Postmortem Interval Estimation Using Protein Chip Technology Combined with Multivariate Analysis Methods / 法医学杂志

OBJECTIVES@#To estimate postmortem interval (PMI) by analyzing the protein changes in skeletal muscle tissues with the protein chip technology combined with multivariate analysis methods.@*METHODS@#Rats were sacrificed for cervical dislocation and placed at 16 ℃. Water-soluble proteins in skeletal muscles were extracted at 10 time points (0 d, 1 d, 2 d, 3 d, 4 d, 5 d, 6 d, 7 d, 8 d and 9 d) after death. Protein expression profile data with relative molecular mass of 14 000-230 000 were obtained. Principal component analysis (PCA) and orthogonal partial least squares (OPLS) were used for data analysis. Fisher discriminant model and back propagation (BP) neural network model were constructed to classify and preliminarily estimate the PMI. In addition, the protein expression profiles data of human skeletal muscles at different time points after death were collected, and the relationship between them and PMI was analyzed by heat map and cluster analysis.@*RESULTS@#The protein peak of rat skeletal muscle changed with PMI. The result of PCA combined with OPLS discriminant analysis showed statistical significance in groups with different time points (P<0.05) except 6 d, 7 d and 8 d after death. By Fisher discriminant analysis, the accuracy of internal cross-validation was 71.4% and the accuracy of external validation was 66.7%. The BP neural network model classification and preliminary estimation results showed the accuracy of internal cross-validation was 98.2%, and the accuracy of external validation was 95.8%. There was a significant difference in protein expression between 4 d and 25 h after death by the cluster analysis of the human skeletal muscle samples.@*CONCLUSIONS@#The protein chip technology can quickly, accurately and repeatedly obtain water-soluble protein expression profiles in rats' and human skeletal muscles with the relative molecular mass of 14 000-230 000 at different time points postmortem. The establishment of multiple PMI estimation models based on multivariate analysis can provide a new idea and method for PMI estimation.

Prokaryotic expression, polyclonal antibody preparation, spatio-temporal expression profile and functional analysis of c-Myc of Helicoverpa armigera (Lepidoptera: Noctuidae) / 生物工程学报

c-Myc protein encoded by c-Myc (cellular-myelocytomatosis viral oncogene) gene regulates the related gene expression through the Wnt/β-catenin signaling pathway, and has received extensive attention in recent years. The purpose of this study was to express Helicoverpa armigera c-Myc gene (Ha-c-Myc) by using prokaryotic expression system, prepare the polyclonal antibody, examine the spatio-temporal expression profile of Ha-c-Myc, and investigate the possible function of Ha-c-Myc in regulating H. armigera sterol carrier protein-2 (SCP-2) gene expression. The Ha-c-Myc gene was amplified by PCR and cloned into a prokaryotic expression plasmid pET-32a(+). The recombinant plasmid pET-32a-Ha-c-Myc was transformed into Escherichia coli BL21. IPTG was used to induce the expression of the recombinant protein. Protein was purified by Ni2+-NTA column and used to immunize New Zealand rabbits for preparing the polyclonal antibody. The Ha-c-Myc expression levels in different developmental stages (egg, larva, prepupa, pupa, and adult) of H. armigera and different tissues (midgut, fat body, head, and epidermis) of the prepupa were determined by real-time quantitative reverse transcription PCR (qRT-PCR). Ha-c-Myc siRNA was synthesized and transfected into H. armigera Ha cells. The relative mRNA levels of Ha-c-Myc and HaSCP-2 in Ha cells were detected by qRT-PCR. Results showed that the pET-32a-Ha-c-Myc recombinant plasmid was constructed. The soluble Ha-c-Myc protein of about 65 kDa was expressed in E. coli. The polyclonal antibody was prepared. Western blotting analysis suggested that the antibody had high specificity. Enzyme linked immunosorbent assay (ELISA) showed that the titer of the antibody was high. Ha-c-Myc gene expressed at all developmental stages, with high levels in the early and late instars of larva, and the prepupal stage. Tissue expression profiles revealed that Ha-c-Myc expressed in various tissues of prepupa, with high expression level in the midgut, but low levels in the epidermis and fat body. RNAi results showed that the knockdown of Ha-c-Myc expression significantly affected transcription of HaSCP-2, leading to a 50% reduction in HaSCP-2 mRNA expression level. In conclusion, the Ha-c-Myc was expressed through a prokaryotic expression system, and the polyclonal anti-Ha-c-Myc antibody was obtained. Ha-c-Myc may promote the expression of HaSCP-2 and play an important role in the lipid metabolism of H. armigera. These results may facilitate further study on the potential role and function mechanism of Ha-c-Myc in H. armigera and provide experimental data for exploring new targets of green pesticides.

