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Tao Zhu

Publications and source records attributed to Tao Zhu.

At least 19 recordsLinked to original sources
PubMed2025

Genetic effects on chromatin accessibility reveal the molecular mechanisms of complex traits in maize.

Cis-regulatory elements (CREs) are critical for modulating gene expression and phenotypic diversity in maize. While genome-wide association study (GWAS) hits and expression quantitative trait loci (eQTLs) are often enriched in CREs, their molecular mechanisms remain poorly understood. Characterizing CREs within accessible chromatin regions (ACRs) offers a powerful approach to link noncoding variants to chromatin structure alterations and phenotypic variation. Here, we generated ATAC-seq profiles from seedling leaves of 214 maize inbred lines, identifying 82 174 consensus ACRs. Notably, 39.55% of these ACRs exhibited significant population-wide chromatin accessibility variation. By mapping chromatin accessibility quantitative trait loci (caQTLs), we discovered 27 004 loci, including 1398 predicted to disrupt transcription factor (TF)-binding sites. Integration with multi-omics data revealed 7405 caACR-target gene pairs and linked 56 caACRs to GWAS signals for 51 agronomic traits, with significant enrichment in flowering-related pathways. Functional candidates such as ZmZIM30 - putatively regulated by caACRs - emerged as key regulators of flowering time. At the fad7 locus associated with linolenic acid content, allelic variants overlapping a caQTL showed differential chromatin accessibility. Our study provides a high-resolution cis-elements of maize leaves, deciphers the genetic basis of chromatin accessibility variation, and bridges noncoding caQTLs to molecular mechanisms underlying GWAS hits.

Zea mays↗
PubMed2006

Deletion of the intracellular domain of coxsackie and adenovirus receptor (CAR) enhances the expression of itself and boosts the efficiency of current adenovirus-mediated gene therapy in ovarian cancer cell lines in vitro.

The failure of adenovirus-mediated gene therapy often derives from the absence of coxsackie and adenovirus receptor (CAR) expression in target cells. We hypothesize that the slight up-regulation of CAR expression might boost the effect of adenovirus-mediated gene therapy in ovarian cancer. To test this hypothesis, we transfected full-length and intracellular-domain-deleted (tailless) CAR plasmids into CAR-deficient ovarian cancer cell line SKOV3. We observed significant elevations of the in vitro killing effect of Adv-TK and oncolytic adenovirus-mediated cytopathic effect (CPE) in transfected sub-clones, and tailless-transfected SKOV3 showed higher CAR expressions than full-length CAR-transfected cells. We conclude that the extracellular domain of CAR is essential for adenovirus-based gene therapy and, furthermore, that its intracellular domain might play an important role in the regulation of its own expression.

Adenoviridae Infections↗
PubMed2006

AlphaCP1 mediates stabilization of hTERT mRNA by autocrine human growth hormone.

We herein demonstrate that autocrine human growth hormone production in human mammary carcinoma cells results in increased telomerase activity as a result of specific up-regulation of telomerase catalytic subunit (human telomerase reverse transcriptase (hTERT)) mRNA and protein. This increase in hTERT gene expression is not due to increased transcriptional activation of the hTERT promoter but is the result of increased stability of hTERT mRNA exerted by CU-rich cis-regulatory sequences present in the 3'-untranslated region of TERT mRNA. Autocrine human growth hormone up-regulates two poly(C)-binding proteins, alphaCP1 and alphaCP2, which bind to these cis-regulatory elements and stabilize hTERT mRNA. We have therefore demonstrated that post-transcriptional modulation of the level of hTERT mRNA is one mechanism for regulation of cellular telomerase activity.

3' Untranslated Regions↗
PubMed2006

HOXB7, a homeodomain protein, is overexpressed in breast cancer and confers epithelial-mesenchymal transition.

