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Differential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

This paper was designed to study stereoselective enrichment and changes in gene expression when zebrafish (Danio rerio) embryo-larvae were exposed to racemic, (-)- or (+)- PCB149 (2,2',3,4',5',6- hexachlorobiphenyl). Based on bioconcentration analysis, non-racemic enrichment was significantly observed after racemic exposure. No isomerization between the two isomers was found after (-)/(+)-PCB149 exposure. Furthermore, based on gene expression-data mining, CYPs genes (cyp2k6, cyp19a1b, and cyp2aa4) were differential genes after (+)-PCB149 exposure. No obvious differences of dysregulation of gene expression caused by racemic and (-)-PCB149, were observed in embryo-larvae. The above results suggested that (-)-PCB149 could be considered as the main factor causing the dysregulation of gene expression in embryo-larvae after racemic exposure; and (+)-PCB149 should be pursued apart from the racemate, when considering the toxicity of chiral PCB149. Thus, the information in our study could provide new insights to assess the environmental risk of chiral PCBs in aquatic systems.

Background: Acute kidney injury (AKI), a common pathological process following hemorrhagic shock, can lead to an internal milieu disorder, which is an important factor of multiple organ failure (MOF). It has been shown that the mesenteric lymph return plays a deleterious effect on MOF induced by hemorrhagic shock. In this study, we investigated the effects of mesenteric lymph duct ligation (MLDL) on gene expression profiles of renal tissue following hemorrhagic shock with fluid resuscitation., Methods: After establishment of hemorrhagic shock model and fluid resuscitation in rats of shock and shock ligation groups, the MLDL was performed in shock ligation group, and only threading under the mesenteric lymph duct in the shock group. Then, the fixed position renal tissue was taken out for homogenate in two groups at 3 h after resuscitation, the total mRNA was extracted, reversely transcribed into cDNAs and marked with Cy3 and Cy5. The cDNAs were subjected for microarray scanning with 12,028 cDNA probes; the differentially expressed genes between two groups were analyzed., Results: In the 5812 valid dates of rat genomes transcription, there were 34 known differentially expressed genes between the two groups, of which 11 genes were up-regulated whereas 23 genes were down-regulated by MLDL. These different expressed genes encoding protein function were mainly involved in signal transduction, transcription regulation, metabolism, transport, cell growth, cell cycle, cell adhesion, cell movement, cellular component, and biological process., Conclusions: The mechanism of MLDL alleviating the AKI aftershock might be associated with up- or down-regulation of the above gene expressions.

Combining information across genes in the statistical analysis of microarray data is desirable because of the relatively small number of data points obtained for each individual gene. Here we develop an estimator of the error variance that can borrow information across genes using the James-Stein shrinkage concept. A new test statistic (FS) is constructed using this estimator. The new statistic is compared with other statistics used to test for differential expression: the gene-specific F test (F1), the pooled-variance F statistic (F3), a hybrid statistic (F2) that uses the average of the individual and pooled variances, the regularized t-statistic, the posterior odds statistic B, and the SAM t-test. The FS-test shows best or nearly best power for detecting differentially expressed genes over a wide range of simulated data in which the variance components associated with individual genes are either homogeneous or heterogeneous. Thus FS provides a powerful and robust approach to test differential expression of genes that utilizes information not available in individual gene testing approaches and does not suffer from biases of the pooled variance approach.

