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Multiple myeloma (MM) is one of hematological malignancies, characterized by malignant proliferation of plasma cells. Biomarkers play an important role in evaluating the development and prognosis of MM. Ubiquitin-conjugating enzyme E2T (UBE2T) is served to connect with particular E3 ubiquitin ligase to degraded-related substrates, contributing to DNA repair in the Fanconi anemia pathway. Also, numerous evidences reported that UBE2T is closely related to cell proliferation and carcinogenesis. However, the relationship between MM and UBE2T has not been studied. Here, we integrated eight datasets and analyzed the relationship of expression of UBE2T and ISS, 1q21, relapse and survival in MM 2684 patients (totally 2893 samples). We found that the expression of UBE2T increased with the deterioration of MM (P = 1.4e-07), especially in the early stage. UBE2T is closely related to IgG serotype MM (P = 6.9e-05). High expression of UBE2T is associated with poor survival and prognosis (EFS: P = 1.43e-03, OS: P = 5.47e-05). UBE2T is likely to play a part in the cell division pathway, affecting the survival and prognosis of MM. Therefore, UBE2T could be considered as an early alternative biomarker for the prognosis of MM.

RNA sequencing (RNA-seq) has become a standard method for profiling gene expression, yet genomic DNA (gDNA) contamination carried over to the sequencing library poses a significant challenge to data integrity. Detecting and correcting this contamination is vital for accurate downstream analyses. Particularly, when RNA samples are scarce and invaluable, it becomes essential not only to identify but also to correct gDNA contamination to maximize the data's utility. However, existing tools capable of correcting gDNA contamination are limited and lack thorough evaluation. To fill the gap, we developed CleanUpRNAseq, which offers a comprehensive set of functionalities for identifying and correcting gDNA-contaminated RNA-seq data. Our package offers three correction methods for unstranded RNA-seq data and a dedicated approach for stranded data. Through rigorous validation on published RNA-seq datasets with known levels of gDNA contamination and real-world RNA-seq data, we demonstrate CleanUpRNAseq's efficacy in detecting and correcting detrimental levels of gDNA contamination across diverse library protocols. CleanUpRNAseq thus serves as a valuable tool for post-alignment quality assessment of RNA-seq data and should be integrated into routine workflows for RNA-seq data analysis. Its incorporation into OneStopRNAseq should significantly bolster the accuracy of gene expression quantification and differential expression analysis of RNA-seq data. [ABSTRACT FROM AUTHOR]

• We introduce a hexagonal convolution neural network for images with hexagonal pixels. • We applied hexCNN to segment spatially resolved transcriptomics data. • HexCNN achieved greater segmentation accuracies than state-of-the-art GNN models. • We noticed considerable dropout events and batch effects hindering further progress. Spatial transcriptomics is a rapidly evolving field that enables researchers to capture comprehensive molecular profiles while preserving information about the physical locations. One major challenge in this research area involves the identification of spatial domains, which are distinct regions characterized by unique gene expression patterns. However, current unsupervised methods have struggled to perform well in this regard due to the presence of high levels of noise and dropout events in spatial transcriptomic profiles. In this paper, we propose a novel hexagonal Convolutional Neural Network (hexCNN) for hexagonal image segmentation on spatially resolved transcriptomics. To address the problem of noise and dropout occurrences within spatial transcriptomics data, we first extend an unsupervised algorithm to a supervised learning method that can identify useful features and reduce noise hindrance. Then, inspired by the classical convolution in convolutional neural networks (CNNs), we designed a regular hexagonal convolution to compensate for the missing gene expression patterns from adjacent spots. We evaluated the performance of hexCNN by applying it to the DLPFC dataset. The results show that hexCNN achieves a classification accuracy of 86.8% and an average Rand index (ARI) of 77.1% (1.4% and 2.5% higher than those of GNNs). The results also demonstrate that hexCNN is capable of removing the noise caused by batch effect while preserving the biological signal differences. [ABSTRACT FROM AUTHOR]

At present, enzyme debridement preparation has shown a good curative effect on eschar removal of burn wounds. Keratinase has shown great potential in enzymatic debridement because of its good fibrin-degrading ability. In this study, the debridement of keratinase was examined by using a third degree burn wound model in rats. We observed the wound, and keratinase shortened the time of eschar dissolution after debridement. Histopathology and immunofluorescence staining showed that the eschar in the keratinase group became thinner, inflammatory cell infiltration in the wound increased, the fluorescence intensity of the macrophage surface marker CD68 increased, and the CD163/CD86 ratio increased. In bone marrow-derived macrophages (BMDMs), there was no significant difference in the activity of CCK-8 in cells in the keratinase group compared with the control group. The fluorescence intensity of the keratinase group was higher than that of the control group. At 12 h, the cell scratches were obviously closed. The number of migrated Transwell cells increased. Flow cytometry and immunofluorescence analysis showed increased expression of CD206 and Arg-1 and decreased expression of CD86 and iNOS. The gene expression of the Arg-1, iNOS and IL-10 was increased, as shown by qPCR. The secretion of IL-10 was increased and TNF-α was decreased, as shown by ELISA. We concluded that keratinase dissolution of eschar not only has a hydrolytic effect on eschar but may also affect immune regulation to enhance the migration and phagocytosis of macrophages, promote the polarization of macrophages, and further enhance the effect of eschar dissolution. Therefore, keratinase may have good prospects for the debridement of burn wounds. [ABSTRACT FROM AUTHOR]