The identification of bZIP gene family in Cannabis sativa L. and its preliminary research of the function in regulation of lipid metabolism / 药学学报

The bZIP (basic leucine zipper) gene family is one of the largest transcription factor families in eukaryotes, and its members play important roles in stress response, secondary metabolism, plant growth, seed development and other aspects. To investigate the biological functions of the bZIP (CsbZIP) gene in Cannabis sativa L., we systematically investigated the CsbZIP gene family using bioinformatics methods based on the whole-genome and transcriptome data. The results showed that 55 CsbZIP gene family members (CsbZIP1-CsbZIP55) were identified and distributed on 10 chromosomes, belonging to 12 subfamilies. The gene structure and protein motif distribution of the same subfamily members were similar. Segment repeats were the main reasons for the expansion of CsbZIP gene family. Cis-elements analysis showed that the promoter regions of 73 lipid synthesis genes contained G-box or A-box element. qRT-PCR showed that the relative expression levels of 7 CsbZIP genes and 7 lipid synthesis genes were relatively high in hemp seed. 7 CsbZIP genes had a significant positive correlation with 7 lipid synthesis genes. This study revealed the structural features, evolutionary patterns and expression patterns of CsbZIP, providing important clues for further study on the regulation of CsbZIP on oil metabolism of hemp seed.

Comparison of pathogenicity and gene expression profiles between adult Schistosoma japonicum isolated from hilly and marshland and lake regions of Anhui Province / 中国血吸虫病防治杂志

Objective To compare the differences in pathogenicity and gene expression profiles between adult Schistosoma japonicum isolated from hilly and marshland and lake regions of Anhui Province, so as to provide the scientific evidence for formulating the precise schistosomiasis control strategy in different endemic foci. Methods C57BL/6 mice were infected with cercariae of S. japonicum isolates from Shitai County (hilly regions) and Susong County (marshland and lake regions) of Anhui Province in 2021, and all mice were sacrificed 44 days post-infection and dissected. The worm burdens, number of S. japonicum eggs deposited in the liver, and the area of egg granulomas in the liver were measured to compare the difference in the pathogenicity between the two isolates. In addition, female and male adult S. japonicum worms were collected and subjected to transcriptome sequencing, and the gene expression profiles were compared between Shitai and Susong isolates of S. japonicum. The differentially expressed genes (DEGs) were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Results The total worm burdens [(14.50 ± 3.96) worms/mouse vs. (16.10 ± 3.78) worms/mouse; t = 0.877, P = 0.392], number of female and male paired worms [(4.50 ± 0.67) worms/mouse vs. (5.10 ± 1.45) worms/mouse; t = 1.129, P = 0.280], number of unpaired male worms [(5.50 ± 4.01) worms/mouse vs. (5.60 ± 1.69) worms/mouse; t = 0.069, P = 0.946], number of eggs deposited in per gram liver [(12 116.70 ± 6 508.83) eggs vs. (16 696.70 ± 4 571.56) eggs; t = 1.821, P = 0.085], and area of a single egg granuloma in the liver [(74 359.40 ± 11 766.34) µm2 vs. (74 836.90 ± 13 086.12) µm2; t = 0.081, P = 0.936] were comparable between Shitai and Susong isolates of S. japonicum. Transcriptome sequencing identified 584 DEGs between adult female worms and 1 598 DEGs between adult male worms of Shitai and Susong isolates of S. japonicum. GO enrichment analysis showed that the DEGs between female adults were predominantly enriched in biological processes of stimulus response, cytotoxicity, multiple cell biological processes, metabolic processes, cellular processes and signaling pathways, cellular components of cell, organelles and cell membranes and molecular functions of binding and catalytic ability, and KEGG enrichment analysis showed that these DEGs were significantly enriched in pathways of vascular endothelial growth factor signaling, glutathione metabolism, arginine and proline metabolism. In addition, the DEGs between male adults were predominantly enriched in biological processes of signaling transduction, multiple cell biological processes, regulation of biological processes, metabolic processes, development processes and stimulus responses, cellular components of extracellular matrix and cell junction and molecular functions of binding and catalytic ability, and these DEGs were significantly enriched in pathways of Wnt signaling, Ras signaling, natural killer cells-mediated cytotoxicity, extracellular matrix-receptor interactions and arginine biosynthesis. Conclusions There is no significant difference in the pathogenicity between S. japonicum isolates from hilly and marshland and lake regions of Anhui Province; however, the gene expression profiles vary significantly between S. japonicum isolates.

