Search tips
Search criteria

Results 1-25 (38)

Clipboard (0)

Select a Filter Below

Year of Publication
1.  Analyses of the mitochondrial mutations in the Chinese patients with sporadic Creutzfeldt–Jakob disease 
Pathogenic mitochondrial DNA (mtDNA) mutations leading to mitochondrial dysfunction can cause a variety of chronic diseases in central nervous system (CNS). However, the role of mtDNA mutations in sporadic Creutzfeldt–Jakob disease (sCJD) has still been unknown. In this study, we comparatively analyzed complete mtDNA sequences of 31 Chinese sCJD patients and 32 controls. Using MITOMASTER and PhyloTree, we characterized 520 variants in sCJD patients and 507 variants in control by haplogroup and allele frequencies. We classified the mtDNAs into 40 sub-haplogroups of 5 haplogroups, most of them being Asian-specific haplogroups. Haplogroup U, an European-specific haplogroups mtDNA, was found only in sCJD. The analysis to control region (CR) revealed a 31% increase in the frequency of mtDNA CR mutations in sCJD versus controls. In functional elements of the mtDNA CR, six CR mutations were in conserved sequence blocks I (CSBI) in sCJD, while only one in control (P<0.05). More mutants in transfer ribonucleic acid-Leu (tRNA-Leu) were detected in sCJD. The frequencies of two synonymous amino-acid changes, m.11467A>G, p.(=) in NADH dehydrogenase subunit 4 (ND4) and m.12372G>A, p.(=) in NADH dehydrogenase subunit 5 (ND5), in sCJD patients were higher than that of controls. Our study, for the first time, screened the variations of mtDNA of Chinese sCJD patients and identified some potential disease-related mutations for further investigations.
PMCID: PMC4266738  PMID: 24667788
2.  Effects of allicin on the proliferation and cell cycle of chondrocytes 
The present study demonstrates the effect of allicin on the proliferation and the cell cycle distribution of the chondrocytes. MTT assay and flow cytometry were used for the evaluation of the effect of allicin on cell proliferative and the cell cycle distribution, respectively of the chondrocytes. The reverse transcription polymerase chain reaction (RT-PCR) and western blot analysis were respectively used for the analysis of mRNA and protein expression levels of cyclin D1, CDK4 and CDK6. The results revealed that exposure of the chondrocytes to allicin at a concentration of 40 µM significantly promoted the cell viability. Treatment of the cells with 10, 20, 30, 40, and 50 μg/mL of allicin enhanced the cell viability by 2.5.47 ± 0.86, 5.43 ± 0.66, 10.74 ± 1.48, 35.89 ± 3.78, and 32.21 ± 2.92%, respectively after 36 h compared to control cells. Allicin exposure caused a marked decrease in the percentage of cells in G0/G1 phase with a subsequent increase in the S phase population. Furthermore, allicin treatment enhanced the expression of cyclin D1, CDK4 and CDK6. Therefore, allicin treatment enhances the proliferation of chondrocytes by promoting the transition from G1 to S phase of the cell cycle through increase in the expression of cyclin D1, CDK4 and CDK6 levels.
PMCID: PMC4680385  PMID: 26722440
Osteoarthritis; chondrocytes; proliferation; viability; transition
3.  Evaluation of Apoptosis Induction by Concomitant Inhibition of MEK, mTOR, and Bcl-2 in Human Acute Myeloid Leukemia Cells 
Molecular cancer therapeutics  2014;13(7):1848-1859.
Aberrant activation of multiple signaling pathways is common in acute myeloid leukemia (AML) cells, which can be linked to a poor prognosis for patients with this disease. Previous research with mTOR or MEK inhibitors revealed cytostatic, rather than cytotoxic, effects in in vitro and in vivo AML models. We evaluated the combination effect of the mTOR inhibitor AZD8055 and the MEK inhibitor selumetinib on human AML cell lines and primary AML samples. This combination demonstrated synergistic proapoptotic effects in AML cells with high basal activation of MEK and mTOR. We next incorporated the BH3 mimetic ABT-737 into this combination regimen to block Bcl-2, which further enhanced the apoptogenic effect of MEK/mTOR inhibition. The combination treatment also had a striking proapoptotic effect in CD33+/CD34+ AML progenitor cells from primary AML samples with NRAS mutations. Mechanistically, up-regulation of the proapoptotic protein Bim, accompanied by the down-regulation of the antiapoptotic protein Mcl-1 (mainly via protein degradation), appeared to play critical roles in enhancing the combination drug effect. Furthermore, the modulation of survivin, Bax, Puma, and XIAP expression suggested a role for mitochondria-mediated apoptosis in the cytotoxicity of the drug combination. Consequently, the concomitant blockade of pro-survival MEK/mTOR signaling and the deactivation of Bcl-2 could provide a mechanism-based integrated therapeutic strategy for the eradication of AML cells.
