Biotin-labeled DNA Probes Research Articles

PARP1 negatively regulates transcription of BLM through its interaction with HSP90AB1 in prostate cancer

BackgroundProstate cancer (PCa) is a prevalent malignant disease affecting a significant number of males globally. Elevated expression of the Bloom’s syndrome protein (BLM) helicase has emerged as a promising cancer biomarker, being associated with the onset and progression of PCa. Nevertheless, the precise molecular mechanisms governing BLM regulation in PCa remain elusive.MethodsThe expression of BLM in human specimens was analyzed using immnohistochemistry (IHC). A 5′-biotin-labeled DNA probe containing the promoter region of BLM was synthesized to pull down BLM promoter-binding proteins. Functional studies were conducted using a range of assays, including CCK-8, EdU incorporation, clone formation, wound scratch, transwell migration, alkaline comet assay, xenograft mouse model, and H&E staining. Mechanistic studies were carried out using various techniques, including streptavidin-agarose-mediated DNA pull-down, mass spectrometry (MS), immunofluorescence (IF), dual luciferase reporter assay system, RT-qPCR, ChIP-qPCR, co-immunoprecipitation (co-IP), and western blot.ResultsThe results revealed significant upregulation of BLM in human PCa tissues, and its overexpression was associated with an unfavorable prognosis in PCa patients. Increased BLM expression showed significant correlations with advanced clinical stage (P = 0.022) and Gleason grade (P = 0.006). In vitro experiments demonstrated that BLM knockdown exerted inhibitory effects on cell proliferation, clone formation, invasion, and migration. Furthermore, PARP1 (poly (ADP-ribose) polymerase 1) was identified as a BLM promoter-binding protein. Further investigations revealed that the downregulation of PARP1 led to increased BLM promoter activity and expression, while the overexpression of PARP1 exerted opposite effects. Through mechanistic studies, we elucidated that the interaction between PARP1 and HSP90AB1 (heat shock protein alpha family class B) enhanced the transcriptional regulation of BLM by counteracting the inhibitory influence of PARP1 on BLM. Furthermore, the combination treatment of olaparib with ML216 demonstrated enhanced inhibitory effects on cell proliferation, clone formation, invasion, and migration. It also induced more severe DNA damage in vitro and exhibited superior inhibitory effects on the proliferation of PC3 xenograft tumors in vivo.ConclusionsThe results of this study underscore the significance of BLM overexpression as a prognostic biomarker for PCa, while also demonstrating the negative regulatory impact of PARP1 on BLM transcription. The concurrent targeting of BLM and PARP1 emerges as a promising therapeutic approach for PCa treatment, holding potential clinical significance.

Glucometer-based electrochemical biosensor for determination of microRNA (let-7a) using magnetic-assisted extraction and supersandwich signal amplification.

A sensitive and portable biosensor is proposed for simple detection of microRNAs based on a supersandwich hybridization signal amplification strategy and a glucometer transducer. The presence of a target microRNA triggers the cascading hybridization chain reaction to create long supersandwich assemblies containing multiple biotin-labelled DNA probes. Then, large amounts of biotin-modified invertase signal molecules can attach to the supersandwich assemblies to generate an amplified signal for the glucometer readout. With such supersandwich format, a single target microRNA can introduce many biotin-invertase signal molecules, resulting in a one-to-multiple amplification effect. Thus, the accurate quantification of microRNAs can be achieved in a simple detection fashion without the requirement of expensive or precise instrumentation. The linear range of the biosensor for microRNA was from 0.05 to 100nM with a detection limit of 48pM. Theproposed biosensor can discriminate the target microRNA from its family members with high selectivity and can be successfully applied to the detection of target microRNA spiked in serum samples with a good recovery (96.0-108.0%). Therefore, the proposed biosensor is expected to provide more information for early and accurate cancer diagnosis.

Detection of Streptavidin Based on Terminal Protection and Cationic Conjugated Polymer-Mediated Fluorescence Resonance Energy Transfer.

