Ion channels are involved in the mechanism of anesthetic action and side effect. The transcription and expression of ion channel genes can be modulated by general anesthetics. The adverse effect of continuous infusion of etomidate has been concerned. However, the effects of etomidate on mRNA expressions of ion channel genes remain unclear. In this study, we exposed Daphnia pulex in 250 μmol/L of etomidate for 240 min and observed the change of heart rate, phototactic behavior and blood glucose during the period of exposure, as well as the mRNA expressions of 120 ion channel genes at the end of the experiment. Compared to the controls, heart rate, phototactic behavior and blood glucose were not influenced by 250 μmol/L of etomidate. According to the quantitative PCR results, 18 of 120 Daphnia pulex ion channel genes transcripts were affected by persistent 240 min exposure to 250 μmol/L of etomidate: 2 genes were upregulated and 16 genes were down-regulated, suggesting that etomidate showed effects on many different ion channels in transcription level. Systematical exploration of transcriptional changes of ion channels could contribute to understanding of the pharmacological mechanism of etomidate.
It is generally considered that various regulatory activities between genes are contained in the gene expression datasets. Therefore, the underlying gene regulatory relationship and the biologically useful information can be found by modeling the gene regulatory network from the gene expression data. In our study, two unsupervised matrix factorization methods, independent component analysis (ICA) and nonnegative matrix factorization (NMF), were proposed to identify significant genes and model the regulatory network using the microarray gene expression data of Alzheimer's disease (AD). By bio-molecular analyzing of the pathways, the differences between ICA and NMF have been explored and the fact, which the inflammatory reaction is one of the main pathological mechanisms of AD, is also emphasized. It was demonstrated that our study gave a novel and valuable method for the research of early detection and pathological mechanism, biomarkers' findings of AD.
Objective The aim of this study is to review the association between long non-coding RNA (lncRNA) and papillary thyroid carcinoma (PTC). Method The relevant literatures about lncRNA associated with PTC were retrospectively analyzed and summarized. Results The expression levels of noncoding RNA associated with MAP kinase pathway and growth arrest (NAMA), PTC susceptibility candidate 3 (PTCSC3), BRAF activated non-coding RNA (BANCR), maternally expressed gene 3 (MEG3), NONHSAT037832, and GAS8-AS1 in PTC tissues were significantly lower than those in non-thyroid carcinoma tissues. The expression levels of ENST00000537266, ENST00000426615, XLOC051122, XLOC006074, HOX transcript antisense RNA (HOTAIR), antisense noncoding RNA in the INK4 locus (ANRIL), and metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) in PTC tissues were upregulated in PTC tissues, comparing with the non-thyroid carcinoma tissues. These lncRNAs were possibly involved in cell proliferation, migration, and apoptosis of PTC. Conclusion LncRNAs may provide new insights into the molecular mechanism and gene-targeted therapy of PTC and become new molecular marker for the diagnosis of PTC.
