Month: February 2020

On the other hand, we observed 7 miRs of which miR-98, miR-486-3p, and miR-874 showed low values of co-expression correlation and miR-124, miR-381, miR-501-5p, and miR-660 showed high values of coexpression correlation in F-BC compared with NF-BC network profile. Out of 49, 8 not predicted miR–mRNA interactions showing inverse correlation could also distinguish F-BC from NF-BC tumors. Among them 5 pairs could be considered as predicted targets albeit using less stringent criteria. From 49 miR–mRNA interactions, 24 showed differentially expressed genes and significant coexpression differences; however, they did not exhibit inverse signal of fold-change value, suggesting that the separation between F-BC from NF-BC tumors could not be exclusively explained by the predominant mechanism of miRs-mediated gene repression. We perBortezomib formed functional analysis using the IPA program on a set formed by 28 unique genes representing 49 predicted/not predicted miRmRNA interactions listed in table S4. The results from functional analysis demonstrated over representation of some biological processes involved with: apoptosis, cell death, and fibroblast proliferation. We present the results of integrated analysis of miR/mRNA data from the same tumor tissue samples to identify genes that could differentiate between tumor harvested from young patients with familial BC and those from sporadic BC, not harboring BRCA1/BRCA2 mutations. We identified a set of 9 miRs whose expression levels, rather than miR identity, were able to correctly separate, with high accuracy, familial and non-familial young BC patients. A subset of these miRs has previously been characterized as BC regulatory genes, including miR-486-3p, miR-98, miR-874, miR-210, miR-124, whereas miR-660 has been associated with other cancers or tissue types. We next identified a set of miRs showing significant negative or positive correlations with those of their targets. Approximately 34,6% retained inversely correlated miR–mRNA interactions. An interaction network revealed changes in the co-expression of these miR-mRNA pairs that were able to distinguish familial from sporadic breast cancer. For instance, a decreased expression of miR-874, miR-98 and miR-486-3p were associated with increased expression of their predicted target genes in F-BC cases. MiR-874, which has been previously associated with unfavorable prognosis in invasive breast cancer was inversely correlated with several of their paired genes, suggesting that miR-874 has a critical role in the regulation of genes preferentially expressed in F-BC. This analysis revealed genes involved in embryonic stem cell self-renewal, such as STAT3 and EZH1. FGD6 is a mediator of EGFR endocytosis and its inhibition in BC coincided with an enhanced EGF-signaling. TBRG1 was previously identified as one of the TGFb1-responsive genes and has been described as a novel growth inhibitor that contributes to the maintenance of chromosomal stability. VPS13A codes for vacuolar sorting proteins, and its loss was observed in colorectal and gastric cancers with high microsatellite instability.

Differences were observed in intrinsic apoptosis induction at the single-cell level. These biological findings imply that apoptosis induction at the single-cell level depends on the stochastic behaviors of intranuclear biological reaction processes generated in the p53 signaling network, including DSB generation and repair. In silico experiments using mathematical modeling and mathematical analysis are one available method of understanding the cell fate decision mechanism as a result of fluctuations of those cellular responses, i.e., cell-to-cell variability in p53 pulses and apoptosis induction under conditions of various stress intensities. Several mathematical models have been used to explore the mechanism by which the dynamics of p53 affect cell cycle arrest and apoptosis induction. Till date, one prominent finding was reported by Zhang et al.; they constructed an integrative model of four modules—generation and repair of IR-induced DSBs module, ATM switch module, p53-Mdm2 oscillator module, and cell fate decision module—and reported the possibility that stochasticity in DSB generation led to cell-to-cell variability in cell fate. However, Zhang’s model did not take into consideration any stochasticity in the generation of the p53 pulse, and the question of whether any effect of IR dose is observed on the dynamics of the p53 signaling network remained unanswered. The cell fate decision mechanism consists of several signal transduction systems that extend into two spaces, the nucleus and cytoplasm. In general, the Tubulin Acetylation Inducer existing probability of intranuclear proteins is much smaller than that of cytoplasmic proteins. Hence, the intranuclear biochemical reaction processes develop notable fluctuations compared with the cytoplasmic ones. We inferred that stochasticity in the dynamics of the p53 signaling network also has a profound relationship with cell-to-cell variability in cell fate. This hypothesis is in agreement with the implication based on the abovementioned biological findings. It is well known that stochastic simulation is useful for exploring the emergence and collapse of biological functions. Our novel mathematical model, which realized stochasticity in both the generation and repair of DSB and the p53 signaling network, has the potential to elucidate the dynamic behavior of the cell fate decision mechanism under conditions of various stress intensities. In this paper, we describe the construction of a massive integrative model that consists of the generation of IR-induced DSB, DSB repair system, p53 signaling network, and apoptosis induction pathway. These, except for the apoptosis induction pathway, are described as intranuclear biochemical reactions. Because they are modeled as stochastic processes, intrinsic noise is introduced into the simulation of intranuclear reactions. In contrast, the apoptosis induction pathway is described as cytoplasmic reactions and is modeled as a deterministic process. To demonstrate the biological validation of the proposed model, we then compared the abovementioned biological findings observed in NIH3T3 cells, MCF7 cells, and fibrosarcoma cells with corresponding simulations of the same results.

