angiogenic properties

BACKGROUND

A new intercellular communication mode established by neoplastic cells and tumor microenvironment components is based on extracellular vesicles (EVs). However, the biological effects of the EVs released by tumor cells on angiogenesis are not completely understood. Here, we aimed to understand the biological effects of EVs isolated from two cell lines of oral squamous cell carcinoma (OSCC) (SCC15 and HSC3) on endothelial cell tubulogenesis.

METHODS

OSCC-derived EVs were isolated with a polymer-based precipitation method, quantified using nanoparticle tracking analysis and verified for EV markers by dot blot. Functional assays were performed to assess the angiogenic potential of the OSCC-derived EVs.

RESULTS

The results showed that EVs derived from both cell lines displayed typical spherical-shaped morphology and expressed the EV markers CD63 and Annexin II. Although the average particle concentration and size were quite similar, SCC15-derived EVs promoted a pronounced tubular formation associated with significant migration and apoptosis rates of the endothelial cells, whereas EVs derived from HSC3 cells inhibited significantly endothelial cell tubulogenesis and proliferation.

CONCLUSION

The findings of this study reveal that EVs derived from different OSCC cell lines by a polymer-based precipitation method promote pro- or anti-angiogenic effects.

Hepatoprotective Activity of Vitamin E and Metallothionein in Cadmium-Induced Liver Injury in Ctenopharyngodon idellus

As an environmental and industrial pollutant, cadmium (Cd) can cause a broad spectrum of toxicological effects. Multiple organs, especially the liver, are considerably affected by Cd in both humans and animals. We investigated the protective effects of metallothionein (MT) and vitamin E (VE) supplementation on Cd-induced apoptosis in the grass carp (Ctenopharyngodon idellus) liver. Grass carp were divided into four groups: the control group, Cd + phosphate-buffered saline (PBS) group, Cd + VE group, and Cd + MT group. All fish were injected with CdCl₂ on the first day and then VE, MT, and PBS were given 4 days postinjection, respectively. The results showed that Cd administration resulted in liver poisoning in grass carp, which was expressed as an increase in Cd contents, malondialdehyde (MDA) concentration, percentage of hepatocyte apoptosis, and apoptosis-related gene mRNA transcript expression. However, VE and MT treatments protected against Cd-induced hepatotoxicity in grass carp by decreasing Cd contents, lipid peroxidation, and histological damage and reducing the percentage of hepatocyte apoptosis by regulating related mRNA transcript expression. These data demonstrate that oxidative stress and activation of the caspase signaling cascade play a critical role in Cd-induced hepatotoxicity. However, VE and MT alleviate Cd-induced hepatotoxicity through their antioxidative and antiapoptotic effects, and MT has a more powerful effect than VE.

Wnt3a promotes pro-angiogenic features in macrophages in vitro: Implications for stroke pathology

Wnt3a is implicated in several key cellular processes and its expression has been reported in different cell types. Here, we report a novel function for Wnt3a in macrophages, whose exposure to this ligand shifts them towards a pro-angiogenic phenotype capable, under oxygen and glucose deprivation, of inducing in vitro tubular pattern structures in endothelial cells resembling capillary-like vasculature. These newly acquired angiogenetic features also include increased proliferation and migration and surprisingly, an increase in cell death. This work provides a new link between Wnt3a and macrophage-mediated angiogenesis under glucose and oxygen deprivation in vitro, which are worth further investigation in pathological conditions including stroke, where the stimulation of the angiogenic process might help to recovery after tissue injury Impact statement This work provides a new link between Wnt3a and macrophage-mediated angiogenesis under glucose and oxygen deprivation in vitro. Our results reveal how Wnt3a shifts macrophages towards a pro-angiogenic phenotype, which is able-in absence of both glucose and oxygen-of inducing angiogenesis in vitro, thus pointing to a synergy between the activation of the pathway and the hypoxia scenario. This work also demonstrates that modulation of cell death is key in order to explain the observed angiogenic effects. We consider all these findings of significant importance, since no connection between Wnt3a, macrophages, and angiogenesis has been established so far. Furthermore, we do believe that this work provides new and interesting results, with Wnt signaling pathway emerging as an interesting target mediating beneficial outcomes during the inflammatory response undoubtedly linked to stroke pathology, where angiogenesis has been already proposed as a potential mechanism to promote recovery after the injury.