N6‐methyladenosine (m6A) plays a key role in many biological processes. However, the function and evolutionary relationship of m6A‐related genes in insects remain largely unknown. Here we analysed the phylogeny of m6A‐related genes among 207 insect species and found that m6A‐related genes are evolutionarily conserved in insects. Subcellular localization experiments of m6A‐related proteins in BmN cells confirmed that BmYTHDF3 was localized in the cytoplasm, BmMETTL3, BmMETTL14, and BmYTHDC were localized in the nucleus, and FL2D was localized to both the nucleus and cytoplasm. We examined the expression patterns of m6A‐related genes during the embryonic development of Bombyx mori. To elucidate the function of BmMETTL3 during the embryonic stage, RNA sequencing was performed to measure changes in gene expression in silkworm eggs after BmMETTL3 knockdown, as well as in BmN cells overexpressing BmMETTL3. The global transcriptional pattern showed that knockdown of BmMETTL3 affected multiple cellular processes, including oxidoreductase activity, transcription regulator activity, and the cation binding. In addition, transcriptomic data revealed that many observed DEGs were associated with fundamental metabolic processes, including carbon metabolism, purine metabolism, amino acid biosynthesis, and the citrate cycle. Interestingly, we found that knockdown of BmMETTL3 significantly affected Wnt and Toll/Imd pathways in embryos. Taken together, these results suggest that BmMETTL3 plays an essential role in the embryonic development of B. mori, and deepen our understanding of the function of m6A‐related genes in insects. [ABSTRACT FROM AUTHOR]

Background: TP53 mutations have a prognostic significance in relapsed and refractory diffuse large B‐cell lymphoma (rrDLBCL) patients, and their treatment still faces a great challenge. This study aimed to evaluate the prognosis of patients with TP53 mutations (TP53mut) in the context of CAR‐T therapy (Chimeric antigen receptor T‐cell therapy) as well as explore the heterogeneity in their cohort and identify the possible risk factors. Methods: A retrospective study was conducted to investigate the clinical characteristics of rrDLBCL patients with TP53 mutations and their prognostic factors, receiving CAR‐T therapy. And the expression level of TP53 and DDX3X, which was an important co‐mutation of TP53 revealed in the cohort, were explored in public databases and cell lines. Results: The median overall survival time of 40 patients with TP53 mutations was 24.5 months, while their median progression‐free survival time after CAR‐T was 6.8 months. There were no significant differences in the ORR (objective remission rate, X2 = 3.0498, p > 0.05) and PFS (after CAR‐T therapy) between the patients with wild‐type and mutated TP53 genes after CAR‐T therapy, while the OS of patients with TP53 mutations was significantly worse (p < 0.01). In patients with TP53 mutations, the performance status (ECOG score) was identified as the most important prognostic factor, while the efficacies of induction and salvage treatments were also correlated with the prognosis. Among molecular indicators, the co‐mutations of Chr‐17 and those located on the exon 5 of the TP53 gene showed a tendency for a worse prognosis. Moreover, the patients with TP53‐DDX3X co‐mutations were identified as a subgroup with an extremely bad prognosis. The expression levels of DDX3X and TP53 were explored in a public database and the cell lines with their co‐mutations, which indicated that inhibiting the DDX3X gene could affect the proliferation of rrDLBCL cells and the expression of TP53. Conclusions: This study indicated rrDLBCL patients with TP53 mutations was still the group of poor prognosis in the CAR‐T therapy era. CAR‐T therapy can benefit some TP53mut patients, and the performance status (ECOG) might help predict their prognosis. The study also revealed a subgroup of TP53‐DDX3X co‐mutations in rrDLBCL, which showed a strong clinical significance. [ABSTRACT FROM AUTHOR]

Background. This study is aimed at identifying the important biomarkers associated with bone metastasis (BM) in breast cancer (BRCA). Methods. The GSE175692 dataset was used to detect significant differential expressed genes (DEGs) between BRCA samples with or without BM, and DEG-related pathways were then explored. Further, we constructed the protein-protein interaction (PPI) network on GEGs and filtered 5 vital nodes. We then performed the Cox regression, Kaplan-Meier analysis, nomogram, and ROC curve to filter the most significant prognosis genes. The GSE14020 and GSE124647 datasets were used to verify the expression and prognostic value of hub genes, respectively. Finally, the gene set enrichment analysis (GSEA) was performed to reveal the potential mechanism. Results. Totally, 74 DEGs were detected, which mainly correlated with infectious disease, signaling molecules, and interaction. The 5 important DEGs were then filtered, and the Cox regression further showed that 2 genes, including prominin 1 (PROM1) and C-C motif chemokine ligand 2 (CCL2), were related to the prognosis of BRCA metastasis patients. Especially, PROM1 presented a better prognostic performance on the survival probability of patients than CCL2. Verification analysis further confirmed the abnormal expression and significant prognostic influence of PROM1. Finally, GSEA revealed that PROM1 was negatively related to IGF1 and mTOR pathways in BRCA metastasis. Conclusion. PROM1 was an important biomarker associated with BRCA bone metastasis and affected the prognosis of metastatic BRCA patients. It may play a vital role in metastatic BRCA by negatively regulating IGF1 and mTOR pathways. [ABSTRACT FROM AUTHOR]

Bleomycin is a common antitumor agent used to treat many different types of malignancies; however, its main side effect is pulmonary fibrosis. The mechanism of bleomycin-induced pulmonary fibrosis (BIPF) has not been fully elucidated. Therefore, to further explore the molecular mechanisms of BIPF, we screened for microRNA (miRNA) and mRNA expression obtained from BIPF samples from the Gene Expression Omnibus database. Subsequently, we identified the differentially expressed miRNAs and genes that overlapped with the differentially expressed miRNAs target genes, predicted by using the miRWalk database selected as a candidate. The candidate genes were visualized based on Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes analyses. A protein-protein interaction network was constructed. Hub differentially expressed genes were selected and corresponding miRNAs to construct a miRNA-mRNA regulation network. Then, we chose three key miRNAs to study their regulatory relationship in bleomycin-induced pulmonary fibrosis. Finally, mouse lung epithelial cells TC-1 and MLE-12 were treated with bleomycin with qPCR to validate the results of three important hub genes and all key miRNAs. And dual-luciferase report experiment was carried out to verify the interaction of mmu-miR-1946a and serpina3n. The results revealed that the imbalance of matrix metalloproteinase-9 (MMP-9) and tissue inhibitor of metalloproteinase-1 (TIMP-1) plays a pivotal role in the occurrence and development of BIPF. In addition, Serpina3n and mmu-miR-1946a were proved interaction and may be involved in the regulation of the balance between MMP-9 and TIMP-1. The experimental results also verify the analysis. Our findings provide new insights into the key mediators and pathways related to the molecular mechanisms of BIPF. [ABSTRACT FROM AUTHOR]

