Genomic-scale analysis of Pasteurella multocida gene expression during growth within liver tissue of chickens with fowl cholera

We have recently reported the gene expression profile of Pasteurella multocida during growth in the blood of chickens with fowl cholera. Here we report the gene expression profile of P. multocida during growth in the livers of similarly infected chickens. We compared expression profiles of bacteria harvested from the livers of infected chickens with late-stage fowl cholera with those of bacteria grown in rich medium. Independent analysis of bacterial expression profiles from three individual chickens indicated that 93 P. multocida genes were always differentially expressed during growth in liver tissue. Of these 93 genes, 49 were upregulated and 44 downregulated in the host. Many of the upregulated genes were involved in energy production and conversion (9/49) and carbohydrate transport and metabolism (8/49), and a number of these have been shown to be induced under anaerobic conditions in other species. The downregulated genes were generally of unknown or poorly characterised functions (14/44). Comparison of the differentially regulated gene sets identified for growth in liver with those identified previously for growth in blood allowed the identification of a core set of 13 upregulated and 16 downregulated genes that were differentially regulated in at least five of the six infections studied.     

Microarray-based gene expression profiles in rabbit retina due to negative pressure suction

We investigated a possible molecular pathogenesis involving retinal ganglion cell apoptosis following transient high intraocular pressure. Changes in the gene expression profiles of the retina were detected via gene chip methodology. Twelve New Zealand white rabbits were randomly assigned to control and 3-min negative pressure suction groups. The control group was treated only with a laser, and the experimental group was also treated with suction for 3 min, using a negative pressure generator. Total RNA was then extracted from the retinal tissue at different recovery stages to analyze gene expression profiles using the Agilent rabbit one-way gene chip. The groups were then compared. Immediately after negative pressure suction induction, 704 genes were differentially expressed. Among these, 485 genes were upregulated, and 219 were downregulated. Expression of the genes encoding CRYAA, CRYAB, and TLR3 genes, which are involved in apoptosis, was elevated. The KRT18 gene, which is involved in apoptosis, had reduced expression. Seven days after negative pressure suction, 482 genes were differentially expressed. Among these, 178 genes were upregulated, and 304 were downregulated. Expression of the genes encoding CRYAB, IL1-BETA and IL1R1, which are involved in apoptosis, was upregulated. Ten days after negative pressure suction, 402 genes were differentially expressed. Of these, 213 genes were upregulated, and 189 were downregulated. Apoptosis genes CRYAB, CRYBA3, CRYBB2, IL1- BETA, and IL1R1 showed higher expression levels. We concluded that negative pressure suction for long periods of time (for example, 3 min) results in changes in gene expression. Genes with higher fold changes help protect retinal ganglion cells from apoptosis. We suggest that promoting the expression of these genes should be considered as a new means for treating ischemic-hypoxic retinopathy.     

Gene and protein expression profiles in the foetal liver of the pregnant rat fed a low protein diet

Foetal growth is particularly sensitive to the protein content of the mother’s diet. Microarray data from the foetal liver of pregnant rats fed normal (HP) or reduced protein diets (LP) were compared by gene set enrichment analysis. Soluble proteins from a second portion of the liver were analysed by two-dimensional gel electrophoresis. Genes associated with progesterone, insulin-like growth factor-1 and vascular endothelial growth factor were upregulated in HP compared to LP, in addition to genes associated with cell differentiation and signalling from the extracellular matrix. In contrast, cytokine signalling was downregulated. Proteomics showed that proteins associated with amino acid metabolism, mitochondrial function and cell motility were differentially abundant in the HP compared to the LP groups. These growth factor and extracellular matrix signalling pathways linked to cell motility may be important mediators of the changes in liver structure that occur in utero and persist into adult life.     

