Global analysis of population stratification using a smart panel of 27 continental ancestry-informative SNPs.

Over the last decade, several panels of ancestry-informative markers have been proposed for the analysis of population genetic structure. The differentiation efficiency depends on the discriminatory ability of the included markers and the reference population coverage. We previously developed a small set of 27 autosomal single nucleotide polymorphisms (SNPs) for analyzing African, European, and East Asian ancestries. In the current study, we gathered a high-coverage reference database of 110 populations (10,350 individuals) from across the globe. The discrimination power of the panel was re-evaluated using four continental ancestry groups (as well as Indigenous Americans). We observed that all the 27 SNPs demonstrated stratified population specificity leading to a striking ancestral discrimination. Five markers (rs728404, rs7170869, rs2470102, rs1448485, and rs4789193) showed differences (δ > 0.3) in the frequency profiles between East Asian and Indigenous American populations. Ancestry components of all involved populations were accurately accessed compared with those from previous genome-wide analyses, thereafter achieved broadly population separation. Thus, our ancestral inference panel of a small number of highly informative SNPs in combination with a large-scale reference database provides a high-resolution in estimating ancestry compositions and distinguishing individual origins. We propose extensive usage in biomedical studies and forensics.

Role of the Fibrinogen Degradation Products and D-Dimer in the Differential Diagnosis of Pulmonary Tuberculosis and Community-Acquired Pneumonia.

BACKGROUND: Differential diagnosis between pulmonary tuberculosis (TB) and community acquired pneumonia (CAP) is often difficult. Pulmonary TB could induce a systemic hypercoagulable state. The present study aims to investigate whether fibrinogen degradation products (FDP) and D-dimer play a diagnostic role for pulmonary TB. METHODS: We retrospectively analyzed the clinical and laboratory characteristics of 192 patients with activated pulmonary TB and 110 patients with CAP. The serum levels of FDP and D-dimer were detected and the diagnostic ability was evaluated. RESULTS: The serum levels of FDP and D-dimer were significantly higher in patients with pulmonary TB compared to CAP (both p < 0.05). ROC curve analyses showed that the diagnostic value of FDP in pulmonary TB was noticeably higher than that of D-dimer (p = 0.0197). Combined detection of FDP and D-dimer may slightly improve the sensitivity of diagnosis for pulmonary TB from CAP. However, the AUC showed no significant differences from FDP alone (p = 0.416). CONCLUSIONS: The serum level of FDP and D-dimer are useful laboratory markers that can be used to distinguish patients with pulmonary TB from patients with CAP.

Marek's disease virus type 1 encoded analog of miR-155 promotes proliferation of chicken embryo fibroblast and DF-1 cells by targeting hnRNPAB.

Marek's disease virus type 1 (MDV-1) is a representative oncogenic Alpha herpesvirus that causes an immunosuppressive and neoplastic lymphoproliferative avian disease, namely Marek's disease (MD). The rapid-onset T-cell lymphoma in chickens induced by MDV-1 has been historically regarded as an ideal natural model for herpesvirus-related cancer research. As a viral analog of cellular miR-155, the MDV-1-encoded miR-M4-5p has been shown to be crucial for the virally-induced MD tumorigenesis. Our previous studies demonstrated that miR-M4-5p induces an over-expression of oncogene c-Myc by targeting LTBP1 and suppressing the TGF-ß signaling pathway during MDV-1 infection. We have now further identified the chicken heterogeneous nuclear ribonucleoprotein AB (hnRNPAB) as a new cellular biological target for miR-M4-5p. Suppression of hnRNPAB expression mediated by miR-M4-5p promotes the proliferation, but not the apoptosis, of both primary chicken embryo fibroblasts (CEFs) and transformed chicken fibroblast DF-1 cell line. HnRNPAB is a member of the hnRNP family of proteins that play important roles in normal biological processes as well as cancer development. Our data suggests that the recognition and down-regulation of hnRNPAB by miR-M4-5p may be one of the important strategies for MDV-1 to trigger the development of MD lymphomas.

Antiproliferative effect of the HSP90 inhibitor NVP-AUY922 is determined by the expression of PTEN in esophageal cancer.