PMCID: PMC4090272  PMID: 24739393
AZD8055; selumetinib; ABT-737; acute myeloid leukemia; apoptosis
4.  Reversal of Acquired Drug Resistance in FLT3-mutated Acute Myeloid Leukemia Cells via Distinct Drug Combination Strategies 
FMS-like tyrosine kinase-3 (FLT3) internal tandem duplication (FLT3-ITD) mutations are common in patients with acute myeloid leukemia (AML). These patients regularly develop resistance to FLT3 inhibitors suggesting that targeted combination drug strategies are needed to enhance AML therapy efficacy.
Experimental Design
Acquired point mutations of FLT3 ITD gene were screened using cDNA-based sequencing approach in vitro sorafenib resistant cells, which were developed by long-term exposure of Ba/F3-ITD to increasing doses of sorafenib, and in FLT3 ITD mutated AML patients, who developed relapse following sorafenib therapy. Drug effects (e.g., proliferation inhibition, apoptosis induction, and changes in signal transduction protein expression) were assessed in AML cells harboring the point mutations in vitro and in FLT3 ITD mutated AML patient samples.
We identified several acquired point mutations in the tyrosine kinase (TK) domains (TKDs) of the FLT3 gene in sorafenib-resistant murine leukemia cell line carrying human FLT3-ITD mutations, which were also detected in two of four sorafenib-resistant patient samples. Engineering these point mutations into Ba/F3-ITD cells generated sub-lines that demonstrated varying degrees of sorafenib (a type II TK inhibitor) resistance. A similar pattern of resistance could be observed by exposing these sub-lines to the other type II TK inhibitors AC220 and MLN518. However, these sub-lines retained sensitivity to the type I TK inhibitors PKC412 or crenolanib. The combination of crenolanib with sorafenib demonstrated marked cytotoxic effects in all of the sorafenib-resistant sub-lines.
These combination strategies could be clinically important in reversing acquired resistance to FLT3 inhibition in AML.
PMCID: PMC4073635  PMID: 24619500
FLT3; sorafenib; crenolanib; drug resistance; drug combination strategies
5.  Transcriptome Complexity in Cardiac Development and Diseases 
With the advancement of transcriptome profiling by micro-arrays and high-throughput RNA-sequencing, transcriptome complexity and its dynamics are revealed at different levels in cardiovascular development and diseases. In this review, we will highlight the recent progress in our knowledge of cardiovascular transcriptome complexity contributed by RNA splicing, RNA editing and noncoding RNAs. The emerging importance of many of these previously under-explored aspects of gene regulation in cardiovascular development and pathology will be discussed.
PMCID: PMC4306672  PMID: 24759793
Cardiovascular diseases; Genes; Molecular biology; Signal transduction
6.  Proteomics Analyses for the Global Proteins in the Brain Tissues of Different Human Prion Diseases*  
Proteomics changes of brain tissues have been described in different neurodegenerative diseases including Alzheimer's disease and Parkinson's disease. However, the brain proteomics of human prion disease remains less understood. In the study, the proteomics patterns of cortex and cerebellum of brain tissues of sporadic Creutzfeldt-Jakob disease, fatal familial insomnia, and G114V genetic CJD were analyzed with isobaric tags for relative and absolute quantitation combined with multidimensional liquid chromatography and MS analysis, with the brains from three normal individuals as controls. Global protein profiling, significant pathway, and functional categories were analyzed. In total, 2287 proteins were identified with quantitative information both in cortex and cerebellum regions. Cerebellum tissues appeared to contain more up- and down-regulated proteins (727 proteins) than cortex regions (312 proteins) of Creutzfeldt-Jakob disease, fatal familial insomnia, and G114V genetic CJD. Viral myocarditis, Parkinson's disease, Alzheimer's disease, lysosome, oxidative phosphorylation, protein export, and drug metabolism-cytochrome P450 were the most commonly affected pathways of the three kinds of diseases. Almost coincident biological functions were identified in the brain tissues of the three diseases. In all, data here demonstrate that the brain tissues of Creutzfeldt-Jakob disease, fatal familial insomnia, and G114V genetic CJD have obvious proteomics changes at their terminal stages, which show the similarities not only among human prion diseases but also with other neurodegeneration diseases. This is the first study to provide a reference proteome map for human prion diseases and will be helpful for future studies focused on potential biomarkers for the diagnosis and therapy of human prion diseases.