Objective: To study the antidepressant-like effect and action mechanism of geniposide and eleutheroside B combination treatment on the lipopolysaccharide (LPS)-induced depression mice model. Methods: Depression mice model was established by lipopolysaccharide (LPS) injection. Totally 48 mice were randomly divided into 6 groups (8 rats per group) according to a random number table, including normal, model, fluoxetine (20 mg/kg), geniposide (100 mg/kg) + eleutheroside B (100 mg/kg), geniposide + eleutheroside B + WAY 100635 (0.03 mg/kg), geniposide + eleutheroside B+ N-methyl-D-aspartic acid receptor (NMDA, 75 mg/kg) groups, respectively. After continuous administration for 10 days, autonomic activity tests after 30 min of administration were performed on the 10th day. On the 11th day, except for the normal group, the mice in the other groups were intraperitoneally injected with LPS (1 mg/kg), and the behavioral tests were performed 4 h later. Enzyme linked immunosorbent assay was used to detect tumor necrosis factor alpha (TNF- α) and interleukin-1 β (IL-1 β) levels in mice serum. The mRNA expression of indoleamine 2,3-dioxygenase (IDO) and nuclear transcription factor (NF- κB) were detected by real-time quantitative polymerase chain reaction. Western-blot analysis was used to detect IDO and NF- κB protein expressions in hippocampus tissue. Results: Compared with the normal group, a single administration of LPS increased the immobility time in the forced swimming test (FST) and tail suspension test (TST, P<0.01), without affecting autonomous activity. Compared with the model group, fluoxetine and geniposide + eleutheroside B administration significantly improved the immobility time of depressed mice in the FST and TST, decreased serum IL-1 β content, inhibited the expression levels of NF- κ B gene and protein in hippocampus tissues (P<0.05 or P<0.01). Compared with the model group, geniposide + eleutheroside B treatment significantly reduced serum TNF-α content and inhibited IDO mRNA and protein expressions in hippocampus (P<0.05 or P<0.01). In addition, NMDA partly prevented the inhibition of IDO mRNA expression by geniposide + eleutheroside B; NMDA and WAY-100635 also partly prevented the reduction of IL-1 ß content induced by geniposide + eleutheroside B treatment (P<0.05 or P<0.01). Conclusions: The combination of geniposide and eleutheroside B showed a certain antidepression-like effect. Its main mechanism of action may be contributed to inhibiting the activation of NF- κB, decreasing the proinflammatory cytokines such as TNF-α, IL-1 β, and inhibiting in the neuroinflammatory reaction. Additionally, it also affects tryptophan metabolism, reduces the expression of a key enzyme of tryptophan metabolism, IDO. And this antidepressant-like effect may be mediated by 5-hydroxytryptamine and glutamate systems. [ABSTRACT FROM AUTHOR]

The present study is aimed at investigating whether Qiliqiangxin (QL) could regulate myocardial energy metabolism in heart failure rats after acute myocardial infarction (AMI) and further exploring the underlying mechanisms. AMI was established by ligating the left anterior descending coronary artery in adult male SD rats. AMI rats with ejection fraction EF < 50 % at two weeks after the operation were chosen as heart failure rats for the main study. Rats were randomized into the sham, MI, MI+QL, and MI+QL+2-MeOE2 groups. The results showed that compared with the MI group, QL significantly improved cardiac function, reduced serum NT-proBNP level, and alleviated myocardial fibrosis. QL also increased myocardial capillary density by upregulated protein expressions of vascular endothelial growth factor (VEGF) and CD31 by regulating the HIF-1α/VEGF pathway. Moreover, QL promoted ATP production, glucose uptake, and glycolysis by upregulating HIF-1α and a series of glycolysis-relevant enzymes in a HIF-1α-dependent manner. QL also improved myocardial glucose oxidation enzyme expression and free fatty acid uptake by a HIF-1α-independent pathway. Our results indicate that QL treatment improves cardiac function through regulating glucose uptake, FFA uptake, and key enzymes of energy metabolism via HIF-1α-dependent and independent mechanisms. [ABSTRACT FROM AUTHOR]

Exosome complex (EXOSC) genes, which encode a multi-protein intracellular complex, mediate the degradation of various types of RNA molecules. EXOSCs, also known as polymyositis/scleroderma complexes, exist in eukaryotic cells and archaea, and primarily mediate 3′ to 5′mRNA degradation. However, how EXOSC genes are implicated in processes of B-cell immune-associated pathways and B-cell tumorigenesis remains unclear. The present bioinformatics study indicated that 6 of 10 EXOSC genes, particularly the EXO.index, were able to predict the survival of patients with mantle cell lymphoma (MCL), by analyzing gene expression profiles of 123 patients with MCL from the Gene Expression Omnibus database. The results suggested that EXOSC gene expression may be a molecular marker for MCL. Compared with the whole transcript profile, patients with MCL with a high EXO.index exhibited poorer survival and decreased RNA levels, which was also verified in a second dataset. The EXOSC genes may be associated with DNA repair and B-cell activation pathways, which may be the cause of poorer survival of patients with MCL. [ABSTRACT FROM AUTHOR]