HDL-associated ApoM is anti-apoptotic by delivering sphingosine 1-phosphate to S1P1 & S1P3 receptors on vascular endothelium

Background

High-density Lipoprotein (HDL) attenuates endothelial cell apoptosis induced by different cell-death stimuli such as oxidation or growth factor deprivation. HDL is the main plasma carrier of the bioactive lipid sphingosine 1-phosphate (S1P), which it is a signaling molecule that promotes cell survival in response to several apoptotic stimuli. In HDL, S1P is bound to Apolipoprotein M (ApoM), a Lipocalin that is only present in around 5% of the HDL particles. The goal of this study is to characterize ApoM-bound S1P role in endothelial apoptosis protection and the signaling pathways involved.

Methods

Human umbilical vein endothelial cells (HUVEC) cultures were switched to serum/grow factor deprivation medium to induce apoptosis and the effect caused by the addition of ApoM and S1P analyzed.

Results

The addition of HDL^+ApoM or recombinant ApoM-bound S1P promoted cell viability and blocked apoptosis, whereas HDL^-ApoM had no protective effect. Remarkably, S1P exerted a more potent anti-apoptotic effect when carried by ApoM as compared to albumin, or when added as free molecule. Mechanistically, cooperation between S1P1 and S1P3 was required for the HDL/ApoM/S1P-mediated anti-apoptotic ability. Furthermore, AKT and ERK phosphorylation was also necessary to achieve the anti-apoptotic effect of the HDL/ApoM/S1P complex.

Conclusions

Altogether, our results indicate that ApoM and S1P are key elements of the anti-apoptotic activity of HDL and promote optimal endothelial function.

Electronic supplementary material

The online version of this article (doi:10.1186/s12944-017-0429-2) contains supplementary material, which is available to authorized users.

6-Gingerol induces autophagy to protect HUVECs survival from apoptosis

6-Gingerol, the major pharmacologically-active component of ginger, has the potential to prevent heart disease. However, the mechanisms are not well understood. In this study, the protective effect of 6-gingerol against hydrogen peroxide-induced apoptosis in human umbilical vein endothelial cells (HUVECs) was investigated. Apoptosis was detected by Hoechst 33342 and Flow cytometry analysis. To further elucidate the crosstalk between apoptosis and autophagy, we tested the expression of autophagy related proteins, LC3B, Bcl-2, Beclin1, AKT, p-AKT, mechanistic target of rapamycin (mTOR), and p-mTOR. Furthermore, mitochondrial membrane potential and the intracellular generation of reactive oxygen species (ROS) were also investigated. Our data revealed that 6-gingerol significantly reduced apoptosis by inducing autophagy. It has been demonstrated that 6-gingerol suppressed the phosphatidylinositol 3-kinase (PI3K)/AKT/mTOR signaling pathway, increased the expression of Beclin1 to promote autophagy, and increased Bcl-2 expression to inhibit apoptosis. In addition, the damage of mitochondrial was protected, and ROS level was decreased by 6-gingerol. These firmly indicate 6-gingerol has a strong protective ability against the apoptosis caused by oxidative stress in HUVECs, and the mechanism may relate to the induction of autophagy. Our data suggest 6-gingerol may be beneficial in the prevention of atherosclerosis.

Fibroblast growth factor rescues brain endothelial cells lacking presenilin 1 from apoptotic cell death following serum starvation

Presenilin 1 (Psen1) is important for vascular brain development and is known to influence cellular stress responses. To understand the role of Psen1 in endothelial stress responses, we investigated the effects of serum withdrawal on wild type (wt) and Psen1−/− embryonic brain endothelial cells. Serum starvation induced apoptosis in Psen1−/− cells but did not affect wt cells. PI3K/AKT signaling was reduced in serum-starved Psen1−/− cells, and this was associated with elevated levels of phospho-p38 consistent with decreased pro-survival AKT signaling in the absence of Psen1. Fibroblast growth factor (FGF1 and FGF2), but not vascular endothelial growth factor (VEGF) rescued Psen1−/− cells from serum starvation induced apoptosis. Inhibition of FGF signaling induced apoptosis in wt cells under serum withdrawal, while blocking γ-secretase activity had no effect. In the absence of serum, FGF2 immunoreactivity was distributed diffusely in cytoplasmic and nuclear vesicles of wt and Psen1−/− cells, as levels of FGF2 in nuclear and cytosolic fractions were not significantly different. Thus, sensitivity of Psen1−/− cells to serum starvation is not due to lack of FGF synthesis but likely to effects of Psen1 on FGF release onto the cell surface and impaired activation of the PI3K/AKT survival pathway.