PMCID: PMC4390265  PMID: 25616867
7.  Nuclear phosphatase PPM1G in cellular survival and neural development 
PPM1G is a nuclear localized serine/threonine phosphatase implicated to be a regulator of chromatin remodeling, mRNA splicing and DNA damage. However, its in vivo function is unknown.
Here we show that ppm1g expression is highly enriched in the central nervous system during mouse and zebrafish development. ppm1g−/− mice were embryonic lethal with incomplete penetrance after E12.5. Rostral defects, including neural tube and craniofacial defects were observed in ppm1g−/− embryos associated with increased cell death in the neural epithelium. In zebrafish, loss of ppm1g also led to neural defects with aberrant neural marker gene expression. Primary fibroblasts from ppm1g−/− embryos failed to grow without immortalization while immortalized ppm1g−/− fibroblasts had increased cell death upon oxidative and genotoxic stress when compared to wild type fibroblasts.
Our in vivo and in vitro studies revealed a critical role for PPM1G in normal development and cell survival.
PMCID: PMC4230483  PMID: 23723158
PPM1G; neural tube; serine threonine phosphatase; PP2Cγ
8.  MicroRNA-21 and the clinical outcomes of various carcinomas: a systematic review and meta-analysis 
BMC Cancer  2014;14:819.
MicroRNA-21 (miR-21) has been suggested to play a significant role in the prognosis of carcinoma. The recognition of novel biomarkers for the prediction of cancer outcomes is urgently required. However, the potential prognostic value of miR-21 in various types of human malignancy remains controversial. The present meta-analysis summarises and analyses the associations between miR-21 status and overall survival (OS) in a variety of tumours.
Eligible published studies were identified by searching the PubMed and Chinese Biomedicine databases. The patients’ clinical characteristics and survival results were pooled, and a pooled hazard ratio (HR) with 95% confidence intervals (95% CI) was used to calculate the strength of this association. A random-effects model was adopted, and then, meta-regression and subgroup analyses were performed. In addition, an analysis of publication bias was also conducted.
Twenty-seven eligible articles (including 31 studies) were identified that included survival data for 3273 patients. The pooled HR suggested that high miR-21 was clearly related to worse overall survival (HR = 2.27, 95% CI: 1.81-2.86), with a heterogeneity measure index of I2 = 76.0%, p = 0.001, showing that miR-21 might be a considerable prognostic factor for poor survival in cancer patients.
MiR-21 might be a potentially useful biomarker for predicting cancer prognosis in future clinical applications.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2407-14-819) contains supplementary material, which is available to authorized users.
PMCID: PMC4232634  PMID: 25376700
miR-21; Cancer; Prognosis; Meta-analysis
9.  Post-transplant lymphoproliferative disorder presenting as a tumor adjacent to the renal allograft: A case report and review of the literature 
Oncology Letters  2014;8(6):2607-2610.
Post-transplant lymphoproliferative disorder (PTLD) is a potentially fatal complication of solid organ transplantation. The current report presents the case of a 42-year-old male who developed PTLD within the first year following renal transplantation. The disorder manifested as a tumor adjacent to the lower pole of the renal allograft and resulted in urinary obstruction. Durable complete remission was achieved as a result of surgical resection followed by a reduction in immunosuppression and low-dose rituximab-based chemotherapy, indicating that this therapeutic strategy may be safe and effective for the treatment of specific cases of localized and resectable PTLD.
