Cunshuan Xu

Comprehensive CircRNA expression profile and selection of key CircRNAs during priming phase of rat liver regeneration

BackgroundRat liver regeneration (LR) proceeds along a process of highly organized and ordered tissue growth in response to the loss or injury of liver tissue, during which many physiological processes may play important roles. The molecular mechanism of hepatocyte proliferation, energy metabolism and substance metabolism during rat LR had been elucidated. Further, the correlation of circular RNA (circRNA) abundance with proliferation has recently been clarified. However, the regulatory capacity of circRNA in rat LR remains a fascinating topic.ResultsTo investigate the regulatory mechanism of circRNA during priming phase of rat LR, high-throughput RNA sequencing technology was performed to unbiasedly profile the expression of circRNA during priming phase of rat LR. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analysis was conducted to predict the functions of differentially expressed circRNAs and their host linear transcripts. Co-expression networks of circRNA-miRNA were constructed based on the correlation analysis between the differentially expressed LR-related circRNAs and the condition of their miRNA binding sites. To excavate the key circRNAs in the early phase of rat LR, we comprehensively evaluated and integrated the relationship of expression level between the circRNAs and the linear transcripts as well as the distribution of miRNA binding sites in circRNA sequences.ConclusionsThis paper is the first to employ the comprehensive circRNA expression profile and to investigate circRNA-miRNA interactions during priming phase of rat LR. Two thousand four hundred twelve circRNAs were detected, and 159 circRNAs deriving from 116 host linear transcripts differentially expressed (pu2009<u20090.05). Six significantly changed circRNAs during priming phase of rat LR were screened as key circle molecules, and then were validated by qRT-PCR. This study will lay the foundation for revealing the functional roles of circRNAs during rat LR and help solve the remaining clinical problems.

Proteomic analysis of the skin of Chinese giant salamander (Andrias davidianus).

UNLABELLEDnThe Chinese giant salamander (Andrias davidianus), renowned as a living fossil, is the largest and longest-lived amphibian species in the world. Its skin has developed mucous gland which could secrete a large amount of mucus under the scraping and electric stimulation, and the molting is the degraded skin stratum corneum. Although several proteomic studies have focused on functional proteomes of mammalian and frog skin, the skin proteome of Chinese giant salamander has not yet been carefully studied. To establish the functional skin proteome of Chinese giant salamander, two-dimensional gel electrophoresis (2DE) and mass spectrometry (MS) were applied to detect the composition and relative abundance of the proteins in the skin, mucus and molting. Our findings indicated that 249 proteins were identified in the skin, 155 proteins in the mucus, and 97 proteins in the molting. Furthermore, Gene Ontology (GO) analysis showed that these proteins participated in various physiological activities, including extracellular matrix organization, defense, immune response, wound healing, respiration, etc. In conclusion, the proteomic results provide new insight in the aspects of the proteomes in the skin, mucus and the molting of Chinese giant salamander.nnnBIOLOGICAL SIGNIFICANCEnThis was the first study to examine the protein expression abundance in the skin, mucus and molting of Chinese giant salamander by a proteomics approach. Meantime, the identification of a more global proteome in normal skin may provide a basis for characterizing and comparing the skin proteomes from other amphibian species.

iTRAQ-Based Quantitative Proteomic Analysis of the Initiation of Head Regeneration in Planarians

The planarian Dugesia japonica has amazing ability to regenerate a head from the anterior ends of the amputated stump with maintenance of the original anterior-posterior polarity. Although planarians present an attractive system for molecular investigation of regeneration and research has focused on clarifying the molecular mechanism of regeneration initiation in planarians at transcriptional level, but the initiation mechanism of planarian head regeneration (PHR) remains unclear at the protein level. Here, a global analysis of proteome dynamics during the early stage of PHR was performed using isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics strategy, and our data are available via ProteomeXchange with identifier PXD002100. The results showed that 162 proteins were differentially expressed at 2 h and 6 h following amputation. Furthermore, the analysis of expression patterns and functional enrichment of the differentially expressed proteins showed that proteins involved in muscle contraction, oxidation reduction and protein synthesis were up-regulated in the initiation of PHR. Moreover, ingenuity pathway analysis showed that predominant signaling pathways such as ILK, calcium, EIF2 and mTOR signaling which were associated with cell migration, cell proliferation and protein synthesis were likely to be involved in the initiation of PHR. The results for the first time demonstrated that muscle contraction and ILK signaling might played important roles in the initiation of PHR at the global protein level. The findings of this research provide a molecular basis for further unraveling the mechanism of head regeneration initiation in planarians.

