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Background. Ewing's sarcoma (ES) is the most common malignant primary bone tumor in children and adolescents. This study is aimed at developing new prognostic markers and building a microRNA-mRNA network in the development of ES. Method. GSE80201 and GSE39262 were downloaded from the Gene Expression Omnibus (GEO) database. Bioinformatics analysis was used to download and process data. The coexpression of differentially expressed microRNAs (DEMs) and genes (DEGs) was selected by using R software. The FunRich database was utilized to perform cellular component (CC), molecular function (MF), and biological process (BP) enrichment analysis. Cytoscape and ClueGO were used to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and construct the mRNA-microRNA network. The Kaplan-Meier Plotter was used to perform prognosis analysis between the expression level of genes we selected and overall survival (OS) of patients with ES. Univariate analysis and multivariate analysis were carried out to research the prognostic value of identified mRNA expression in ES according to TCGA database. Results. By using bioinformatics analysis, 10 DEMs and 5 target mRNAs were identified. Based on the KmPlot software, COL1A2, COL3A1, and TGFBI were significantly related to the OS of patients with ES. High COL3A1 mRNA expression was correlated with distant metastasis, margin status, and poor overall survival of ES. Besides, multivariate analysis indicated that COL3A1 was an independent risk factor for ES patients. Conclusions. In conclusion, our results suggest that COL3A1 and its related molecules may be a potential diagnostic and prognostic biomarker for patients with ES. [ABSTRACT FROM AUTHOR]

Circular RNAs (circRNAs) are endogenous RNAs with a covalently closed continuous loop, generated through various backsplicing events of pre-mRNA. An accumulating number of studies have shown that circRNAs are potential biomarkers for major human diseases such as cancer and Alzheimer's disease. Thus, identification and prediction of human disease-associated circRNAs are of significant importance. To this end, a computational analysis-assisted strategy is indispensable to detect, verify, and quantify circRNAs for downstream applications. In this review, we briefly introduce the biology of circRNAs, including the biogenesis, characteristics, and biological functions. In addition, we outline about 30 recent bioinformatic analysis tools that are publicly available for circRNA study. Principles for applying these computational strategies and considerations will be briefly discussed. Lastly, we give a complete survey on more than 20 key computational databases that are frequently used. To our knowledge, this is the most complete and updated summary on publicly available circRNA resources. In conclusion, this review summarizes key aspects of circRNA biology and outlines key computational strategies that will facilitate the genome-wide identification and prediction of circRNAs. [ABSTRACT FROM AUTHOR]

CIP2A, cancerous inhibitor of protein phosphatase 2A, was initially recognized as an oncoprotein. Recently several studies revealed that CIP2A could function as a prognosis biomarker, however, the result remained not comprehensive, partly due to small number of patients included individually. Here we carried out a meta-analysis of published studies to assess the prognostic significance of CIP2A in solid tumors. All eligible studies were identified through searching PubMed, Embase and Web of Science database. In this meta-analysis, 22 studies involving 4,579 participants were included, and we verified that CIP2A over-expression was significantly related with poor overall survival (pooled HR = 1.844, 95% CI = 1.528–2.225, P<0.001) and short disease free survival (pooled HR = 1.808, 95% CI = 1.591–2.055, P<0.001) in solid tumors. Additionally, subgroup analysis suggested that the trend of a poor overall survival with an increased CIP2A expression was present in East-Asian and European patients, as well as in lung cancer and colorectal cancer. To sum up, CIP2A over-expression was associated with poor survival in human solid tumors and might be a predictive factor of poor prognosis. [ABSTRACT FROM AUTHOR]

Itch is described as an unpleasant or irritating skin sensation that elicits the desire or reflex to scratch. MrgprA3, one of members of the Mrgprs family, is specifically expressed in a subpopulation of dorsal root ganglion (DRG) in the peripheral nervous system (PNS). These MrgprA3-expressing DRG neurons have been identified as itch-specific neurons. They can be activated by the compound, chloroquine, which is used as a drug to treat malaria. In the present study, we labeled these itch-specific neurons using the method of molecular genetic markers, and then studied their electrophysiological properties. We also recorded the cutaneous MrgprA3 − neurons retrogradely labeled by Dil dye (MrgprA3 − -Dil). We first found that MrgprA3 + neurons have a lower excitability than MrgprA3 − neurons (MrgprA3 − -non-Dil and MrgprA3 − -Dil). The number of action potential (AP) was reduced more obviously in MrgprA3 + neurons than that of in MrgprA3 − neurons. In most cases, MrgprA3 + neurons only generated single AP; however, in MrgprA3 − neurons, the same stimulation could induce multiple AP firing due to the greater voltage-gated potassium (Kv) current existence in MrgprA3 + than in MrgprA3 − neurons. Thus, Kv current plays an important role in the regulation of excitability in itch-specific neurons. [ABSTRACT FROM AUTHOR]

