Chaoneng Ji

Methionine synthase A2756G polymorphism and cancer risk: a meta-analysis.

Polymorphisms in methionine synthase (MTR) gene may be involved in carcinogenesis by affecting DNA methylation. However, association studies on MTR A2756G polymorphism in cancers have reported conflicting results. Therefore we performed a meta-analysis to better assess the associations. A total of 24 896 cancer patients and 33 862 controls from 52 articles for MTR A2756G were investigated. Overall, individuals carrying MTR 2756GG genotype had a subtly reduced cancer risk under a recessive genetic model (odds ratio (OR), 0.92; P=0.053; 95% confidence interval (95% CI), 0.84–1.00; I2=0.0%; Pheterogeneity=0.61). In the subgroup analyses by ethnicity, 2756GG was associated with a significantly reduced cancer risk in European populations (OR, 0.83; P=0.001; 95% CI, 0.74–0.93; I2=0.0%; Pheterogeneity=0.99). However, in Asian populations, a significantly elevated association between 2756GG genotype and cancer risk was observed (OR, 1.33; P=0.012; 95% CI, 1.06–1.65; I2=0.0%; Pheterogeneity=0.50). In studies stratified by tumor site, there was a significantly reduced risk of acute lymphoblastic leukemia (ALL) (OR, 0.54; P=0.049; 95% CI, 0.29–1.00; I2=10.7%; Pheterogeneity=0.33) and colorectal cancer (OR, 0.63; P=0.004; 95% CI, 0.47–0.87; I2=0.0%; Pheterogeneity=0.73) in European populations. Our study indicates that MTR A2756G polymorphism is a candidate gene polymorphism for cancer susceptibility regardless of environmental factors. Large-scale, well-designed, and population-based studies are required to further investigate gene–gene and gene–environment interactions on MTR A2756G polymorphism and tissue-specific cancer risk in an ethnicity-specific population.

Polymorphisms of tumor necrosis factor-alpha are associated with increased susceptibility to gastric cancer: a meta-analysis

AbstractWe conducted a meta-analysis to assess the association between tumor necrosis factor-alpha (TNF-alpha) gene TNFA-308 (G > A) and TNFA-857 (C > T) polymorphisms and gastric cancer (GC) susceptibility. We also performed subgroup analyses based on ethnicity (Caucasian, east Asian, and other populations) and tumor location [noncardia gastric cancer (NCGC)]. There were 3,335 GC patients and 5,286 controls for TNFA-308, and 1,118 GC patients and 1,591 controls for TNFA-857 in our analysis. Overall, allele contrast (A vs. G) of TNFA-308 polymorphism produced significant results in worldwide populations [Pheterogeneity = 0.05, random-effects (RE) odds ratio (OR) 1.19; 95% confidence interval (CI) 1.03–1.37, P = 0.02] and Caucasian populations (Pheterogeneity = 0.15, fixed-effects (FE), OR 1.27; 95% CI 1.11–1.45, P = 0.0005). Similar results were also obtained in recessive models and homozygote contrasts. No significant association was observed in NCGC and east Asian subgroup analysis. T variant of TNFA-857 produced significant results only in allele contrast (Pheterogeneity = 0.38, FE OR 1.17; 95% CI 1.01–1.35, P = 0.04). In conclusion, TNFA-308 locus of TNF-alpha would be a risk factor for GC, especially in Caucasian populations. Besides, TNFA-857 locus may be related to GC risk, which demonstrated changeability of results in different contrasts.

Molecular cloning and characterization of a novel human cAMP response element-binding (CREB) gene (CREB4)

AbstractCyclic adenosine monophosphate (cAMP) response element-binding (CREB) proteins are a family of mammalian transcription activators. We identified a novel human CREB gene (CREB4) that was 1592bp long and encoded a protein of 395 amino acid residues. The protein shared high homology to mouse CREB3 (identity 62%, similarity 72%). The expression pattern of the human CREB4 gene showed transcripts in prostate, brain, pancreas, skeletal muscle, small intestine, testis, leukocyte, and thymus, whereas in heart, lung, liver, kidney, placenta, spleen, ovary, and colon, specific bands of the transcript could not be detected. The CREB4 gene consisted of ten exons and nine introns and was mapped to chromosome 1q21.3 by means of a bioinformatics analysis.