Epithelial-mesenchymal transition (EMT) is increasingly recognized as a mechanism whereby cells in primary noninvasive tumors acquire properties essential for migration and invasion. Microarray analyses of microdissected epithelial cells from bone metastasis revealed a HOXB7 overexpression that was 3-fold higher than in primary breast carcinomas and 18-fold higher compared with normal breast. This led us to investigate the role of HOXB7 in neoplastic transformation of breast cells. Expression of HOXB7 in both MCF10A and Madin-Darby canine kidney (MDCK) epithelial cells resulted in the acquisition of both phenotypic and molecular attributes typical of EMT. Loss of epithelial proteins, claudin 1 and claudin 7, mislocalization of claudin 4 and E-cadherin, and the expression of mesenchymal proteins, vimentin and alpha-smooth muscle actin, were observed. MDCK cells expressing HOXB7 exhibited properties of migration and invasion. Unlike MDCK vector-transfected cells, MDCK-HOXB7 cells formed highly vascularized tumors in mice. MDCK-HOXB7 cells overexpressed basic fibroblast growth factor (bFGF), had more active forms of both Ras and RhoA proteins, and displayed higher levels of phosphorylation of p44 and p42 mitogen-activated protein kinase (MAPK; extracellular signal-regulated kinases 1 and 2). Effects initiated by HOXB7 were reversed by specific inhibitors of FGF receptor and the Ras-MAPK pathways. These data provide support for a function for HOXB7 in promoting tumor invasion through activation of Ras/Rho pathway by up-regulating bFGF, a known transcriptional target of HOXB7. Reversal of these effects by HOXB7-specific siRNA further suggested that these effects were mediated by HOXB7. Thus, HOXB7 overexpression caused EMT in epithelial cells, accompanied by acquisition of aggressive properties of tumorigenicity, migration, and invasion.

Animals↗
PubMed2006

RUNX3 is frequently inactivated by dual mechanisms of protein mislocalization and promoter hypermethylation in breast cancer.

A tumor suppressor function has been attributed to RUNX3, a member of the RUNX family of transcription factors. Here, we examined alterations in the expression of three members, RUNX1, RUNX2, and RUNX3, and their interacting partner, CBF-beta, in breast cancer. Among them, RUNX3 was consistently underexpressed in breast cancer cell lines and primary tumors. Fifty percent of the breast cancer cell lines (n = 19) showed hypermethylation at the promoter region and displayed significantly lower levels of RUNX3 mRNA expression (P < 0.0001) and protein (P < 0.001). In primary Singaporean breast cancers, 9 of 44 specimens showed undetectable levels of RUNX3 by immunohistochemistry. In 35 of 44 tumors, however, low levels of RUNX3 protein were present. Remarkably, in each case, protein was mislocalized to the cytoplasm. In primary tumors, hypermethylation of RUNX3 was observed in 23 of 44 cases (52%) and was undetectable in matched adjacent normal breast epithelium. Mislocalization of the protein, with or without methylation, seems to account for RUNX3 inactivation in the vast majority of the tumors. In in vitro and in vivo assays, RUNX3 behaved as a growth suppressor in breast cancer cells. Stable expression of RUNX3 in MDA-MB-231 breast cancer cells led to a more cuboidal phenotype, significantly reduced invasiveness in Matrigel invasion assays, and suppressed tumor formation in immunodeficient mice. This study provides biological and mechanistic insights into RUNX3 as the key member of the family that plays a role in breast cancer. Frequent protein mislocalization and methylation could render RUNX3 a valuable marker for early detection and risk assessment.

Antimetabolites, Antineoplastic↗
PubMed2006

Biodegradation of dibenzofuran by Janibacter terrae strain XJ-1.

The dibenzofuran (DF)-degrading bacterium, Janibacter terrae strain XJ-1, was isolated from sediment from East Lake in Wuhan, China. This strain grows aerobically on DF as the sole source of carbon and energy; it has a doubling time of 12 hours at 30 degrees C; and it almost completely degraded 100 mg/L(-1) DF in 5 days, producing 2,2',3-trihydroxybiphenyl, salicylic acid, gentisic acid, and other metabolites. The dbdA (DF dioxygenase) gene cluster in the strain is almost identical to that on a large plasmid in Terrabacter sp. YK3. Unlike Janibacter sp. strain YY-1, XJ-1 accumulates gentisic acid rather than catechol as a final product of DF degradation.

Actinomycetales↗
PubMed2006

Polyamine analogues down-regulate estrogen receptor alpha expression in human breast cancer cells.