N6-methyladenosine (m6A) is the most abundant eukaryote mRNA modification, modulated by regulators known as epigenetic writers, erasers and readers, which are known to serve crucial roles in mRNA metabolism. However, the role of m6A during B-cell development and B-cell tumorigenesis remains poorly understood. By analyzing the gene expression profile of 123 mantle cell lymphoma cases from the Gene Expression Omnibus database, the present study demonstrated that one-half of the m6A regulators were able to predict patient survival in mantle cell lymphoma, notably the m6A.index. The expression levels of the m6A regulators were regarded as good classifiers in mantle cell lymphoma. The m6A.index-low mantle cell lymphoma type exhibited a poor patient survival and lower mRNA levels from the total transcriptome. The m6A regulators may be associated with the cell division and the RNA metabolic pathways, which may result in poor survival of patients with mantle cell lymphoma. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are confirmed to be tumor promoters or suppressors in multiple squamous cell carcinomas (SCCs). miR‐99a‐5p has been demonstrated to be downregulated in cancerous tissues, but its functional role in head and neck SCC (HNSCC) and its mechanism of action have not been fully elucidated. Here, we studied the expression of miR‐99a‐5p in HNSCC and performed a clinical value assessment and then extracted mature expression data from The Cancer Genome Atlas (TCGA) and microarrays from Gene Expression Omnibus (GEO). Furthermore, biological analysis was constructed via online prediction tools. The results revealed that miR‐99a‐5p expression was markedly lower in HNSCC tissues than in normal tissues, which also showed significance in the prognosis of HNSCC. However, its diagnostic value could not be verified due to the lack of body fluid samples. Additionally, miR‐99a‐5p was expressed at higher levels in patients with low histological grade neoplasms than those with high histological grade neoplasms. The age of the patient might also be a possible clinical parameter affecting miR‐99a‐5p expression. Furthermore, miR‐99a‐5p significantly influenced HNSCC progression by regulating the PI3K‐Akt signaling pathway, in which the key target genes were upregulated in 519 HNSCC tissues compared to 44 normal tissues, as determined by the Gene Expression Profiling Interactive Analysis (GEPIA). In conclusion, our study may provide insights into the expression and mechanism of miR‐99a‐5p in HNSCC. Further studies are required to elucidate the role of miR‐99a‐5p and its potential clinical applications for HNSCC. [ABSTRACT FROM AUTHOR]

We previously reported that BMP9 inhibited breast cancer progression. However, the precise molecular mechanism is still unknown. Based on our RNA-sequencing (RNA-seq) results, BMP9 significantly down-regulated the expression of long non-coding RNA SNHG3. Exogenous BMP9 promoted autophagy and inhibited migration and invasion in MDA-MB-231 cells, which was effectively blunted by SNHG3 overexpression. Interestingly, SNHG3 was negatively connected with autophagy. Knockdown of SNHG3 induced autophagy by increasing the formation of autophagic vacuoles and thus inhibited the migration and invasion of MDA-MB-231 cells. Mechanically, BMP9-SNHG3 activated AMPK, AKT and mTOR signaling pathways to induce autophagy and inhibit migration and invasion. Meanwhile, BMP9 regulated SNHG3 transcription by suppressing c-Myc entry into the nucleus. In conclusion, BMP9 promotes autophagy and inhibits migration and invasion in breast cancer cells through the c-Myc/SNHG3/mTOR signaling axis, which might offer a fresh perspective on BMP9's breast cancer-inhibiting properties. [Display omitted] • In addition to inhibiting metastasis of BC, BMP9 was found to induce autophagy, which was mediated by SNHG3. • SNHG3 knockdown inhibited metastasis by promoting the synthesis of autophagic vesicles. • BMP9-SNHG3 promoted autophagy and inhibited metastasis through AMPK, AKT and mTOR pathways. • BMP9 regulated the expression of SNHG3 by blocking c-Myc nuclear transport. • The newly revealed BMP9/c-Myc/SNHG3/mTOR axis may be a therapeutic target for BC. [ABSTRACT FROM AUTHOR]

Cardiac microvascular endothelial cells (CMECs) are important angiogenic components and are injured rapidly after cardiac ischaemia and anoxia. Cardioprotective effects of Qiliqiangxin (QL), a traditional Chinese medicine, have been displayed recently. This study aims to investigate whether QL could protect CMECs against anoxic injury and to explore related signalling mechanisms. CMECs were successfully cultured from Sprague-Dawley rats and exposed to anoxia for 12 hrs in the absence and presence of QL. Cell migration assay and capillary-like tube formation assay on Matrigel were performed, and cell apoptosis was determined by TUNEL assay and caspase-3 activity. Neuregulin-1 (NRG-1) siRNA and LY294002 were administrated to block NRG-1/ErbB and PI3K/Akt signalling, respectively. As a result, anoxia inhibited cell migration, capillary-like tube formation and angiogenesis, and increased cell apoptosis. QL significantly reversed these anoxia-induced injuries and up-regulated expressions of NRG-1, phospho-ErbB2, phospho-ErbB4, phospho-Akt, phospho-mammalian target of rapamycin (mTOR), hypoxia-inducible factor-1α (HIF-1α) and vascular endothelial growth factor (VEGF) in CMECs, while NRG-1 knockdown abolished the protective effects of QL with suppressed NRG-1, phospho-ErbB2, phospho-ErbB4, phospho-Akt, phospho-mTOR, HIF-1α and VEGF expressions. Similarly, LY294002 interrupted the beneficial effects of QL with down-regulated phospho-Akt, phospho-mTOR, HIF-1α and VEGF expressions. However, it had no impact on NRG-1/ErbB signalling. Our data indicated that QL could attenuate anoxia-induced injuries in CMECs via NRG-1/ErbB signalling which was most probably dependent on PI3K/Akt/mTOR pathway. [ABSTRACT FROM AUTHOR]