CD31 signals confer immune privilege to the vascular endothelium

Constitutive resistance to cell death induced by inflammatory stimuli activating the extrinsic pathway of apoptosis is a key feature of vascular endothelial cells (ECs). Although this property is central to the maintenance of the endothelial barrier during inflammation, the molecular mechanisms of EC protection from cell-extrinsic, proapoptotic stimuli have not been investigated. We show that the Ig-family member CD31, which is expressed by endothelial but not epithelial cells, is necessary to prevent EC death induced by TNF-α and cytotoxic T lymphocytes in vitro. Combined quantitative RT-PCR array and biochemical analysis show that, upon the engagement of the TNF receptor with TNF-α on ECs, CD31 becomes activated and, in turn, counteracts the proapoptotic transcriptional program induced by TNF-α via activation of the Erk/Akt pathway. Specifically, Akt activation by CD31 signals prevents the localization of the forkhead transcription factor FoxO3 to the nucleus, thus inhibiting transcription of the proapoptotic genes CD95/Fas and caspase 7 and de-repressing the expression of the antiapoptotic gene cFlar. Both CD31 intracellular immunoreceptor tyrosine-based inhibition motifs are required for its prosurvival function. In vivo, CD31 gene transfer is sufficient to recapitulate the cytoprotective mechanisms in CD31(-) pancreatic β cells, which become resistant to immune-mediated rejection when grafted in fully allogeneic recipients.

Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis

BACKGROUND

Apoptosis is a critical process in endothelial cell (EC) biology and pathology, which has been extensively studied at protein level. Numerous gene expression studies of EC apoptosis have also been performed, however few attempts have been made to use gene expression data to identify the molecular relationships and master regulators that underlie EC apoptosis. Therefore, we sought to understand these relationships by generating a Bayesian gene regulatory network (GRN) model.

RESULTS

ECs were induced to undergo apoptosis using serum withdrawal and followed over a time course in triplicate, using microarrays. When generating the GRN, this EC time course data was supplemented by a library of microarray data from EC treated with siRNAs targeting over 350 signalling molecules.The GRN model proposed Vasohibin-1 (VASH1) as one of the candidate master-regulators of EC apoptosis with numerous downstream mRNAs. To evaluate the role played by VASH1 in EC, we used siRNA to reduce the expression of VASH1. Of 10 mRNAs downstream of VASH1 in the GRN that were examined, 7 were significantly up- or down-regulated in the direction predicted by the GRN.Further supporting an important biological role of VASH1 in EC, targeted reduction of VASH1 mRNA abundance conferred resistance to serum withdrawal-induced EC death.

CONCLUSION

We have utilised Bayesian GRN modelling to identify a novel candidate master regulator of EC apoptosis. This study demonstrates how GRN technology can complement traditional methods to hypothesise the regulatory relationships that underlie important biological processes.

Revisiting the pathogenesis of rheumatic fever and carditis

Rheumatic fever is one of the most-neglected ailments, and its pathogenesis remains poorly understood. The major thrust of research has been directed towards cross-reactivity between streptococcal M protein and myocardial α-helical coiled-coil proteins. M protein has also been the focus of vaccine development. The characteristic pathological findings suggest that the primary site of rheumatic-fever-related damage is subendothelial and perivascular connective tissue matrix and overlying endothelium. Over the past 5 years, a streptococcal M protein N-terminus domain has been shown to bind to the CB3 region in collagen type IV. This binding seems to initiate an antibody response to the collagen and result in ground substance inflammation. These antibodies do not cross-react with M proteins, and we believe that no failure of immune system and, possibly, no molecular mimicry occur in rheumatic fever. This alternative hypothesis shares similarity with collagen involvement in both Goodpasture syndrome and Alport syndrome.