Diagnostic criteria and research progress on heart allograft pathology / 器官移植

With the improvement of surgical technique of heart transplantation and clinical application of potent immunosuppressant, the quantity of heart transplantation and the survival time of heart allograft have been significantly improved. However, a series of complications, such as right ventricular failure, ischemia-reperfusion injury, acute rejection, "Quilty lesion", infection and chronic rejection characterized by transplant coronary artery disease (TCAD) may still occur at different stages after heart transplantation. The application of endomyocardial biopsy (EMB) makes it possible to observe and understand the pathological features of multiple complications of heart allograft including rejection, which has become the most accurate diagnostic tool for postoperative complications. In this article, the brief history of heart allograft pathology, main postoperative complications and pathological diagnostic criteria, and cutting edge research progress on diagnostic criteria of rejection were illustrated, aiming to bring clinical benefits to more recipients undergoing heart transplantation.

Differential expression profile of circRNAs in oral leukoplakia / 口腔疾病防治

Objective@#To investigate the differences and clinical significance of circRNA expression profiles in oral leukoplakia (OLK) tissues and normal oral mucosal (NOM) tissues.@*Methods@# High-throughput sequencing was used to detect differentially expressed circRNAs in 6 pairs of OLK and NOM tissues, and qRT-PCR was used to verify the expression of 10 circRNAs screened in 6 pairs of OLK and NOM tissues. The ring formation of circRNA was verified by RNase R digestion and Sanger sequencing, and the target circHLA-C was further verified by qRT-PCR in 20 pairs of OLK and NOM tissues. CircHLA-C was visualized using the UCSC genome browser (genome.ucsc.edu). The function of differentially expressed circRNAs was analyzed by GO and KEGG enrichment analyses. TargetScan and miRanda predicted the downstream miRNAs and mRNAs of the target circRNAs, and a ceRNA network related to the identified circRNAs was constructed in Cytoscape.@* Results@#Sequencing analysis showed that 366 circRNAs were significantly differentially expressed in OLK tissues, including 65 upregulated and 301 downregulated circRNAs. After qRT-PCR verification, 7 of the 10 screened circRNAs were expressed consistent with the sequencing results. The upregulated circHLA-C was confirmed to be a real circRNA with back-splice junction sites by RNase R digestion and Sanger sequencing. Correlation analysis showed a positive correlation between circHLA-C and the degree of OLK dysplasia. ROC curve analysis suggested that circHLA-C had potential value in diagnosing OLK with high accuracy and specificity.@*Conclusion@#CircRNA was significantly abnormally expressed in OLK tissues, and the upregulation of circHLA-C may be related to the degree of OLK dysplasia, providing guiding value for the diagnosis of OLK in the future.

Expression analysis of miRNA profiles in apheresis platelets at the end of storage / 中国输血杂志

【Objective】 To investigate the changes of platelet microRNA (miRNA) expression profiles of storage in vitro, and to explore the molecular mechanism of miRNAs involved in the regulation of platelet storage lesion (PSL). 【Methods】 20 platelet samples (5 mL / sample) were collected from apheresis platelet donors, fully mixed and stored in a shaker with (22±2) ℃ horizontal agitation, sampled on day 1 and day 5, and sequenced by DNA nanoball (DNB) sequencing technology. The miRNAs with more than 2 times expressions (P<0.01) were considered as significantly differences between d5 and d1 groups. The miRanda and TargetScan softwares were used to predict the target genes. Gene Ontology (GO) function enrichment analysis and Kyoto Encyclopedia of genes and genomes (KEGG) pathway enrichment analysis were performed on the target genes of significant differentially expressed miRNAs. The expression of miRNAs was verified by real-time fluorescence quantitative PCR (qRT-PCR). 【Results】 Compared with d1 group, 315 miRNAs with significantly different expression (P<0.01) were screened in d5 group, including 146 up-regulated miRNAs (such as miR-146a, let-7b), and 169 down-regulated miRNAs (such as mir-30d, mir-142). Among 126 known miRNAs, 43 were up-regulated and 83 were down-regulated. There are 189 new miRNA sequences. The enriched GO terms of target genes of differentially expressed miRNAs in d5 and d1 groups included cell components, organelles, cell membrane and other cell structures, molecular functions such as adhesion, catalysis and activity, and biological processes such as cell processing, metabolism, biological regulation and stress. The corresponding pathways in the top 10 of KEGG enrichment were mainly signal transduction, secretion, membrane transport, amino acid metabolism, polysaccharide metabolism, protein synthesis and environmental adaptation. The 6 randomly selected differentially expressed miRNAs verified by qRT-PCR were consistent with those of DNB sequencing. 【Conclusion】 The expression profiles of platelets miRNAs have changed significantly between the d1 and d5 of storage in vitro. Functional prediction suggested that these miRNAs might be involved in the regulation of platelet PSL.