Rationale: Noncoding RNAs (ncRNAs) such as microRNAs (miRs or miRNAs) play important roles in the control of cellular processes through posttranscriptional gene regulation. However, ncRNA research is limited to utilizing RNA agents synthesized in vitro. Recombinant RNAs produced and folded in living cells shall better recapitulate biologic RNAs. Methods: Herein, we developed a novel platform for in vivo fermentation production of humanized recombinant ncRNA molecules, namely hBERAs, carrying payload miRNAs or siRNAs. Target hBERAs were purified by anion exchange FPLC method. Functions of hBERA/miRNAs were investigated in human carcinoma cells and antitumor activities were determined in orthotopic osteosarcoma xenograft spontaneous lung metastasis mouse models. Results: Proper human tRNAs were identified to couple with optimal hsa-pre-miR-34a as new fully-humanized ncRNA carriers to accommodate warhead miRNAs or siRNAs. A group of 30 target hBERAs were all heterogeneously overexpressed (each accounting for >40% of total bacterial RNA), which facilitated large-scale production (8-31 mg of individual hBERAs from 1L bacterial culture). Model hBERA/miR-34a-5p and miR-124-3p were selectively processed to warhead miRNAs in human carcinoma cells to modulate target gene expression, enhance apoptosis and inhibit invasiveness. In addition, bioengineered miR-34a-5p and miR-124-3p agents both reduced orthotopic osteosarcoma xenograft tumor growth and spontaneous pulmonary metastases significantly. Conclusion: This novel ncRNA bioengineering technology and resulting recombinant ncRNAs are unique additions to conventional technologies and tools for basic research and drug development.

Dimethomorph (DMM) is a broad-spectrum fungicide used globally in agricultural production, but little is known regarding the immunotoxicity of DMM in humans. In this study, the immunotoxicity of DMM on human Jurkat T cells was evaluated in vitro. The results indicated that the half-effective concentration (EC50) of DMM for Jurkat cells was 126.01 mg/L (0.32 mM). To further elucidate the underlying mechanism, transcriptomics based on RNA sequencing for exposure doses of EC25 (M21) and EC10 (L4) was performed. The results indicated that compared to untreated samples (Ctr), 121 genes (81 upregulated, 40 downregulated) and 30 genes (17 upregulated, 13 downregulated) were significantly differentially regulated in the L4 and M21 samples, respectively. A gene ontology analysis indicated that the significantly differentially expressed genes (DEGs) were mostly enriched in the negative regulation of cell activities, and a KEGG pathway analysis indicated that the DEGs were mainly enriched in the immune regulation and signal transduction pathways. A quantitative real-time PCR for the selected genes showed that compared to the high-dose exposure (M21), the effect of the low-dose DMM exposure (L4) on gene expression was more significant. The results indicated that DMM has potential immunotoxicity for humans, and this toxicity cannot be ignored even at low concentrations. [ABSTRACT FROM AUTHOR]

Neuroprotection in acute stroke has not been successfully translated from animals to humans. Animal research on promising agents continues largely in rats and mice which are commonly available to researchers. However, controversies continue on the most suitable species to model the human situation. Generally, putative agents seem less effective in mice as compared with rats. We hypothesized that this may be due to inter-species differences in stroke response and that this might be manifest at a genetic level. Here we used whole-genome microarrays to examine the differential gene regulation in the ischemic penumbra of mice and rats at 2 and 6 h after permanent middle cerebral artery occlusion (pMCAO; Raw microarray CEL data files are available in the GEO database with an accession number GSE163654). Differentially expressed genes (adj. p ≤ 0.05) were organized by hierarchical clustering, correlation plots, Venn diagrams and pathway analyses in each species and at each time-point. Emphasis was placed on genes already known to be associated with stroke, including validation by RT-PCR. Gene expression patterns in the ischemic penumbra differed strikingly between the species at both 2 h and 6 h. Nearly 90% of significantly regulated genes and most pathways modulated by ischemia differed between mice and rats. These differences were evident globally, among stroke-associated genes, immediate early genes, genes implicated in stress response, inflammation, neuroprotection, ion channels, and signal transduction. The findings of this study may have significant implications for the choice of species for screening putative stroke therapies. [ABSTRACT FROM AUTHOR]