Third, regulation by miRNAs occurs at the network level. In this study, we selectively investigated the function of let-7b, but other miRNAs that contributed to the disease and their communication with let-7b, especially for the up-stream signal of let-7b and its role in CTEPH, still needed further study and evaluation. Fourth, our previous study of miRNA profile of PASMCs culture from pulmonary endarterectomy tissue also found let-7d, another member of let-7 family, was decreased and involved in the cell proliferation, which indicated the importance of let-7 family in pathogenesis of CTEPH. A hypothesis about the mechanism leading to the decrease of let-7 family is still needed to be set in our further study.The present study replicated and extended our previous findings regarding the effects of exposure of rats to GAS extract. Immunologically, exposure to GAS led to an increase in sera antiGAS antibodies as well as to the presence of antibodies in the striatum, PFC and thalamus, as we have previously found. Behaviorally, GAS exposure led to impaired food manipulation and increased marble-burying without a concomitant increase in activity level. These behavioral alterations may be relevant to symptoms commonly observed in GAS-related neuropsychiatric disorders, including impaired fine motor control, anxiety and compulsions. A novel finding of the present study is that GAS-exposure led to an increase in the level of TH and of D1 and D2 dopamine receptors in the striatum and PFC. These results add to our previous findings of altered dopamine function following GAS exposure. Specifically, the D2 antagonist, haloperidol, ameliorated motor impairment in GAS-exposed rats ; anti-D1 and anti-D2 IgG were detected in the sera of these rats ; and their dopamine level in the frontal cortex and basal ganglia was increased. Involvement of the dopaminergic system has been repeatedly implicated in the pathogenesis of GAS-related neuropsychiatric disorders: Anti-dopaminergic drugs such as haloperidol are used to treat motor symptoms in GAS-related disorders ; anti-D1 and anti-D2 antibodies were detected in the sera of SC and PANDAS patients ; and increased levels of TH were found in brains of rats injected with antibodies purified from SC patients. Interestingly, sera and IgG from SC and PANDAS patients and from GAS-exposed rats led to increased CAM-KII activity in vitro, and CAM-KII activity has been shown to up-regulate the D2 dopamine receptor promoter in vitro. There are previous reports that antibodies to neuronal cell surface can lead to changes in the function and level of their targeted protein, thus leading to neuronal and behavioral alterations. For instance, anti-AMPA receptor antibodies in AMPA receptor encephalitis as well as WY 14643 anti-NMDA receptor antibodies in anti-NMDA receptor encephalitis and in paraneoplastic syndrome were reported to decrease synaptic density of the receptor.