Bioinformatics analysis of expression profiles of long noncoding RNA in endometrial cancer / 上海交通大学学报（医学版）

Objective • To analyze the differentially expressed profiles of long noncoding RNA (lncRNA) in endometrial cancer (EC) tissues and normal endometrial tissues. Methods • The RNA was extracted from 21 EC tissues and 5 normal endometrial tissues, respectively, and lncRNAs expression profiles were analyzed and screened by transcriptome sequencing technology. Gene Ontology (GO) function analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were carried out for the differentially expressed lncRNAs, and their expression differences between the transcriptome sequencing and TCGA database were analyzed. Results • There were 3 060 differentially expressed lncRNAs, of which 2 046 were upregulated and 1 014 were down-regulated. GO functional analysis showed that these lncRNAs were associated with cell adhesion, immune response, inflammatory response and cell proliferation. KEGG pathway analysis showed that these lncRNAs were mainly enriched on the pathways, such as PI3KAkt signaling pathway, cell adhesion and cytokine-cytokine receptor interaction. Intersection analysis showed that 57 lncRNAs were up-regulated or downregulated simultaneously in the sequencing results and TCGA database. Conclusion • The expression of lncRNAs in EC tissues and normal endometrial tissues are significantly different, suggesting that it may play an important role in the occurrence and development of EC.

Screening chronic periodontitis-related genes using whole-genome expression profiling / 中国组织工程研究

BACKGROUND: Whole-genome expression profiling is a technical method for gene expression research, with high sensitivity and specificity. This technique can be used to detect differential genes related to chronic periodontitis in the whole genome, therefore efficiently and quickly finding chronic periodontitis-related factors. OBJECTIVE: To screen genes related to chronic periodontitis by using the whole-genome expression profiling. METHODS: Normal periodontal ligament tissue of 15 patients with orthodontic extraction was selected as control group, and periodontal tissue of 21 patients with chronic periodontitis was selected as experimental group. To screen up-regulated and down-regulated genes. the genome-wide expression profile chips of four chronic periodontitis tissues and four healthy tissues were compared. The expression of the differential gene PI3K-Akt signal pathway was verified by real-time PCR (7 normal cases and 13 cases of chronic periodontitis) and western blot (4 normal cases and 4 cases of chronic periodontitis). The experimental protocol was approved by the Ethics Committee of the First Affiliated Hospital of Hainan Medical University (approval No. HNM20180034) and informed consent was obtained from each patient. RESULTS AND CONCLUSION: Analysis of the whole genome expression profile chip revealed that 1 565 up-regulated genes and 1 849 down-regulated genes were significantly differentially expressed in chronic periodontitis samples. The enrichment analysis revealed that the expression of PI3K-Akt signaling pathway was significantly different in chronic periodontitis (P < 0.001). Real-time PCR and western blot assay results indicated that PI3K and Akt expression was higher in the experimental group than in the control group (P < 0.05). All the findings indicate that the genome-wide expression profile chip is fast and highly sensitive to screen the changes in chronic periodontitis-related genes. Significantly differential expression of PI3K-Akt signal pathway in chronic periodontitis provides an experimental basis for the treatment of chronic periodontitis.

Analysis on Gene Set Enrichment of Related Signaling Pathways and Immune Infiltration in Intracranial Aneurysm / 中国实验方剂学杂志

Objective::Based on gene array technology, gene set enrichment analysis (GSEA) and immune infiltration analysis were performed on chip data of intracranial aneurysm (IA) mRNA expression profile, in order to provide theoretical basis for understanding the formation mechanism of IA. Method::The GSE75436 raw data were obtained from the gene expression omnibus (GEO). GSEA of biological process (BP) in gene ontology (GO) and Kyoto gene and genome encyclopedia (KEGG) signaling pathways were analyzed for gene expression profile by R software. The CIBERSORT deconvolution method was used to analyze the infiltration ratio of 22 types of immune cells in the expression profile. And COREMINE database was used to predict traditional Chinese medicines (TCMs), which were significant correlation with the enrichment result. Result::The GSEA results showed that the changes in gene expression of IA samples mainly involved in the regulation of cytokines, activation and differentiation of leukocyte, inflammatory immune response and other processes. The infiltration matrix analysis of immune cells showed that mast cells resting and neutrophils were significantly reduced in IA samples. The comparison of paired samples showed that mast cells and natural killer cells (NK cells) were significantly activated in the IA samples of the same individual, while neutrophils and T cells CD4 naive were significantly reduced. Through COREMINE prediction, it was found that Stephaniae Tetrandrae Radix was correlated with the activation of granulocytes, Sapindi Mukorossi Semen and Pistaciae Chinensis Cortex were correlated with the activation of neutrophils, Trichosanthis Semen, Paeoniae Radix Alba and Ligustri Lucidi Fructus were correlated with the cytotoxicity mediated by NK cells. Conclusion::Activation of mast cells and NK cells are closely associated with the occurrence and development of IA. The inflammatory immune processes and pathways such as nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) signaling pathway and cytotoxicity mediated by NK cells may be important factors in the pathogenesis of IA, and TCMs such as Stephaniae Tetrandrae Radix may be the potential molecular drug sources.