Deoxythymidilate kinase (DTYMK) has been identified as a putative oncogene associated with the incidence of hepatocellular carcinoma (HCC), but the mechanisms whereby it regulates this cancer type remain uncertain. The present study was therefore designed to explore the role of DTYMK in HCC and to evaluate the underlying molecular mechanisms. MiRNAs associated with DTYMK expression levels in HCC were identified through analyses of both clinical samples and publically available gene expression datasets. We then assessed the putative functions of DTYMK and miR-148b-3p in this oncogenic context through studies of HCC cells and a murine xenograft model system. Correlation analyses and in vitro experiments led us to confirm DTYMK as a target of miR-148b-3p. In addition, we assessed dTTP levels associated with the DTYMK pathway in HCC cells to understand the functional implications of our experimental findings. We found that HCC tissues and cells exhibited marked DTYMK upregulation and miR-148b-3p downregulation, with the expression levels of DTYMK and miR-148b-3p being negatively correlated with one another. The impact of overexpressing DTYMK in tumor cells was partially reversed upon cellular transfection with miR-148b-3p mimics, providing conclusive evidence that DTMYK is a target of this miRNA. Importantly, DTYMK-related dTTP levels were also impacted by miR-148b-3p mimic transfection. DTYMK is a key regulator of HCC progression, and its expression is suppressed by miR-148b-3p, suggesting that this miR-148b-3p/DTYMK regulatory axis may be amenable to therapeutic targeting in patients with HCC. [ABSTRACT FROM AUTHOR]

Several gene expression studies have been previously conducted to characterize molecular basis of Wooden Breast myopathy in commercial broiler chickens. These studies have generally used a limited sample size and relied on a binary disease outcome (unaffected or affected by Wooden Breast), which are appropriate for an initial investigation. However, to identify biomarkers of disease severity and development, it is necessary to use a large number of samples with a varying degree of disease severity. Therefore, in this study, we assayed a relatively large number of samples (n = 96) harvested from the pectoralis major muscle of unaffected (U), partially affected (P) and markedly affected (A) chickens. Gene expression analysis was conducted using the nCounter MAX Analysis System and data were analyzed using four different supervised machine-learning methods, including support vector machines (SVM), random forests (RF), elastic net logistic regression (ENET) and Lasso logistic regression (LASSO). The SVM method achieved the highest prediction accuracy for both three-class (U, P and A) and two-class (U and P+A) classifications with 94% prediction accuracy for two-class classification and 85% for three-class classification. The results also identified biomarkers of Wooden Breast severity and development. Additionally, gene expression analysis and ultrastructural evaluations provided evidence of vascular endothelial cell dysfunction in the early pathogenesis of Wooden Breast. [ABSTRACT FROM AUTHOR]

Motivation Several methods have been proposed for the paired RNA-seq analysis. However, many of them do not consider the heterogeneity in treatment effect among pairs that can naturally arise in real data. In addition, it has been reported in literature that the false discovery rate (FDR) control of some popular methods has been problematic. In this paper, we present a full hierarchical Bayesian model for the paired RNA-seq count data that accounts for variation of treatment effects among pairs and controls the FDR through the posterior expected FDR. Results Our simulation studies show that most competing methods can have highly inflated FDR for small to moderate sample sizes while PairedFB is able to control FDR close to the nominal levels. Furthermore, PairedFB has overall better performance in ranking true differentially expressed genes (DEGs) on the top than others, especially when the sample size gets bigger or when the heterogeneity level of treatment effects is high. In addition, PairedFB can be applied to identify the biologically significant DEGs with controlled FDR. The real data analysis also indicates PairedFB tends to find more biologically relevant genes even when the sample size is small. PairedFB is also shown to be robust with respect to the model misspecification in terms of its relative performance compared to others. Availability and implementation Software to implement this method (PairedFB) can be downloaded at: https://sites.google.com/a/udel.edu/qiujing/publication. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Uptake of Ca2+ into the mitochondrial matrix controls cellular metabolism and survival-death pathways. Several genes are implicated in controlling mitochondrial Ca2+ uptake (mitochondrial calcium regulatory genes, MCRGs), however, less is known about the factors which influence their expression level. Here we have compared MCRG mRNA expression, in neural cells of differing type (cortical neurons vs. astrocytes), differing neuronal subtype (CA3 vs. CA1 hippocampus) and in response to Ca2+ influx, using a combination of qPCR and RNA-seq analysis. Of note, we find that the Mcu-regulating Micu gene family profile differs substantially between neurons and astrocytes, while expression of Mcu itself is markedly different between CA3 and CA1 regions in the adult hippocampus. Moreover, dynamic control of MCRG mRNA expression in response to membrane depolarization-induced Ca2+ influx is also apparent, resulting in repression of Letm1, as well as Mcu. Thus, the mRNA expression profile of MCRGs is not fixed, which may cause differences in the coupling between cytoplasmic and mitochondrial Ca2+, as well as diversity of mitochondrial Ca2+ uptake mechanisms. [ABSTRACT FROM AUTHOR]