A high-throughput fluorescence resonance energy transfer (FRET)-based endothelial cell apoptosis assay and its application for screening vascular disrupting agents

In this study, we developed a high-throughput endothelial cell apoptosis assay using a fluorescence resonance energy transfer (FRET)-based biosensor. After exposure to apoptotic inducer UV-irradiation or anticancer drugs such as paclitaxel, the fluorescence of the cells changed from green to blue. We developed this method into a high-throughput assay in 96-well plates by measuring the emission ratio of yellow fluorescent protein (YFP) to cyan fluorescent protein (CFP) to monitor the activation of a key protease, caspase-3, during apoptosis. The Z' factor for this assay was above 0.5 which indicates that this assay is suitable for a high-throughput analysis. Finally, we applied this functional high-throughput assay for screening vascular disrupting agents (VDA) which could induce endothelial cell apoptosis from our in-house compounds library and dioscin was identified as a hit. As this assay allows real time and sensitive detection of cell apoptosis, it will be a useful tool for monitoring endothelial cell apoptosis in living cell situation and for identifying new VDA candidates via a high-throughput screening.

Fibroblast growth factor 2 is a key determinant of vascular sprouting during bovine luteal angiogenesis

Fibroblast growth factor (FGF) 2 and vascular endothelial growth factor (VEGF) A are thought to be key controllers of luteal angiogenesis; however, their precise roles in the regulation and coordination of this complex process remain unknown. Thus, the temporal and spatial patterns of endothelial network formation were determined by culturing mixed cell types from early bovine corpora lutea on fibronectin in the presence of FGF2 and VEGFA (6 h to 9 days). Endothelial cells, as determined by von Willebrand factor immunohistochemistry, initially grew in cell islands (days 0–3), before undergoing a period of vascular sprouting to display a more tubule-like appearance (days 3–6), and after 9 days in culture had formed extensive intricate networks. Mixed populations of luteal cells were treated with SU1498 (VEGF receptor 2 inhibitor) or SU5402 (FGF receptor 1 inhibitor) or control on days 0–3, 3–6 or 6–9 to determine the role of FGF2 and VEGFA during these specific windows. The total area of endothelial cells was unaffected by SU1498 treatment during any window. In contrast, SU5402 treatment caused maximal reduction in the total area of endothelial cell networks on days 3–6 vs controls (mean reduction 81%;P<0.001) during the period of tubule initiation. Moreover, SU5402 treatment on days 3–6 dramatically reduced the total number of branch points (P<0.001) and degree of branching per endothelial cell island (P<0.05) in the absence of changes in mean island area. This suggests that FGF2 is a key determinant of vascular sprouting and hence critical to luteal development.

Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers

We present a novel algorithm to estimate genome-wide gene networks consisting of more than 20,000 genes from gene expression data using nonparametric Bayesian networks. Due to the difficulty of learning Bayesian network structures, existing algorithms cannot be applied to more than a few thousand genes. Our algorithm overcomes this limitation by repeatedly estimating subnetworks in parallel for genes selected by neighbor node sampling. Through numerical simulation, we confirmed that our algorithm outperformed a heuristic algorithm in a shorter time. We applied our algorithm to microarray data from human umbilical vein endothelial cells (HUVECs) treated with siRNAs, to construct a human genome-wide gene network, which we compared to a small gene network estimated for the genes extracted using a traditional bioinformatics method. The results showed that our genome-wide gene network contains many features of the small network, as well as others that could not be captured during the small network estimation. The results also revealed master-regulator genes that are not in the small network but that control many of the genes in the small network. These analyses were impossible to realize without our proposed algorithm.

Biological assessment of robust noise models in microarray data analysis

Motivation: Although several recently proposed analysis packages for microarray data can cope with heavy-tailed noise, many applications rely on Gaussian assumptions. Gaussian noise models foster computational efficiency. This comes, however, at the expense of increased sensitivity to outlying observations. Assessing potential insufficiencies of Gaussian noise in microarray data analysis is thus important and of general interest.

Results: We propose to this end assessing different noise models on a large number of microarray experiments. The goodness of fit of noise models is quantified by a hierarchical Bayesian analysis of variance model, which predicts normalized expression values as a mixture of a Gaussian density and t-distributions with adjustable degrees of freedom. Inference of differentially expressed genes is taken into consideration at a second mixing level. For attaining far reaching validity, our investigations cover a wide range of analysis platforms and experimental settings. As the most striking result, we find irrespective of the chosen preprocessing and normalization method in all experiments that a heavy-tailed noise model is a better fit than a simple Gaussian. Further investigations revealed that an appropriate choice of noise model has a considerable influence on biological interpretations drawn at the level of inferred genes and gene ontology terms. We conclude from our investigation that neglecting the over dispersed noise in microarray data can mislead scientific discovery and suggest that the convenience of Gaussian-based modelling should be replaced by non-parametric approaches or other methods that account for heavy-tailed noise.