Heat shock protein 90 (HSP90), a molecular chaperone, has provoked great interest as a promising molecular target for cancer treatment, due to its involvement in regulating the conformation, stability and functions of key oncogenic proteins. At present, a variety of chemical compounds targeting HSP90 have been developed and have shown convincing anti-neoplastic activity in various preclinical tumor models. The aim of our study was to evaluate the antitumor effects of a novel HSP90 inhibitor, NVP-AUY922, in esophageal squamous cancer cells (ESCC). Four ESCC cell lines (TE-1, TE-4, TE-8, TE-10) were examined. NVP-AUY922 potently inhibited the proliferation of ESCC, particularly in PTEN-null TE-4 cells with a 2-3 times lower IC50 than the other three cell lines. Western blot analysis showed that PTEN-null TE-4 cells exhibited higher AKT and ERK activity, which contribute to cell proliferation and survival. NVP-AUY922 significantly suppressed the activity of AKT and ERK in TE-4 but not in PTEN-proficient TE-10 cells. Genetic modification experiments demonstrated that the sensitivity to NVP-AUY922 was decreased by exogenous transduction of PTEN in TE-4 and increased by silencing PTEN expression in intact PTEN-expressing TE-10, suggesting that the expression of PTEN may be associated with cell sensitivity in HSP90 inhibition. Furthermore, the enhanced activity of AKT in PTEN-silenced TE-10 was more easily suppressed by NVP-AUY922. Collectively, NVP-AUY922 exhibits a strong antiproliferative effect, revealing its potential as a novel therapeutic alternative to current ESCC treatment. The effect may be improved further by impeding PTEN expression.

Esophageal cancer exhibits resistance to a novel IGF-1R inhibitor NVP-AEW541 with maintained RAS-MAPK activity.

AIM: To assess the effects of a novel type 1 insulin-like growth factor receptor (IGF-1R) inhibitor, NVP-AEW541, on cell proliferation and signal transduction of esophageal cancer. MATERIALS AND METHODS: Cell proliferation assay and western blot were conducted to assess the antitumor effects of NVP-AEW541. Genetic modification of RAS by expression vector was applied for overexpression of mutant RAS. RESULTS: More than 2 µmol/l of NVP-AEW541 was required to effectively inhibit the proliferation of esophageal cancer. NVP-AEW541 potently blocked the activation of IGF-1R and protein kinase B (PKB, also known as AKT), but not of mitogen-activated protein kinase kinase (MEK) and extracellular-signal-regulated kinases (ERK). Active RAS was not reduced by NVP-AEW541 in esophageal cancer cells TE-1, suggesting that insensitivity of esophageal cancer to NVP-AEW541 is due to the maintained RAS-MAPK activity, which did not arise from RAS mutation. Moreover, the transduction of mutant RAS reduced the sensitivity of TE-1 cells to NVP-AEW541. CONCLUSION: Stimulation of RAS-MAPK pathway is associated with resistance to NVP-AEW541 in esophageal cancer. Combining NVP-AEW541 with inhibitors/antibodies against RAS-MAPK signaling molecules might be more effective for use against esophageal cancer.

Oral administration of FAK inhibitor TAE226 inhibits the progression of peritoneal dissemination of colorectal cancer.

Peritoneal dissemination is one of the most terrible types of colorectal cancer progression. Focal adhesion kinase (FAK) plays a crucial role in the biological processes of cancer, such as cell attachment, migration, proliferation and survival, all of which are essential for the progression of peritoneal dissemination. Since we and other groups have reported that the inhibition of FAK activity exhibited a potent anticancer effect in several cancer models, we hypothesized that TAE226, a novel ATP-competitive tyrosine kinase inhibitor designed to target FAK, can prevent the occurrence and progression of peritoneal dissemination. In vitro, TAE226 greatly inhibited the proliferation and migration of HCT116 colon cancer cells, while their adhesion on the matrix surface was minimally inhibited when FAK activity and expression was suppressed by TAE226 and siRNA. In vivo, when HCT116 cells were intraperitoneally inoculated in mice, the cells could attach to the peritoneum and begin to grow within 24 h regardless of the pretreatment of cells with TAE226 or FAK-siRNA, suggesting that FAK is not essential, at least for the initial integrin-matrix contact. Interestingly, the treatment of mice before and after inoculation significantly suppressed cell attachment to the peritoneum. Furthermore, oral administration of TAE226 greatly reduced the size of disseminated tumors and prolonged survival in tumor-bearing mice. Taken together, a possible strategy for inhibiting peritoneal dissemination by targeting FAK with TAE226 appears to be applicable through anti-proliferative and anti-invasion/anti-migration mechanisms.