Objective To study the effect of silencing the NOD-like receptor family, pyrin domain containing protein 3 (NLRP3) gene on the production of inflammatory factors induced by lipopolysaccharide (LPS) and adenosine triphosphate (ATP) in rat brain microvascular endothelial cells (BMECs), and whether NLRP3 inflammasome signaling pathway plays a role in the BMEC model of cerebral small vessel disease induced by proinflammatory agents. Methods BMECs from male Wistar rats were extracted in vitro and the morphology and purity of endothelial cells were identified. BMECs in normal culture were divided into blank control group and LPS+ATP group. The expression levels of NLRP3 inflammasome and downstream inflammatory factor Caspase-1 were detected by Western blot and real-time polymerase chain reaction, and compared by student’s t test between the two groups. Small interfering RNA (siRNA) was used to silence the specific gene NLRP3 in BMECs. After transfection of siRNA NLRP3 and siRNA plasmid negative control into BMECs, the transfected cells were divided into four groups, namely, siNC group (non silenced target gene), siNLRP3 group (silenced target gene), siNC+LPS+ATP group (non silenced target gene and added proinflammatory agents) and siNLRP3+LPS+ATP group (silenced target gene and added proinflammatory agents). The expression levels of NLRP3 and Caspase-1 were detected by Western blot and real-time polymerase chain reaction, and analyzed by analysis of variance for 2-factor factorial design. Results The microvascular segments of rat BMECs were “beaded” after 24 h of isolation and culture; after 48 h, “island” cell clusters were formed; after 72 h, “paving stone” like monolayer cells adhered to the wall and grew. After that, the cells gradually became dense and reached the convergence degree of 80%. The positive rate of BMECs detected by immunofluorescence staining was 96%. In the normally cultured cells, the protein and mRNA expression levels of NLRP3 and Caspase-1 in the LPS+ATP group were higher than those in the blank control group (P<0.05). In the RNA interference cultured cells, the protein and mRNA expression levels of NLRP3 and Caspase-1 in the siNLRP3 group were lower than those in the siNC group, and those expression levels in the siNLRP3+LPS+ATP group were lower than those in the siNC+LPS+ATP group (P<0.05); the protein and mRNA expression levels of NLRP3 and Caspase-1 in the siNC+LPS+ATP group were higher than those in the siNC group, and those expression levels in the siNLRP3+LPS+ATP group were higher than those in the siNLRP3 group (P<0.05). Plasmid transfection and proinflammatory agents intervention had statistically significant interaction effect on the mRNA expression of NLRP3 and Caspase-1 (P<0.05). Conclusions LPS and ATP can promote the release of NLRP3 and Caspase-1 in BMECs. Silencing NLRP3 gene expression can reduce the induction of proinflammatory agents. NLRP3 inflammasome signaling pathway may play a role in the cerebral small vessel disease cell model of rat BMECs induced by proinflammatory agents.
Using modular identification methods in gene-drug multiplex networks to infer new gene-drug associations can identify new therapeutic target genes for known drugs. In this paper, based on the gene expression data and drug response data of lung cancer in the genomics of drug sensitivity in cancer (GDSC) database, a multiple network algorithm is proposed. First, a heterogeneous network of genes of lung cancer and drugs in different cell lines is constructed, and then a network module identification method based on graph entropy is used. In this heterogeneous network, network modules are identified, and five lung cancer gene-drug association modules are identified through iterative convergence. Compared with other methods, the algorithm has better results in terms of running time, accuracy and robustness, and the identified modules have obvious biological significance. The research results in this article have guiding significance for the medication and treatment of lung cancer, and can provide references for the treatment of other diseases with the same targeted genes.
Objective To integrate the result of whole genome expression data and whole genome promoter CpG island methylation data, to screen the epigenetic modulated differentially expressed genes from transformed porcine bone marrow mesenchymal stem cells (BMSCs) after long-term cultivation. Methods Bone marrow from 6 landrace pigs, 3-month-old about 50 kg weight, was aspirated from the medullary cavity of the proximal tibia. The BMSCs were isolated, and purified by Ficoll density gradient centrifugation combined with adherent culture method. The transfor mation of BMSCs was tested by several methods including cell morphology observation, karyotype analysis, clone forming in soft agarose, serum requirement assay, and tumor forming in mice. The Agilent Pig 4x44k Gene Expression Microarray was used to investigate the differentially expressed mRNA. The methylated genes expression profile was performed using customized pig methylation chip. The gene expression and DNA methylation profiles were integrated to find out the epigenetic modulated differentially expressed genes, and to complete the bioinformatic analysis. Results BMSCs showed a change in appearance, from the initial spindle shape to a more flatted morphology then to small contact shape. After additional passages, BMSCs gradually acquired recovery of proliferating capacity and transformation properties such as anchorage-independent growth, chromosomal abnormality, and tumor formation in nude mice. The gene chip analysis demonstrated that 257 genes were upregulated and 315 genes were downregulated during long-term cultures as well as multiple signal pathways transduction involved, such as cell cycle, ECM-receptor interaction, focal adhesion, regulation of actin cytoskeleton, pathways in cancer, and P53. The analysis from methylation chip of coding genes suggested epigenetic regulation was involved in BMSCs spontaneous transformation and play a important role on it; 962 genes were hypermethylated and 1219 genes were hypomethylated, which were involved in the biological process of cellular metabolic, structure, and tumor generation. The combined analysis of genes regulated by methylation in the transformation process of BMSCs found that the methylation changes of the 35 genes were contrary to the direction of expression change (correlation coefficient r=–0.686, P=0.000); in which the methylation level of 21 genes promoter regions were increased while the gene expression decreased, and the methylation level of the 14 genes promoter regions decreased and the gene expression increased. At the same time, KEGG enrichment analysis revealed multiple genes regulated by methylation, involved in stem cell differentiation and multiple cell signaling pathways. Among the 14 down-regulated genes, many of them have the role of regulating the interaction of tumor and immunization, and the change of the methylation status of the CDKN3 promoter region may be closely related to the cell oncology. Conclusion The results deepen our understanding of the crucial role of coding genes methylation modification in BMSCs transformation, and may provide new approach to establish safe criteria for BMSCs clinical applications and transformation prevention.