In this paper, a fast and simple strategy for sensitive detection of streptavidin (SA) was proposed based on terminal protection of small molecule-linked DNA and cationic conjugated polymer-mediated fluorescence resonance energy transfer (FRET). In principle, we designed a biotin-labelled DNA probe (P1) as the recognitive probe of SA, along with a complementary DNA probe (P2) to form double-stranded DNA (dsDNA) with P1. SYBR Green I (SG I) as a fluorescent dye was further used to specifically bind to dsDNA to emit stronger fluorescence. The cationic poly[(9,9-bis(6′-N,N,N-triethy-lammonium)hexyl) fluorenylene phenylene dibromide] (PFP) acted as the donor to participate in the FRET and transfer energy to the recipient SG I. In the absence of SA, P1 could not hybridize with P2 to form dsDNA and was digested by exonuclease I (Exo I); thus, only a weak FRET signal would be observed. In the presence of SA, biotin could specifically bind to SA, which protected P1 from Exo I cleavage. Then, P1 and P2 were hybridized into dsDNA. Therefore, the addition of SG I and PFP led to obvious FRET signal due to strong electrostatic interactions. Then, SA can be quantitatively detected by monitoring FRET changes. As the whole reagent reaction was carried out in 1.5 mL EP and detected in the colorimetric dish, the operation process of the detection system was relatively simple. The response time for each step was also relatively short. In this detection system, the linear equation was obtained for SA from 0.1 to 20 nM with a low detection limit of 0.068 nM (S/N = 3). In addition, this strategy has also achieved satisfactory results in the application of biological samples, which reveals the application prospect of this method in the future.

Point-of-care detection of 16S rRNA of Staphylococcus aureus based on multiple biotin-labeled DNA probes

A visual method that combines multiple biotin-labeled DNA probes and lateral-flow nucleic acid biosensor was developed to detect Staphylococcus aureus. The 16S rRNA from Staphyloccocus aureus (S. aureus), coupled with multiple biotin-labeled DNA probes, was functionalized in a signal structure for lateral-flow point-of-care detection. The secondary structure of the 16S rRNA was unwound by two specific capture probes modified by Fam and multiple bridge probes, which extended additional sequences for use as initiators. By utilizing the initiators, each target 16S rRNA with multiple DNA probes could tether a number of biotin molecules, so that a large number of streptavidin-labeled gold nanoparticles could be introduced in the lateral flow assay. The images of the lateral flow detection results obtained using a smartphone were transmitted to a computer via Wi-Fi or Bluetooth connection for quantitative processing by ImageJ. The limit of detection was 103 cfu/mL without sample enrichment, and decreased to 0.12 cfu/mL following a 3-h enrichment of samples in growth medium. Notably, this method presented high specificity and applicability for the detection of S. aureus in food samples. In short, the developed visual non-specific operation method is very suitable for point-of-care diagnosis of pathogens in resource-limited countries.

Fluorescence hydrogel array based on interfacial cation exchange amplification for highly sensitive microRNA detection

Despite the great success of fluorescence sensing array application in bioanalysis, the photo-quenching problem accompanied with high surface fluorophore density has become the bottleneck for its further sensitivity improvement. Herein, a fluorescence polyethylene glycol (PEG) hydrogel array was developed for highly sensitive microRNA detection based on interfacial cation exchange amplification coupled with DNA hybridization chain reaction (HCR). The carboxylate PEG hydrogel array was fabricated on glass slide via photo polymerization and modified with miRNA capture probe, target miRNA binding triggered HCR in hydrogel with biotin labelled DNA probes to generate numerous DNA polymer chains where biotinylated CdS QDs were subsequently conjugated with a streptavidin bridge. Interfacial cation exchange amplification was triggered in hydrogel upon the introduction of Ag+ and Rhod-5N, and abundant Cd2+ was released from CdS to bind with Rhod-5N for substantial fluorescence enhancement. The aqueous-like environment of hydrogel eliminated the fluorescence quenching and simplified experiment process by performing cation exchange reaction at interface with direct result. The linear range for model target miRNA-21 was 1 fM to 500 pM with a detection limit of 0.835 fM. Taking advantage of the nonfouling property of PEG hydrogel, direct quantification of miRNA-21 was achieved from crude cancer cell lysates with a detection limit down to 10 equivalent cells. The expressions of circulating miRNA-21 in clinical serum samples were also assessed with comparable results from RT-PCR. The developed hydrogel array provides a universal platform for highly sensitive fluorescence sensing, and would benefit clinical non-invasive disease diagnosis.