PMCID: PMC4214511  PMID: 25364435
post-transplant lymphoproliferative disorder; Epstein-Barr virus; early-onset; kidney transplantation
10.  Nonreference Medical Image Edge Map Measure 
Edge detection is a key step in medical image processing. It is widely used to extract features, perform segmentation, and further assist in diagnosis. A poor quality edge map can result in false alarms and misses in cancer detection algorithms. Therefore, it is necessary to have a reliable edge measure to assist in selecting the optimal edge map. Existing reference based edge measures require a ground truth edge map to evaluate the similarity between the generated edge map and the ground truth. However, the ground truth images are not available for medical images. Therefore, a nonreference edge measure is ideal for medical image processing applications. In this paper, a nonreference reconstruction based edge map evaluation (NREM) is proposed. The theoretical basis is that a good edge map keeps the structure and details of the original image thus would yield a good reconstructed image. The NREM is based on comparing the similarity between the reconstructed image with the original image using this concept. The edge measure is used for selecting the optimal edge detection algorithm and optimal parameters for the algorithm. Experimental results show that the quantitative evaluations given by the edge measure have good correlations with human visual analysis.
PMCID: PMC4123524  PMID: 25132844
11.  Post-transplant recurrent pericarditis with pericardial tamponade is successfully treated with colchicine: A case report 
Recurrent pericarditis is a rare complication following renal transplantation. Colchicine, an inhibitor of microtubule polymerization, has been recommended for the treatment of recurrent acute pericarditis in non-transplant patients and is commonly used for the treatment of gout in transplant patients. However, the use of colchicine for the treatment of recurrent pericarditis in renal transplant patients has rarely been reported. In the present study, a rare case of recurrent pericarditis, manifested as large pericardial effusion and pericardial tamponade within the first year following renal transplantation, was successfully treated with colchicine. Therefore, low-dose colchicine may be a safe and effective option for the treatment of recurrent pericarditis in renal transplant patients.
PMCID: PMC4113640  PMID: 25120603
kidney transplant; recurrent pericarditis; pericardial tamponade; colchicine
12.  Expression of Chemerin and Its Receptors in Rat Testes and Its Action on Testosterone Secretion 
The Journal of endocrinology  2014;220(2):155-163.
The novel adipokine chemerin plays a role in regulating lipid and carbohydrate metabolism, and recent reports of elevated chemerin levels in polycystic ovarian syndrome elevated chemerin levels with polycystic ovary syndrome and preeclampsia point to an emerging role for chemerin in reproduction. We hypothesized that chemerin, like other adipokines, may function to regulate male gonadal steroidogenesis. Here we show that chemerin and its three receptors chemokine-like receptor 1 (CMKLR1), G-protein coupled receptor 1 (GPR1) and chemokine (C-C motif) receptor-like 2 (CCRL2) were expressed in male reproductive tracts, liver and white adipose tissue. CMKLR1 and GPR1 protein were localized specifically in the Leydig cells of human and rat testes by immunohistochemistry. The expression of chemerin and its receptors in rat testes was developmentally regulated and highly expressed in Leydig cells. In vitro treatment with chemerin suppressed the human chorinoic gonadotropin (hCG)-induced testosterone production from primary Leydig cells, which was accompanied by the inhibition of 3beta-hydroxysteroid dehydrogenase (3beta-HSD) gene and protein expression. The hCG-activated p44/42 mitogen-activated-protein kinase (MAPK) (Erk1/2) pathway in Leydig cells was also inhibited by chemerin co-treatment. Together, these data suggest chemerin is a novel regulator of male gonadal steroidogenesis.
PMCID: PMC3932185  PMID: 24301613
chemerin; steroidogenesis; testosterone; adipokine; Leydig cell
13.  Rare V203I mutation in the PRNP gene of a Chinese patient with Creutzfeldt–Jakob disease 
Prion  2013;7(3):259-262.
Here, we report a Chinese case of Creutzfeldt–Jakob disease (CJD) with a rare mutation in the prion protein gene (PRNP) leading to an exchange of amino acid from valine (Val) to isoleucine (I) at codon 203 (V203I). The 80-y-old male presented with sudden memory loss, rapid loss of vocabulary, inattention and slow responses, accompanied by dizziness, blurred vision and ataxia. Two weeks after admission, he exhibited tremor, myoclonus and bilateral Babinski signs. At the end of the clinical course, he developed severe akinetic mutism. The cerebrospinal fluid (CSF) was positive for 14-3-3 protein. Increased bilateral signal intensity in the frontal and parietal lobes was seen on diffusion-weighted imaging (DWI); periodic activity was recorded on an electroencephalogram (EEG). There was no family history of similar symptoms. The total clinical course was approximately two months.
PMCID: PMC3783113  PMID: 23764840
14-3-3 protein; PRNP; Creutzfeldt–Jakob disease; V203I; mutation
14.  Bipolar loop-like non-volatile strain in the (001)-oriented Pb(Mg1/3Nb2/3)O3-PbTiO3 single crystals 
Scientific Reports  2014;4:4591.