This study investigated the effects of glycinin on the growth, intestinal oxidative status, tight junction components, cytokines and apoptosis signalling factors of fish. The results showed that an 80 g/kg diet of glycinin exposure for 42 d caused poor growth performance and depressed intestinal growth and function of juvenile Jian carp (Cyprinus carpio var. Jian). Meanwhile, dietary glycinin exposure induced increases in lipid peroxidation and protein oxidation; it caused reductions in superoxide dismutase (SOD), catalase and glutathione peroxidase (GPx) activities; and it increased MnSOD, CuZnSOD, GPx1b and GPx4a mRNA levels, suggesting an adaptive mechanism against stress in the intestines of fish. However, dietary glycinin exposure decreased both the activity and mRNA levels of nine isoforms of glutathione-S-transferase (GST) (α, μ, π, ρ, θ, κ, mGST1, mGST2 and mGST3), indicating toxicity to this enzyme activity and corresponding isoform gene expressions. In addition, glycinin exposure caused partial disruption of intestinal cell–cell tight junction components, disturbances of cytokines and induced apoptosis signalling in the distal intestines>mid intestines>proximal intestines of fish. Glycinin exposure also disturbed the mRNA levels of intestinal-related signalling factors Nrf2, Keap1a, Keap1b, eleven isoforms of protein kinase C and target of rapamycin/4E-BP. Interestingly, glutamine was observed to partially block those negative influences. In conclusion, this study indicates that dietary glycinin exposure causes intestinal oxidative damage and disruption of intestinal physical barriers and functions and reduces fish growth, but glutamine can reverse those negative effects in fish. This study provides some information on the mechanism of glycinin-induced negative effects. [ABSTRACT FROM PUBLISHER]

This study aimed to investigate the effects of threonine (Thr) on the digestive and absorptive ability, proliferation and differentiation of enterocytes, and gene expression of juvenile Jian carp (Cyprinus carpio var. Jian). First, seven isonitrogenous diets containing graded levels of Thr (7.4–25.2 g/kg diet) were fed to the fishes for 60 days. Second, enterocyte proliferation and differentiation were assayed by culturing enterocytes with graded levels of Thr (0–275 mg/l) in vitro. Finally, enterocytes were cultured with 0 and 205 mg/l Thr to determine protein synthesis. The percent weight gain (PWG), specific growth rate, feed intake, feed efficiency, protein retention value, activities of trypsin, lipase and amylase, weights and protein contents of hepatopancreas and intestine, folds heights, activities of alkaline phosphatase (AKP), γ- glutamyl transpeptidase and Na+/K+-ATPase in all intestinal segments, glutamate-oxaloacetate transaminase (GOT) and glutamate-pyruvate transaminase (GPT) activities in hepatopancreas, and 4E-BP2 gene expression in muscle, hepatopancreas and intestinal segments were significantly enhanced by Thr (p<0.05). However, the plasma ammonia concentration and TOR gene expression decreased (p<0.05). In vitro, Thr supplement significantly increased cell numbers, protein content, the activities of GOT, GPT, AKP and Na+/K+-ATPase, and protein synthesis rate of enterocytes, and decreased LDH activity and ammonia content in cell medium (p<0.05). In conclusion, Thr improved growth, digestive and absorptive capacity, enterocyte proliferation and differentiation, and protein synthesis and regulated TOR and 4E-BP2 gene expression in juvenile Jian carp. The dietary Thr requirement of juvenile Jian carp was 16.25 g/kg diet (51.3 g/kg protein) based on quadratic regression analysis of PWG. [ABSTRACT FROM AUTHOR]

β-conglycinin has been identified as one of the major feed allergens. However, studies of β-conglycinin on fish are scarce. This study investigated the effects of β-conglycinin on the growth, digestive and absorptive ability, inflammatory response, oxidative status and gene expression of juvenile Jian carp (Cyprinus carpio var. Jian) in vivo and their enterocytes in vitro. The results indicated that the specific growth rate (SGR), feed intake, and feed efficiency were reduced by β-conglycinin. In addition, activities of trypsin, chymotrypsin, lipase, creatine kinase, Na+,K+-ATPase and alkaline phosphatase in the intestine showed similar tendencies. The protein content of the hepatopancreas and intestines, and the weight and length of the intestines were all reduced by β-conglycinin. β-conglycinin increased lipid and protein oxidation in the detected tissues and cells. However, β-conglycinin decreased superoxide dismutase (SOD), catalase (CAT), glutathione-S-transferase (GST), glutathione peroxidase (GPx) and glutathione reductase (GR) activities and glutathione (GSH) content in the intestine and enterocytes. Similar antioxidant activity in the hepatopancreas was observed, except for GST. The expression of target of rapamycin (TOR) gene was reduced by β-conglycinin. Furthermore, mRNA levels of interleukin-8 (IL-8), tumor necrosis factor-α (TNF-α), and transforming growth factor-β (TGF-β) genes were increased by β-conglycinin. However, β-conglycinin increased CuZnSOD, MnSOD, CAT, and GPx1b gene expression. In conclusion, this study indicates that β-conglycinin induces inflammation and oxidation, and causes dysfunction of intestinal digestion and absorption in fish, and finally reduces fish growth. The results of this study provide some information to the mechanism of β-conglycinin-induced negative effects. [ABSTRACT FROM AUTHOR]

The present study was conducted to test the hypothesis that dietary arginine promotes digestion and absorption capacity, and, thus, enhances fish growth. This improvement might be related to the target of rapamycin (TOR) and eIF4E-binding protein (4E-BP). A total of 1200 juvenile Jian carp, Cyprinus carpio var. Jian, with an average initial weight of 6·33 (se 0·03) g, were fed with diets containing graded concentrations of arginine, namely, 9·8 (control), 12·7, 16·1, 18·5, 21·9 and 24·5 g arginine/kg diet for 9 weeks. An real-time quantitative PCR analysis was performed to determine the relative expression of TOR and 4E-BP in fish muscle, hepatopancreas and intestine. Dietary arginine increased (P < 0·05): (1) glutamate-oxaloacetate transaminase and glutamate-pyruvate transaminase activities in muscle and hepatopancreas; (2) intestine and hepatopancreas protein content, folds height, and trypsin, chymotrypsin, lipase, Na+/K+-ATPase, alkaline phosphatase, γ-glutamyl transpeptidase and creatine kinase activities in intestine; (3) Lactobacillus counts; (4) relative expression of TOR in the muscle, hepatopancreas and distal intestine (DI); (5) relative expression of 4E-BP in proximal intestine (PI) and mid-intestine (MI), as compared with the control group. In contrast, dietary arginine reduced (P < 0·05): (1) plasma ammonia content; (2) Aeromonas hydrophila and Escherichia coli counts; (3) relative expression of TOR in PI and MI; (4) relative expression of 4E-BP in the muscle, hepatopancreas and DI. The arginine requirement estimated by specific growth rate using quadratic regression analysis was found to be 18·0 g/kg diet. These results indicate that arginine improved fish growth, digestive and absorptive ability and regulated the expression of TOR and 4E-BP genes. [ABSTRACT FROM PUBLISHER]