Background: Clusterin, a heterodimeric glycoprotein of approximately 80 kDa, exists extensively in human body fluids. The abnormal expression of clusterin is closely related to the occurrence, progression, and prognosis of tumors. Up to now, few studies have focused on clusterin in human testicular cancer. This study describes an extensive exploration of the presence and expression of clusterin in testicular seminoma. Methods: Tumor tissues and normal testis tissues were collected from 13 patients with testicular seminoma and 16 patients undergoing surgical castration for prostate cancer. Real-time polymerase chain reaction (PCR) was performed to detect the expression difference of clusterin mRNA between testicular seminoma and normal testis. Western blot and immunohistochemical analysis were performed to detect the presence and expression difference of clusterin protein between two groups. Results: Real-time PCR showed the expression of clusterin mRNA in testicular seminoma to be significantly lower than in normal testis (only 13% relative quantification). Western blot analysis indicated marked reductions in the expression of clusterin protein in testicular seminoma. Similar results were observed upon immunohistochemical analysis. Conclusion: In testicular seminoma and normal testis, clusterin exists in its heterodimeric secretory isoform. Clusterin expression is significantly lower in testicular seminoma than in normal testis. This is the first comprehensive study of the presence and expression of clusterin in human testicular cancer. © 2013 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Objective: Retinal vascular endothelial cell (RVECs) injury is a major cause of morbidity and mortality among the patients with diabetes. RVECs dysfunction is the predominant pathological manifestation of vascular complication in diabetic retinopathy. N6-methyladenosine (m6A) serves as the most prevalent modification in eukaryotic mRNAs. However, the role of m6A RNA modification in RVECs dysfunction is still unclear. Methods: RT-qPCR analysis and western blot were conducted to detect the change of m6A RNA modification in diabetic retinopathy. CCK-8 assay, transwell experiment, wound healing assay, tube formation experiment, m6A-IP-qPCR were performed to determine the role of YTHDC1 in RVECs. Retinal trypsin digestion test and H&E staining were used to evaluate histopathological changes. Results: The levels of m6A RNA methylation were significantly up-regulated in HG-induced RVECs, which were caused by increased expression of YTHDC1. YTHDC1 regulated the viability, proliferation, migration and tube formation ability in vitro. YTHDC1 overexpression impaired RVECs function by repressing CDK6 expression, which was mediated by YTHDC1-dependent mRNA decay. Moreover, it showed sh-YTHDC1 inhibited CDK6 nuclear export. Sh-YTHDC1 promotes the mRNA degradation of CDK6 in the nucleus but does not affect the cytoplasmic CDK6 mRNA. In vivo experiments showed that overexpression of CDK6 reversed the protective effect of sh-YTHDC1 on STZ-induced retinal tissue damage. Conclusion: YTHDC1-mediated m6A methylation regulates diabetes-induced RVECs dysfunction. YTHDC1-CDK6 signaling axis could be therapeutically targeted for treating DR. [ABSTRACT FROM AUTHOR]

Temperature plays an important role in the heap bioleaching. The maldistribution of ventilation in the heap leads to local hyperthermia, which does exert a tremendous stress on bioleaching microbes. In this study, the genome-wide expression profiles of Acidithiobacillus ferrooxidans at 40 °C were detected using the microarray. The results showed that some classic proteases like Lon and small heat-shock proteins were not induced, and heat-inducible membrane proteins were suggested to be under the control of σE. Moreover, expression changes of energy metabolism are noteworthy, which is different from that in heterotrophic bacteria upon heat stress. The induced enzymes catalyzed the central carbon metabolism pathway that might mainly provide precursors of amino acids for protein synthesis. These results will deepen the understanding of the mechanisms of heat-shock response on autotrophic bacteria. [ABSTRACT FROM AUTHOR]

The objective of this study was to investigate changes in gene expression of intestinal IGF-I, IGFBPs, and IGF-I receptor in pigs in response to weaning and different rearing environment. Pigs were weaned early at 12 days of age and either remained on-site in a separate facility (CON) or were moved to a segregated site with reduced infection pressure (segregated early weaning; SEW). Small intestinal samples were collected from a total of 15 pigs killed at 11 (pre-weaning), 15 (3 days post-weaning), and 34 days of age. Intestinal IGF-I mRNA levels were higher (P<0.01) in SEW than in CON pigs at 3 days post-weaning, but not at 34 days of age. Weaning reduced (P<0.05) both IGF-IR mRNA levels and specific binding of IGF-1 in the jejunum in both groups at day 34, but only in SEW pigs (P<0.05) at day 3 post-weaning. Weaning resulted in a major reduction (P<0.05) in intestinal IGFBP-2 mRNA, with no difference between SEW and CON. Intestinal IGFBP-3 mRNA levels were unaffected by weaning or post-weaning environment. Weaning did not affect intestinal IGFBP-4 mRNA levels, except for an increase (P<0.05) in CON pigs compared to pre-weaning, and to SEW pigs at 3 days post-weaning. The abundance of IGFBP-5 mRNA in the gut was highly variable with no apparent treatment effect. Intestinal IGFBP-6 mRNA levels were reduced (P<0.05) after weaning, with lower (P<0.05) levels in SEW pigs than in CON pigs at 34 days of age. This study documents the changes in IGF-1, IGF-IR, and IGFBP mRNA abundance, and in IGF-1 binding during post-weaning adaptation of the intestine in early-weaned pigs. In addition, the relative differences observed in intestinal expression of IGF-1, IGF-IR, and in IGF-1 binding between the post-weaning environments are consistent with previous observations in a companion study indicating that segregated early weaning enhances post-weaning intestinal maturation in pigs. [Copyright &y& Elsevier]