Based on these in silico results, we selectively focused on let-7b to study its cellular function relevant to the disease, because the predicted targets of it were likely to be involved in CTEPH pathogenesis. Let-7b has been reported to be an antioncogenic miRNA which is frequently lost in many tumors. By the preliminary correlation analysis with clinical characteristics of CTEPH patients, we found that circulating let-7b levels were decreased in patients with negative AVR, which was generally regarded to be related with serious pulmonary WZ8040 vascular remodeling. This illuminating result indicated the possible role of let-7b in pulmonary vascular biology of CTEPH pathogenesis. In the further mechanism study, we found that let-7b could target ET-1 and TGFBR1, which have been reported to be closely related to the pathogenesis of CTEPH. Antagonizing let-7b could up-regulate ET-1 and TGFBR1 expression, which promoted PAECs and PASMCs migration. These effects would lead to persistent constriction or remodeling of pulmonary vascular bed and promote CTEPH development. Positive correlation was also found between let-7b and PAI-1 or D-Dimer, which were regarded to be elevated in thrombotic diseases. Therefore, the positive correlation gave no direct indication for the role of let-7b in coagulation process of CTEPH. The exact mechanism still needs further study. It was mainly secreted by endothelial cells and mediate vascular constriction and PASMCs proliferation through endothelin A and B receptors. In CTEPH patients, increases of ET-1 were significantly correlated with clinical characteristics. In addition, elevated serum ET-1 was demonstrated to be a predictor of bad pulmonary endarterectomy outcome. Endothelin receptor antagonists have emerged as cornerstone treatment for PAH for more than 10 years. In CTEPH patients, especially inoperable ones, ETAs were also of benefit in hemodynamics. ET-1 expression was a complex biological process. In the present study, we showed a new aspect of ET-1 expression regulation at the posttranscriptional level by a miRNA. The down-regulation of let-7b was correlated with elevation of plasma ET-1 level, and this might be accomplished through two ways. First, ET-1 was a direct target of let-7b, and it was derepressed when let-7b was down-regulated. Second, TGF-b was one of the most potent regulators of ET-1 expression. It strongly increased ET-1 mRNA and protein expression in endothelial, and specifically, TGF-b induced ET-1 expression preferentially through the TGFBR1/Smad3 pathway. Our results suggested that decreased let-7b up-regulated the expression of TGFBR1, which was in turn possibly involved in the elevation of ET-1 in CTEPH patients. In addition, ET-1 is a mitogenic growth factor especially in pulmonary circulation. By wound healing assay, we further illustrated that derepression of ET1 by let-7b partially participated in the PAECs migration, and the elevated ET-1 could induce PASMCs migration. The aberrant migration of PAECs and PASMCs was further related to the pulmonary vascular remodeling of CTEPH patients. Besides regulation of ET-1 expression, TGFBR1 and downstream signals played an important role in biology of pulmonary vessels.

Although Schaadt et al. have previously developed models to predict the substrate specificity of Gefitinib transporters for A. thaliana proteins, one limitation of their models is that only 61 proteins were used in the training dataset for model development. Chen et al. have developed models to predict the substrate specificity for electron transporters, protein/mRNA transporters, ion transporters, and other transporters, and more recently improved this method to differentiate transporters from non-transporters using a probability distribution function for each query protein. This improved method, which is essentially a combination of the original Chen et al. model and the Ou et al. model, is limited in that the proposed threshold of 0.65 is not reliable for the prediction of transporters. Barghash et al. model is also limited to classifying transporters of only four substrates and at TC family/subfamily level. The models developed in the present study can simultaneously predict whether a query protein is a transporter or non-transporter protein and its substrate specificity for seven transporter protein classes. One advantage of our model is that it can differentiate cation and anion transporters. Our PSSM-based model demonstrated superior performance with respect to substrate specificity prediction. However, this model was computationally demanding when the PSSM profile was generated from the UniRef90 database. We observed that our TrSSP web server would take approximately 6–15 minutes per sequence to run when the UniRef90 database was used for PSSM generation. To significantly reduce the PSSM computational time, we implemented parallel computing for PSSM generation and used the UniProt/ SwissProt database as the reference database, which reduced the runtime of our TrSSP server to approximately 10 minutes for approximately 200 sequences with no impact on model performance. During vaginal transmission of HIV-1, virions in semen must traverse the thin layer of cervicovaginal mucus coating the vaginal epithelium before they can encounter and potentially infect target cells. Due to the presence of substantial quantities of secreted and transudated antibodies, CVM possesses both diffusional and immunological barrier properties against sexually transmitted viruses. In women with healthy vaginal microflora, lactobacilli secrete substantial levels of lactic acid, producing an acidic environment that inactivates leukocytes within minutes. Thus, few immune cells capable of opsonization and antibody-dependent cell-mediated cytotoxicity are actually present in healthy CVM secretions, which also exhibit limited complement activity. Neutralization, a process in which secreted or topically-applied Ab engage the gp120/gp41 trimeric glycoproteins on HIV at sufficient stoichiometry to preclude their attachment to target cells, is thus generally thought to be a critical component of sterilizing immunity against initial HIV infections in the vagina. Effective neutralization in the vaginal lumen that directly reduces the rates of acquiring initial infections, rather than attempting to clear infections, may be especially important since HIV infections remain difficult to cure.