Differential proteome analysis of the cell differentiation regulated by BCC, CRH, CXCR4, GnRH, GPCR, IL1 signaling pathways in Chinese fire-bellied newt limb regeneration

Following amputation, the newt has the remarkable ability to regenerate its limb, and this process involves dedifferentiation, proliferation and differentiation. To investigate the potential proteome during a dynamic network of Chinese fire-bellied newt limb regeneration (CNLR), two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and mass spectrum (MS) were applied to examine changes in the proteome that occurred at 11 time points after amputation. Meanwhile, several proteins were selected to validate their expression levels by Western blot. The results revealed that 1476 proteins had significantly changed as compared to the control group. Gene Ontology annotation and protein network analysis by Ingenuity Pathway Analysis 9.0 (IPA) software suggested that the differentially expressed proteins were involved in 33 kinds of physiological activities including signal transduction, cell proliferation, cell differentiation, etc. Among these proteins, 407 proteins participated in cell differentiation with 212 proteins in the differentiation of skin cell, myocyte, neurocyte, chondrocyte and osteocyte, and 37 proteins participated in signaling pathways of BCC, CRH, CXCR4, GnRH, GPCR and IL1 which regulated cell differentiation and redifferentiation. On the other hand, the signal transduction activity and cell differentiation activity were analyzed by IPA based on the changes in the expression of these proteins. The results showed that BCC, CRH, CXCR4, GnRH, GPCR and IL1 signaling pathways played an important role in regulating the differentiation of skin cell, myocyte, neurocyte, chondrocyte and osteocyte during CNLR.

Interleukin 18 augments growth ability via NF-κB and p38/ATF2 pathways by targeting cyclin B1, cyclin B2, cyclin A2, and Bcl-2 in BRL-3A rat liver cells.

Interleukin 18 (IL-18) is a pleiotropic cytokine and capable of stimulating proliferation of certain cell types. Nonetheless, its effect on normal liver cells cultured remains unclear. In the present study, we discovered that IL-18 expression level was remarkably elevated at 3.3 and 8.6h after synchronized BRL-3A rat liver cells (G0 phase) re-entering the cell cycle. In addition, recombinant rat IL-18 (rrIL-18) at dosages 5-10 ng/ml increased the cell viability compared to untreated cells (with medium only) at 24 and 48 h (P<0.05). At the same time, the percentage of BrdU-labeling cells was also significantly increased (P<0.01). On the other hand, knockdown of IL-18 expression with short interference RNA (siRNA), the cell viability began to decline at 24h and significantly decreased compared to negative control (NC) at 48 and 72 h after transfection (P<0.05). Meanwhile, the number of cells in division phase (G2/M) was reduced in parallel. Further, after treatment with rrIL-18 (5 ng/ml), IL-18 and its receptor subunit IL-18Rα increased both at mRNA and protein levels. Moreover, the expression levels of adaptor molecule MyD88, transcription factor NF-κB and its downstream targets cyclin B1 and cyclin B2 were remarkably enhanced in BRL-3A cells stimulated by rrIL-18. Furthermore, transcription factor ATF2 and its targeted genes cyclin A2, Bcl-2 were also markedly increased after treatment with rrIL-18. These results demonstrated that IL-18 can augment cell proliferation via NF-κB and p38/ATF2 pathway by targeting cyclin B1, cyclin B2, cyclin A2 and Bcl-2 in BRL-3A rat liver cells.

A preliminary in vivo study of the effects of OPN on rat liver regeneration induced by partial hepatectomy

Osteopontin (OPN) is a member of Th1 cytokine secreted by activated lymphocytes and macrophages. However, it deserves to be studied whether OPN could promote cell activation or proliferation, and then facilitate hepatic self-repair during liver regeneration (LR). This study is designed to further reveal the effects of OPN on LR in vivo. Firstly, quantitative reverse transcription-PCR (qRT-PCR) and western blot (WB) were utilized to validate the expression profile of endogenous OPN in rat regenerating livers after partial hepatectomy (PH). Then OPN expression vector, two shRNA expression vectors and their respective test vectors were successfully constructed. Afterwards, test vectors were administrated into mouse livers via tail vein to find the more efficient shRNA. Furthermore, OPN expression vector and the more efficient shRNA expression vector were injected into rat regenerating livers, and then the changes in liver regeneration and hepatic microstructure were respectively detected by liver regeneration rate and HE staining, while the expressions of several marker genes were detected by qRT-PCR and WB. Endogenous OPN was strikingly up-regulated in both mRNA and protein level during LR, especially at 12 and 72xa0h after PH. The shRNA expression vector Opn(313) was found to be more efficient than Opn(887) in silencing the expression of Opn. Then OPN expression vector and Opn(313) were injected into rat remnant livers, and it showed that OPN overexpression aggravated hepatic necrosis and leukocytes infiltration, while OPN silencing inhibited liver regeneration rate and the expressions of PCNA and CCL2, but augmented that of BAX. In conclusion, OPN might enhance inflammation and cell proliferation, attenuate cell apoptosis, and ultimately facilitate liver regeneration at the termination stage of liver regeneration.