Background: Osteoarthritis (OA) is the most common chronic joint disease and how ferroptosis contributes to OA has garnered much attention recently. Bioinformatics promoted the discovery of ferroptosis-related biomarkers for OA. But since OA is a whole-joint disease, sensitive biomarkers for OA are still limited. We herein focused on subchondral bone, a joint component often-ignored by existing bioinformatic reports, to identify ferroptosis-related diagnostic biomarkers for OA. Method: Microarray datasets GSE51588 and GSE55457 were downloaded from Gene Expression Omnibus database. Ferroptosis-related differential expression genes (Ferr-DEGs) between OA and normal samples were identified and their functional enrichment was analyzed. Common genes for OA diagnosis were selected from Ferr-DEGs using the combination of SVM-RFE, LASSO regression, and RandomForest machine learning algorithms. Common genes' diagnostic value was verified by receiver operating characteristic (ROC) curve and their association with immune infiltration was analyzed by CIBERSORT. Finally, candidate gene's expression was verified in chondrocytes from OA patients and in an in vitro IL-1β-induced OA model, by RT-PCR. Results: Two ferroptosis-related genes, LPCAT3 and PGD, were identified as OA diagnostic biomarkers and confirmed by ROC diagnostic test. The association of LPCAT3 and PGD with the infiltration of several types of immune cells was identified. The decreased expression of LPCAT3 and PGD was both confirmed in OA chondrocytes and IL-1β-induced OA condition. Conclusions: We identified ferroptosis-related genes LPCAT3 and PGD as potential diagnostic biomarkers for OA, which may offer insight into the role of ferroptosis in OA and provides useful information for the diagnosis and treatment of OA. [ABSTRACT FROM AUTHOR]

The Dalbergia plants are widely distributed across more than 130 tropical and subtropical countries and have significant economic and medicinal value. Codon usage bias (CUB) is a critical feature for studying gene function and evolution, which can provide a better understanding of biological gene regulation. In this study, we comprehensively analyzed the CUB patterns of the nuclear genome, chloroplast genome, and gene expression, as well as systematic evolution of Dalbergia species. Our results showed that the synonymous and optimal codons in the coding regions of both nuclear and chloroplast genome of Dalbergia preferred ending with A/U at the third codon base. Natural selection was the primary factor affecting the CUB features. Furthermore, in highly expressed genes of Dalbergia odorifera, we found that genes with stronger CUB exhibited higher expression levels, and these highly expressed genes tended to favor the use of G/C-ending codons. In addition, the branching patterns of the protein-coding sequences and the chloroplast genome sequences were very similar in the systematic tree, and different with the cluster from the CUB of the chloroplast genome. This study highlights the CUB patterns and features of Dalbergia species in different genomes, explores the correlation between CUB preferences and gene expression, and further investigates the systematic evolution of Dalbergia, providing new insights into codon biology and the evolution of Dalbergia plants. [ABSTRACT FROM AUTHOR]

Background: To screen efficacious neoantigens for the development of LIHC mRNA vaccines, construct LIHC immune clusters, and therefore select patients who might benefit from vaccination. Methods: RNA-seq data and clinical information of 371 TCGA-LIHC and 231 ICGC-LIHC cohorts were downloaded. Differentially expressed genes and their associations with prognosis were analyzed by GEPIA, genetic alterations were examined in the cBioPortal portal, and the association between genes and immune infiltrating cells was explored by TIMER. The immune clusters were constructed by consistency clustering, and the immune landscape was described using CIBERSORT. Results: POLR3C and KPNA2 were identified as LIHC tumor neoantigens related to inferior prognosis and antigen-presenting cell infiltration. In addition, three immune clusters (IC1, IC2 and IC3) with significant differences in molecular, immune cytological, and clinical features were identified in both the TCGA and ICGC LIHC cohorts. Immune "hot" phenotype IC3 displayed a better survival than IC2, and immune "cold" phenotype IC1 exhibited a high tumor mutation burden. Conclusion: In conclusion, for the development of anti-LIHC mRNA vaccines, we identified efficacious neoantigens POLR3C and KPNA2, profiled the tumor microenvironment of LIHC, and identified IC1 patients as the subgroup who might not most benefit from vaccination. [ABSTRACT FROM AUTHOR]

Galectin-1 is highly expressed in blastocysts and trophoblast giant cells during implantation, and dysregulated galectin-1 is associated with many pregnancy-related abnormalities. Elevated galectin-1 contributes to cancer cells invasion. Here, we found that galectin-1 is expressed in mouse oocytes, preimplantation embryos (all stages), and trophoblast stem (TS) cells. Peak levels of galectin-1 mRNA and protein were detected on day 4 and day 5 after the induction of TS cells differentiation. Overexpression of galectin-1 increased TS cells migration and invasion, whereas knockdown of galectin-1 attenuated these effects. Additionally, knockdown of galectin-1 in TS cells decreased the expression of matrix metalloproteinase (MMP) 2/9, ZEB-1, Snail, N-cadherin, TGF-β, Nodal, and phospho-Smad2/3, whereas the expression of E-cadherin was increased. In contrast, overexpression of galectin-1 in TS cells increased the expression of MMP2/9, ZEB-1, and N-cadherin, whereas the expression of E-cadherin was decreased. These findings suggest a potential role of galectin-1 in the differentiation of mouse TS cells. [ABSTRACT FROM AUTHOR]

