Fuchun Zhang

Transcriptome analysis of hepatocytes after partial hepatectomy in rats

After partial hepatectomy (PH), the recovery of liver mass is mainly mediated by proliferation and enlargement of hepatocytes. Therefore, measuring the transcriptional profiling of hepatocytes after PH will be helpful in exploring the mechanism of liver regeneration (LR). Firstly, hepatocytes were isolated from rat regenerating liver at different time points following PH, and then global gene expression analysis of hepatocytes was performed using Rat Genome 230 2.0 Array. The results demonstrated that 1,417 genes in the array (including 767 known genes) were identified to be LR-related. Clustering analysis demonstrated that 767 known genes fell into six classes with distinct expression kinetics. When gene expression patterns were combined with gene functions, genes involved in acute-phase response and defense response were rapidly elevated in early phases; those in cell proliferation and DNA replication were significantly up-expressed in middle phase; a growing number of cell adhesion-involved genes were up-regulated as regeneration progressed; those in amino acid and lipid metabolism showed persistent down-regulation during LR. Based on the above analyses, it was suggested that hepatocyte defense mechanism was quickly triggered after PH; cell proliferation became active in middle phase; cell adhesion was strengthened in late phase; amino acid and lipid metabolism were attenuated during LR. Additionally, comparative analysis between transcriptional profiling of hepatocytes and regenerating liver indicated a major contribution of hepatocytes to LR.

Characterization of a novel β-helix antifreeze protein from the desert beetle Anatolica polita.

Many ectotherms organisms produce antifreeze proteins (AFPs) which inhibit the growth of ice by binding to the surface of ice crystals. In this study, a novel antifreeze protein gene from the desert beetle Anatolica polita (named as Apafp752) was expressed in a high level in Escherichia coli strain BL21 (DE3). An approximately 30kDa fusion protein thioredoxin (Trx)-ApAFP752 was purified through Ni-NTA affinity chromatography and gel filtration chromatography. The activity of the purified fusion protein Trx-ApAFP752 was analyzed by thermal hysteresis activity (THA) and cryoprotection assay. The results suggested that Trx-ApAFP752 conferred freeze resistance on bacterium in a concentration- and time-dependent manner and the cryoprotective effect increased under alkaline conditions. Circular Dichroism (CD) spectrum analysis showed that the recombinant protein of ApAFP752 possessing β-sheet as the main structure was stable under a wide range of pH from 2.0 to 11.0 and thermal stability below 50°C. The predicted 3D structure showed that Trx-ApAFP752 could form a β-helix structure on the antifreeze protein part, which placed most of the Thr in a regular array on one side of the protein to form a putative ice-binding surface.

Expression patterns of the cell junction-associated genes during rat liver regeneration.

To study actions of the genes associated with tight junction, adherent junction, focal adhesion, and gap junction during liver regeneration (LR), these genes were obtained by collecting data from databases and thesis, and their expression profiles in rat regenerating liver were detected employing Rat Genome 230 2.0 array. Next the LR-associated genes were identified by comparing the difference between sham operation (SO) and partial hepatectomy (PH) groups. 79, 53, 109, 53 genes involved in the above four junctions were found to be LR-associated. The initial and total expression numbers of these genes occurring in the initial phase of LR, G0/G1, cell proliferation, cell differentiation, and structure-functional rebuilding were 124, 43, 122, 10, and 249, 145, 957, 306, respectively, illustrating that genes were initially expressed mainly in the initiation stage, and functioned in different phases. Up-regulation and down-regulation to a total of 972 and 540 times, as well as, 41 types of expression patterns showed that the physiological and biochemical activities were diverse and complicated in LR. According to the data, there was an increase in the forepart and prophase, but a decrease in late-metaphase and anaphase for gap junction assembly. Focal adhesion formation displayed an enhancement in forepart, prophase, and anaphase; and formation of tight junctions and adherent junctions last throughout the LR.