Summary: Hematogenous metastasis is one of the most important factors determining the outcome of the patients with salivary adenoid cystic carcinoma (SACC). In the present study, we examined expression profile of genes in SACC cell lines to look for molecules responsible for its unique metastatic trait. A transcriptomic microarray analysis between the lower lung-metastatic rate cell line SACC-83 and the higher lung-metastatic rate cell line SACC-LM were performed, and eight genes, showed by microarray to be highly expressed in SACC-LM, were picked for validation by quantitative real-time PCR. Among the genes, the expression of epiregulin, a novel member of epidermal growth factor family, was 350-folds higher in SACC-LM than in SACC-83. Accordingly, we examined the effects of epiregulin on migration and invasion in SACC-83 as well as its targeted downstream molecules, and found that epiregulin could promote in vitro migration and invasion in SACC-83. Furthermore, epiregulin not only induced activation of both ERK1/2 and Akt, but also expression of COX-2. In addition, all these effects could be partially blocked by U0126, a specific inhibitor of mitogen-activated protein kinase kinase (MEK or MAPKK), or LY294002, a specific inhibitor of phosphatidylinositol 3-kinase (PI3K). Conclusively, the results suggest that epiregulin may play an important role in lung metastasis of SACC. [Copyright &y& Elsevier]

The purpose of this study was to explore the effect of the traditional Chinese medicine Fuyou formula on precocious puberty (PP). The Fy formula may exert an effect in female rats with PP and GT-7 cells through the GPR54/GnRH signaling pathway. To confirm the effect of the Fy formula on PP through the GPR54/GnRH signaling pathway, we first treated GT1-7 cells with the Fy formula and observed changes in the expression of related genes and proteins and in GnRH secretion. Then, we randomly divided young female Sprague-Dawley rats into the control group, model group, leuprorelin group and the Fy formula group. A PP model was established by injection of danazol on postnatal day 5, and the Fy formula was administered on PND15. The time of vaginal opening, the wet weights of the ovary and uterus, serum hormone levels and the expression of hypothalamic-related genes were observed. We found that the Fy formula delayed vaginal opening, decreased the wet weights and coefficients of the ovary and uterus, decreased the levels of serum hormones (E2, follicle-stimulating hormone and luteinizing hormone) and the cellular GnRH level, and downregulated the gene expression of Kiss1, GPR54 and GnRH in the hypothalamus and the gene and protein expression of GPR54 and GnRH in GT1-7 cells. In conclusion, the Fy formula may alleviate PP via the GPR54/GnRH signaling pathway. [ABSTRACT FROM AUTHOR]

Over the past decade, a large amount of RNA sequencing (RNA-seq) data were deposited in public repositories, and more are being produced at an unprecedented rate. However, there are few open source tools with point-and-click interfaces that are versatile and offer streamlined comprehensive analysis of RNA-seq datasets. To maximize the capitalization of these vast public resources and facilitate the analysis of RNA-seq data by biologists, we developed a web application called OneStopRNAseq for the one-stop analysis of RNA-seq data. OneStopRNAseq has user-friendly interfaces and offers workflows for common types of RNA-seq data analyses, such as comprehensive data-quality control, differential analysis of gene expression, exon usage, alternative splicing, transposable element expression, allele-specific gene expression quantification, and gene set enrichment analysis. Users only need to select the desired analyses and genome build, and provide a Gene Expression Omnibus (GEO) accession number or Dropbox links to sequence files, alignment files, gene-expression-count tables, or rank files with the corresponding metadata. Our pipeline facilitates the comprehensive and efficient analysis of private and public RNA-seq data. [ABSTRACT FROM AUTHOR]

Acute myeloid leukemia (AML) is a malignant hematological disease in which nearly half have normal cytogenetics. We have tried to find some significant molecular markers for this part of the cytogenetic normal AML, which hopes to provide a benefit for the diagnosis, molecular typing and prognosis prediction of AML patients. In the present study, we calculated and compared the gene expression profiles of cytogenetically normal acute myeloid leukemia (CN-AML) patients in database of The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and dataset Vizome (a total of 632 CN-AML samples), and we have demonstrated a correlation between PDE7B gene and CN-AML. Then we proceeded to a survival analysis and prognostic risk analysis between the expression levels of PDE7B gene and CN-AML patients. The result showed that the event-free survival (EFS) and overall survival (OS) were significantly shorter in CN-AML patients with high PDE7B levels in each dataset. And we detected a significantly higher expression level of PDE7B in the leukemia stem cell (LSC) positive group. The Cox proportional hazards regression model showed that PDE7B is an independent risk predictor for CN-AML. All results indicate that PDE7B is an unfavorable prognostic factor for CN-AML. [ABSTRACT FROM AUTHOR]

Background: Multiple myeloma (MM) is the plasma cell tumor, which is characterized by clonal proliferation of tumor cells, with high risk of progression to renal impairment, bone damage and amyloidosis. Although the survival rate of patients with MM has improved in the past decade, most people inevitably relapse. The treatment and prognosis of MM are still urgent problems. Breast Cancer Antiestrogen Resistance 3 (BCAR3) is a protein-coding gene that is associated with many tumors. However, there have been few studies on the relationship of BCAR3 and MM.Methods: We analyzed 1878 MM patients (1930 samples) from 7 independent datasets. First, we compared the BCAR3 expression level of MM patients in different stages and MM patients with different amplification of 1q21. Second, we analyzed BCAR3 expression levels in MM patients with different molecular subtypes. Finally, we explored the event-free survival rate (EFS) and overall survival rate (OS) of MM patients with high or low BCAR3 expression, including patients before and after relapse, and their therapeutic responses to bortezomib and dexamethasone.Results: The expression of BCAR3 showed a decreasing trend in stages I, II and III (P = 0.00068). With the increase of 1q21 amplification level, the expression of BCAR3 decreased (P = 0.022). Patients with high BCAR3 expression had higher EFS and OS (EFS: P < 0.0001, OS: P < 0.0001). The expression of BCAR3 gene before relapse was higher than that after relapse (P = 0.0045). BCAR3 is an independent factor affecting prognosis (EFS: P = 5.17E-03; OS: P = 3.33E-04).Conclusion: We found that high expression level of BCAR3 predicted better prognosis of MM patients. Low expression of BCAR3 at diagnosis can predict early relapse. BCAR3 is an independent prognostic factor for MM. BCAR3 can be used as a potential biomarker. [ABSTRACT FROM AUTHOR]