Abstract 2096: High sensitivity of cutaneous T-cell lymphoma (CTCL) to CABE, a component of propolis

Abstract Cutaneous T-cell lymphoma (CTCL) is a heterogeneous group of diseases characterized by clonal expansion of malignant T-cells in the skin. In the course of our quest to screen and identify a potent, selective anti-proliferative drug for CTCL, we discovered that caffeic acid benzyl ester (CABE), a natural component of edible plant species found in high concentrations in propolis, showed increased potency for CTCL (IC50 4 μM) in vitro compared to other tumor types such as melanoma (IC50 25 μM), glioma (IC50 25 μM), multiple myeloma (MM) (IC50 70 μM), head and neck squamous cell carcinoma (HNSCC) (IC50 25 μM), ovarian cancer (OC) (IC50 17 μM), breast carcinoma (IC50 43 μM), and Hodgkin's B-cell lymphoma (IC50 33 μM). Cell death in CTCL MJ and HH cell lines was accompanied by increased caspase-3 and poly (ADP-ribose) (PARP) cleavage and annexin V staining. There is growing evidence that CABE and its analogs exert their anticancer activity by modulating expression level of key transcription factors. Here, we evaluated the effects of CABE on the activity of different transcription factors and the expression of total and phosphorylated proteins in MJ cells by use of the transcription factor activation profiling array (TFAPA) and the reverese-phase protein array profiling (RPPA) assays. The activity of 48 transcription factors (TFs) and expression of 225 unique total and phosphorylated proteins could be monitored simultaneously by using a collection of biotin-labeled DNA probes and 225 unique antibodies. TFAPA analysis revealed that 18 TFs (including STAT1, STAT4, and RXR) were up-regulated and 3 TFs (STAT3, STAT5, and SATB1) were down-regulated to a variable extent in cells treated with 10 μM CABE for 5 h as compared to vehicle-treated control. RPPA analysis revealed 41 differentially expressed proteins between vehicle control and cells treated with 10 μM CABE. These can be functionally categorized into functional groups: DNA repair, cell cycle, apoptosis, phosphoinositide 3-kinase (PI3K)/AKT/mTOR, and receptor kinase pathways. Our results suggest that CABE targets multiple signaling pathways in CTCL in vitro, warranting the development of a pre-clinical animal model for the testing of CABE efficacy in vivo. Acknowledgement: These studies were supported in part by the grant from Moleculin, LLC Citation Format: Arumugam Jayakumar, Radjendirane Venugopal, Rafal Zielinski, Aleksandra Rusin, Izabela Fokt, Stanislaw Skora, Xiao Ni, Madeleine Duvic, Waldemar Priebe. High sensitivity of cutaneous T-cell lymphoma (CTCL) to CABE, a component of propolis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2096. doi:10.1158/1538-7445.AM2015-2096

RNA imaging: seeing is believing.

RNA imaging: seeing is believing.

Protein Z/protein Z-dependent protease inhibitor system in loco in human gastric cancer

In gastric cancer, hemostatic system components contribute to cancer progression, as activation of factor X (FX) was observed. The protein Z (PZ)/protein Z-dependent protease inhibitor (ZPI) complex inhibits factor Xa proteolytic activity. The purpose of this study was to determine the distribution of ZPI and PZ in relation to FX, and prothrombin fragment (F1 + 2), a standard marker for blood coagulation activation, in human gastric cancer tissue. ABC procedures and a double staining method employed polyclonal antibodies against PZ, FX, and F1 + 2 and a monoclonal antibody against ZPI. In situ hybridization (ISH) methods employed biotin-labeled 25-nucleotide single-stranded DNA probes directed to either PZ or ZPI mRNAs. FX and components of PZ/ZPI coagulation inhibitory system were observed in cancer cells. F1 + 2 was observed in gastric cancer cells as well. Double staining studies revealed FX/PZ, FX/ZPI, and PZ/ZPI co-localization on gastric cancer cells. ISH studies demonstrated the presence of PZ mRNA and ZPI mRNA in gastric cancer cells indicating induced synthesis of these proteins. The co-localization of PZ/ZPI and FX in gastric cancer cells indicates in loco that these proteins may play a role in anticoagulant events at the tumor tissue.