Recombinant protein SMBPRG4 containing two Somatomedin B domains and a small amount of glycosylation of repetitive sequences of proteoglycan 4 was cloned according to PGR4 gene polymorphism. Mature purification process was established and recombinant protein SMBPRG4, with high-level expression was purified. By using size-exclusion chromatogaraphy and dynamic light scattering, we found that the recombinant protein self-aggregate to dimeric form. Structure prediction and non-reducing electrophoresis revealed that SMBPRG4 was a non-covalently bonded dimer.
Cancer gene expression data have the characteristics of high dimensionalities and small samples so it is necessary to perform dimensionality reduction of the data. Traditional linear dimensionality reduction approaches can not find the nonlinear relationship between the data points. In addition, they have bad dimensionality reduction results. Therefore a multiple weights locally linear embedding (LLE) algorithm with improved distance is introduced to perform dimensionality reduction in this study. We adopted an improved distance to calculate the neighbor of each data point in this algorithm, and then we introduced multiple sets of linearly independent local weight vectors for each neighbor, and obtained the embedding results in the low-dimensional space of the high-dimensional data by minimizing the reconstruction error. Experimental result showed that the multiple weights LLE algorithm with improved distance had good dimensionality reduction functions of the cancer gene expression data.
Lung adenocarcinoma is a prevalent histological subtype of non-small cell lung cancer with different morphologic and molecular features that are critical for prognosis and treatment planning. In recent years, with the development of artificial intelligence technology, its application in the study of pathological subtypes and gene expression of lung adenocarcinoma has gained widespread attention. This paper reviews the research progress of machine learning and deep learning in pathological subtypes classification and gene expression analysis of lung adenocarcinoma, and some problems and challenges at the present stage are summarized and the future directions of artificial intelligence in lung adenocarcinoma research are foreseen.
Synergistic effects of drug combinations are very important in improving drug efficacy or reducing drug toxicity. However, due to the complex mechanism of action between drugs, it is expensive to screen new drug combinations through trials. It is well known that virtual screening of computational models can effectively reduce the test cost. Recently, foreign scholars successfully predicted the synergistic value of new drug combinations on cancer cell lines by using deep learning model DeepSynergy. However, DeepSynergy is a two-stage method and uses only one kind of feature as input. In this study, we proposed a new end-to-end deep learning model, MulinputSynergy which predicted the synergistic value of drug combinations by integrating gene expression, gene mutation, gene copy number characteristics of cancer cells and anticancer drug chemistry characteristics. In order to solve the problem of high dimension of features, we used convolutional neural network to reduce the dimension of gene features. Experimental results showed that the proposed model was superior to DeepSynergy deep learning model, with the mean square error decreasing from 197 to 176, the mean absolute error decreasing from 9.48 to 8.77, and the decision coefficient increasing from 0.53 to 0.58. This model could learn the potential relationship between anticancer drugs and cell lines from a variety of characteristics and locate the effective drug combinations quickly and accurately.