Retinoic acid (RA) is the most biologically active metabolite of vitamin A and is important for stomach physiological function. However, little is known about the metabolic status of RA in human gastric lesions. From 2015 to 2018, 1,392 local residents in Lujiang County were recruited into a cross-sectional survey program, which included a questionnaire interview and blood collection. We detected the mRNA and protein expression of RA metabolism-relevant factors in gastric tissues from 68 local patients with gastric lesions. The effects of all-trans retinoic acid (ATRA) supplementation were investigated in a gastric precancerous lesions (GPLs) rat model. In the cross-sectional survey, no significant differences in the level of RA precursor (P > 0.05) between the H. pylori seronegative and seropositive residents were observed. However, the mRNA and protein expression of RA synthesizing enzymes (RDH10 and ALDH1A1) were significantly decreased and catabolic enzyme (CYP26B1) was significantly increased in the patients (P < 0.05). Consistently, in the GPL rat model, we observed a similar disorder; however, ATRA supplementation significantly not only corrected the disorder by increasing Rdh10, Aldh1a1 and decreasing Cyp26b1, but also reduced claudin-18 (P < 0.05). Our study suggested that RA metabolism is disrupted in individuals with gastric lesions, while ATRA supplementation can prevent GPL from progressing to gastric cancer. [ABSTRACT FROM AUTHOR]

Nonsense-mediated mRNA decay (NMD) and its regulation play an important role in eliminating faulty transcripts and controlling gene expression. However, measuring NMD activity and characterizing its targets remain challenging. In this study, we set out to establish Nanopore direct RNA sequencing in combination with quantitative real-time PCR (qPCR) as a method for analyzing NMD activity and its targets in cultured cell lines and clinical tissue samples. Nanopore RNA sequencing could detect more isoforms than short-read sequencing, especially in identifying novel isoforms and predicting isoforms annotated with premature termination codon (PTC). Changes in transcriptional isoforms of five genes (PRS, RPL12, SRSF2, PPIA, and TMEM208) could faithfully reflect NMD activity in the three cell lines and prostate cancer (PCA) samples. NMD activity in PCA samples varied, but some patients showed an increased trend. Together, Nanopore sequencing was superior in identifying NMD targets and evaluating NMD activity compared with short-read sequencing, and the NMD markers we screened may be used for measuring NMD activity in clinical patients. • Nanopore sequencing predicted transcripts with PTC and detected novel isoforms. • A set of NMD markers were screened based on Nanopore sequencing at transcriptional level. • Verification experiment by qPCR confirmed the NMD marker could faithfully reflect NMD activity. [ABSTRACT FROM AUTHOR]

Objective: To observe the effect of kisspeptin on the endocrine function of rat luteal cells. Design: Experimental animal study. Setting: Research institute laboratory. Animal(s): Immature Sprague-Dawley rats. Intervention(s): The expression of kisspeptin and its receptor, GPR54, in immature rat ovaries treated with gonadotropin was observed via immunohistochemistry and real-time polymerase chain reaction. Then recombinant kisspeptin was used to examine the effect on the endocrine function of rat luteal cells. Main Outcome Measure(s): Expression and localization of kisspeptin, localization of GPR54, P and E2 secretion, expression of steroidogenic enzymes, and phosphorylation of Erk1/2. Result(s): Real-time polymerase chain reaction indicated that ovarian KiSS-1 mRNA levels increased significantly, showing a peak at the luteal period in gonadotropin-primed immature rats. Immunostaining analysis showed that after gonadotropin treatment, kisspeptin was strongly localized in theca cells, the interstitial compartment, and the corpus luteum and that GPR54 protein was clearly detected in the corpus luteum of rat ovaries. In cultured luteal cells, kisspeptin treatment augmented basal and hCG-induced P levels but not E2 production, with concomitant increases detected in the transcript levels of key steroidogenic enzymes (StAR, CYP11A, and 3β-HSD). Furthermore, treatment with kisspeptin increased the phosphorylation of Erk1/2 mitogen-activated protein kinase in cultured luteal cells. Conclusion(s): The kisspeptin/GPR54 signaling system could stimulate P secretion in rat luteal cells via the Erk1/2 mitogen-activated protein kinase signaling pathway, suggesting an important role for the function of the corpus luteum. [ABSTRACT FROM AUTHOR]