DAXX interacts with phage ΦC31 integrase and inhibits recombination

Phage ΦC31 integrase has potential as a means of inserting therapeutic genes into specific sites in the human genome. However, the possible interactions between ΦC31 integrase and cellular proteins have never been investigated. Using pLexA-ΦC31 integrase as bait, we screened a pB42AD-human fetal brain cDNA library for potential interacting cellular proteins. Among 61 positives isolated from 106 independent clones, 51 contained DAXX C-terminal fragments. The strong interaction between DAXX and ΦC31 was further confirmed by co-immunoprecipitation. Deletion analysis revealed that the fas-binding domain of DAXX is also the region for ΦC31 binding. Hybridization between a ΦC31 integrase peptide array and an HEK293 cell extract revealed that a tetramer, 451RFGK454, in the C-terminus of ΦC31 is responsible for the interaction with DAXX. This tetramer is also necessary for ΦC31 integrase activity as removal of this tetramer resulted in a complete loss of integrase activity. Co-expression of DAXX with ΦC31 integrase in a HEK293-derived ΦC31 integrase activity reporter cell line significantly reduced the ΦC31-mediated recombination rate. Knocking down DAXX with a DAXX-specific duplex RNA resulted in increased recombination efficiency. Therefore, endogenous DAXX may interact with ΦC31 causing a mild inhibition in the integration efficiency. This is the first time that ΦC31 was shown to interact with an important cellular protein and the potential effect of this interaction should be further studied.

An unannotated α/β hydrolase superfamily member, ABHD6 differentially expressed among cancer cell lines

Abhydrolase domain containing (Abhd) gene was a small group belongs to α/β hydrolase superfamily. Known members of this group are all found to be involved in important biochemical processes and related to various diseases. In this paper, we report the tissue distribution, subcellular location and differential distribution among cancer cell lines of Abhd6, one unannotated member of this group.

The Secondary Structure of Calcineurin Regulatory Region and Conformational Change Induced by Calcium/Calmodulin Binding

The protein serine/threonine phosphatase calcineurin (CN) is activated by calmodulin (CaM) in response to intracellular calcium mobilization. A widely accepted model for CN activation involves displacement of the CN autoinhibitory peptide (CN467–486) from the active site upon binding of CaM. However, CN activation requires calcium binding both to the low affinity sites of CNB and to CaM, and previous studies did not dissect the individual contributions of CNB and CaM to displacement of the autoinhibitory peptide from the active site. In this work we have produced separate CN fragments corresponding to the CNA regulatory region (CNRR381–521, residues 381–521), the CNA catalytic domain truncated at residue 341, and the CNA-CNB heterodimer with CNA truncated at residue 380 immediately after the CNB binding helix. We show that the separately expressed regulatory region retains its ability to inhibit CN phosphatase activity of the truncated CN341 and CN380 and that the inhibition can be reversed by calcium/CaM binding. Tryptophan fluorescence quenching measurements further indicate that the isolated regulatory region inhibits CN activity by occluding the catalytic site and that CaM binding exposes the catalytic site. The results provide new support for a model in which calcium binding to CNB enables CaM binding to the CNA regulatory region, and CaM binding then instructs an activating conformational change of the regulatory region that does not depend further on CNB. Moreover, the secondary structural content of the CNRR381–521 was tentatively addressed by Fourier transform infrared spectroscopy. The results indicate that the secondary structure of CNRR381–521 fragment is predominantly random coil, but with significant amount of β-strand and α-helix structures.

A global genomic view of MIF knockdown-mediated cell cycle arrest.