Strain has been widely used to manipulate the properties of various kinds of materials, such as ferroelectrics, semiconductors, superconductors, magnetic materials, and “strain engineering” has become a very active field. For strain-based information storage, the non-volatile strain is very useful and highly desired. However, in most cases, the strain induced by converse piezoelectric effect is volatile. In this work, we report a non-volatile strain in the (001)-oriented Pb(Mg1/3Nb2/3)O3-PbTiO3 single crystals and demonstrate an approach to measure the non-volatile strain. A bipolar loop-like S-E curve is revealed and a mechanism involving 109° ferroelastic domain switching is proposed. The non-volatile high and low strain states should be significant for applications in information storage.
PMCID: PMC3975321  PMID: 24699506
15.  A Small Peptide with Potential Ability to Promote Wound Healing 
PLoS ONE  2014;9(3):e92082.
Wound-healing represents a major health burden, such as diabetes-induced skin ulcers and burning. Many works are being tried to find ideal clinical wound-healing biomaterials. Especially, small molecules with low cost and function to promote production of endogenous wound healing agents (i.e. transforming growth factor beta, TGF-β) are excellent candidates. In this study, a small peptide (tiger17, c[WCKPKPKPRCH-NH2]) containing only 11 amino acid residues was designed and proved to be a potent wound healer. It showed strong wound healing-promoting activity in a murine model of full thickness dermal wound. Tiger17 exerted significant effects on three stages of wound healing progresses including (1) the induction of macrophages recruitment to wound site at inflammatory reaction stage; (2) the promotion of the migration and proliferation both keratinocytes and fibroblasts, leading to reepithelialization and granulation tissue formation; and (3) tissue remodeling phase, by promoting the release of transforming TGF-β1 and interleukin 6 (IL-6) in murine macrophages and activating mitogen-activated protein kinases (MAPK) signaling pathways. Considering its easy production, store and transfer and function to promote production of endogenous wound healing agents (TGF-β), tiger17 might be an exciting biomaterial or template for the development of novel wound-healing agents.
PMCID: PMC3960170  PMID: 24647450
16.  Single Domain SmCo5@Co Exchange-coupled Magnets Prepared from Core/shell Sm[Co(CN)6]·4H2O@GO Particles: A Novel Chemical Approach 
Scientific Reports  2013;3:3542.
SmCo5 based magnets with smaller size and larger maximum energy product have been long desired in various fields such as renewable energy technology, electronic industry and aerospace science. However, conventional relatively rough synthetic strategies will lead to either diminished magnetic properties or irregular morphology, which hindered their wide applications. In this article, we present a facile chemical approach to prepare 200 nm single domain SmCo5@Co core/shell magnets with coercivity of 20.7 kOe and saturation magnetization of 82 emu/g. We found that the incorporation of GO sheets is responsible for the generation of the unique structure. The single domain SmCo5 core contributes to the large coercivity of the magnets and the exchange-coupled Co shell enhances the magnetization. This method can be further utilized in the synthesis other Sm-Co based exchange-coupled magnets.
PMCID: PMC3868969  PMID: 24356309
17.  Nek9 regulates spindle organization and cell cycle progression during mouse oocyte meiosis and its location in early embryo mitosis 
Cell Cycle  2012;11(23):4366-4377.
Nek9 (also known as Nercc1), a member of the NIMA (never in mitosis A) family of protein kinases, regulates spindle formation, chromosome alignment and segregation in mitosis. Here, we showed that Nek9 protein was expressed from germinal vesicle (GV) to metaphase II (MII) stages in mouse oocytes with no detectable changes. Confocal microscopy identified that Nek9 was localized to the spindle poles at the metaphase stages and associated with the midbody at anaphase or telophase stage in both meiotic oocytes and the first mitotic embyros. Depletion of Nek9 by specific morpholino injection resulted in severely defective spindles and misaligned chromosomes with significant pro-MI/MI arrest and failure of first polar body (PB1) extrusion. Knockdown of Nek9 also impaired the spindle-pole localization of γ-tubulin and resulted in retention of the spindle assembly checkpoint protein Bub3 at the kinetochores even after 10 h of culture. Live-cell imaging analysis also confirmed that knockdown of Nek9 resulted in oocyte arrest at the pro-MI/MI stage with abnormal spindles, misaligned chromosomes and failed polar body emission. Taken together, our results suggest that Nek9 may act as a MTOC-associated protein regulating microtubule nucleation, spindle organization and, thus, cell cycle progression during mouse oocyte meiotic maturation, fertilization and early embryo cleavage.
