COL4A1, negatively regulated by XPD and miR-29a-3p, promotes cell proliferation, migration, invasion and epithelial-mesenchymal transition in liver cancer cells.

OBJECTIVE: Collagen type IV alpha 1 (COL4A1) exerts tumor-promoting functions in several tumors. However, its role in liver cancer remains not fully understood. Hence, this study aims to investigate the role of COL4A1 in regulating liver cancer cell behaviors and to validate its upstream regulatory mechanism. METHODS: Expression of xeroderma pigmentosum D (XPD) and COL4A1 was examined by qRT-PCR and western blot. Cell proliferation, migration, and invasion were evaluated. The protein levels of N-cadherin, vimentin, and E-cadherin were determined by western blot to evaluate epithelial-mesenchymal transition (EMT). The interaction between miR-29a-3p and COL4A1 was analyzed by luciferase reporter assay. RESULTS: COL4A1 overexpression significantly promoted cell proliferation, migration, invasion, and EMT in Hep3B cells. In contrast, COL4A1 silencing yielded the opposite effects in HepG2 cells. Expression of COL4A1 was increased, whereas expression of XPD and miR-29a-3p was decreased in HCC tissues compared to controls. COL4A1 mRNA level was negatively correlated with expression of XPD and miR-29a-3p in HCC tissues. Furthermore, XPD silencing-mediated up-regulation of COL4A1 expression was attenuated by miR-29a-3p mimic. Moreover, miR-29a-3p mimic inhibited Hep3B cell proliferation, migration, and invasion by directly targeting COL4A1. CONCLUSION: COL4A1 is negatively regulated by XPD-miR-29a-3p axis and promotes liver cancer progression in vitro.

Proteomic changes in maize as a response to heavy metal (lead) stress revealed by iTRAQ quantitative proteomics.

Lead (Pb), a heavy metal, has become a crucial pollutant in soil and water, causing not only permanent and irreversible health problems, but also substantial reduction in crop yields. In this study, we conducted proteome analysis of the roots of the non-hyperaccumulator inbred maize line 9782 at four developmental stages (0, 12, 24, and 48 h) under Pb pollution using isobaric tags for relative and absolute quantification technology. A total of 252, 72 and 116 proteins were differentially expressed between M12 (after 12-h Pb treatment) and CK (water-mocked treatment), M24 (after 24-h Pb treatment) and CK, and M48 (after 48-h Pb treatment) and CK, respectively. In addition, 14 differentially expressed proteins were common within each comparison group. Moreover, Cluster of Orthologous Groups enrichment analysis revealed predominance of the proteins involved in posttranslational modification, protein turnover, and chaperones. Additionally, the changes in protein profiles showed a lower concordance with corresponding alterations in transcript levels, indicating important roles for transcriptional and posttranscriptional regulation in the response of maize roots to Pb pollution. Furthermore, enriched functional categories between the successive comparisons showed that the proteins in functional categories of stress, redox, signaling, and transport were highly up-regulated, while those in the functional categories of nucleotide metabolism, amino acid metabolism, RNA, and protein metabolism were down-regulated. This information will help in furthering our understanding of the detailed mechanisms of plant responses to heavy metal stress by combining protein and mRNA profiles.

Targeting exogenous GDNF gene to the bovine somatic cell beta-casein locus for the production of transgenic bovine animals.

Considerable attention is currently being directed toward methods for producing recombinant human proteins in the mammary glands of genetically modified transgenic livestock. However, the expression of inserted genes in transgenic animals is variable and often very low because of the randomness of the site of transgene integration. One possible strategy to avoid the expression problem associated with random integration is to use site-specific integration by targeting integration to a high expression locus and, thereby, to improve expression of the transferred gene. In the present study, we focused on glial cell line-derived neurotrophic factor (GDNF), a novel type of neurotrophic factor first cloned in 1993. Research has shown that GDNF may have potential applications in the treatment of Parkinson's disease and other diseases of the central nervous system since it acts as a protective factor for central dopaminergic neurons. Here, we constructed a gene targeting vector to knock-in the human GDNF gene at the bovine beta-casein gene locus as a first step to producing transgenic animals with a high level of expression of human GDNF protein in their mammary glands. Bovine fetal fibroblast cells were transfected with linearized pNRTCNbG by electroporation. Three cell clones were identified with successful targeting to the beta-casein locus; and were confirmed using both polymerase chain reaction analysis and sequencing. Gene-targeted cells were used as nuclear donors; a total of 161 embryos were reconstructed, 23 of which developed to the blastocyst stage. These blastocysts were transferred to 8 recipient cows, but no offspring were obtained.

Effects of Tripterygium wilfordii glycosides on regulatory T cells and Th17 in an IgA nephropathy rat model.

In this study, we examined the effects of Tripterygium wilfordii glycosides (TWGs) on Th17 and regulatory T cells (Tregs) in an immunoglobulin A nephropathy (IgAN) rat model. IgAN model rats were randomly divided into the model group, TWG treatment group, and prednisone group. Normal rats were included as controls. There were 6 rats in each group. The urine protein levels and the number of red blood cells in urine were analyzed at 24 h. IgA deposition in renal tissue was detected by fluorescence microscopy. The concentration of interleukin-17 in serum was detected by an enzyme-linked immunosorbent assay and the number of Tregs in blood was analyzed by flow cytometry. TWGs and prednisone significantly reduced urine protein levels and urine red blood cells at 24 h in IgAN model rats (P < 0.01), but prednisone had a greater effect than did TWGs (P < 0.05). TWGs and prednisone reduced IgA deposition in renal tissue, but prednisone had a greater effect than TWGs. T. wilfordii glycosides and prednisone significantly decreased the serum IL-17 level in an IgAN rat model and increased the number of Tregs in the blood (P < 0.01). There was no significant difference between prednisone and TWGs (P > 0.05). In conclusion, TWGs had therapeutic effects on IgAN model rats and may regulate the immune balance of Th17 and Tregs.