Functional and genomic characterization of three novel cell lines derived from a metastatic gallbladder cancer tumor

BACKGROUND: Gallbladder cancer (GBC) is the most common tumor of the biliary tract. The incidence of GBC shows a large geographic variability, being particularly frequent in Native American populations. In Chile, GBC represents the second cause of cancer-related death among women. We describe here the establishment of three novel cell lines derived from the ascitic fluid of a Chilean GBC patient, who presented 46% European, 36% Mapuche, 12% Aymara and 6% African ancestry. RESULTS: After immunocytochemical staining of the primary cell culture, we isolated and comprehensively characterized three independent clones (PUC-GBC1, PUC-GBC2 and PUC-GBC3) by short tandem repeat DNA profiling and RNA sequencing as well as karyotype, doubling time, chemosensitivity, in vitro migration capability and in vivo tumorigenicity assay. Primary culture cells showed high expression of CK7, CK19, CA 19-9, MUC1 and MUC16, and negative expression of mesothelial markers. The three isolated clones displayed an epithelial phenotype and an abnormal structure and number of chromosomes. RNA sequencing confirmed the increased expression of cytokeratin and mucin genes, and also of TP53 and ERBB2 with some differences among the three cells lines, and revealed a novel exonic mutation in NF1. The PUC-GBC3 clone was the most aggressive according to histopathological features and the tumorigenic capacity in NSG mice. CONCLUSIONS: The first cell lines established from a Chilean GBC patient represent a new model for studying GBC in patients of Native American descent.

Cloning and function analysis of elongase of very long chain fatty acid gene Bmelo424 in silkworm / 生物工程学报

Genes belonging to the elongases of very long chain fatty acid (ELOVL) family affect many physiological functions in organism. In this paper, Bmelo424 gene, a member of the ELOVL family in silkworm, was cloned and its ORF was 558 bp. Its protein sequence was predicted to have four transmembrane domains, six serine phosphorylation sites, eight threonine phosphorylation sites and four tyrosine phosphorylation sites, and its subcellular localization was in the endoplasmic reticulum. Secondary structure analysis showed that the percentage of alpha-helix and beta-strand was 26.7% and 20% respectively. The results of fluorescence quantitative PCR showed that Bmelo424 gene was expressed in all tissues of silkworm, especially with the highest expression in head. By heterologous expression of Bmelo424 gene in Saccharomyces cerevisiae, the effect of Bmelo424 gene on fatty acid elongation was studied. GC-MS results indicated that the fatty acid content of C16:1n-7 in S. cerevisiae with pYES2-Bmelo424 recombinant plasmid increased significantly, whereas the content of C16:0, C18:0 and C18:1n-9 decreased. The results of temperature stress revealed that Bmelo424 gene could improve the low temperature adaptability of S. cerevisiae, but its high temperature adaptability decreased. This provides a reference for exploring the function of Bmelo424 gene in silkworm.

Long non-coding RNAs show different expression profiles and display competing endogenous RNA potential in placenta accreta spectrum disorders / 南方医科大学学报

OBJECTIVE@#To investigate the expression profile of long non-coding RNAs (lncRNA) and identify potential lncRNA-related competing endogenous RNAs (ceRNA) in placenta accrete spectrum disorders (PAS).@*METHODS@#Five tissue specimens of placental implantation and 5 adjacent normal placental tissues were collected from cesarean section deliveries complicated by PAS in our hospital between December, 2017 and June, 2018. Human microarrays were used to identify the lncRNAs that were differentially expressed in PAS, and 5 of the identified lncRNAs were further validated using qRT-PCR. GO and KEGG pathway analyses were performed to indentify the most significant enrichment functions. A ceRNA network was constructed based on ENST00000511361 (RP5-875H18.4), NR_027457 (LINC00221) and NR_126415 (FOXP4-AS1) to pinpoint the potential lncRNAs-related ceRNA.@*RESULTS@#A total of 329 lncRNAs and 179 mRNAs were identified to have differential expression in PAS. The results of qRT-PCR were consistent with the human microarrays results. Transforming growth factor-β (TGF-β) signaling pathway was the most significantly enriched pathway. The constructed ceRNA network suggested that RP5-875H18.4--miRNA-218--SLIT2 had a potential ceRNA regulatory mechanism in PAS.@*CONCLUSIONS@#The differentially expressed lncRNAs are involved in the occurrence and progression of PAS possibly by regulating the TGF-β signaling pathway. The ceRNA network of RP5-875H18.4--miRNA-218--SLIT2 may play a role in the occurrence of PAS.