We applied in the previous study miRNA microarray screening analysis to identify several differentially expressed miRNAs, including miR-183 in normal, eutopic, and ectopic endometrium. Knockdown of miR-183 expression induced the invasiveness and inhibition of apoptosis in endometrial stromal cells. The current study aims to identify the miR-183 targets with relevance to cell functions in endometrial stromal cells, to verify the interaction of miR-183 with its target genes, and to confirm the role of miR-183 in the process of endometriosis. Using microarray analysis, we identified 27 differentially expressed genes (19 were upregulated and 8 downregulated), from which we selected 4 downregulated genes (ITGB1, AMIGO2, VAV3, and PSEN2) based on GO databases for functional analysis and significant pathway analysis. Western blotting analyses showed that integrin ?1 (ITGB1), but not AMIGO2, was affected by miR-183 overexpression, whereas no protein expression of VAV3 and PSEN2 was detected. Luciferase reporter assay verified that ITGB1 is a target gene of miR-183. Moreover, we found that ITGB1 is overexpressed in the endometrium of endometriosis patients. Furthermore, overexpression of ITGB1 rescued the repressive effects of miR-183 on the invasiveness of endometrial stromal cells. These findings, together with the fact that ITGB1 is a critical factor for cell adhesion and invasiveness, suggest that miR-183 may be involved in the development of endometriosis by regulating ITGB1 in endometrial stromal cells. [ABSTRACT FROM AUTHOR]

Abstract: T-cell surface glycoprotein CD8 consists of two distinguished chains, termed α and β chains, and functions as a co-receptor for the T-cell receptor by binding to MHC class I proteins. In this study we report the cloning and identification of both CD8α and CD8β genes from orange-spotted grouper (Epinephelus coioides). The predicted grouper CD8α and CD8β proteins were structurally similar to other fish especially to those of Pleuronectiformes. Real-time RT-PCR revealed that the CD8 mRNA was much higher in the thymus than in other immune organs, and the expression level were very low in stomach, liver, and brain. During embryonic development of the grouper, the highest CD8 transcripts were detected in the multi-cell stage, followed by muscle burl stage, which suggested that the multi-cell stage may be critical in CD8 transcript synthesis. Moreover, CD8 mRNA levels were examined in lymphocytes at different time treated with lipopolysaccharide (LPS), polyriboinosinic polyribocytidylic acid (PolyI:C), phytohemagglutinin (PHA), and concanavalin A (ConA). The result showed that the CD8 mRNA levels were significantly affected in time-dependent manner by PolyI:C, PHA, and ConA, but not by LPS. [Copyright &y& Elsevier]

Alternative pre-mRNA splicing, which produces various mRNA isoforms with distinct structures and functions from a single gene, is regulated by specific RNA-binding proteins and is an essential method for regulating gene expression in mammals. Recent studies have shown that abnormal change during neuronal development triggered by splicing mis-regulation is an important feature of various neurological diseases. Polypyrimidine tract binding protein 1 (PTBP1) is a kind of RNA-binding proteins with extensive biological functions. As a well-known splicing regulator, it affects the neuronal development process through its involvement in axon formation, synaptogenesis, and neuronal apoptosis, according to the most recent studies. Here, we summarized the mechanism of alternative splicing, structure and function of PTBP1, and the latest research progress on the role of alternative splicing events regulated by PTBP1 in axon formation, synaptogenesis and neuronal apoptosis, to reveal the mechanism of PTBP1-regulated changes in neuronal development process. • Abnormal change during neuronal development triggered by splicing mis-regulation is an important feature of various neurological diseases. • As a well-known splicing regulator, PTBP1 is a kind of RNA binding protein with extensive biological functions. • PTBP1 participates in the regulation of the neuronal development process through its involvement in axon formation, synaptogenesis, and neuronal apoptosis. [ABSTRACT FROM AUTHOR]

It has been well documented that BST2 restricts the release of enveloped viruses by cross-linking newly produced virions to the cell membrane. However, it is less clear whether and how BST2 inhibits the release of enveloped viruses which bud via the secretory pathway. Here, we demonstrated that BST2 restricts the release of Japanese encephalitis virus (JEV) whose budding occurs at the ER-Golgi intermediate compartment, and in turn, JEV infection downregulates BST2 expression. We further found that the JEV envelope protein E, but not other viral components, significantly downregulates BST2 with the viral protein M playing an auxiliary role in the process. Envelope protein E-mediated BST2 downregulation appears to undergo lysosomal degradation pathway. Additional study revealed that the transmembrane domain and the coiled-coil domain (CC) of BST2 are the target domains of viral protein E and that the N- and C-terminal membrane anchors and the CC domain of BST2 are essential for blocking JEV release. Our results together indicate that the release of enveloped viruses whose budding take place in an intracellular compartment can be restricted by BST2. [ABSTRACT FROM AUTHOR]

Abstract: The C-type lectin receptors (CLRs) expressed on dendritic cells (DCs), in particular DC-SIGN and DCIR, likely play an important role in HIV-1 early infection. Here, we systematically compared the capture and transfer capability of DC-SIGN and DCIR using a wide range of HIV-1 isolates. Our results indicated that DC-SIGN plays a stronger role than DCIR in DC-mediated HIV-1 capture and transfer. This was further strengthened by the data from transient and stable transfectants, showing that DC-SIGN had better capability, compared with DCIR in HIV-1 capture and transfer. Following constructing and analyzing a series of soluble DC-SIGN and DCIR truncates and chimeras, we demonstrated that the neck domain, but not the CRD, renders DC-SIGN higher binding affinity to gp120 likely via the formation of tetramerization. Our findings provide insights into CLR-mediated HIV-1 capture and transfer, highlighting potential targets for intervention strategies against gp120-CLR interactions. [Copyright &y& Elsevier]