A Repeat Sequence Causes Competition of ColE1-Type Plasmids

Plasmid pSW200 from Pantoea stewartii contains 41 copies of 15-bp repeats and has a replicon that is homologous to that of ColE1. Although deleting the repeats (pSW207) does not change the copy number and stability of the plasmid. The plasmid becomes unstable and is rapidly lost from the host when a homoplasmid with the repeats (pSW201) is present. Deleting the repeats is found to reduce the transcriptional activity of RNAIp and RNAIIp by about 30%, indicating that the repeats promote the transcription of RNAI and RNAII, and how the RNAI that is synthesized by pSW201 inhibits the replication of pSW207. The immunoblot analysis herein demonstrates that RNA polymerase β subunit and σ70 in the lysate from Escherichia coli MG1655 bind to a biotin-labeled DNA probe that contains the entire sequence of the repeat region. Electrophoretic mobility shift assay also reveals that purified RNA polymerase shifts a DNA probe that contains four copies of the repeats. These results thus obtained reveal that RNA polymerase holoenzyme binds to the repeats. The repeats also exchange RNA polymerase with RNAIp and RNAIIp in vitro, revealing the mechanism by which the transcription is promoted. This investigation elucidates a mechanism by which a plasmid prevents the invasion of an incompatible plasmid and maintains its stability in the host cell during evolution.

Genome Mutation Revealed by Artificial Hybridization between Chrysanthemum yoshinaganthum and Chrysanthemum vestitum Assessed by FISH and GISH

Present study has been done to investigate artificial interspecific crossability between Japanese Chrysanthemum yoshinaganthum (2n=36) and Chinese C. vestitum (2n=54), which were cultured in vitro and in vivo and characterization of their artificial hybrid chromosomes and type of changes assessed by FISH and GISH. GISH was applied by using biotin-labeled total genomic DNA probe of C. vestitum, which were mixed with blocking DNA of C. yoshinaganthum. Approximately 18 yellow-green colored chromosomes of C. vestitum were detected by the probe, approximately 18 yellow-red- mixed colored chromosomes could be common chromosomes of the two species, and nine chromosomes were relatively red of Ch. yoshinaganthum that were not detected by the probe. The expected average of FISH six signals of 5S rDNA sites and ten of 45S rDNA were observed on the chromosomes of three and six hybrid plants, respectively. Multicolor FISH signals showed unexpected average of seven and 14 yellow signals of 5S rDNA sites on seven and thirteen chromosomes simultaneous with ten and 11 red signals of 45S rDNA sites on ten and 11 chromosomes which were detected by the probes respectively. FISH mapping of the 5S rDNA at terminal sites was detected in hybrid chromosomes, for the first time. Yellow-color signals of the telomeres were detected by the biotin-labeled probe of the PCR-amplified telomeric probe in interphase and terminal sites in metaphase. All chromosomes that showed terminal signals except four chromosomes showed subterminal sites of telomeres indicating the presence of translocations.

Co-localization of Protein Z, Protein Z-Dependent protease inhibitor and coagulation factor X in human colon cancer tissue: Implications for coagulation regulation on tumor cells

IntroductionSeveral hemostatic system components, including factor X (FX), contribute to cancer progression. The Protein Z (PZ)/protein Z-dependent protease inhibitor (ZPI) complex directly inhibits factor Xa proteolytic activity. The aim of this study was to determine the antigenic distribution of ZPI and PZ, in relation to FX, as well as indicators of blood coagulation activation (F1+2 and fibrin) in human colon cancer tissue. Materials & methodsStudies were performed on human colon cancer fragments. Immunohistochemical (IHC) ABC procedures and double staining method employed polyclonal antibodies against PZ, FX, F1+2 and monoclonal antibodies against ZPI and fibrin. In-situ hybridization (ISH) methods employed biotin-labeled 25-nucleotide single-stranded DNA probes directed to either FX, PZ or ZPI mRNAs. ResultsExpression of FX, PZ and ZPI in association with colon cancer cells was observed by IHC. Moreover, the presence of both F1+2 and fibrin in association with colon cancer cells was found, which indicates that blood coagulation activation proceeds extravascularly at the tumor site. Furthermore, expression of FX and PZ was visualized in association with endothelial cells. In turn, colon cancer-associated macrophages were characterized by FX , PZ and ZPI presence. The double staining studies revealed strong FX/PZ, FX/ZPI, as well as PZ/ZPI co-localization on colon cancer cells. ISH studies revealed the presence of FX mRNA, PZ mRNA and ZPI mRNA in colon cancer cells indicating induced synthesis of these proteins. ConclusionsThe localization of PZ/ZPI and FX in colon cancer cells indicates that PZ/ZPI may contribute to anticoagulant events at the tumor site. Strong co-localization of PZ/ZPI and FX in cancer cells, and the presence of the mRNAs encoding the proteins, suggests their role in the tumor's biology. However, the presence of F1+2 and fibrin at the colon cancer site also suggests that the regulation of FXa by the PZ/ZPI complex at this site is incomplete.