The critical role of polyamines in cell growth has led to the development of a number of agents that interfere with polyamine metabolism including a novel class of polyamine analogues, oligoamines. Here we demonstrate that oligoamines specifically suppress the mRNA and protein expression of estrogen receptor alpha (ERalpha) and ERalpha target genes in ER-positive human breast cancer cell lines, whereas neither ERbeta nor other steroid hormonal receptors are affected by oligoamines. The constitutive expression of a cytomegalovirus promoter-driven exogenous ERalpha in ER-negative MDA-MB-231 human breast cancer cells was not altered by oligoamines, suggesting that oligoamines specifically suppress ERalpha transcription rather than affect mRNA or protein stability. Further analysis demonstrated that oligoamines disrupted the DNA binding activity of Sp1 transcription factor family members to an ERalpha minimal promoter element containing GC/CA-rich boxes. Treatment of MDA-MB-231 cells with the JNK-specific inhibitor SP600125 or expression of the c-Jun dominant negative inhibitor TAM67 blocked the oligoamine-activated JNK/c-Jun pathway and enhanced oligoamine-inhibited ERalpha expression, suggesting that AP-1 is a positive regulator of ERalpha expression and that oligoamine-activated JNK/AP-1 activity may antagonize the down-regulation of ERalpha induced by oligoamines. Taken together, these results suggest a novel antiestrogenic mechanism for specific polyamine analogues in human breast cancer cells.

Breast Neoplasms↗
PubMed2006

Benzoylphenylurea sulfur analogues with potent antitumor activity.

A novel series of BPU analogues were synthesized and evaluated for antitumor activity. In particular, BPU sulfur analogues 6n and 7d were shown to possess up to 10-fold increased potency, when compared to 1 (NSC-639829), against cancer cell lines. 6n was more effective than 1 in causing apoptosis of MCF-7 cells. When compared to other drugs with a similar mechanism of action, 6n retained significant ability to inhibit tubulin assembly, with an IC(50) of 2.1 microM.

Antineoplastic Agents↗
PubMed2006

HFIP-induced structures and assemblies of the peptides from the transmembrane domain 4 of membrane protein Nramp1.

Membrane protein Nramp1 (natural resistance-associated macrophage protein 1) is a pH-dependent divalent metal cation transporter that regulates macrophage activation in infectious and autoimmune diseases. A naturally occurring glycine to aspartic acid substitution at position 169 (G169D) within the transmembrane domain 4 (TM4) of Nramp1 makes mice susceptible to Leishmania donovani, Salmonella typhimurium, and Mycobacterium bovis. Here we present a structural and self-assembling study on two synthetic 24-residue peptides, corresponding to TM4 of mouse Nramp1 and its G169D mutant, respectively, in 1,1,1,3,3,3-hexafluoroisopropanol-d(2) (HFIP-d(2)) aqueous solution by nuclear magnetic resonance (NMR) spectroscopy. The results show that amphipathic alpha-helical structures are formed from residue Ile173 to Tyr187 for the wild-type peptide and from Trp168 to Tyr187 for the G169D mutant, respectively. The segment of the N-terminus from Leu167 to Leu172 is poorly structured for the wild-type peptide, whereas it is well defined for the G169D mutant. Both peptides aggregate to form a tetramer and the monomeric peptides in peptide bundles are structurally and orientationally similar. The intermolecular interactions in assemblies could be stronger in the C-terminal regions related to residues Phe180-Leu184 than those in the central helical segments for both peptides. The G169D mutation may change the size of the opening on the termini of assembly.

Amino Acid Sequence↗
PubMed2006

Construction and characterization of a rock-cluster-based EST analysis pipeline.

Open access to vast amount of expression sequence tags (ESTs) data in the public databases has provided a powerful platform for gene identification, gene expression studies and comparative/functional genomic studies. To facilitate management of large-scale EST data, high performance cluster and analysis softwares, especially parallel softwares, are fundamentally essential. We reported herein a convenient approach to construct a high performance computating (HPC) cluster based on popular Rocks and a perl-scripted analysis pipeline for EST pre-processing, clustering, assembling and annotation and any other desired analysis modules through parallel computing. We tested the system using different datasets on increasing nodes. Our present results showed that the cluster and pipeline accelerate the EST analysis without artificial interference.

Cluster Analysis↗
PubMed2006

[Cannabinoid receptor 1 expression and pathological changes in rat hippocampus after deprivation of rapid eye movement sleep].