Induction of Functional Hepatocyte-Like Cells by Overexpression of FOXA3 and HNF4α in Rat Bone Marrow Mesenchymal Stem Cells

Liver regeneration has always been of great therapeutic interest, particularly to generate hepatocytes from other types of cells including adult stem cells and induced pluripotent stem cells. In this study, it was found that overexpression of both FOXA3 and HNF4α can convert rat bone marrow mesenchymal stem cells (BMSCs) to functional hepatocyte-like cells (HLCs). The results show that these HLCs had the typical hepatocyte morphology with unique hepatocyte markers such as ALB, G6P, KRT18, TAT, TTR, KRT19 and AFP. Simultaneously, they also exhibited hepatic functions such as glycogen storage, indocyanine green absorption, and cytoplasmic accumulation of neutral triglycerides and lipids. In addition to that, these functions could be maintained in the process of cell culture, thus suggesting that FOXA3 and HNF4α are powerful transcription factors for inducing rat BMSCs to differentiate into functional HLCs, and this study will provide a novel method to generate HLCs.

Overexpression of transcription factor Foxa2 and Hnf1α induced rat bone mesenchymal stem cells into hepatocytes

Hepatocytes differentiated from induced pluripotent stem cells and adult stem cells could be utilized as a tool for the study of liver diseases, screening for drug metabolism and hepatotoxicity. Thus further investigationxa0ofxa0thexa0method to efficiently generate hepatocytes is in great need. Bone Mesenchymal Stem Cells (BMSCs) were collected from rat femurs and tibias. FOXA2 and HNF1α genes were constructed into a lentiviral vector and introduced into BMSCs by a lentivirus-mediatedxa0overexpression system. Three weeks after the induction, the expressions of FOXA2 and HNF1α, and liver specific genes were analyzed, and hepatocyte-function related assays were performed. Overexpression of both FOXA2 and HNF1α induced the BMSCs to differentiate into hepatocyte-like cells (HLCs). Hepatocyte-specific gene and protein were detected by RT-PCR, Western Blot and Immunofluorescence. These HLCs also exerted some typical hepatocyte functions such as glycogen storage, indocyanine green absorption and lipid accumulation. The combination of FOXA2 and HNF1α can effectively induce BMSCs to differentiate into HLCs. This is a novel and efficient method to prepare HLCs within a short timeline.

The Chinese giant salamander exemplifies the hidden extinction of cryptic species

Overexploitation, habitat destruction, human-driven climate change and disease spread are resulting in the extinction of innumerable species, with amphibians being hit harder than most other groups [1]. Few species of amphibians are widespread, and those that are often represent complexes of multiple cryptic species. This is especially true for range-restricted salamanders [2]. Here, we used the widespread and critically endangered Chinese giant salamander (Andrias davidianus) to show how genetically uninformed management efforts can negatively affect species conservation. We find that this salamander consists of at least five species-level lineages. However, the extensive recent translocation of individuals between farms, where the vast majority of extant salamanders now live, has resulted in genetic homogenization. Mitochondrial DNA (mtDNA) haplotypes from northern China now predominate in farms. Unfortunately, hybrid offspring are being released back into the wild under well-intentioned, but misguided, conservation management. Our findings emphasize the necessity of genetic assessments for seemingly well-known, widespread species in conservation initiatives. Species serve as the primary unit for protection and management in conservation actions [3], so determining the taxonomic status of threatened species is a major concern, especially for amphibians. The level of threat to amphibians may be underestimated, and existing conservation strategies may be inadvertently harmful if conducted without genetic assessment.

Integrative proteomic and microRNA analysis of the priming phase during rat liver regeneration

The partial hepatectomy (PH) model provides an effective medium for study of liver regeneration (LR). Considering that LR is regulated by microRNAs (miRNAs), investigation of the regulatory role of miRNAs is critical for revealing how regenerative processes are initiated and controlled. Using high-throughput sequencing technology, we examined miRNA expression profiles of the regenerating rat liver after PH, and found that 23 miRNAs were related to rat LR. Among them, several miRNAs were significantly altered at 2h and 6h after PH, corresponding to the priming phase of LR. Furthermore, we examined the protein profiles in the regenerating rat liver at 2h and 6h after PH by iTRAQ coupled with LC-MS/MS, and found that 278 proteins were significantly changed. Subsequently, an integrative proteomic and microRNA analysis by Ingenuity Pathway Analysis 9.0 (IPA) software showed that miR-125a, miR-143, miR-150, miR-181c, miR-182, miR-183, miR-199a, miR-429 regulated the priming phase of rat LR by modulating the expression of proteins involved in networks critical for cell apoptosis, cell survival, cell cycle, inflammatory response, metabolism, etc. Thus, our studies provide novel evidence for a functional molecular network populated by the down-regulated targets of the up-regulated miRNAs in the priming phase of rat LR.