Recent studies found that TIPE2 was involved in cancer development. However, little is known about TIPE2 in lung cancer. Our study aims to clarify the role of TIPE2 in lung carcinogenesis. We examined the expression of TIPE2 in lung squamous cancer (LSC), small cell lung cancer and lung adenocarcinoma (AdC) tissues and found that TIPE2 expression was lost in small cell lung cancer, compared with adjacent non-tumor tissues. Overexpression of TIPE2 significantly inhibited the growth of lung cancer cell H446 in vitro and even suppressed tumor formation in vivo. Flow cytometry analysis found TIPE2 overexpression promoted apoptosis of H446. In TIPE2 over-expression cells, caspase-3, caspase-9, and Bax were significantly up-regulated while Bcl-2 was down-regulated. Moreover, coincident results were shown by immunohistochemistry in tumors from nude mice. TIPE2 inhibited the phosphorylation of Akt, while promoting the phosphorylation of P38, but had no effect on IκBα and ERK pathway. Taken together, TIPE2 promoted lung cancer cell apoptosis through affecting apoptosis-related molecules caspase-3, caspase-9, Bcl-2 and Bax, possibly via regulating P38 and Akt pathways, indicating that TIPE2 might be a novel marker for lung cancer diagnosis and therapy. [ABSTRACT FROM AUTHOR]

Epilepsy is a common neurological disease. Understanding the mechanisms of epileptogenesis at the cellular and molecular levels may provide novel targets for preventing this disorder. Brain-derived neurotrophic factor ( BDNF) and its receptor tropomyosin-related kinase type B ( Trk B) are believed to be critical for epileptogenesis. Previous studies have revealed possible changes in the expression of full-length Trk B receptors ( Trk B. FL) and truncated Trk B receptors ( Trk B. T) in neurodegenerative disorders. In this study, we investigated alterations in Trk B receptor expression and Trk B signalling activity in a rat hippocampal neuronal model of spontaneous recurrent epileptiform discharges ( SREDs) and the effects on the epileptiform discharges. To induce epileptiform discharges, we established a model with Mg2+-free treatment. We found a dramatic upregulation of Trk B. T and a decrease in Trk B. FL in the SREDs model. Calpain contributed to the downregulation of Trk B. FL. The upregulation of Trk B. T required transcription and translation activity. Furthermore, BDNF induced the activation of Trk B. FL signalling. However, Trk B. FL signalling was inhibited in the SREDs model. Although calpain inhibitors prevented a decrease in Trk B. FL, they did not restrain the downregulation of Trk B. FL signalling activity in the model. However, a SREDs model with a translation inhibitor prevented the increase in Trk B. T and re-activated Trk B. FL signalling activity. Finally, we used electrophysiology to observe that a downregulation of Trk B. T could relieve the representative epileptiform discharges in the model. These results, taken together, demonstrate that alterations in Trk B. FL signalling may be regulated via Trk B. T receptors. Upregulation of Trk B. FL signalling suppresses epileptiform discharges in the SREDs model. [ABSTRACT FROM AUTHOR]