Simple Summary: Immune checkpoint inhibitors (ICIs) changed the standard care of patients with lung squamous cell carcinoma (LUSC). It is an urgent need to precisely predict the population's response to ICIs. The aim of the study was to explore novel biomarkers for LUSC immunotherapy and the potential mechanism. Five hundred and twenty-five Chinese patients with LUSC who underwent targeted sequencing were involved, and TP53 and LRP1B were the genes most frequently correlated to tumor mutational burden (TMB). Further analysis demonstrated that TP53/LRP1B co-wild was associated with improved survival of immunotherapy. Compared with those with TP53/LRP1B mutant, patients with TP53/LRP1B co-wild had lower TMB and chromosome instability, while stronger cytotoxic immune cell infiltrations, which might be the reason for the better clinical outcomes of immunotherapy. These results indicated that TP53/LRP1B co-wild might be regarded as a potential biomarker for guiding anti-PD-L1 immunotherapy in LUSC. Immunotherapy brought long-term benefits for partial patients with lung squamous cell carcinoma (LUSC). The predictor of anti-PD-L1 therapy was controversial and limited in LUSC. We aimed to explore novel biomarker for LUSC immunotherapy and the potential mechanism. Five hundred and twenty-five Chinese patients (Geneplus cohort) with LUSC underwent targeted sequencing and were involved to explore the genomic profiling. TP53 and LRP1B were the most frequently recurrent genes and correlated to higher tumor mutational burden (TMB). We observed that LUSC patients with TP53 and LRP1B co-wild (co-wild type) were associated with better survival of anti-PD-L1 therapy compared with TP53 mutant or LRP1B mutant (mutant type) in POPAR/OAK cohort. Copy-number variation (CNV) and whole genome doubling (WGD) data from TCGA LUSC cohort were obtained to assess the CNV events. There were fewer CNV alterations and lower chromosome instability in patients with TP53/LRP1B co-wild compared with those with TP53/LRP1B mutant. RNA expression data from the TCGA LUSC cohort were collected to explore the differences in RNA expression and tumor immune microenvironment (TIME) between mutant and co-wild groups. The TP53/LRP1B co-wild type had a significantly increased proportion of multiple tumor-infiltrating lymphocytes (TILs), including activated CD8 T cell, activated dendritic cell (DC), and effector memory CD8 T cell. Immune-related gene sets including checkpoint, chemokine, immunostimulatory, MHC and receptors were enriched in the co-wild type. In conclusion, TP53/LRP1B co-wild LUSC conferred an elevated response rate in anti-PD-L1 therapy and improved survival, which was associated with a chromosome-stable phenotype and an activated immune microenvironment. [ABSTRACT FROM AUTHOR]

Background. Insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) plays a key role in tumorigenesis and tumor progression. Lung cancer is the leading cause of cancer-related death in men and women all over the world. However, the relationship between IGF2BP3 and small-cell lung cancer (SCLC) has not been reported yet. Methods. SCLC and normal samples (GSE19945 and GSE149507) were obtained in the Gene Expression Omnibus (GEO) dataset. Differential genes were screened by R software, and functional analysis and signal pathway enrichment analysis were carried out. In addition, we used the survival analysis database to analyze the relationship between prognosis and gene expression. Besides, immunohistochemistry (IHC) and quantitative real-time PCR (qPCR) were used for further research. Results. Five differentially expressed miRNAs and 9 differentially expressed mRNAs were selected by using R software. Survival analysis database results show that C7, CLIC5, PRDX1, IGF2BP3, and LDB2 were related the overall survival of patients with SCLC. Furthermore, multivariate analysis included that IGF2BP3 was independent risk factors for SCLC patients. Besides, gene function and signal pathway enrichment analysis showed that differentially expressed miRNAs were involved in the process of tumorigenesis and development. Furthermore, IHC and qPCR outcomes showed that the expression level of hsa-miR-182, hsa-miR-183, and IGF2BP3 was differentially expressed in normal lung tissues (NLTs) and SCLC tissues (SCLCTs). Conclusions. Our results concluded that hsa-miR-182, hsa-miR-183, and IGF2BP3 may take part in the development of SCLC. [ABSTRACT FROM AUTHOR]

The Brakeless protein performs many important functions during Drosophila development, but how it controls gene expression is poorly understood. We previously showed that Brakeless can function as a transcriptional co-repressor. In this work, we perform transcriptional profiling of brakeless mutant embryos. Unexpectedly, the majority of affected genes are down-regulated in brakeless mutants. We demonstrate that genomic regions in close proximity to some of these genes are occupied by Brakeless, that over-expression of Brakeless causes a reciprocal effect on expression of these genes, and that Brakeless remains an activator of the genes upon fusion to an activation domain. Together, our results show that Brakeless can both repress and activate gene expression. A yeast two-hybrid screen identified the Mediator complex subunit Med19 as interacting with an evolutionarily conserved part of Brakeless. Both down- and up-regulated Brakeless target genes are also affected in Med19-depleted embryos, but only down-regulated targets are influenced in embryos depleted of both Brakeless and Med19. Our data provide support for a Brakeless activator function that regulates transcription by interacting with Med19. We conclude that the transcriptional co-regulator Brakeless can either activate or repress transcription depending on context. [ABSTRACT FROM AUTHOR]

Positive Transcription Elongation Factor b (P-TEFb) is a kinase consisting of Cdk9 and Cyclin T that releases RNA Polymerase II (Pol II) into active elongation. It can assemble into a larger Super Elongation Complex (SEC) consisting of additional elongation factors. Here, we use a miRNA-based approach to knock down the maternal contribution of P-TEFb and SEC components in early Drosophila embryos. P-TEFb or SEC depletion results in loss of cells from the embryo posterior and in cellularization defects. Interestingly, the expression of many patterning genes containing promoter-proximal paused Pol II is relatively normal in P-TEFb embryos. Instead, P-TEFb and SEC are required for expression of some non-paused, rapidly transcribed genes in pre-cellular embryos, including the cellularization gene Serendipity-α. We also demonstrate that another P-TEFb regulated gene, terminus, has an essential function in embryo development. Similar morphological and gene expression phenotypes were observed upon knock down of Mediator subunits, providing in vivo evidence that P-TEFb, the SEC and Mediator collaborate in transcription control. Surprisingly, P-TEFb depletion does not affect the ratio of Pol II at the promoter versus the 3’ end, despite affecting global Pol II Ser2 phosphorylation levels. Instead, Pol II occupancy is reduced at P-TEFb down-regulated genes. We conclude that a subset of non-paused, pre-cellular genes are among the most susceptible to reduced P-TEFb, SEC and Mediator levels in Drosophila embryos. [ABSTRACT FROM AUTHOR]