CT23 knockdown attenuating malignant behaviors of hepatocellular carcinoma cell is associated with upregulation of metallothionein 1

The cancer-testis antigen 23 (CT23) gene has been reported in association with the pathogenesis and progress of hepatocellular carcinoma (HCC). However, the alterations of gene expression profiling induced by CT23 knockdown in HCC cells remains largely unknown. In this study, the RNA interfering (RNAi) method was used to silence CT23 expression in BEL-7404 cells. Microarray analysis was performed on mRNA extracted from the CT23 knockdown cells and the control cells to determine the alterations of gene expression profiles. The result showed a total of 1051 genes expressed differentially (two-fold change), including 470 genes upregulated and 581 gene downregulated in the CT23 knockdown cells. A bioinformatic analysis showed that the functional differentially expressed genes (DEGs) were linked to cell proliferation, migration, and apoptosis, and metallothionein 1 (MT1) attained the maximum enrichment scores in functional annotation, classification, and pathway analysis of DEGs. Furthermore, Western blot analysis and cell behaviors assays verified that CT23 modulates cell proliferation, migration, and apoptosis by regulating MT1 expression in HCC cells and non-neoplastic hepatocytes. In summary, downregulated CT23 gene in BEL-7404 cells might change the expressions of carcinogenesis and progression related genes in HCC by upregulating MT1 expression, which would provide insight into searching for a novel therapeutic target for HCC.     

Identification of potential key genes associated with osteosarcoma based on integrated bioinformatics analyses

Due to high rates of metastasis and poor clinical outcomes for patients, it is important to study the pathomechanisms of osteosarcoma. However, due to the fact that osteosarcoma shows significant interindividual variation and high heterogeneity, the identification of differentially expressed genes (DEGs) at the population level cannot answer many important questions related to osteosarcoma tumorigenesis. Therefore, a new strategy to identify dysregulated genes in osteosarcoma samples is required. The aim of this study was to improve our understanding of osteosarcoma pathogenesis by identifying genes with universal aberrant expression in osteosarcoma samples. Because the relative expression ordering of genes is stable in normal bone tissues but is disrupted in osteosarcoma tissues, we used the RankComp algorithm to identify DEGs in normal and osteosarcoma tissue samples. We then calculated the dysregulation frequency for each gene. Genes with deregulation frequencies above 80% were deemed to be universal DEGs. Next, coexpression, pathway enrichment, and protein-protein interaction network analyses were performed to characterize the functions of these genes. From 188 samples of osteosarcoma obtained from four datasets measured on different platforms, 51 universal DEGs were identified, including 4 universally upregulated genes and 47 universally downregulated genes. Genes that were differentially coexpressed with these universal DEGs were found to be enriched in 46 cancer-related pathways. In addition, functional and network analyses showed that genes with high dysregulation frequencies were involved in cancer-related functions. Thus, the commonly aberrant genes identified in osteosarcoma tissues may be important targets for osteosarcoma diagnosis and therapy.     

Gene expression changes induced by valproate in the process of rat hippocampal neural stem cells differentiation

Valproate (VPA), an effective clinical approved anti‐epileptic drug and mood stabilizer, has been believed to induce neuronal differentiation at the expense of inhibiting astrocytic and oligodendrocytic differentiation. Nevertheless, the involving mechanisms of it remain unclear yet. In the present study, we explored the global gene expression changes of fetus rat hippocampal neural stem cells following VPA treatment by high‐throughput microarray. We obtained 874 significantly upregulated genes and 258 obviously downregulated genes (fold change > 2 and P < 0.05). Then, we performed gene ontology and pathway analyses of these differentially expressed genes and chose several genes associated with nervous system according to gene ontology analysis to conduct expression analysis to validate the reliability of the array results as well as reveal possible mechanisms of VPA. To get a better comprehension of the differentially regulated genes by VPA, we conducted protein–protein association analysis of these genes, which offered a source for further studies. In addition, we made the overlap between the VPA‐downregulated genes and the predicted target genes of VPA‐upregulated microRNAs (miRNAs), which were previously demonstrated. These overlapped genes may provide a source to find functional VPA/miRNA/mRNA axes during neuronal differentiation. This study first constructed a comprehensive potential downstream gene map of VPA in the process of neuronal differentiation.     