Background: Identifying differentially expressed genes has been an important and widely used approach to investigate gene functions and molecular mechanisms. A related issue that has drawn much less attention but is equally important is the identification of constantly expressed genes across different conditions. A common practice is to treat genes that are not significantly differentially expressed as significantly equivalently expressed. Such naive practice often leads to large false discovery rate and low power. The more appropriate way for identifying constantly expressed genes should be conducting high dimensional statistical equivalence tests. A well-known equivalence test, the two one-sided tests (TOST), can be used for this purpose. However, due to the small sample sizes often associated with genomics data, the variance estimator in the TOST test could be unstable. Hence it would be fitting to examine the application of shrinkage variance estimators to the TOST test in high dimensional settings. Result: In this paper, we study the effect of shrinking the variance estimators in the TOST test in high dimensional settings through simulation studies. In addition, we derive analytic formulas for the p-value of the resultant shrinkage variance TOST test and apply it to a real data set. [ABSTRACT FROM AUTHOR]

Objective To investigate the expression of Toll - like receptor 4 (TLR4) protein in hippocampus of rat model with temporal lobe epilepsy after status epilepticus (SE) and explore its function in the pathogenesis of temporal lobe epilepsy. Methods Rat model with temporal lobe epilepsy was induced by lithium chloride (LiCl)-pilocarpine. Total protein was extracted from hippocampus and rat brain slices were obtained at different time points (0, 1, 6, 12, 24, 48 h and 7, 10, 30, 50 d) after SE. Western blotting and immunohistochemical staining were used for detection of the expression of TLR4 in the hippocampus. Results The results of Western blotting showed the TLR4 protein expression at 0, 1, 6, 12, 24, 48 h and 7, 10, 30 d after SE was higher than that in the control group (P < 0.05, for all), and the TLR4 protein expression at 50 d after SE showed no significant difference compared with the control group (P = 0.714). There was no significant difference between LiCl group and control group (P = 0.590). The results of immunohistochemistry showed the number of TLR4 positive neuron in CA3 area at 1, 6, 12, 24, 48 h and 7, 10, 30, 50 d after SE was higher than that in the control group (P < 0.05, for all), but showed no significant difference at 0 h after SE (P = 0.326). There was no significant difference between LiCl group and model group at 0 h after SE (P = 0.451). The difference in CA1 and CA2 area in different groups was not statistically significant (P > 0.05). Conclusion TLR4 protein was mainly expressed in cytoplasm of pyramidal cells in CA3 area of hippocampus. TLR4 protein expression in the hippocampus was increased in varying degrees at different observation time points after SE, indicating that TLR4 may play an important role in the development of epilepsy [ABSTRACT FROM AUTHOR]

Recently, TiO nanotube layers are widely used in orthopedics and dental applications because of their good promotion effect on bone cells. Furthermore, peptide sequences such as arginine-glycine-aspartic acid are used to modify Ti implant for binding to cell surface integrins through motif. In this study, a cellular adhesive peptide of arginine-glycine-aspartic acid-cysteine (RGDC) was immobilized onto anodized TiO nanotubes on Ti to examine its in vitro responses on rat bone marrow stromal cells (BMSCs). Materials were characterized by scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy techniques. High-resolution C1s scans suggested the presence of RGDC on the surface and SEM images confirmed the nanotubes were not destroyed after modification. BMSCs adhesion and osteogenic gene expression were detected in TiO nanotube layers with and without RGDC modification by fluorescence microscopy, confocal laser scanning microscopy, SEM, and realtime polymerase chain reaction (Real-time PCR). Results showed that the TiO nanotube layers immobilized with RGDC increased BMSCs adhesion compared to nonfunctionalized nanotubes after 4 h of cultivation. Furthermore, the osteogenic gene expression of BMSCs was dramatically enhanced on the TiO nanotube layers immobilized with RGDC (10 mM) compared to the TiO nanotube layers immobilized with RGDC (1 mM) and non-functionalized anodized Ti. Our results from in vitro study provided evidence that Ti anodized to possess nanotubes and then further functionalized with RGDC should be further studied for the design of better biomedical implant surfaces. [ABSTRACT FROM AUTHOR]