Protein Z is present in human breast cancer tissue

Thromboembolic complications are common findings in breast cancer patients [1, 2]. Hemostatic system components play a role in tumor progression, independent of their role in hemostasis [1, 2]. Since the report of multifactorial activation of factor X in cancer patients [1], inhibitors which control the activity of this factor have attracted attention. Protein Z (PZ), a vitamin K-dependent plasma nonpeptidase glycoprotein [3, 4], is involved in one mechanism responsible for the direct inhibition of factor Xa. PZ circulates in plasma complexed with PZ-dependent protease inhibitor (ZPI) and enhances the rate of ZPImediated factor Xa inhibition [5, 6]. The presence of ZPI in breast cancer tissue was previously reported [7], while information on PZ in tumor malignant tissue is lacking. The purpose of the present study was to evaluate the localization of PZ (both protein and mRNA) at the primary site of human breast cancer. Tumor fragments were obtained during the surgical treatment of 13 previously untreated breast cancer patients (clinical stage T1-2N0M0). Studies were performed on 4 cases of G2 and 9 cases of G3 invasive ductal carcinomas. Immunohistochemical studies (IHC) were performed (Vectastain Kits, Vector Laboratories, Burlingame, CA, USA) [7] employing a polyclonal antibody against homogeneous, plasma-derived human PZ (prepared in rabbits, and purified from immune sera by protein A-Sepharose chromatography). The antibody did not cross-react with all other purified human plasma vitamin K-dependent proteins including prothrombin, protein C, protein S, factor VII, factor X, and factor IX by ELISA. Controls consisted of omission of the primary antibody from the procedure. The control fragments of normal breast tissues obtained from neoplasm-free surgical margins were processed simultaneously as well. Antigen staining was detected by the dark brown reaction product. A semiquantitative analysis of PZ IHC expression in cancer cells (based on both the percentage of cancer cells with PZ positive staining and the intensity of staining) was performed [7]. Immunoreactive score (IRS) values of 1–4 were interpreted as weak, 5–8 as medium, and 9–12 as strong PZ expression. In situ hybridization (ISH) method employed a biotin-labeled 25-nucleotide single-stranded DNA probe (probe sequence: 50 Biotin-CGTCATACCGCATGTGCA CATGGAC-Biotin 30) specific for PZ mRNA. The probe was synthesized by Sigma-Aldrich, Poznan, Poland. The ISH protocol of R&D Systems (R&D Systems, Minneapolis, MN, USA) was followed. Hybrids were detected with rabbit anti-biotin monoclonal antibodies according to the IHC ABC technique associated with ImmunoMax amplification technique described in detail elsewhere [7]. Negative controls included hybridization without addition of the molecular probe and incubation of slides in a RNase A solution (R&D Systems, Minneapolis, MN, USA) before hybridization. Reaction results appeared as dark brown staining. E. Sierko M. Z. Wojtukiewicz (&) Department of Oncology, Medical University, 12 Ogrodowa St, Bialystok, Poland e-mail: mzwojtukiewicz@gmail.com

Streptavidin-modified magnetic poly(2-hydroxyethyl methacrylate-co-glycidyl methacrylate) microspheres for selective isolation of bacterial DNA