Molecular characterization and functional analysis of Cashmere goat mammalian target of rapamycin.

The mammalian target of rapamycin (mTOR) is an evolutionarily conserved protein kinase that belongs to the phosphatidylinositol kinase-related kinase family. We describe our molecular characterization of mTOR and its function (GenBank accession HM114224) in Cashmere goat (Capra hircus). The goat mTOR complementary DNA is 8617 bp, comprising an open reading frame of 7650 bp--corresponding to a polypeptide of 2549 amino acids--and a 909 bp 3' untranslated region with a polyA tract and a polyadenylation signal at nucleotides 8575-8580. In a bioinformatics analysis, goat mTOR has typical sites of activity and domains. mTOR mRNA was measured in brain, heart, testis, liver, spleen, kidney, and lung by real-time polymerase chain reaction, and the expression of mTOR in fetal fibroblasts was detected by western blot. The viability of fetal fibroblasts was inhibited on treatment with CCI-779, a specific inhibitor of mTOR. Our data supplied evidence that the transcription of mTOR was detected in the seven tissues in Cashmere goat, and mTOR protein was translated in fetal fibroblasts. The proliferation of fetal fibroblasts decreases on inhibition of mTOR.

Autophagy: Can it become a potential therapeutic target?

Autophagy is a cellular lysosomal degradation pathway involved in proteins and organelles recycling for promoting cell survival, development and homeostasis. It is a multistep process and genetic studies have identified many proteins that participate in autophagosome formation and fusion with lysosomes, and various signaling factors that associate with the regulation of autophagy. In general, autophagy acts as a cell protector and its dysfunction is correlated with diverse pathologies, such as neurodegeneration, liver, heart and muscle diseases, cancer, inflammation and ageing. However, its role in cell death increases the complexity of the autophagic degradation system. A broad understanding of autophagy, ranging from detailed processes, including induction, formation and degradation, to function in physiology and pathology, revealed by accumulating studies, may be helpful for formulating therapeutic strategies for autophagy-associated human diseases.

IGF-IR and its inhibitors in gastrointestinal carcinomas (Review).

The type I insulin-like growth factor receptor (IGF-IR) and its associated signaling system play a significant role in tumorigenesis, tumor survival and progression, and cancer therapeutic resistance, and thus has provoked great interest as a promising target for cancer treatment. In this report we present the role of IGF-IR in gastrointestinal carcinomas whose pathology has been identified as tightly correlated with an abnormal expression and activation of IGF-IR. Reported data from experimental studies suggest the feasibility of targeted IGF-IR therapy in gastrointestinal carcinomas. Many types of inhibitors against IGF-IR have been developed. Inhibitors with anti-IGF-IR monoclonal antibodies and tyrosine kinase inhibitors currently undergoing preclinical and clinical evolution are also reviewed.

Progress in researches about focal adhesion kinase in gastrointestinal tract.

Focal adhesion kinase (FAK) is a 125-kDa non-receptor protein tyrosine. Growth factors or the clustering of integrins facilitate the rapid phosphorylation of FAK at Tyr-397 and this in turn recruits Src-family protein tyrosine kinases, resulting in the phosphorylation of Tyr-576 and Tyr-577 in the FAK activation loop and full catalytic FAK activation. FAK plays a critical role in the biological processes of normal and cancer cells including the gastrointestinal tract. FAK also plays an important role in the restitution, cell survival and apoptosis and carcinogenesis of the gastrointestinal tract. FAK is over-expressed in cancer cells and its over-expression and elevated activities are associated with motility and invasion of cancer cells. FAK has been proposed as a potential target in cancer therapy. Small molecule inhibitors effectively inhibit the kinase activity of FAK and show a potent inhibitory effect for the proliferation and migration of tumor cells, indicating a high potential for application in cancer therapy.