The WRKY domain is the defining feature of the WRKY transcription factor family, which is a superfamily involved in regulating various physiological programs that are unique in plants. The WRKY genes have not been analyzed in spinach, a nutritious vegetable crop. We analyzed the spinach WRKY gene family and studied their phylogeny and gene expression in various tissues of spinach. Based on the Neighbor-joining phylogenetic tree, 48 SpWRKY genes in spinach genome can be divided into seven groups (I, IIa to IIe, III) as established in other plants; in addition, two novel SpWRKY genes are designated as group IV. SpWRKY genes were randomly distributed in six chromosomes, and 14 of them located in unassigned scaffolds. There is no tandem duplication, while seven paralogs were detected in the SpWRKY family. RNA-Seq and WGCNA analyses revealed significantly high expressions of 5 genes during female flower development. qRT-PCR results showed that most of the SpWRKY genes are expressed in roots, leaves and female flowers, and only 10 genes were expressed in stems and male flowers. The study provided fundamental information and a foundation for studying the function of spinach WRKY genes. [ABSTRACT FROM AUTHOR]

• The LIM protein Lmpt regulates Drosophila motility by acting as a repressor of Wnt signaling. • Lmpt is closely associated with the stability of muscle tissue and metabolic function. • Involvement of Lmpt in Wnt signaling increases the possibility that mammalian Fhl2 and other LIM proteins may also play a role in Wnt signaling. • A new addition to the important role of LIM domain proteins in the Drosophila. LIM domain is considered to be important in mediating protein–protein interactions, and members of the LIM protein family can co-regulate tissue-specific gene expression by interacting with different transcription factors. However, its exact function in vivo remains unclear. Our study demonstrates that the LIM protein family member Lmpt may act as a cofactor that interacts with other transcription factors to regulate cellular functions. In this study, we generated Lmpt knockdown Drosophila (Lmpt-KD) using the UAS-Gal4 system. We assessed the lifespan and motility of Lmpt-KD Drosophila and analyzed the expression of muscle-related and metabolism-related genes using qRT-PCR. Additionally, we utilized Western blot and Top-Flash luciferase reporter assay to evaluate the level of the Wnt signaling pathway. Our study revealed that knockdown of the Lmpt gene in Drosophila resulted in a shortened lifespan and reduced motility. We also observed a significant increase in oxidative free radicals in the fly gut. Furthermore, qRT-PCR analysis indicated that knockdown of Lmpt led to decreased expression of muscle-related and metabolism-related genes in Drosophila, suggesting that Lmpt plays a crucial role in maintaining muscle and metabolic functions. Finally, we found that reduction of Lmpt significantly upregulated the expression of Wnt signaling pathway proteins. Our results demonstrate that Lmpt is essential for motility and survival in Drosophila and acts as a repressor in Wnt signaling. [ABSTRACT FROM AUTHOR]

The Notch signalling pathway in the mammalian ovary regulates granulosa cell proliferation. However, the effects of Notch signalling on steroidogenesis are unclear. In this study we cultured mouse ovarian granulosa cells from preantral follicles in vitro and observed the effect of Notch signalling on steroidogenesis through overexpression, knockdown and inhibition of Notch signalling. Activation of Notch signalling decreased progesterone and oestrogen secretion. In contrast, inhibition of Notch signalling increased the production of progesterone and oestrogen. Expression of the genes for steroidogenic-related enzymes, including 3β-hydroxysteroid dehydrogenase, p450 cholesterol side-chain cleavage enzyme and aromatase, was repressed after stimulation of Notch signalling. The expression of upstream transcription factors, including steroidogenic factor 1 (SF1), Wilms' tumour 1 (Wt1), GATA-binding protein 4 (Gata4) and Gata6, was also inhibited after stimulation of Notch signalling. Production of interleukin (IL)-6 was positively correlated with Notch signalling and negatively correlated with the expression of these transcription factors and enzymes. In conclusion, Notch signalling regulated progesterone and oestrogen secretion by affecting the expression of upstream transcription factors SF1, Wt1, Gata4 and Gata6, as well as downstream steroidogenic-related enzymes. IL-6, which may be regulated directly by Notch signalling, may contribute to this process. Our findings add to the understanding of the diverse functions of Notch signalling in the mammalian ovary. Steroid hormone synthesis is one function of granulosa cells and plays an important role in the maturation and function of reproductive organs. In this study we found that Notch signalling affected progesterone and oestradiol secretion by granulosa cells via regulation of interleukin-6 expression. This finding adds to our understanding of the diverse functions of Notch signalling in the mammalian ovary. [ABSTRACT FROM AUTHOR]