Identification of Putative Biomarkers for the Early Stage of Porcine Spermatogonial Stem Cells Using Next-Generation Sequencing

To identify putative biomarkers of porcine spermatogonial stem cells (pSSCs), total RNA sequencing (RNA-seq) analysis was performed on 5- and 180-day-old porcine testes and on pSSC colonies that were established under low temperature culture conditions as reported previously. In total, 10,184 genes were selected using Cufflink software, followed by a logarithm and quantile normalization of the pairwise scatter plot. The correlation rates of pSSCs compared to 5- and 180-day-old testes were 0.869 and 0.529, respectively and that between 5- and 180-day-old testes was 0.580. Hierarchical clustering data revealed that gene expression patterns of pSSCs were similar to 5-day-old testis. By applying a differential expression filter of four fold or greater, 607 genes were identified between pSSCs and 5-day-old testis, and 2118 genes were identified between the 5- and 180-day-old testes. Among these differentially expressed genes, 293 genes were upregulated and 314 genes were downregulated in the 5-day-old testis compared to pSSCs, and 1106 genes were upregulated and 1012 genes were downregulated in the 180-day-old testis compared to the 5-day-old testis. The following genes upregulated in pSSCs compared to 5-day-old testes were selected for additional analysis: matrix metallopeptidase 9 (MMP9), matrix metallopeptidase 1 (MMP1), glutathione peroxidase 1 (GPX1), chemokine receptor 1 (CCR1), insulin-like growth factor binding protein 3 (IGFBP3), CD14, CD209, and Kruppel-like factor 9 (KLF9). Expression levels of these genes were evaluated in pSSCs and in 5- and 180-day-old porcine testes. In addition, immunohistochemistry analysis confirmed their germ cell-specific expression in 5- and 180-day-old testes. These finding may not only be useful in facilitating the enrichment and sorting of porcine spermatogonia, but may also be useful in the study of the early stages of spermatogenic meiosis.     

Differential endocrine regulation of genes enriched in initial segment and distal caput of the mouse epididymis as revealed by genome-wide expression profiling

We have performed genome-wide expression profiling of endocrine regulation of genes expressed in the mouse initial segment (IS) and distal caput of the epididymis by using Affymetrix microarrays. The data revealed that of the 15 020 genes expressed in the epididymis, 35% were enriched in one of the two regions studied, indicating that differential functions can be attributed to the IS and the more distal caput regions. The data, furthermore, showed that 27% of the genes expressed in the IS and/or distal caput epididymidis are under the regulation of testicular factors present in the duct fluid, while bloodborne androgens can regulate for 14% of them. This is in line with the high testis dependency of epididymal physiology. We then focused on genes with moderate or strong expression, showing strict segment enrichment and strong dependency on testicular factors. Analyses of the 59 genes, including upregulated and downregulated genes, fulfilling the criteria indicated that the expression of 18 (17 downregulated genes; 1 upregulated gene) of 19 gonadectomy-responsive genes enriched in the IS was not maintained by the androgen treatment, whereas the expression of all six downregulated genes enriched in the distal caput and the majority of those with no strict segment enrichment of expression (28 of 34; consisting of 23 downregulated and 5 upregulated genes) were maintained by androgens. Hence, it is evident that testicular factors other than androgens are important for the expression of IS-enriched genes, whereas the expression of distal caput-enriched genes is typically regulated by androgens. Identical data were obtained by independent clustering analyses performed for the expression data of 3626 epididymal genes. Several novel genes with putative involvement in epididymal sperm maturation, such as a disintegrin and metallopeptidase domain 28 (Adam28) and a solute carrier organic anion transporter family, member 4C1 (Slco4c1), were identified, indicating that this approach is successful for identifying novel epididymal genes.     

Gene Expression Profile in the Long-Living Lotus: Insights into the Heat Stress Response Mechanism

Lotus (Nelumbo Adans) is an aquatic perennial plant that flourished during the middle Albian stage. In this study, we characterized the digital gene expression signatures for China Antique lotus under conditions of heat shock stress. Using RNA-seq technology, we sequenced four libraries, specifically, two biological replicates for control plant samples and two for heat stress samples. As a result, 6,528,866 to 8,771,183 clean reads were mapped to the reference genome, accounting for 92–96% total clean reads. A total of 396 significantly altered genes were detected across the genome, among which 315 were upregulated and 81 were downregulated by heat shock stress. Gene ontology (GO) enrichment of differentially expressed genes revealed protein folding, cell morphogenesis and cellular component morphogenesis as the top three functional terms under heat shock stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis led to the identification of protein processing in endoplasmic reticulum, plant-pathogen interactions, spliceosome, endocytosis, and protein export as significantly enriched pathways. Among the upregulated genes, small heat shock proteins (sHsps) and genes related to cell morphogenesis were particularly abundant under heat stress. Data from the current study provide valuable clues that may help elucidate the molecular events underlying heat stress response in China Antique lotus.