The dispersion copolymerization of 2-hydroxyethyl methacrylate (HEMA) with glycidyl methacrylate (GMA) in a toluene/2-methylpropan-1-ol mixture in the presence of Fe3O4 nanoparticles coated with oleic acid, produced monodisperse magnetic poly(2-hydroxyethyl methacrylate-co-glycidyl methacrylate) (P(HEMA-GMA)) microspheres. Oxirane groups of the microspheres were ammonolyzed and then functionalized with streptavidin using cyanuric chloride. The final product contained 0.67mg of streptavidin per gram of wet magnetic P(HEMA-GMA) microspheres. The microspheres were characterized by elemental analysis, scanning electron microscopy, IR, UV–VIS and atomic absorption spectroscopy. The streptavidin-modified magnetic P(HEMA-GMA) microspheres were used for immobilization of biotinylated DNA and subsequent selective isolation of target DNA from complex samples using DNA/DNA hybridisation. Based on the highly selective recognition of streptavidin with a biotin-labeled DNA probe, DNA sensor was constructed for magnetic separation of DNA from real samples.

In Situ Hybridization for Coccidioides immitis 5.8S Ribosomal RNA Sequences in Formalin-fixed, Paraffin-embedded Pulmonary Specimens Using a Locked Nucleic Acid Probe

Coccidioides immitis/Coccidioides posadasii are common causes of pulmonary infection in certain geographic areas, and are highly infectious when working with culture isolates in the laboratory. Rapid techniques to accurately identify this pathogen in tissues may be of benefit for diagnosis and in limiting the exposure of laboratory personnel to this agent. Locked nucleic acids (LNA) are modified nucleotides in which a ribonucleoside is linked between the 2'-oxygen and the 4'-carbon atoms with a methylene unit. LNA oligonucleotides exhibit increased thermal stability and make excellent probes for in situ hybridization (ISH). In this study, ISH utilizing a biotin-labeled LNA probe targeting Coccidioides sp. ribosomal RNA sequences in 6 formalin-fixed, paraffin-embedded pulmonary tissue specimens from 6 patients with culture positive or histologic findings suggestive of Coccidioides sp. infection is described. The cultures of the pulmonary specimens confirmed C. immitis in 3 of 6 patients. The ISH procedure with the LNA probe was positive in all 6 cases, although the number of organisms that were highlighted varied from rare to numerous. ISH with a biotin-labeled DNA probe of the same sequence was positive in 4 of the 6 cases and the signal intensity and number of organisms was much less than that observed with the LNA probe. Negative control tissues containing a variety of different fungal pathogens including Aspergillus sp., Fusarium sp., Blastomyces dermatitidis, Candida sp, Histoplasma capsulatum, and Zygomyces did not hybridize with the LNA and DNA probes. ISH with an LNA oligonucleotide probe targeting Coccidioides sp. ribosomal RNA is useful for rapid ISH. ISH could be rapidly performed when fungal pathogens are observed in tissue but cultures are negative or have not been performed.

Down-regulation of PROS1 Gene Expression by 17β-Estradiol via Estrogen Receptor α (ERα)-Sp1 Interaction Recruiting Receptor-interacting Protein 140 and the Corepressor-HDAC3 Complex

Pregnant women show a low level of protein S (PS) in plasma, which is known to be a risk for deep venous thrombosis. 17Beta-estradiol (E(2)), an estrogen that increases in concentration in the late stages of pregnancy, regulates the expression of various genes via the estrogen receptor (ER). Here, we investigated the molecular mechanisms behind the reduction in PS levels caused by E(2) in HepG2-ERalpha cells, which stably express ERalpha, and also the genomic ER signaling pathway, which modulates the ligand-dependent repression of the PSalpha gene (PROS1). We observed that E(2) repressed the production of mRNA and antigen of PS. A luciferase reporter assay revealed that E(2) down-regulated PROS1 promoter activity and that this E(2)-dependent repression disappeared upon the deletion or mutation of two adjacent GC-rich motifs in the promoter. An electrophoretic mobility shift assay and DNA pulldown assay revealed that the GC-rich motifs were associated with Sp1, Sp3, and ERalpha. In a chromatin immunoprecipitation assay, we found ERalpha-Sp protein-promoter interaction involved in the E(2)-dependent repression of PROS1 transcription. Furthermore, we demonstrated that E(2) treatment recruited RIP140 and the NCoR-SMRT-HDAC3 complex to the PROS1 promoter, which hypoacetylated chromatin. Taken together, this suggested that E(2) might repress PROS1 transcription depending upon ERalpha-Sp1 recruiting transcriptional repressors in HepG2-ERalpha cells and, consequently, that high levels of E(2) leading to reduced levels of plasma PS would be a risk for deep venous thrombosis in pregnant women.