Abstract: The mechanistic target of rapamycin (mTOR) plays a key role in growth and development. In the present study, a cDNA encoding mTOR protein was identified from common carp Cyprinus carpio muscle. The open reading frame of this cDNA encodes 2515 deduced amino acid residues that showed high sequence similarity with its zebrafish Danio rerio counterparts. Bioinformatic analysis showed that the protein belongs to the PI-3 kinase family. The putative protein has FAT, FRB, PI3Kc, and FATC domains, which are highly conserved among the vertebrate orthologs. Real-time quantitative PCR analysis revealed that the abundance of mTOR mRNA was the highest in the heart at 18–31g and muscle at 31–75g of common carp. As the common carp grew (18–40g), the mTOR expression gradually decreased in the hepatopancreas and heart, but increased in the muscle, hind kidney, spleen, gill, head kidney, foregut, midgut, and hindgut. Then the mTOR expression kept a constant in all examined tissues during the common carp grew (40–75g). The present study identified the mTOR gene and determined its gene expression profile in various tissues of the common carp with body weight increased. These findings will help better understand the biological role of mTOR in the juvenile fish. [Copyright &y& Elsevier]

Abstract: The effects of dietary choline on growth, digestive and absorptive capacities, and target of rapamycin (TOR) and eIF4E-binding protein2 (4E-BP2) gene expression in muscle, hepatopancreas and intestine of juvenile Jian carp (Cyprinus carpio var. Jian) were assessed. A total of 1200 juvenile Jian carp with an average initial weight of 7.94±0.03g were fed six semi-purified diets containing 165 (unsupplemented control group), 310, 607, 896, 1167 and 1820mgcholinekg−1 diet for 65days. Specific growth rate (SGR), feed intake, feed efficiency, protein retention value, protein content and lipid content of fish carcasses were significantly improved by dietary choline supplementation; whereas, protein efficiency ratio and body ash content were not significantly different among dietary groups. Patterns of differences in intestine length, relative gut length, intestine weight, hepatopancreas protein content, intestinal folds height in three intestinal segments, trypsin and chymotrypsin activities in intestine and hepatopancreas, α-amylase and creatine kinase activities in intestine, Na+/K+-ATPase activity in distal intestine and relative expression of TOR gene in distal intestine and 4E-BP2 gene in muscle responded similar to SGR; whereas, the trends of hepatosomatic index, lipase activity in intestine and hepatopancreas, Na+/K+-ATPase activity in proximal intestine and mid intestine, TOR gene expression in muscle and hepatopancreas, and 4E-BP2 gene expression in proximal intestine, mid intestine and distal intestine were opposite. Alkaline phosphatase and γ-glutamyl transpeptidase activities in intestinal segments were not significantly different among dietary groups. These results indicated that dietary choline could improve fish growth, enhance digestive and absorptive ability and regulate TOR and 4E-BP2 gene expression in tissues. The dietary choline requirement of Jian carp estimated by the broken-line model based on SGR was 566mgcholinekg−1 diet in the form of choline chloride. [Copyright &y& Elsevier]

Abstract: GPI-anchored membrane cytokines have been shown to play an important role in host immune response against tumor cells. In the present study, we constructed the tumor vaccine expressing mIL-21 in the GPI-anchored form and investigated its anti-tumor effect in C57BL/6 mice model. The fusion genes containing mIL-21 and the GPI anchor signal sequence was acquired by overlaping PCR, inserted into plasmid pcDNA3.1 to form the pcDNA3.1 mIL-21-GPI recombinant, which was transfected into the B16F10 cells, and the tumor vaccine based on B16F10 cells expressing the GPI-anchored membrane mIL-21 was generated. Through transfection, it was found that GPI-anchored membrane mIL-21 has no proliferate impact on B16F10 cells, but it was functional and reflected in inducing CD3-activated murine splenocytes proliferation response to B16F10 cells, improving the cytotoxicities of CTL and NK cells, increasing the numbers of splenocytes-producing IFN-γ in mice, augmenting therapeutic effect of tumor and prolonging longevity effects in tumor-bearing mice injected with the inactivated GPI-anchored mIL-21 tumor vaccine. We concluded the expression of mIL-21 on the B16F10 cells surface in the GPI-anchored form was proved to be effective in activating immune responses against tumor cells, and our results provided a good foundation for further investigating the immunotherapy of tumor by GPI-mIL-21. [Copyright &y& Elsevier]

Abstract: Background: FAS-670 A/G single nucleotide polymorphism has been demonstrated to affect the expression of FAS gene by altering the transcriptional activity of FAS gene promoter. Downregulation of FAS with resultant resistance to death signals has been found in many cancers. We carried out a case-control study to investigate the biological significance of this polymorphism in nasopharyngeal carcinoma (NPC). Methods: FAS-670 A/G polymorphism was examined in a Chinese population of 237 patients with NPC and 264 control subjects using the polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) technique. Results: There were no significant differences in the genotype or allele distribution of FAS-670 A/G polymorphism between cases and controls. FAS-670 (AG+GG) genotype and G allele showed significant associations with an increasing risk of lymph node metastasis (OR=2.08, P =0.01; OR=1.67, P =0.011, respectively) and distant metastasis (OR=3.87, P =0.015; OR=1.81, P =0.03, respectively) of NPC patients. In addition, FAS-670 (AG+GG) genotype showed an increasing incidence of advanced clinical stage, but this finding was not statistically significant (OR=1.79, P =0.066). Conclusion: The FAS-670 G allele could be used as a genetic risk marker for the metastasis of NPC patients. [Copyright &y& Elsevier]