Microarray technology is commonly used to identify differentially expressed (DE) genes across conditions. A related issue that has rarely been discussed but is equally important is to identify commonly expressed genes or constantly expressed genes across different organs, tissues, or species. A common practice in the literature for such studies is to apply the differential expression analysis and conclude that a gene is unchanged if there is no statistical evidence to conclude for differential expression. However, genes that are not statistically significantly DE could be (1) truly non-DE genes or (2) truly DE genes not detected by the statistical test of differential expression due to lack of power resulted from high noise level or lack of replication. Therefore, the practice of treating non-statistically significantly DE genes as non-DE genes has the risk of including genes that are truly DE without controlling such errors. We argue that if one wants to identify genes that are truly non-DE, one needs to show statistical evidence through valid statistical tests with the appropriate type I error rate control. In this paper, we consider the identification of non-DE genes through statistical equivalence tests under the framework of multiple testing. In particular, we consider the average equivalence criterion and study the power and false discovery rate (FDR) of the standard average equivalence test, the “two one-sided tests” (TOST), through extensive simulation studies based on real microarray data sets. We study the effects of various factors that can affect the power and FDR of the equivalence test including the proportion of non-DE genes. We also compare the ROC curves of the equivalence test with those of the naive method of selecting genes that are not statistically significant DE. [ABSTRACT FROM AUTHOR]

The pathophysiology of atopic dermatitis (AD) is complex. CD4+ T cells play an essential role in the development of lesions in AD. However, the underlying mechanism remains unclear. In the present study, we investigated the differentially expressed genes (DEGs) between adult AD lesioned and non-lesioned skin using two datasets from the Gene Expression Omnibus (GEO) database. 62 DEGs were shown to be related to cytokine response. Compared to non-lesioned skin, lesioned skin showed immune infiltration with increased numbers of activated natural killer (NK) cells and CD4+ T memory cells (p < 0.01). We then identified 13 hub genes with a strong association with CD4+ T cells using weighted correlation network analysis. Single-cell analysis of AD detected a novel CD4+ T subcluster, CD4+ tissue residency memory cells (TRMs), which were verified through immunohistochemistry (IHC) to be increased in the dermal area of AD. The significant relationship between CD4+ TRM and AD was assessed through further analyses. FOXO1 and SBNO2, two of the 13 hub genes, were characteristically expressed in the CD4+ TRM, but down-regulated in IFN-γ/TNF-α-induced HaCaT cells, as shown using quantitative polymerase chain reaction (qPCR). Moreover, SBNO2 expression was associated with increased Th1 infiltration in AD (p < 0.05). In addition, genes filtered using Mendelian randomization were positively correlated with CD4+ TRM and were highly expressed in IFN-γ/TNF-α-induced HaCaT cells, as determined using qPCR and western blotting. Collectively, our results revealed that the newly identified CD4+ TRM may be involved in the pathogenesis of adult AD. • Single-cell analysis detects two fates of CD4+ TRM in atopic dermatitis. • Transcriptomic features of JUND+CD4+ TRM indicate their anti-apoptosis and pro-inflammatory activity in atopic dermatitis. • JUND+CD4+ TRM appear to upregulate IFN-γ+ cell infiltration. • MMP12 and TNFRSF6B are positively associated with immune infiltration of JUND+CD4+ TRM in atopic dermatitis. [ABSTRACT FROM AUTHOR]