β-Catenin Up-regulates Atoh1 Expression in Neural Progenitor Cells by Interaction with an Atoh1 3′ Enhancer

Atoh1, a basic helix-loop-helix transcription factor, plays a critical role in the differentiation of several epithelial and neural cell types. We found that beta-catenin, the key mediator of the canonical Wnt pathway, increased expression of Atoh1 in mouse neuroblastoma cells and neural progenitor cells, and baseline Atoh1 expression was decreased by siRNA directed at beta-catenin. The up-regulation of Atoh1 was caused by an interaction of beta-catenin with the Atoh1 enhancer that could be demonstrated by chromatin immunoprecipitation. We found that two putative Tcf-Lef sites in the 3' enhancer of the Atoh1 gene displayed an affinity for beta-catenin and were critical for the activation of Atoh1 transcription because mutation of either site decreased expression of a reporter gene downstream of the enhancer. Tcf-Lef co-activators were found in the complex that bound to these sites in the DNA together with beta-catenin. Inhibition of Notch signaling, which has previously been shown to induce bHLH transcription factor expression, increased beta-catenin expression in progenitor cells of the nervous system. Because this could be a mechanism for up-regulation of Atoh1 after inhibition of Notch, we tested whether siRNA to beta-catenin prevented the increase in Atoh1 and found that beta-catenin expression was required for increased expression of Atoh1 after Notch inhibition.

Identification of the promoter region of the P2RX4 gene

The human P2X(4) purinergic receptor is an ATP gated cation-selective channel, which can be upregulated following nerve injury or stimulation by various cytokines. However, the transcriptional control of this regulation is unknown. In this study, the transcription initiation site was estimated to be 72 bp upstream of ATG start codon by using a novel sequencing based primer extension method with 5'-FAM tagged primers. To delineate the promoter region of the P2RX4 gene which encodes the P2X(4) receptor, we constructed 8 fragments (size range 100-4500 bp) covering the 4.5 Kb upstream region of the P2RX4 gene. A dual-colour luciferase reporter vector system was used to measure the promoter activities in both transfected HEK-293 cells and COS-7 cells for each fragment extracted from 5 to 7 randomly picked colonies. The 62 bp sequence upstream of the initiation site showed promoter activity. A putative GATA-2 binding site (-29 to -20) within this region was required for high promoter activity and GATA-2 was found to be one of the transcriptional factors binding to P2RX4 promoter by both fluorescent super electrophoresis mobility shift assay and immunoprecipitation using streptavidin coated Dynabeads and biotin-labeled double-strand DNA probes. A single nucleotide polymorphism with minor allele frequency of 0.23 was found within the GATA-2 binding site of P2RX4 promoter region which significantly reduced gene transcription. In conclusion, our data has identified the first transcription factor involved in P2X receptor expression.

Microarray of DNA–protein complexes on poly-3-hydroxybutyrate surface for pathogen detection

A novel strategy was developed for the specific immobilization of DNA probes on poly-3-hydroxybutyrate (PHB) surface by using the substrate-binding domain (SBD) of PHB depolymerase as an active binding motif. To demonstrate whether this method can be used for the detection of clinical pathogens, the pathogen-specific biotin-labeled DNA probes were immobilized via core streptavidin (cSA) fused to the SBD. The pathogen-specific 15-mer oligonucleotide probes were designed for four model pathogens, while the target DNAs were prepared by PCR using universal primers. The complex of pathogen-specific probes and cSA-SBD fusion protein was immobilized on the PHB-coated slide by microspotting. This DNA-protein complex microarray was able to successfully diagnose Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Furthermore, the specific pathogens could be diagnosed in the presence of other microorganisms. Thus, the DNA-protein complex microarray platform technology employing PHB and the SBD reported here can be widely used for the detection of DNA-DNA and DNA-biomolecule interactions without synthetic or chemical modification of biomolecules or solid surface.