PMCID: PMC3552919  PMID: 23159858
meiosis; microtubule-organizing center (MTOC) spindle; oocyte; γ-tubulin
18.  Biomonitoring of Non-Dioxin-Like Polychlorinated Biphenyls in Transgenic Arabidopsis Using the Mammalian Pregnane X Receptor System: A Role of Pectin in Pollutant Uptake 
PLoS ONE  2013;8(11):e79428.
Polychlorinated biphenyls (PCBs) are persistent organic pollutants damaging to human health and the environment. Techniques to indicate PCB contamination in planta are of great interest to phytoremediation. Monitoring of dioxin-like PCBs in transgenic plants carrying the mammalian aryl hydrocarbon receptor (AHR) has been reported previously. Herein, we report the biomonitoring of non-dioxin-like PCBs (NDL-PCBs) using the mammalian pregnane X receptor (PXR). In the transgenic Arabidopsis designated NDL-PCB Reporter, the EGFP-GUS reporter gene was driven by a promoter containing 18 repeats of the xenobiotic response elements, while PXR and its binding partner retinoid X receptor (RXR) were coexpressed. Results showed that, in live cells, the expression of reporter gene was insensitive to endogenous lignans, carotenoids and flavonoids, but responded to all tested NDL-PCBs in a dose- and time- dependent manner. Two types of putative PCB metabolites, hydroxy- PCBs and methoxy- PCBs, displayed different activation properties. The vascular tissues seemed unable to transport NDL-PCBs, whereas mutation in QUASIMODO1 encoding a 1,4-galacturonosyltransferase led to reduced PCB accumulation in Arabidopsis, revealing a role for pectin in the control of PCB translocation. Taken together, the reporter system may serve as a useful tool to biomonitor the uptake and metabolism of NDL-PCBs in plants.
PMCID: PMC3827382  PMID: 24236133
19.  Analyses of the Survival Time and the Influencing Factors of Chinese Patients with Prion Diseases Based on the Surveillance Data from 2008–2011 
PLoS ONE  2013;8(5):e62553.
Prion diseases are kinds of progressive, incurable neurodegenerative disorders. So far, survival time of the patients with these diseases in China is unclear.
Based upon the surveillance data from Chinese Creutzfeldt-Jakob disease (CJD) surveillance network from January 2008 to December 2011, a retrospective follow-up survey was performed. The survival times of Chinese patients with prion diseases and the possible influencing factors were analyzed.
Median survival time of 121 deceased patients was 7.1 months, while those for sporadic CJD (sCJD), familial CJD (fCJD) and fatal familial insomnia (FFI) cases were 6.1, 3.1 and 8.2 months, respectively. 74.0% of sCJD patients, 100% of fCJD cases and 91.7% FFI cases died within one year. The general socio-demographic factors, abnormalities in clinical examinations, clinical manifestations, and social factors did not significantly influence the survival times of Chinese prion patients.
Survival time of Chinese patients with prion diseases was comparable with that of many Western countries, but obviously shorter than that of Japan. Patients with acute onset and rapid progression had significantly short survival times.
PMCID: PMC3645993  PMID: 23671608
20.  Analysis of Transcriptome Complexity via RNA-Seq in Normal and Failing Murine Hearts 
Circulation research  2011;109(12):1332-1341.
Accurate and comprehensive de novo transcriptome profiling in heart is a central issue to better understand cardiac physiology and diseases. Although significant progress has been made in genome-wide profiling for quantitative changes in cardiac gene expression, current knowledge offers limited insights to the total complexity in cardiac transcriptome at individual exon level.
To develop more robust bioinformatic approaches to analyze high-throughput RNA sequencing (RNA-Seq) data, with the focus on the investigation of transcriptome complexity at individual exon and transcript levels.
Methods and Results
In addition to overall gene expression analysis, the methods developed in this study were used to analyze RNA-Seq data with respect to individual transcript isoforms, novel spliced exons, novel alternative terminal exons, novel transcript clusters (i.e., novel genes) and long non-coding RNA genes. We applied these approaches to RNA-Seq data obtained from mouse hearts following pressure-overload induced by trans-aortic constriction. Based on experimental validations, analyses of the features of the identified exons/transcripts, and expression analyses including previously published RNASeq data, we demonstrate that the methods are highly effective in detecting and quantifying individual exons and transcripts. Novel insights inferred from the examined aspects of the cardiac transcriptome open ways to further experimental investigations.