Differences in circRNA expression profiles between HER-2-positive breast cancer cells and normal mammary epithelial cells / 中华肿瘤杂志

Objective@#To investigate the differential expression profiles of circular RNA (circRNA) in human epidermal growth factor receptor 2 (HER-2) positive breast cancer cells and normal mammary epithelial cells, and to develop novel diagnostic and therapeutic markers for HER-2 positive breast cancer.@*Methods@#Total RNA were extracted from HER-2 positive breast cancer cell SK-BR-3 and normal mammary epithelial cell MCF10A. RNA quality was detected using NanoDrop ND-1000. Rnase R was applied to remove linear RNA and enrich circRNAs. After amplification and reverse transcription into fluorescent complementary RNA (cRNA) using random primer, the labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays. The raw data were extracted and the acquired array images were subjected to quantile normalization followed by heat map and volcano plot analysis. The expression of circRNAs with large fold change was verified by real-time quantitative polymerase chain reaction (RT-qPCR). Finally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed in the differentially expressed circRNAs and circRNA-microRNA (miRNA) network was constructed.@*Results@#The total RNA extracted from SK-BR-3 and MCF10A had high integrity and quality. The expression profiles of circRNA in SK-BR-3 and MCF10A cells were significantly different shown by fluorescent expression signals. Compared with MCF10A cells, there were 6 584 up-regulated circRNAs and 6254 down-regulated circRNAs in SK-BR-3 cells. There were 348 circRNAs with |log2FC|≥2, of which 153 were up-regulated and 195 were down-regulated. Moreover, 8 circRNAs with |log2FC|>5. Among them, 5 were up-regulated in SK-BR-3 cells, including hsa_circRNA_074595 (|log2FC|=7.84), hsa_circRNA_074598 (|log2FC|=6.50), hsa_circRNA_085362 (|log2FC|=5.86), hsa_circRNA_101379 (|log2FC|=5.71) and hsa_circRNA_406683 (|log2FC|=5.34); as well as 3 were down-regulated, including hsa_circRNA_021714 (|log2FC|=5.46), hsa_circRNA_100777 (|log2FC|=5.40), and hsa_circRNA_100796 (|log2FC|=5.03). The expression levels of hsa_circRNA_074595, hsa_circRNA_074598 and hsa_circRNA_100777 were further validated by RT-qPCR in consistent with the results of microarray. GO analysis showed that differentially expressed circRNAs were significantly enriched in the biological process of heart development (P<0.001), cellular component in the cell adhesion-related components (P<0.001), molecular function in protein serine/threonine kinase activity (P<0.001). KEGG analysis revealed that differentially expressed circRNAs were significantly enriched in the PI3K-Akt signaling pathway.@*Conclusions@#The expression profile of circRNA in HER-2 positive breast cancer cells is significantly different from that in normal mammary epithelial cells. The differentially expressed circRNAs may be served as potential diagnostic or therapeutic targets for HER-2 positive breast cancer.

Cloning and expression analysis of ATP/ADP transporter protein gene PgAATP1 in Panax ginseng / 中草药

Objective: To clone the full-length cDNA of the ATP/ADP transporter protein (AATP) genes in Panax ginseng to provide resources and some knowledge necessary for the further gene function study. Methods: The mRNA sequence of the AATP genes in other plants were downloaded on the website of NCBI and used to perform local Blast alignment in the transcriptome of Jilin ginseng from 14 tissues. The AATP gene in Panax ginseng was cloned by PCR, and analyzed using bioinformatics software and online resources. The expression pattern of PgAATP1 gene in 14 tissues of Panax ginseng was analyzed using the expression profile of transcriptome and its expression level under methyl jasmonate was deceted by quantitative real-time PCR. Results: A full-length cDNA sequence was successfully cloned from Panax ginseng and named as PgAATP1, which was 1866 bp in length and encoded 621 amino acids. The relative molecular mass of PgAATP1 protein calculated was 67 897.23, and the isoelecric point calculated was 9.58. It was found that the protein was similar to the plastid AATP in other species. The expression of this gene was high in all tissues but higherin fruit flesh and leaf blade, and the expression of PgAATP1 gene was up-regulated by methyl jasmonate. Conclusion: We have obtained the full-length of PgAATP1 gene. This gene expressed higher in tissues of vigorous starch synthesis and responsing to methyl jasmonate.