OBJECTIVE: To observe the expression of cannabinoid receptor 1 (CB1R) mRNA and pathological changes in rat hippocampus after deprivation of rapid eye movement (REM) sleep. METHODS: Totally 42 Sprague-Dawley male rats were randomly divided into cage control (CC), tank control (TC) and the sleep deprivation groups (SD). The SD and TC rats were sacrificed at the end of 1 d, 3 d and 5 d sleep deprivation periods, respectively. The modified multiple platform methods were established for the REM sleep deprivation. CB1R mRNA was measured by reverse transcription-polymerase chain reaction (RT-PCR). The hippocampus sections of different stages were observed with electron microscope. RESULT: In SD 1 d group, the expression of CB1R mRNA was significantly increased compared with the CC, TC, SD 3 d and SD 5 d groups (P <0.05) while in SD 3 d group it was reduced. The expression of CB1R mRNA of SD 5 d group was significantly higher than that of the SD 3 d group (P <0.05). Neuron apoptosis was found in SD 3 d and SD 5 d groups. CONCLUSION: Sleep deprivation can cause brain injury with the changes of CB1R mRNA expression.

Animals↗
PubMed2006

Down-regulation of MT1-MMP expression suppresses tumor cell invasion in metastatic human SW626 ovarian cancer cells.

Membrane-type 1 matrix metalloproteinase (MT1-MMP/MMP-14) is a key enzyme involved in degradation of extracellular matrix (ECM) and various surface-associated proteins that control cell growth, differentiation and survival, plays crucial roles in molecular carcinogenesis, tumor cell growth, invasion, and angiogenesis. We tested the inhibitory effect of antisense MT1-MMP on the ability of metastatic human ovarian carcinoma cell line SW626 in proliferation and invasion. RT-PCR was used to amplify MT1-MMP cDNA fragments with two different restriction sites at its 5'-end. Antisense MT1-MMP cloned in eukaryotic expression vector pMMP14as was transfected into SW626 cells. MT1-MMP protein expression, activities of MMP-2 and MMP-9, changes of cell proliferation, and cell invasion ability were detected by Western blot, optimized gelatin zymography, MTT assay and matrigel in vitro invasion assay, respectively. After 48 h transfection, decreased expression of endogenous MT1-MMP protein was detected in pMMP14as-transfected SW626 cells and showed significantly lower proliferation level when compared with control cells. The activation of proMMP-2 was inhibited markedly, and the mean percentage of invasive cells was 63.30+/-5.80% in pMMP14as-transfected cells, which was less than that (97.60+/-7.50%) in control cells (P<0.05). Both cell proliferation and invasion in SW626 cells were inhibited effectively by antisense MT1-MMP transfection, suggesting that MT1-MMP may be a proper target molecule for anti-invasion therapy for human ovarian cancers.

Blotting, Western↗
PubMed2006

[Expression and clinical significance of Pin1 and Cyclin D1 in cervical cancer cell lines and cervical epithelial tissues].

BACKGROUND & OBJECTIVE: Peptidyl-prolyl cis/trans isomerase Pin1 is prevalently overexpressed in human cancers. Up-regulation of Pin1 elevates the expression of Cyclin D1, and plays an important role in tumorigenesis and tumor progression. This study was to investigate the expression and clinical significance of Pin1 and Cyclin D1 in cervical cancer cell lines and cervical epithelial tissues. METHODS: The expression of Pin1 and Cyclin D1 in cervical cancer cell lines HeLa, SiHa, C33a and Caski were detected by reverse transcription-polymerase chain reaction (RT-PCR) and Western blot. Their expression in 88 samples of cervical tissues, including 10 samples of normal cervix, 21 samples of cervical intraepithelial neoplasia (CIN), and 57 samples of invasive cervical cancer, were detected by immunohistochemistry. RESULTS: The mRNA and protein levels of Pin1 were significantly higher in HeLa, SiHa, C33a, and Caski cells than in normal cervical epithelial tissues (P<0.05). The expression of Pin1 increased progressively along with the disease process from normal cervix to CIN, and to invasive cervical cancer (0%, 47.62%, 64.91%, P<0.05). Pin1 expression had no relation to disease stage (FIGO), pathologic grade, and pelvic lymph node metastasis status (P>0.05). The positive rate of Pin1 was significantly higher in cervical adenocarcinoma than in cervical squamous cell carcinoma (100% vs. 60.0%, P<0.05). In cervical cancer tissues, the overexpression of Pin1 was positively correlated to that of Cyclin D1 (P<0.05). CONCLUSIONS: Pin1 is overexpressed in HeLa, SiHa, C33a and Caski cell lines as well as in cervical cancer tissues. The overexpression of Pin1 is closely related to Cyclin D1 expression in cervical cancer. The aberrant expression of Pin1 and Cyclin D1 might contribute to tumorigenesis of cervical cancer.