Our work provided a comprehensive set of methods to analyze mouse cardiac transcriptome complexity at individual exon and transcript levels. Applications of the methods may infer important new insights to gene regulation in normal and disease hearts in terms of exon utilization and potential involvement of novel components of cardiac transcriptome.
PMCID: PMC3243366  PMID: 22034492
RNA-Seq; transcriptome profiling; hypertrophy; heart failure
21.  Heat shock protein 70 selectively mediates the degradation of cytosolic PrPs and restores the cytosolic PrP-induced cytotoxicity via a molecular interaction 
Virology Journal  2012;9:303.
Although the aggregation of PrPSc is thought to be crucial for the neuropathology of prion diseases, there is evidence in cultured cells and transgenic mice that neuronal death can be triggered by the accumulation of cytosolic PrPs, leading to the hypothesis that the accumulation of PrPs in the cytosol of neurons may be a primary neurotoxic culprit. Hsp70, a molecular chaperone involved in protein folding/refolding and degradation in the cytoplasm, has a protective effect in some models of neurodegenerative diseases, e.g., Alzheimer’s and Parkinson’s diseases, but its role in prion diseases remains unclear.
To study the role of Hsp70 in prion diseases, we used immunoprecipitation to first identify a molecular interaction between Hsp70 and PrPs. Using immunofluorescence, we found that Hsp70 colocalized with cytosolic PrPs in HEK293 cells transiently transfected with plasmids for Cyto-PrP and PG14-PrP but not with wild-type PG5-PrP or endoplasmic reticulum (ER)-retained PrPs (3AV-PrP and ER-PrP). Using western blot analysis and apoptosis assays of cultured cells, we found that the overexpression of Hsp70 by transfection or the activation of Hsp70 by geldanamycin selectively mediated the degradation of cytosolic PrPs and restored cytosolic PrP-induced cytotoxicity. Moreover, we found that Hsp70 levels were up-regulated in cells expressing Cyto-PrP and in hamster brains infected with the scrapie agent 263K.
These data imply that Hsp70 has central role in the metabolism of cytosolic PrPs
PMCID: PMC3544727  PMID: 23216755
Hsp70; Cytosolic PrP; Apoptosis; Prion disease; Geldanamycin
22.  Global impact of RNA splicing on transcriptome remodeling in the heart *  
In the eukaryotic transcriptome, both the numbers of genes and different RNA species produced by each gene contribute to the overall complexity. These RNA species are generated by the utilization of different transcriptional initiation or termination sites, or more commonly, from different messenger RNA (mRNA) splicing events. Among the 30 000+ genes in human genome, it is estimated that more than 95% of them can generate more than one gene product via alternative RNA splicing. The protein products generated from different RNA splicing variants can have different intracellular localization, activity, or tissue-distribution. Therefore, alternative RNA splicing is an important molecular process that contributes to the overall complexity of the genome and the functional specificity and diversity among different cell types. In this review, we will discuss current efforts to unravel the full complexity of the cardiac transcriptome using a deep-sequencing approach, and highlight the potential of this technology to uncover the global impact of RNA splicing on the transcriptome during development and diseases of the heart.
PMCID: PMC3411092  PMID: 22843179
Alternative RNA splicing; Transcriptome; Gene regulation; Heart; RNA-seq
23.  The first Chinese case of Creutzfeldt-Jakob disease patient with R208H mutation in PRNP 
Prion  2011;5(3):232-234.
A case of Creutzfeldt-Jakob disease (CJD) with a rare mutation of the prion protein (PrP) gene (PRNP) at codon 208 (R208H), while the codon 129 was a methionine homozygous genotype is reported. The patient initial displayed hand tremor, dizziness and progressive cognitive dysfunction. Subsequently, other symptoms gradually appeared, including cerebellar ataxia and mental disorder. No periodic activity was recorded at electroencephalography (EEG) and 14-3-3 protein in cerebrospinal fluid was negative. Total clinical course was about four months. Retrospective investigation of this family across seven generations did not figure out clear family history. However, genetic analyses revealed six first-degree family members with the R208H allele.