Bioinformatic analysis on related genes of lung adenocarcinoma / 中国肿瘤生物治疗杂志

@# To indentify the candidate genes and signaling pathways in lung adenocarcinoma by analyzing gene profiles with bioinformatics. Methods: The expression profiles of GSE40791, GSE68571, GSE43458, and GSE18842 were down-loaded from the Gene Expression Omnibus (GEO) database. The four microarray datasets were integrated to obtain the differentially expressed genes related to lung adenocarcinoma. STRING database was used to construct the protein-protein interaction (PPI) network of differentially expressed genes, and to further explore the gene modules and the key genes. DAVID was used to perform the gene enrichment analysis of each gene module, and to explore the regulatory function of each gene module in adenocarcinoma cells, as well as the relationship between the key genes in the module and the prognosis of the patients. Results: Thirty-seven up-regulated genes and 120 down-regulated genes were obtained from the primary screen, and the protein-protein interaction(PPI) network was successfully constructed. According to MCODE algorithm, we constructed gene modules and calculated the core genes (KIF14, SEPP1, SPP1, RBP4) in the PPI network. Finally, four modules were proved to be involved in regulation of cell cycle, blood coagulation, cell adhesion and cell metabolism, and four key genes were proved to be differentially expressed between lung adenocarcinoma tissues and normal tissues (all P<0.05). Survival analysis showed that expressions of KIF14, SEPP1 and SPP1 had significant effect on the prognosis of lung adenocarcinoma (P<0.01 or P<0.05), while RBP4 exerted insignificant difference in the survival rate of lung adenocarcinoma patients (P>0.05). Conclusion: With bioinformatics, three differentially expressed genes between lung adenocarcinoma tissues and normal adjacent tissues were finally screened out and proved to be closely related to the prognosis of patients, which provided new thoughts in the diagnosis and prognosis prediction of lung adenocarcinoma and improved the study efficiency on the mechanism of lung adenocarcinoma.

Effects of Dendrobium officinale Polysaccharides on Gene Expression Profile of HUVEC / 中国药房

OBJECTIVE： To investigate the effects of Dendrobium officinale polysaccharides on gene expression profile of HUVEC. METHODS： HUVEC was selected as objects. MTS method was used to detect the effects of different doses of D. officinale polysaccharides （50， 100， 200， 400， 800 μg/mL） on the proliferation activity of HUVEC. The growth inhibitory concentration of 30％ cells （IC30） was calculated to screen the dose of follow-up tests. cDNA microarray assay was used to detect the changes of gene expression profile for HUVEC after treated with D. officinale polysaccharides for 24 h， so as to screen differentially expressed genes. GO enrichment analysis and KEGG pathway enrichment analysis were performed for top 5 differentially expressed genes by using DAVID bioinformatics resource database. Real-time fluorescence quantitative polymerase chain reaction （qRT-PCR） was used to validate the results of microarray detection with immunity-related differentially expressed genes as objects. RESULTS： After treated with 100， 200， 400， 800 μg/mL D. officinale polysaccharides， survival rate of HUVEC  were decreased significantly （P＜0.05 or P＜0.01）. IC30 value was 408 μg/mL. After treated with 400 μg/mL （by IC30） D. officinale polysaccharides， there were 91 differentially expressed genes in HUVEC cells， of which 84 were up-regulated and 7 were down-regulated. Top 5 genes of up-regulated and down- regulated expression were SELE， CCL2， CXCL6， IL8， ICAM1 as well as VWCE， CPT1A， CLU， CCL14， CINS4， which may be mainly associated with immune conditions and inflammatory responses. The differentially expressed genes mainly distributed in extracellular domain， and were enriched in biological processes such as production and response of cytokines and stimulus response， and played molecular functions such as chemokine and its receptor activity. The up-regulated genes as SELE， ICAM1 and CXCL2 were mainly enriched in TNF signaling pathway， influenza A （H1N1）， herpes simplex virus infection and other pathways. The down-regulated gene CCL14 was mainly enriched in chemokine signaling pathway. Results of qRT-PCR validation tests showed that relative expression of ICAM1 was increased significantly， while that of CCL14 was decreased significantly （P＜0.05）， which was in agreement with microarray detection results. CONCLUSIONS： After treated with D. officinale polysaccharides， the expression of 91 genes in HUVEC cells are different significantly， mainly being up-regulated. The differentially expressed genes may participate in immune regulation through TNF signaling pathway， influenza A （H1N1） and herpes simplex virus infection.