Microarray Approach Reveals the Relevance of Interferon Signaling Pathways with Rat Liver Restoration Post 2/3 Hepatectomy at Cellular Level

The immunomodulator interferons are assumed not only to fight tumor progress but also to inhibit liver regeneration by inactivating Kupffer cells. The potential mechanism is still poorly characterized. In particular, the relevance of interferon signaling to liver regeneration at cellular level still remains unknown. In this study, 8 types of rat liver cells from the regenerating liver at 10 recovery time points were separately isolated by percoll density gradient centrifugation and immunomagnetic bead. Transcription profiles of interferon-signaling pathway genes in each cell type along the time course of liver restoration were detected using Rat Genome 230 2.0 Array covering about 12,727 known genes. The chip data demonstrated that hepatocyte mainly up-regulated the IFN-alpha1-mediated JAK/STAT pathway genes; biliary epithelial cell mostly expressed the IFN-beta1-mediated p38 MAPK pathway genes; while the IFN-gamma-activated JAK/STAT pathway genes were down-regulated particularly in HSC, KC, and DC during liver regeneration. It is inferred that STAT3, in contrast to STAT1, seemingly takes a more active role in IFN-alpha1-mediated JAK/STAT pathway in hepatocyte; IFN-beta1-mediated p38 MAPK pathway possibly to some extent affects inflammation and apoptosis of biliary epithelial cell during liver regeneration; IFN-gamma-induced JAK/STAT pathway may be associated with the attenuated apoptosis induction in HSC, KC, and DC. Our data suggested that a better understanding about how interferon signals at liver cell level might be helpful in developing an effective approach to protecting against the inhibition of regeneration.

Analysis of gene expression profiles of liver stellate cells during liver regeneration in rats.

This study performed a large-scale, high-throughput analysis of transcriptional profiling of liver stellate cells (LSCs) at the cellular level to investigate changes in the biological activity of LSCs during rat liver regeneration (LR) and the relation of these changes to LR. First, a rat liver regeneration model was established by partial hepatectomy (PH). Stellate cells were isolated in high purity and yield from the regenerating rat liver by Percoll density gradient centrifugation and immunomagnetic bead sorting. The changes in gene expression of LSCs after PH were examined using a rat genome 230 2.0 array composed of 24622 genes. The results indicated that 10241 of the 24622 genes investigated on the array were differentially expressed in LSCs. Of the 10241 genes, 1563 known genes were related to LR, which were grouped into three major gene expression clusters according to three-fold cut-off threshold: the upregulated gene cluster, the down-regulated gene cluster, and the cluster composed of genes showing complex changes in expression. Additionally, the genes were grouped into those involved in transcription regulation, signal transduction, transport, cellular metabolism, inflammation and immunity by functional analysis. When gene expression profiles were combined with the results of gene functional analysis, most of the genes involved in cytokine secretion and retinol metabolism in LSCs were significantly enriched in the cluster characterized by decreased expression, whereas genes involved in lipid metabolism were mostly enriched in the cluster showing increased expression. Based on further analysis of genes expressed in a phase-dependent manner during LR, it was suggested that lipid metabolism in LSCs was enhanced in the whole regeneration process, and that immune response and cytokine secretion were impaired during all three regenerative phases.

Transcriptional profiles of biliary epithelial cells from rat regenerating liver after partial hepatectomy

It has been widely accepted that hepatocytes are critical for liver regeneration (LR), but very little is known about the role of biliary epithelial cells (BECs) in this event, so this study aims to manifest the relevance of BECs with LR. High purity population of BECs was obtained using Percoll gradient centrifugation combined with immunomagnetic-bead separation technique. Transcriptional profiles of BECs from rat regenerating liver after 2/3 hepatectomy were monitored with rat genome 230 2.0 array. Microarray analysis results were evaluated by RT-PCR assays. Of all the genes on the array, 1262 known genes and 1026 unknown genes were related to LR. 79 of 1262 known genes showed a ≥ 20-fold change in expression level, mainly participating in primary metabolism and inflammatory response. In contrast to the regenerating liver, BEC division did not occur at proliferative phase of LR; alterations in nucleic acid, lipid and protein metabolism were significantly different from each other or within the same substance metabolism at different phases; the active signaling pathways in priming phase were mediated mainly by G protein-coupled receptor, small GTPase and Wnt receptor. Transport-related genes showed up-regulated expression mainly in priming and proliferative phases, possibly linked to cell membrane formation and transport function recovery of BECs in the late phase. In brief, comparative analysis of biological activities of BECs and the regenerating liver reveals that biological activities at the cellular level are not always consistent with those at tissue level, suggesting the necessity of cell level investigation on liver regeneration. Finally, expression of BEC markers in hepatocytes may suggest the potential of hepatocytes to transdifferentiate into BEC.