Reconstruction of a chicken BF2 protein complex and identification of binding nonamer peptides derived from avian influenza virus hemagglutinin.

In order to reconstruct the system for identification of short antigenic peptides, the chicken BF2 gene of Chinese Sanhuang (SH) chicken line was linked to the beta(2)m gene via (G4S)3, a linker encoding a 15-amino acid glycine-rich peptide, by splicing overlap extension PCR (SOE-PCR). The MBP-BF2-(G4S)3-beta(2)m fusion protein was expressed and purified in a pMAL-p2X/E. coli TB1 system. The purified MBP-BF2-(G4S)3-beta(2)m protein was cleaved by Factor Xa protease, and further purified by DEAE-Sepharose chromatography. The conformation of the BF2-(G4S)3-beta(2)m protein was determined by circular dichroism (CD). In addition, the refolded BF2-(G4S)3-beta2m protein was used to bind three predicted nonameric peptides derived from the hemagglutinins of the avian influenza virus (AIV) H5N1 and H9N2 subtypes. The BF2-(G4S)3-beta2m-associated peptides were detected by mass spectrometry. The molecular weights and amino acid sequences of the peptides were confirmed by primary and tandem mass spectrometry analysis, respectively. The results indicate that the secondary structures and predicted three-dimensional crystal structure of BF2-(G4S)3-beta(2)m are similar to those of the monomers of chicken BF2 and beta(2)m. The BF2-(G4S)3-beta(2)m protein could bind two of the three predicted nonamer peptides derived from AIV hemagglutinin. The experimental system demonstrated that the reconstructed BF2-(G4S)3-beta(2)m protein complex can be used to identify nonamer peptides, including T-cell epitopes in chicken.

[Cloning and construction of nucleic acid vaccine of FABP gene cDNA from Echinococcus granulosus].

Specific primers were designed according to published nucleotide sequence of FABP (fatty acid binding protein) gene in the GenBank database. The kozak sequence (CCACC) was introduced at the upstream of initiator. The total RNA was extracted from protoscoleces of Echinococcus granulosus (Inner Mongol isolate). The FABP gene cDNA fragment was amplified by RT-PCR and cloned into pMD19-T vector for sequencing and analyzing. The cloned FABP gene cDNA was with 402bp. The ORF encoded 133 amino acids. The amplified cDNA fragment was subcloned into pCDNA3.1 (+) vector. The results showed that the nucleic acid vaccine candidate pcDNA-FABP-NM has been constructed.

Secondary structure and 3D homology modeling of grass carp (Ctenopharyngodon idellus) major histocompatibility complex class I molecules.

No information to date is available on the structure of fish major histocompatibility complex (MHC) class I and beta2-microglobulin (beta2m) proteins. In the present study, grass carp (Ctenopharyngodon idellus) MHC class I (Ctid-MHC I) and beta(2)-microglobulin (Ctid-beta2m) genes were expressed as soluble maltose binding protein (MBP)-proteins and purified in a pMAL-p2X/Escherichia coli TB1 system. The expressed proteins were purified on amylase affinity columns followed by DEAE-Sepharose. The purified products were identified by Western blotting with anti-MBP polyclonal antibodies. The MBP-Ctid-MHC I and MBP-Ctid-beta2m were cleaved separately with Factor Xa, mixed together and purified on DEAE-Sepharose. The secondary structures were analyzed by circular dichroism (CD) spectrophotometry. The three-dimensional (3D) structure of their peptide-binding domain (PBD) was modeled based sequence homology. The sequence lengths of the alpha-helix, beta-sheet, turn, and random coil in the Ctid-MHC I protein were 79aa, 75aa, 20aa, and 99aa, respectively. In the 97aa of Ctid-beta2m, the contents of the alpha-helix, beta-sheet, turn, and random coil were 0aa, 41aa, 12aa, and 44aa, respectively. The Ctid-beta2m protein displayed a typical beta-sheet. Homology modeling of the Ctid-MHC I and Ctid-beta2m proteins demonstrated similarities with the structure of human MHC class I proteins.

Characterisation of grass carp (Ctenopharyngodon idellus) MHC class I domain lineages.