Background/Aims: Pulmonary fibrosis is a common outcome of various interstitial lung diseases. Prodigiosin (PG) is a series of red pigment with methoxypyrrole ring. This studyinvestigates therole of prodigiosin in pulmonary fibrosis and its underlying mechanisms. Methods: A pulmonary fibrosis rat model was established by intra-trachealinjection ofbleomycin A5. Rats were divided into 4 groups: Normal group, pulmonary fibrosis Model group, Prodigiosin treatment group and hydrocortisone treatmentgroup. HE and Masson staining were carried outto evaluate histopathological changes. The content of hydroxyproline in lung tissue was determined by alkaline hydrolysis. The expression of PICP and PIIINP was examined by ELISA. The mRNA expression of miR-410, TGF-β1 and ADAMTS1 in lung homogenate were detected by RT-PCR. The bronchoalveolar lavage fluid (BALF) and lung tissues of rats were collected and analyzed. Human embryonic pulmonary fibroblast (HEPF) was used for study in vitro. A dual-luciferase reporter assay was conducted to examine the effect of miR-410 on ADAMTS1 expression. Cell transfection was conducted to inhibit miR-410. MTT assay was performed to investigate cell proliferation. The expressions of miR-410, TGF-β1, ADAMTS1and other fibrosis related biomarkers (Col I, Col III, and α-SMA) wereexamined by RT-PCR and Western Blot. Results: HE and Masson staining showed thickened alveolar septum, hyperplasticcapillaries, and large areas of collagen fiber deposition in pulmonary fibrosis model rats. Rats in prodigiosin and hydrocortisone treatment groups had alleviated symptoms. There was high hydroxyproline expression in model rats, whereas the expression of hydroxyproline reduced after prodigiosin or hydrocortisone treatments. RT-PCR results showed high miR-410,high TGF-β1 and low ADAMTS1 in lung tissue of model rats. The expression of PICP and PIIINP werehigher in BALF of model group than in treatment groups. Prodigiosin and hydrocortisone treatment significantly reduced PICP and PIIINP content. RT-PCR and Western Blot analysis showed that prodigiosin inhibited expression of miR-410 and TGF-β1, but up-regulated ADAMTS1 expression. MTT assay indicated that prodigiosin inhibited HEPF proliferation induced by miR-410 overexpression. Conclusion: Prodigiosin down-regulates the expression of miR-410 and TGF-β1, up-regulates ADAMTS1, leading to decrease accumulation of fibrotic proteins. It could be used in alleviating pulmonary fibrosis. [ABSTRACT FROM AUTHOR]

Understanding the cellular-molecular substrates of heart disease is key to the development of cardiac specific therapies and to the prevention of off-target effects by non-cardiac targeted drugs. One of the primary targets for therapeutic intervention has been the human ether a go-go (hERG) K+ channel that, together with the KCNQ channel, controls the rate and efficiency of repolarization in human myocardial cells. Neither of these channels plays a major role in adult mouse heart function; however, we show here that the hERG homolog seizure (sei), along with KCNQ, both contribute significantly to adult heart function as they do in humans. In Drosophila, mutations in or cardiac knockdown of sei channels cause arrhythmias that become progressively more severe with age. Intracellular recordings of semi-intact heart preparations revealed that these perturbations also cause electrical remodeling that is reminiscent of the early afterdepolarizations seen in human myocardial cells defective in these channels. In contrast to KCNQ, however, mutations in sei also cause extensive structural remodeling of the myofibrillar organization, which suggests that hERG channel function has a novel link to sarcomeric and myofibrillar integrity. We conclude that deficiency of ion channels with similar electrical functions in cardiomyocytes can lead to different types or extents of electrical and/or structural remodeling impacting cardiac output. [ABSTRACT FROM AUTHOR]

• Panobinostat reverses the expression of hepaCAM in prostate cancer. • Panobinostat affected the status of histone acetylation through blocking HDACs activity. • Panobinostat can overcome the resistance for androgen deprivation therapy. • Panobinostat and hepaCAM Synergistically inhibited prostate cancer cells growth. Increased expression of histone deacetylases (HDACs) affiliated to the epigenetic regulation is common aberration in prostate cancer (PCa). We have confirmed that hepatocyte cell adhesion molecule (hepaCAM), acting as a tumor suppressor gene, is rarely expressed in PCa previously, However, the mechanisms of which is still unknown. The level of histone acetylation reportedly may involve anti-oncogene transcription and expression. In this study, we investigated the effect of panobinostat, the broad-spectrum histone deacetylases inhibitor, on PCa LNCaP and DU145 cell growth, and observed re-expression of hepaCAM when treated with panobinostat. We demonstrated that intranuclear acetylation of lys9 of histone H3 (Ac-H3K9) were increased, while that of both mRNA and protein of HDAC1, HDAC3, and HDAC4 were decreased when the treating concentration of panobinostat increased. We confirmed the relationship between histone acetylation and the expression of hepaCAM and AR in prostate cancer tissues. We also confirmed that panobinostat could overcome the resistance for androgen deprivation therapy (ADT). Further, we combined panobinostat with Ad-hepaCAM, which resulted in significantly increased antitumor activity and significant attenuation of the proliferation-associated genes CCND1 and PCNA compared to each single treatment. In conclusion, panobinostat may enhance the acetylation of lys9 of histone 3 and reverse the hepaCAM expression through its inhibitory effect on HDACs activity in PCa LNCaP and DU145 cells; Ad-hepaCAM combined with panobinostat may synergistically inhibit the growth of LNCaP and DU145 cells, via a potential mechanism associated with the down-regulation of the expression of CCND1 and PCNA. These findings suggest that this therapeutic strategy should be further developed in clinical trials. [ABSTRACT FROM AUTHOR]