Influence of sirolimus-induced TGF-ß secretion on mouse Treg cell proliferation.

We examined the effects of co-culturing CD4+ CD25+ Treg cells with sirolimus or cyclosporin A on Treg cell proliferation and differentiation and on transforming growth factor-ß (TGF-ß) and Foxp3 expression. CD4+ CD25+ Treg cells were harvested from mononuclear cells of spleens of C57BL/6 mice using immunomagnetic beads and divided into control, sirolimus, and cyclosporine groups. Following a 96-h co-culture, Treg cells were assayed by flow cytometry. FoxP3 and TGF-ß mRNA levels and secretion were assayed by reverse transcription polymerase chain reaction and enzyme-linked immunosorbent assay. Smad protein of the TGF-ß signaling pathway was assayed by western blot and its effect on CD4+ CD25+ FoxP3+ Treg cell proliferation was determined. Sirolimus-promoted differentiation and proliferation was examined using a TGF-ß neutralizing antibody. Sirolimus-treated CD4+ T cell TGF-ß secretion increased 2.5X over control levels (P < 0.01), but that of the cyclosporine group decreased marginally (P > 0.05). The CD4+ cell proportion decreased significantly (41.25 vs 69.22%, P < 0.01) and slightly (65.21 vs 69.22, P > 0.05) in the cyclosporine and sirolimus groups, respectively. T cell Foxp3 mRNA expression was significantly higher in the sirolimus-treated than in the cyclosporine (53.7 vs 40.2%, P < 0.05) and control groups (P < 0.01), but was significantly lower in the cyclosporine group than in controls (23.6 vs 40.2%, P < 0.01). Overall, sirolimus promoted CD4+ CD25+ Treg cell proliferation and growth in vitro, whereas cyclosporin A inhibited proliferation. Sirolimus might promote CD4+ CD25+ FoxP3+ regulatory T cell proliferation by inducing TGF-ß secretion in vivo.

Predicting bacterial essential genes using only sequence composition information.

Essential genes are those genes that are needed by organisms at any time and under any conditions. It is very important for us to identify essential genes from bacterial genomes because of their vital role in synthetic biology and biomedical practices. In this paper, we developed a support vector machine (SVM)-based method to predict essential genes of bacterial genomes using only compositional features. These features are all derived from the primary sequences, i.e., nucleotide sequences and protein sequences. After training on the multiple samplings of the labeled (essential or not essential) features using a library for SVM, we obtained an average area under the ROC curve (AUC) of about 0.82 in a 5-fold cross-validation for Escherichia coli and about 0.74 for Mycoplasma pulmonis. We further evaluated the performance of the method proposed using the dataset consisting of 16 bacterial genomes, and an average AUC of 0.76 was achieved. Based on this training dataset, a model for essential gene prediction was established. Another two independent genomes, Shewanella oneidensis RW1 and Salmonella enterica serovar Typhimurium SL1344 were used to evalutate the model. Results showed that the AUC sores were 0.77 and 0.81, respectively. For the convenience of the vast majority of experimental scientists, a web server has been constructed, which is freely available at http://cefg.uestc.edu.cn:9999/egp.

Linkage and mapping analyses of the normal marking gene +P in the silkworm (Bombyx mori) using SSR markers.

In the silkworm, Bombyx mori, normal markings are mainly controlled by the +P gene, which is located on the second chromosome. Due to a lack of crossing over in females, reciprocal backcrossed F1 (BC1) progenies were used for linkage analysis and mapping of the +P gene based on an SSR linkage map using silkworm strains P50 and H9, which are normal marking and sex-limited marking, respectively. The +P gene was found to be linked to 3 SSR markers. Using a reciprocal BC1M cross, we constructed a linkage map of 22.5 cM, with +P mapped at 11.3 cM and the nearest SSR marker S0206 at a distance of 3.0 cM. Based on a fine genome map of domesticated silkworms, Kaikoblast analysis showed that the physical distance between the nearest markers (containing the +P gene) is 995 kb. Further analysis showed that BGIBMGA009689, BGIBMGA009688, and BGIBMGA009687 are closer to +P, and that BGIBMGA009689 is closest to +P, with a physical distance of 19.1 kb.

Co-evolution of genomic islands and their bacterial hosts revealed through phylogenetic analyses of 17 groups of homologous genomic islands.

Horizontal gene transfer is an important mechanism for the evolution of microbial genomes, and many horizontal gene transfer events are facilitated by genomic islands (GIs). Until now, few reports have provided evidence for the co-evolution of horizontally transferred genes and their hosts. We obtained 17 groups of homologous GIs, all of which appear in 8 or more bacterial strains of the same species or genus. Using phylogenetic analyses, we found that the topological structure of a distance tree based on the proteins of each group of homologous GIs was consistent with that based on the complete proteomes of the hosts. This result clearly indicates that GIs and their bacterial hosts have co-evolved. In addition to presenting and providing evidence for a novel concept, i.e., the co-evolution of GIs and their bacterial hosts, we also describe a new and interesting detail for the phylogenetic analysis of horizontally transferred genes: consistent phylogenetic trees can be obtained by focusing on homologous GIs despite the commonly accepted theory that the phylogenies of horizontally transferred sequences and host organisms should be inconsistent.