In order to characterise grass carp MHC class I (Ctid-MHC I) sequences, 26 Ctid-MHC I genes were cloned from 12 individuals and their alpha domain lineages were analysed. Simultaneously, a quantitative reverse transcription-polymerase chain reaction (Q-RT-PCR) assay was developed to detect Ctid-MHC I tissue-specific expression. The results suggested that Ctid-MHC I could be divided into eight lineages (Ctid-NA-Ctid-NH). Based on whether they contained the motif of eight key amino acids (YYRTKWYY), Ctid-MHC I lineages were divided into two groups [Ctid-MHC I (8(+)) and Ctid-MHC I (8(-))]. The expression analysis showed that the Ctid-MHC I locus/loci appeared in the kidney, gill, intestine, heart, spleen, liver, and brain. A GenBank homology BLAST was performed independently with each alpha domain, and Ctid-MHC I alpha1, alpha2, and alpha3 were categorised into two (V and IX), five (II, IV-VII), and four (IV-VII) domain lineages, respectively. Based on the alphabetic labelling system created in our earlier studies, one alpha1 (IX), four alpha2 (IV-VII), and unique alpha3 (V-VII) domain lineages were observed in grass carp and across the teleostean species.

Reconstruction of a swine SLA-I protein complex and determination of binding nonameric peptides derived from the foot-and-mouth disease virus.

No experimental system to date is available to identify viral T-cell epitopes in swine. In order to reconstruct the system for identification of short antigenic peptides, the swine SLA-2 gene was linked to the beta(2)m gene via (G4S)3, a linker encoding a 15-amino acid glycine-rich sequence (G4S)3, using splicing overlap extension-PCR (SOE-PCR). The maltose binding protein (MBP)-SLA-2-(G4S)3-beta(2)m fusion protein was expressed and purified in a pMAL-p2X/Escherichia coli TB1 system. The purified MBP-SLA-2-(G4S)3-beta(2)m protein was cleaved by factor Xa protease, and further purified by DEAE-Sepharose chromatography. The conformation of the SLA-2-(G4S)3-beta(2)m protein was determined by circular dichroism (CD) spectrum. In addition, the refolded SLA-2-(G4S)3-beta(2)m protein was used to bind three nonameric peptides derived from the foot-and-mouth disease virus (FMDV) O subtype VP1. The SLA-2-(G4S)3-beta(2)m-associated peptides were detected by mass spectrometry. The molecular weights and amino acid sequences of the peptides were confirmed by primary and secondary spectra, respectively. The results indicate that the SLA-2-(G4S)3-beta(2)m was 41.6kDa, and its alpha-helix, beta-sheet, turn, and random coil by CD estimation were 78 aa, 149 aa, 67 aa, and 93 aa, respectively. SLA-2-(G4S)3-beta(2)m protein was able to bind the nonameric peptides derived from the FMDV VP1 region: 26-34 (RRQHTDVSF) and 157-165 (RTLPTSFNY). The experimental system demonstrated that the reconstructed SLA-2-(G4S)3-beta(2)m protein complex can be used to identify nonameric peptides, including T-cell epitopes in swine.

Extensive analysis of different allelelic structures of the chicken BF2 and beta2m proteins.

No information is available to date on the different allelelic structures of the chicken MHC class I (BF2) and beta2m proteins. To elucidate the structure, new allelic beta2m and five different BF2 genes were expressed solubly and purified in a pMAL-p2X/E. coli TB1 system. The 2D structure was detected by circular dichroism (CD) spectroscopy, and the 3D structures of their peptide-binding domain (PBD) were analyzed by homology modeling. The sequence lengths of the alpha-helix, beta-sheet, turn, and random coil in the five BF2 proteins were 69-73 aa, 67-72 aa, 35-37 aa, and 94-98 aa, respectively. The new beta2m protein displayed a typical beta-sheet. Homology modeling of the different BF2 and beta2m proteins demonstrated similarities to the structure of human and rat MHC class I proteins. The 3D structure, however, revealed that the BF2 and beta2m structures were unique. The correct refolding of recombinant BF2 and beta2m proteins might be a powerful tool to further detect antigenic peptides.