Crystallization and preliminary X-ray analysis of cecropin B from Bombyx mori

Cecropin B is a 37-residue cationic antimicrobial peptide derived from the haemolymph of Bombyx mori. The precise mechanism by which cecropins exert their antimicrobial and cytolytic activities is not well understood. Crystals of cecropin B were obtained by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitant at 289 K. The crystal diffracted to 1.43 A resolution using X-ray radiation and belonged to the orthorhombic space group P1, with unit-cell parameters a = 15.08, b = 22.75, c = 30.20 A, alpha = 96.9, beta = 103.1, gamma = 96.5 degrees. The asymmetric unit contained only one molecule of cecropin B, with a calculated Matthews coefficient of 2.48 A(3) Da(-1) and a solvent content of 50.4%.

MiR-429 regulates rat liver regeneration and hepatocyte proliferation by targeting JUN/MYC/BCL2/CCND1 signaling pathway

Increasing evidence indicates that miR-429 is involved in tumor suppression in various human cancers. However, its role in liver regeneration remains unexplored. Liver regeneration is a highly orchestrated process that can be regulated by microRNAs (miRNAs), although the mechanisms are largely unclear. In this study, we aimed to identify the role of miR-429 in hepatocyte proliferation during liver regeneration. First, we performed microarray analysis and qRT-PCR. Results indicated that miR-429 level in rat liver markedly decreased 30 h after partial hepatectomy, and miR-429 overexpression disrupted BRL-3A proliferation and the transition of G1 to S phase in rat hepatocyte and promoted hepatocyte apoptosis. By contrast, miR-429 down-regulation had inverse effects. MiR-429 negatively regulated JUN expression in vitro and in vivo. After using JUN siRNA, we found that JUN inhibition mediates the effect of miR-429 in hepatocyte proliferation and growth and miR-429 negatively regulates JUN/MYC/BCL2/CCND1 signaling pathways. Our results also indicated that miR-429 inhibits hepatocyte proliferation and liver regeneration by targeting JUN/MYC/BCL2/CCND1.

Cloning and characterization of metallothionein gene (HcMT) from Halostachys caspica and its expression in E. coli

Halostachys caspica is a short shrub distributed in the semi-arid and saline-alkali area, which evolved various mechanisms for modulating salt and metal level. In the present study, a Type 2 metallothionein (HcMT) gene was cloned from the salt induced suppression subtractive hybridization (SSH) cDNA library of H.caspica. Quantitative real time PCR (qRT-PCR) analysis indicated that HcMT gene was up-regulated under the stress of Cu(2+), Zn(2+) and Cd(2+), and the tolerance of E. coli strain harboring with the recombinant HcMT (pET-32a-HcMT) to Cu(2+), Zn(2+) and Cd(2+) was enhanced compared to strain with control vector (pET-32a). Moreover, the purified TrxA-HcMT fusion protein from E. coli cells grown in the presence of 0.3mM CuSO4, 0.3mM ZnSO4, or 0.1mM CdCl2 could bind more metal ions than TrxA alone. The predicted 3D structure showed that HcMT could form a single metal-thiolate cluster, which confers the ability to bind five divalent metal ions through fourteen cysteine residues. These data indicate that HcMT may be involved in processes of metal tolerance in H. caspica and could be employed as a potential candidate for heavy metal phytoremediation.

EXPRESSION PROFILES OF THE CELL MIGRATION-ASSOCIATED GENES DURING RAT LIVER REGENERATION

Cell migration plays the essential role in embryogenesis, wound healing, immunization, infection, and cancer metastasis. To study actions of cell migration-associated genes in liver regeneration, these genes were obtained by seaching for the related databases and literatures, and comprehensive analysis for the gene expression change during the regenerating process in liver was detected by Rat Genome 230 2.0 array, and identification of the LR-associated genes was through comparing the discrepancy in gene expression between sham operation and partial hepatectomy groups. The initially and totally expressed numbers of these genes in the initial phase of LR, G0/G1 transition, cell proliferation, cell differentiation, and structural-functional reconstruction were 88, 16, 79, 9, and 177, 90, 632, 207, respectively, illustrating that the associated genes triggered their expression mainly in the priming stage, and worked in different phases. Their expression similarity was classified into five groups and their expression patterns were categorized into 38 types, and the overall times of up-regulation and down-regulation were 589 and 427. Based on expression profiles and expression patterns of cell migration-associated genes in LR, it was confirmed that cell migration-associated genes rise in mRNA levels.