Macrophage immigration inhibitory factor (MIF) is a ubiquitously expressed proinflammatory mediator that has also been implicated in cell growth, cell cycle and carcinogenesis. In this study, we demonstrate siRNA-mediated knockdown of MIF results in G0/G1 cell cycle arrest in HEK293 cells. To elucidate the molecular mechanism of cell cycle perturbation following MIF knockdown, we employed microarray to investigate the genome-wide expression profile in MIF-deficient cells and normal cells. Quantitative real-time PCR were used to confirm the differential expression patterns of ~50 transcripts involved in cell cycle and signaling identified by microarray. The dynamic model of MIF-dependent signaling pathways linked to cell cycle machinery were constructed through analyzing gene expression data in the context of known biological pathways. The results demonstrate that knockdown of MIF could inhibit G1/S transition through inhibition of MAPK, PI3K/Akt, NF-κB, c-Myc-dependent pathway and activation of TGF-β, p53-dependent pathway. Meanwhile, inhibition of E2F-, NFκB, c-Myc, and Ap-1-mediated transcription and stimulation of p53 and FoxO4 transcriptional activity will lead to differential expression of cell cycle regulators and subsequent cell cycle arrest in G0/G1 phase in MIF-knockdown cells. This study provides novel insights into the pleiotropic activities of endogenous MIF, especially its essential and crucial role in cell proliferation and the cell cycle.

UBE1DC1, an ubiquitin-activating enzyme, activates two different ubiquitin-like proteins.

Ubiquitin and ubiquitin‐like proteins are known to be covalently conjugated to a variety of cellular substrates via a three‐step enzymatic pathway. These modifications lead to the degradation of substrates or change its functional status. The ubiquitin‐activating enzyme (E1) plays a key role in the first step of ubiquitination pathway to activate ubiquitin or ubiquitin‐like proteins. Ubiquitin‐activating enzyme E1‐domain containing 1 (UBE1DC1) had been proved to activate an ubiquitin‐like protein, ubiquitin‐fold modifier 1 (Ufm1), by forming a high‐energy thioester bond. In this report, UBE1DC1 is proved to activate another ubiquitin‐like protein, SUMO2, besides Ufm1, both in vitro and in vivo by immunological analysis. It indicated that UBE1DC1 could activate two different ubiquitin‐like proteins, SUMO2 and Ufm1, which have no significant similarity with each other. Subcellular localization in AD293 cells revealed that UBE1DC1 was especially distributed in the cytoplasm; whereas UBE1DC1 was mainly distributed in the nucleus when was cotransfected with SUMO2. It presumed that UBE1DC1 greatly activated SUMO2 in the nucleus or transferred activated‐SUMO2 to nucleus after it conjugated SUMO2 in the cytoplasm. J. Cell. Biochem. 104: 2324–2334, 2008.

A novel splice variant of the cell adhesion molecule contactin 4 (CNTN4) is mainly expressed in human brain

AbstractAxon-associated cell adhesion molecules (AxCAMs) of the immunoglobulin superfamily play important roles in the formation, maintenance, and plasticity of functional neuronal networks. Contactin4 (CNTN4, BIG-2) is a member of the TAG-1/F3 subgroup of AxCAMs. We have cloned a novel splice variant of CNTN4, and term it CNTN4A. The complete nucleotide sequence of CNTN4 is also obtained by combining the insert sequences of two clones, which were isolated when screening the human fetal brain cDNA library with CNTN4A as a probe. CNTN4A protein has an N-terminal cleavable signal peptide, two FNIII-like domains, and a glycosyl phosphatidylinositolanchoring domain. According to the search of the human genome database, CNTN4 was mapped to 3p25–26, a region very close to the breakpoints of the 3p syndrome. Expression analysis of CNTN4A shows that CNTN4A is mainly expressed in brain.

Molecular cloning and characterization of a novel human Rab (Rab2B) gene

AbstractRab proteins are small-molecular-weight guanosine triphosphatases (GTPases) that control vesicular traffic in eukaryotic cells. The small GTPase Rab2 is a resident of pre-Golgi intermediates and is required for protein transport from the endoplasmic reticulum to the Golgi complex. We identified a novel human Rab (Rab2B) gene that was 2312 bp in length and encoded a protein of 216 amino acid residues. The protein shared high homology with mouse Rab2 (identity 83%, similarity 91%). The expression pattern of the human Rab2B gene showed that there is a transcript in kidney, prostate, lung, liver, thymus, colon, pancreas, and skeletal muscle, and low levels in placenta, whereas specific bands of the transcript could not be detected in heart, brain, spleen, testis, ovary, small intestine, and leukocyte. Overexpression has been observed in colon adenocarcinoma CX-1. The Rab2B gene consists of nine exons and eight introns and is mapped to chromosome 14q11.1–14q11.2 by bioinformatics analysis.