Microbe-associated molecular pattern (MAMP)-triggered immunity (MTI) is an important component of the plant innate immunity response to invading pathogens. Although several MTI responses can be measured in different plant species, their magnitude is probably plant species specific and even cultivar specific. In this study, a genome-wide transcriptome analysis of two soybean parental lines and two progeny lines treated for 30 min with the MAMPs flg22 and chitin was carried out. This analysis revealed a clear variation in gene expression, under both untreated and flg22+chitin-treated conditions. In addition, genes with potential additive and non-additive effects were identified in the two progeny lines, with several of these genes having a potential function in the control of innate immunity. The data presented herein represent the basis for further functional analysis that can lead to a better understanding of the soybean innate immunity response. [ABSTRACT FROM AUTHOR]

Background:This study aimed to identify major proteins in the pathogenesis of coronary artery in-stent restenosis (ISR) in diabetic minipigs with sirolimus-eluting stenting, and to investigate the roles of key candidate molecules, particularly ADAM10, in human arterial smooth muscle cells (HASMCs). Methods and Results:The stents were implanted in the coronary arteries of 15 diabetic and 26 non-diabetic minipigs, and angiography was repeated at six months. The intima of one vascular segment with significant ISR and one with non-ISR in diabetic minipigs were isolated and cultured in conditioned medium (CM). The CM was analyzed by LC-MS/MS to uncover proteins whose levels were significantly increased (≥1.5-fold) in ISR than in non-ISR tissues. After literature searching, we focused on the identified proteins, whose biological functions were most potentially related to ISR pathophysiology. Among them, ADAM10 was significantly increased in diabetic and non-diabetic ISR tissues as compared with non-ISR controls. In cell experiments, retrovirus-mediated overexpression of ADAM10 promoted growth and migration of HASMCs. The effects of ADAM10 were more remarkable in high-glucose culture than in low-glucose culture. Using shRNA and an inhibitor of γ-secretase (GSI), we found that the influences of ADAM10 were in part mediated by Notch1 and notch 3 pathway, which up-regulated Notch downstream genes and enhanced nuclear translocation of the small intracellular component of Notch1 and Notch3. Conclusions:This study has identified significantly increased expression of ADAM10 in the ISR versus non-ISR segment in diabetic minipigs and implicates ADAM10 in the enhanced neointimal formation observed in diabetes after vascular injury. [ABSTRACT FROM AUTHOR]

Abstract: Objective: We aim to check if serum levels of receptor for advanced glycation endproduct (RAGE) ligands S100B, S100A6 and S100P were related to myocardial injury in acute coronary syndrome (ACS). Methods: Serum levels of S100B, S100A6, S100P, and soluble RAGE (sRAGE) were analyzed in 882 patients. Based upon clinical and laboratory findings, they were assigned into control (n =251), stable angina (n =211), and ACS (n =420). To verify clinical data of ACS, forty Sprague-Dawley rats were subjected to cardiac ischemia–reperfusion (I/R) injury by occluding proximal (large infarct size; n =20) or distal (small infarct size; n =20) left anterior descending coronary artery, and another 20 rats were in sham-operation group. The expressions of S100B, S100A6, S100P and RAGE in the myocardium were analyzed. Results: Serum levels of S100B, S100A6 and S100P were higher in ACS group than in stable angina and control groups, and sRAGE levels were higher in ACS patients versus controls (all p <0.01). S100B and S100P levels correlated significantly with CK-MB and troponin I levels in ACS group (all p <0.05). In multivariable regression analysis, S100B, S100A6, S100P and conventional risk factors were independently associated with ACS. In animal models, the expressions of S100B, S100A6 and S100P were closely related to infarct size (all p <0.05). Conclusion: This study indicates that serum levels of S100B, S100A6 and S100P are associated with ACS, and serum levels and myocardial expression of these proteins are related to infarct size. [Copyright &y& Elsevier]