Peroxisome Proliferator-activated Receptor γ Interacts with CIITA·RFX5 Complex to Repress Type I Collagen Gene Expression

Recent reports demonstrate that peroxisome proliferator-activated receptor gamma (PPARgamma), a member of the nuclear receptor superfamily, acts as a repressor of type I collagen synthesis. Our data demonstrate that exogenously expressed PPARgamma down-regulates collagen expression in a dose-responsive manner in human lung fibroblast cells. Silencing PPARgamma using lentiviruses expressing short hairpin RNAs partially reverses interferon-gamma (IFN-gamma)-induced repression and activates collagen mRNA levels. Previous studies indicate that IFN-gamma represses collagen gene expression and induces major histocompatibility complex II (MHC II) expression by activating the formation of a regulatory factor for X-box 5 (RFX5) complex with class II transactivator (CIITA). This report demonstrates that PPARgamma is within the RFX5.CIITA complex as judged by co-immunoprecipitation and DNA affinity precipitation studies. Most importantly, occupancy of PPARgamma on the collagen transcription start site and MHC II promoter increases with IFN-gamma treatment. The PPARgamma agonist, troglitazone, sensitizes the cells to IFN-gamma treatment by increasing recruitment of PPARgamma to collagen gene while repressing collagen expression, and these effects are blocked by the PPARgamma antagonist T0070907. PPARgamma may mediate IFN-gamma-stimulated collagen transcription down-regulation and MHC II up-regulation by interacting with CIITA as well as regulating CIITA expression. Therefore, PPARgamma is a critical target for investigations into therapeutics of diseases involving extracellular matrix remodeling and the immune response.

Detection of BCRabl in Acute Leukemia by Molecular and Cytogenetic Methods.

Background: The Philadelphia chromosome (Ph), t(9;22)(q34;q11), is detected by karyotyping in a minority of patients with acute leukemia. Ph results in fusion of the c-abl oncogene on chromosome 9 with the breakpoint cluster region BCR gene on chromosome 22. The purpose of this study was to compare reverse trascriptase-polymerase chain reaction (RT-PCR) for BCR/abl fusion to cytogenetic methods for Ph detection in patients with acute leukemia. Methods and Results: Peripheral blood and bone marrow samples from cases of adult acute myelogenous leukemia (AML) and acute lymphoblastic leukemia (ALL) were examined for Ph by RT-PCR, karyotyping, and fluorescence in situ hybridization (FISH). Using total cellular RNA and a single primer pair, cDNA was transcribed, amplified, electorphoresed, and probed for BCR/abl fusion. Patient cells and SUPB15 and K562 cell lines were used as breakpoint controls. Karyotyping was done by standard Giemsa banding. FISH was performed on bone marrow smears using digxigenin-labeled DNA probes for major and minor bcr breakpoints (corresponding to involvement of major bcr exons 2/3 and minor bcr exon 1, respectively) and biotin-labeled DNA probes for abl. Rhodamine-conjugated antidigoxigenin and fluorescein-conjugated avidin yielded red and green fluorescent signals, respectively. A total of 32 samples from patients with AML were studied, 20 from patients with de novo or relapsed AML and 12 from patients in remission. Five of 32 cases of AML (16%) were RT-PCR+/Ph+ all with major bcr breakpoints between exons 3 and 4. One of the 32 cases (3%) was RT-PCR+/Ph+; this case was the only positive remission sample. Of the four T-PCR+/Ph- cases, one showed t(2;17), one showed t(9;11), and two had a normal karyotype. FISH was done in three RT-PCR+ cases, yielding positive results with the major probe in two. A total of 22 samples from patients with ALL were studies, 15 from patients with de novo or relapsed ALL and seven from patient remission. Seven of 22 cases of ALL (32%) were RT-PCR+, four with major-bcr breakpoints between exons 3 and 4, and three with breakpoints in the minor-bcr. Two of the 22 (9%) cases were RT-PCR+/Ph+. Of the five RT-PCR+/Ph- cases, two showed a 22q- but lacked the typical Ph break on chromosome 9, 1 showed a 12p-, and two had a normal karyotype. FISH was performed in four RT-PCR+ cases, yielding positive results with the major probe in two cases and with the minor probe in two cases. Conclusions: RT-PCR is more sensitive than karyotyping, detecting masked Ph or translocations not found by cytogenetic analysis. FISH is a helpful adjunctive test when used to confirm BCR/abl fusion in RT-PCR+/Ph- cases.