Expression of MiR-455-5p in epithelial ovarian cancer and its target gene function / 实用肿瘤学杂志

Objective The aim of this study was to investigate the expression of miR-455-5p in epithelial ovarian cancer and its effect on the development of epithelial ovarian cancer. Methods The miRNA expression data of normal ovarian epithelial tis-sues and epithelial ovarian cancer tissues GSE83693 were downloaded from the GEO database. Differential expression analysis was used to obtain differential expression data of miRNAs in epithelial ovarian cancer. The expression of miR-455 -5p was analyzed whether there is difference expression between normal ovarian epithelium and epithelial ovary cancer tissues; qRT-PCR was used to verify the differential expression prediction results; bio-informatics software was used to analyze the KEGG pathway enrichment and GO gene function annotation of miR-455-5p target genes,and to explore the disorders of dyregulated miR-455-5p in the devel-opment of epithelial ovarian cancer. Results A total of 101 cases of differentially expressed miRNAs were screened,34 cases were up-regulated and 67 cases were down-regulated. Among them,miR-455-5p was down-regulated significantly(P<0. 01),and the different fulds were -2. 9019. The results of qRT-PCR showed that the expression of miR-455-5p in epithelial ovarian cancer cells(SKOV-3,OVCAR-3 and A2780)was significantly lower than that in normal ovarian epithelial cells(IOSE-80),and the dif-ferential expression was statistically significant(P<0. 05). The results of KEGG pathway enrichment analysis showed that miR-455-5p regulated target genes mainly involved in five pathways,including TGF-β signaling pathway,Hippo signaling pathway,ECM-receptor interaction,transcriptional dysregulation pathway in cancer,and chronic granule cellular leukemia,which were associated with tumors. GO functional annotation analysis showed that the target genes regulated by miR-455-5p in the above pathway was mainly involved in protein phosphorylation,promoted cell proliferation and migration,inhibited apoptosis,promoted epithelial-mesenchymal transition,regulated transcription and regulated cell cycle,etc. ,which associated with tumorigenesis. Conclusion The expression of miR-455-5p is down-regulated in epithelial ovarian cancer. The miR-455-5p target genes are involved in the pathogenesis and function of epithelial ovarian cancer,and are associated with the development of epithelial ovarian cancer.

Application of multiple support vector machine recursive feature elimination model in cancer feature gene selection / 国际生物医学工程杂志

Objective To analyze the cancergene expression profile data using multi-support vector machine recursive feature elimination algorithm (MSVM-RFE) and calculate the genetic ranking score to obtain the optimal feature gene subset. Methods Gene expression profiles of bladder cancer, breast cancer, colon cancer and lung cancer were downloaded from GEO (Gene Expression Omnibus) database.The differentially expressed genes were obtained by differential expression analysis. The differential gene expressions were sequenced by MSVM-RFE algorithm and the average test errors of each gene subset were calculated. Then the optimal gene subsetsof four kinds of cancer were obtained according to the minimum average test errors. Based on the datasets of four kinds of cancer characteristic genes before and after screening, linear SVM classifiers were constructed and the classification efficiencies of the optimal feature gene subsets were verified. Results Using the optimal feature gene subsetobtained by MSVM-RFE algorithm, the classification accuracy was improved from (96.77±1.28)％to (99.85±0.46)％for the bladder cancer data, improved from (83.77±4.93)％to (88.30±3.85)％for the breast cancer data, and improved from (72.69±2.41)％to (90.21±3.31)％for the lung cancer data.Besides, theoptimal feature gene subsetkept the classification accuracy of colon cancer classifierat a high level (>99.5％). Conclusions The feature gene extraction based on MSVM-RFE algorithm can improve the classification efficiency of cancer.

Microarray Analysis of Gene Expression Changes in Neuroplastin 65-Knockout Mice: Implications for Abnormal Cognition and Emotional Disorders / 神经科学通报·英文版

Neuroplastin 65 (Np65) is an immunoglobulin superfamily cell adhesion molecule involved in synaptic formation and plasticity. Our recent study showed that Np65-knockout (KO) mice exhibit abnormal cognition and emotional disorders. However, the underlying mechanisms remain unclear. In this study, we found 588 differentially-expressed genes in Np65-KO mice by microarray analysis. RT-PCR analysis also revealed the altered expression of genes associated with development and synaptic structure, such as Cdh1, Htr3a, and Kcnj9. In addition, the expression of Wnt-3, a Wnt protein involved in development, was decreased in Np65-KO mice as evidenced by western blotting. Surprisingly, MRI and DAPI staining showed a significant reduction in the lateral ventricular volume of Np65-KO mice. Together, these findings suggest that ablation of Np65 influences gene expression, which may contribute to abnormal brain development. These results provide clues to the mechanisms underlying the altered brain functions of Np65-deficient mice.