Contact:peter.sykacek@boku.ac.at

Availability:http://bioinf.boku.ac.at/alexp/robmca.html.

Transcriptional regulation of the vascular endothelial glycome by angiogenic and inflammatory signalling

Vascular endothelial cells undergo many molecular changes during pathological processes such as inflammation and tumour development. Tumours such as malignant lymphomas affecting bone marrow are dependent on interactions with endothelial cells for (1) site-specific homing and (2) tumour-induced angiogenesis. Modifications in glycosylation are responsible for fine-tuning of distinct endothelial surface receptors. In order to gain a comprehensive insight into the regulation of the endothelial glycome, comprising genes encoding for sugar transporters (sugar s/t), glycosyltransferases (GT), glycan-degrading enzymes (GD) and lectins (GBP), we performed gene profiling analysis of the human bone marrow-derived microvascular endothelial cell line HBMEC-60 that resembles closely in its biological behaviour primary bone marrow endothelial cells. HBMEC were activated by either angiogenic VEGF or the inflammatory cytokine TNF. Approximately 48% (207 genes) of the 432 glycome genes tested were found to be expressed in HBMEC-60 cells. Inflammatory and angiogenic signals produce different profiles of up- or down-regulated glycome genes, most prominent changes were seen under TNF stimulation in terms of signal intensity and number of alterations. Stimulation by VEGF and TNF affected primarily genes encoding for glycosyltransferases and in particular those important for terminal modulation. For instance, an enhanced alpha2,6 sialylation was observed after TNF stimulation at the transcriptional and glycan expression level whereas transcription of ST3Gal1 sialylating in alpha2,3 position was enhanced after VEGF stimulation. Transcriptional analysis of the glycome gives insights into the differential regulation of glycosylation pathways and may help to understand the functional impact of endothelial glycosylation.

Inference of gene regulatory networks using time-series data: a survey

The advent of high-throughput technology like microarrays has provided the platform for studying how different cellular components work together, thus created an enormous interest in mathematically modeling biological network, particularly gene regulatory network (GRN). Of particular interest is the modeling and inference on time-series data, which capture a more thorough picture of the system than non-temporal data do. We have given an extensive review of methodologies that have been used on time-series data. In realizing that validation is an impartible part of the inference paradigm, we have also presented a discussion on the principles and challenges in performance evaluation of different methods. This survey gives a panoramic view on these topics, with anticipation that the readers will be inspired to improve and/or expand GRN inference and validation tool repository.

Analysis of PPARalpha-dependent and PPARalpha-independent transcript regulation following fenofibrate treatment of human endothelial cells

Fenofibrate is a synthetic ligand for the nuclear receptor peroxisome proliferator-activated receptor (PPAR) alpha and has been widely used in the treatment of metabolic disorders, especially hyperlipemia, due to its lipid-lowering effect. The molecular mechanism of lipid-lowering is relatively well defined: an activated PPARalpha forms a PPAR-RXR heterodimer and this regulates the transcription of genes involved in energy metabolism by binding to PPAR response elements in their promoter regions, so-called "trans-activation". In addition, fenofibrate also has anti-inflammatory and anti-athrogenic effects in vascular endothelial and smooth muscle cells. We have limited information about the anti-inflammatory mechanism of fenofibrate; however, "trans-repression" which suppresses production of inflammatory cytokines and adhesion molecules probably contributes to this mechanism. Furthermore, there are reports that fenofibrate affects endothelial cells in a PPARalpha-independent manner. In order to identify PPARalpha-dependently and PPARalpha-independently regulated transcripts, we generated microarray data from human endothelial cells treated with fenofibrate, and with and without siRNA-mediated knock-down of PPARalpha. We also constructed dynamic Bayesian transcriptome networks to reveal PPARalpha-dependent and -independent pathways. Our transcriptome network analysis identified growth differentiation factor 15 (GDF15) as a hub gene having PPARalpha-independently regulated transcripts as its direct downstream children. This result suggests that GDF15 may be PPARalpha-independent master-regulator of fenofibrate action in human endothelial cells.