Adenocarcinoma↗
PubMed2006

[Fluid management in orthotopic liver transplantation].

OBJECTIVE: To investigate the influential factors of fluid management during orthotopic liver transplantation surgery. METHODS: Ninety-six patients scheduled for orthotopic liver transplantation were divided into two groups according to the liver function: the decompensatory group (Child-Pugh score C, n=50) and the compensatory group (Child-Pugh score A or B, n=46). According to the intraoperative bleeding amount, the compensatory group was further divided into subgroup A (< 2,000 ml) and subgroup B (> or = 2,000 ml). Plasma albumin concentration and the parameters of blood coagulation were measured before and after the surgery. The intraoperative bleeding amount and the amount of the blood products infused were recorded. RESULTS: Before the surgery, prothrombin time (PT) and activated partial thromboplastin time (APTT) were significantly longer in decompensatory group than in compensatory group (both P<0.05); blood platelets (PLT) and fibrinogen were significantly lower in decompensatory group than in compensatory group (both P<0.05). After the surgery, there were no significant differences in PT, APTT, PLT, and fibrinogen between the two groups (all P>0.05). The amounts of the blood products infused intraoperatively in subgroup A were significantly lower than those in the decompensatory group (all P<0.05). There was no significant difference in the amount of the infused blood products between the subgroup B and decompensatory group (all P>0.05). CONCLUSION: During orthotopic liver transplantation surgery, patients with decompensatory liver function, or those who suffered large amounts of intraoperative bleeding, need infusion of larger amount of blood products.

Adolescent↗
PubMed2006

[Short hairpin RNA silences Pin1 and affects proliferation and apoptosis in HeLa cell line].

OBJECTIVE: To study the effect of short hairpin RNA (shRNA) on the expression of Pin1 mRNA and protein and its influence on the proliferation and apoptosis in HeLa cell lines. METHODS: The recombinant plasmid pSIREN-Pin1 expressing Pin1-targeted shRNA was constructed and then transfected into cervical cancer cell lines by lipofectamine (HeLa/p-shRNA), the control vector pSIREN-Con (HeLa/p-Con) and culture media (HeLa) as control, respectively. The Pin1 mRNA and protein expression were detected by RT-PCR and immunoblotting. The proliferation of cells after transfection was detected by methyl thiazolyl tetrazolium (MTT) and colony formation in soft agar. Flow cytometry (FCM) was used to test the apoptosis of cells marked with fluorescein isothiocyanate (FITC)-annexin V. RESULTS: After transfected with pSIREN-Pin1 for 48 h, the expression of Pin1 mRNA and protein in HeLa cells were 0.19 +/- 0.05 and 0.33 +/- 0.14 respectively. Compared with HeLa/p-Con cells (0.84 +/- 0.16, 0.79 +/- 0.17) and HeLa cells (0.89 +/- 0.11, 0.81 +/- 0.15), the difference was significant respectively (P < 0.05). The proliferation was suppressed significantly in HeLa/p-shRNA cells. The colony ratios are as follows: HeLa/p-shRNA, (12 +/- 3)%; HeLa/p-Con, (20 +/- 5)%; HeLa, (24 +/- 4)% (P < 0.05). The apoptosis ratio was (24.3 +/- 5.7)% in HeLa/p-shRNA cells. It was significantly higher than that in HeLa/p-Con cells (5.0 +/- 1.4)% and HeLa cells (1.8 +/- 0.4)% (P < 0.05). CONCLUSIONS: RNA interference through Pin1-targeted shRNA can effectively inhibit the expression of target gene, and might be potentially useful in gene therapy of Pin1 related cervical cancers. Silencing Pin1 gene can suppress the proliferation and promote the apoptosis in HeLa cells.

Apoptosis↗