PMCID: PMC3226051  PMID: 21791975
creutzfeldt-Jakob disease; PRNP; R208H
24.  Protein Disulfide Isomerase Regulates Endoplasmic Reticulum Stress and the Apoptotic Process during Prion Infection and PrP Mutant-Induced Cytotoxicity 
PLoS ONE  2012;7(6):e38221.
Protein disulfide isomerase (PDI), is sorted to be enzymatic chaperone for reconstructing misfolded protein in endoplasmic reticulum lumen. Recently, PDI has been identified as a link between misfolded protein and neuron apoptosis. However, the potential for PDI to be involved in the pathogenesis of prion disease remains unknown. In this study, we propose that PDI may function as a pleiotropic regulator in the cytotoxicity induced by mutated prion proteins and in the pathogenesis of prion diseases.
Methodology/Principal Findings
To elucidate potential alterations of PDI in prion diseases, the levels of PDI and relevant apoptotic executors in 263K infected hamsters brain tissues were evaluated with the use of Western blots. Abnormal upregulation of PDI, Grp78 and Grp58 was detected. Dynamic assays of PDI alteration identified that the upregulation of PDI started at the early stage and persistently increased till later stage. Obvious increases of PDI and Grp78 levels were also observed in cultured cells transiently expressing PrP mutants, PrP-KDEL or PrP-PG15, accompanied by significant cytotoxicities. Excessive expression of PDI partially eased ER stress and cell apoptosis caused by accumulation of PrP-KDEL, but had less effect on cytotoxicity induced by PrP-PG15. Knockdown of endogenous PDI significantly amended cytotoxicity of PrP-PG15, but had little influence on that of PrP-KDEL. A series of membrane potential assays found that apoptosis induced by misfolded PrP proteins could be regulated by PDI via mitochondrial dysfunction. Moreover, biotin-switch assays demonstrated active S-nitrosylted modifications of PDI (SNO-PDI) both in the brains of scrapie-infected rodents and in the cells with misfolded PrP proteins.
Current data in this study highlight that PDI and its relevant executors may function as a pleiotropic regulator in the processes of different misfolded PrP proteins and at different stages during prion infection. SNO-PDI may feed as an accomplice for PDI apoptosis.
PMCID: PMC3369880  PMID: 22685557
25.  Multiple injuries after earthquakes: a retrospective analysis on 1,871 injured patients from the 2008 Wenchuan earthquake 
Critical Care  2012;16(3):R87.
Multiple injuries have been highlighted as an important clinical dimension of the injury profile following earthquakes, but studies are scarce. We investigated the pattern and combination of injuries among patients with two injuries following the 2008 Wenchuan earthquake. We also described the general injury profile, causes of injury and socio-demographic characteristics of the injured patients.
A retrospective hospital-based analysis of 1,871 earthquake injured patients, totaling 3,177 injuries, admitted between 12 and 31 May 2008 to the People's Hospital of Deyang city (PHDC). An electronic, webserver-based database with International Classification of Diseases (ICD)-10-based classification of earthquake-related injury diagnoses (IDs), anatomical sites and additional background variables of the inpatients was used. We analyzed this dataset for injury profile and number of injuries per patient. We then included all patients (856) with two injuries for more in-depth analysis. Possible spatial anatomical associations were determined a priori. Cross-tabulation and more complex frequency matrices for combination analyses were used to investigate the injury profile.
Out of the 1,871 injured patients, 810 (43.3%) presented with a single injury. The rest had multiple injuries; 856 (45.8%) had two, 169 (9.0%) patients had three, 32 (1.7%) presented with four injuries, while only 4 (0.2%) were diagnosed with five injuries. The injury diagnoses of patients presenting with two-injuries showed important anatomical intra-site or neighboring clustering, which explained 49.1% of the combinations. For fractures, the result was even more marked as spatial clustering explained 57.9% of the association pattern. The most frequent combination of IDs was a double-fracture, affecting 20.7% of the two-injury patients (n = 177). Another 108 patients (12.6%) presented with fractures associated with crush injury and organ-soft tissue injury. Of the 3,177 injuries, 1,476 (46.5%) were fractures. Most injuries were located in the head (22.9%) and lower extremities (30.8%).
Multiple injuries are put forward as an important component of the injury profile after this earthquake. A pattern of injury combinations and spatial aggregation of injuries was also found. Clinical diagnosis and treatment should be adapted to care of these patients. More studies are needed to generalize these findings.
PMCID: PMC3580632  PMID: 22594875

Results 1-25 (38)