Antiapoptotic activities of bcl-2 correlate with vascular maturation and transcriptional modulation of human endothelial cells

Overexpression of a caspase-resistant form of Bcl-2 (D34A) in human umbilical vein endothelial cells (ECs) implanted into immunodeficient mice promotes the maturation of human EC-lined microvessels invested by vascular smooth muscle cells (VSMCs) of mouse origin. In contrast, EC implants not overexpressing Bcl-2 form only simple, uncoated EC tubes. Here the authors compare the phenotypes of vessels formed in vivo and the transcriptomes in vitro of EC expressing different forms of Bcl-2. Wild-type Bcl-2, like the caspase-resistant D34A Bcl-2 mutant, is antiapoptotic in vitro and promotes VSMC recruitment in vivo, whereas a G145E mutant that has diminished antiapoptotic activity in vitro does not promote vessel maturation in vivo. The D34A and wild-type forms of Bcl-2, but not the G145E mutant form of Bcl-2, significantly regulate RNA transcripts previously associated with EC-VSMC interactions and VSMC biology, including matrix Gla protein, insulin-like growth factor-binding protein (IGFBP)-2, matrix metalloproteinase (MMP)-14, ADAM17, stanniocalcin-1, and targets of the nuclear factor (NF)-kappa B, cAMP response element-binding (CREB), and activator protein 1 (AP1) transcription factor families. These effects of Bcl-2 on the transcriptome are detected in ECs cultured as angiogenic three-dimensional (3-D) tubes but are attenuated in ECs cultured as 2-D monolayers. Bcl-2-regulated transcription in ECs may contribute to vascular maturation, and support design of tissue engineering strategies using EC.

Left ventricular assist device-induced molecular changes in the failing myocardium

PURPOSE OF REVIEW

There is considerable increase in the use of left ventricular assist devices for the treatment of severe heart failure. Traditionally viewed as a bridge to transplantation and more recently as a destination therapy, left ventricular assist device support is now recognized to offer potential for myocardial recovery through reverse remodeling, a potential that is further enhanced by combination with pharmacologic therapy. In this study, we examine the molecular changes associated with left ventricular assist device support and how these may contribute to the recovery process.

RECENT FINDINGS

Studies in both patients and experimental models have demonstrated that improved function is associated with alterations in several key pathways including cell survival, cytokine signaling, calcium handling, adrenergic receptor signaling, cytoskeletal and contractile proteins, energy metabolism, extracellular matrix, and endothelial and microvascular functions. Moreover, the unique research opportunities offered by left ventricular assist device analysis are beginning to distinguish changes associated with recovery from those of mechanical unloading alone and identify potential predictors and novel therapeutic targets capable of enhancing myocardial repair.

SUMMARY

Significant progress has been made toward revealing molecular changes associated with myocardial recovery from heart failure. These studies also offer new insight into the pathogenesis of heart failure and point to novel therapeutic strategies.

Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models

MOTIVATION

Statistical inference of gene networks by using time-course microarray gene expression profiles is an essential step towards understanding the temporal structure of gene regulatory mechanisms. Unfortunately, most of the current studies have been limited to analysing a small number of genes because the length of time-course gene expression profiles is fairly short. One promising approach to overcome such a limitation is to infer gene networks by exploring the potential transcriptional modules which are sets of genes sharing a common function or involved in the same pathway.

RESULTS

In this article, we present a novel approach based on the state space model to identify the transcriptional modules and module-based gene networks simultaneously. The state space model has the potential to infer large-scale gene networks, e.g. of order 10(3), from time-course gene expression profiles. Particularly, we succeeded in the identification of a cell cycle system by using the gene expression profiles of Saccharomyces cerevisiae in which the length of the time-course and number of genes were 24 and 4382, respectively. However, when analysing shorter time-course data, e.g. of length 10 or less, the parameter estimations of the state space model often fail due to overfitting. To extend the applicability of the state space model, we provide an approach to use the technical replicates of gene expression profiles, which are often measured in duplicate or triplicate. The use of technical replicates is important for achieving highly-efficient inferences of gene networks with short time-course data. The potential of the proposed method has been demonstrated through the time-course analysis of the gene expression profiles of human umbilical vein endothelial cells (HUVECs) undergoing growth factor deprivation-induced apoptosis.

AVAILABILITY

Supplementary Information and the software (TRANS-MNET) are available at http://daweb.ism.ac.jp/~yoshidar/software/ssm/.