Background and Objective: S100A8 and S100A9, two members of the S100 protein family, have been reported in association with the tumor cell differentiation and tumor progression. Previous study has showed that their expression in stromal cells of colorectal carcinoma (CRC) is associated with tumor size. Here, we investigated the clinical significances of S100A8 and S100A9 in tumor cells of CRC and their underlying molecular mechanisms. Methods: Expression of S100A8 and S100A9 in colorectal carcinoma and matching distal normal tissues were measured by reverse transcriptase polymerase chain reaction (RT-PCR), immunohistochemistry and western blot. CRC cell lines treated with the recombinant S100A8 and S100A9 proteins were used to analyze the roles and molecular mechanisms of the two proteins in CRC in vitro. Results: S100A8 and S100A9 were elevated in more than 50% of CRC tissues and their expression in tumor cells was associated with differentiation, Dukes stage and lymph node metastasis. The CRC cell lines treatment with recombinant S100A8 and S100A9 proteins promoted the viability and migration of CRC cells. Furthermore, the two recombinant proteins also resulted in the increased levels of β-catenin and its target genes c-myc and MMP7. β-catenin over-expression in CRC cells by Adβ-catenin increased cell viability and migration. β-catenin knock-down by Adsiβ-catenin reduced cell viability and migration. Furthermore, β-catenin knockdown also partially abolished the promotive effects of recombinant S100A8 and S100A9 proteins on the viability and migration of CRC cells. Conclusions: Our work demonstrated that S100A8 and S100A9 are linked to the CRC progression, and one of the underlying molecular mechanisms is that extracellular S100A8 and S100A9 proteins contribute to colorectal carcinoma cell survival and migration via Wnt/β-catenin pathway. [ABSTRACT FROM AUTHOR]

Background: The plasminogen activator inhibitor-1 (PAI-1) is expressed in many cancer cell types and allows the modulation of cancer growth, invasion and angiogenesis. To date, studies investigated the association between a functional polymorphism in PAI-1 (4G/5G) and risk of cancer have shown inclusive results. Methods: A meta-analysis based on 25 case-control studies was performed to address this issue. Odds ratios (OR) with corresponding 95% confidence intervals (CIs) were used to assess the association. The statistical heterogeneity across studies was examined with I2 test. Results: Overall, a significant increased risk of cancer was associated with the PAI-1 4G/4G polymorphism for the allele contrast (4G vs. 5G: OR = 1.10, CI = 1.03–1.18, I2 = 49.5%), the additive genetic model (4G/4G vs. 5G/5G: OR = 1.21, CI = 1.06–1.39, I2 = 51.9%), the recessive genetic model (4G/4G vs. 4G/5G+5G/5G: OR = 1.11, CI = 1.04–1.18, I2 = 20.8%). In the subgroup analysis by ethnicity, the results indicated that individuals with 4G/4G genotype had a significantly higher cancer risk among Caucasians (4G/4G vs. 5G/5G: OR = 1.31, 95%CI = 1.09–1.59, I2 = 59.6%; 4G/4G vs. 4G/5G: OR = 1.12, 95%CI = 1.04–1.21, I2 = 3.6%; recessive model: OR = 1.12, 95%CI = 1.05–1.21, I2 = 25.3%). Conclusions: The results of the present meta-analysis support an association between the PAI-1 4G/5G polymorphism and increasing cancer risk, especially among Caucasians, and those with 4G allele have a high risk to develop colorectal cancer and endometrial cancer. [ABSTRACT FROM AUTHOR]

Objective: To investigate firstly the relationship between semenogelin I (Sg I) expression and seminal vesiculitis. Seminal vesiculitis is one of the most common diseases in male urogenital system. However, the cause and the pathogenesis of seminal vesiculitis remain unknown. Sg I, mainly synthesized and secreted by seminal vesicle, is abundant in human seminal plasma and has antibacterial activity.Materials and Methods: Tissue samples were collected from 15 normal cases and 28 patients with seminal vesiculitis. Reverse transcription-polymerase chain reaction was performed to detect the expression difference of Sg I messenger ribonucleic acid (RNA) between normal seminal vesicle tissues and seminal vesiculitis tissues. Immunohistochemistry was applied to detect the expression difference of Sg I protein between the 2 groups.Results: Reverse transcription-polymerase chain reaction showed the expression of Sg I messenger RNA in seminal vesiculitis tissues to be significantly lower than in normal seminal vesicle tissues. In most cases with seminal vesiculitis (78.6%), the same result was observed upon immunohistochemical analysis at the protein level.Conclusion: Abnormal expression of Sg I is closely related to seminal vesiculitis. Low expression of Sg I may play an important role in the occurrence and the development of seminal vesiculitis through weakening the antibacterial activity of seminal vesicle. [ABSTRACT FROM AUTHOR]