A simple one-step assay platform based on fluorescence quenching of macroporous silicon.

We synthesized 3D macroporous silicon through a simple electrochemical dissolution process and systematically estimated its protein adsorption and effect on fluorescence emission. Compared with conventional 2D polystyrene plate, the macroporous silicon showed a superior protein adsorption capacity and significant fluorescence quenching effect. We developed a 3D macroporous silicon-based adenosine assay system through the following fabrication process: streptavidin molecules that have been immobilized on the surface of macroporous silicon are attached with biotin-linked and adenosine-specific DNA aptamer, followed by hybridization between the attached aptamer and fluorescent chemical (carboxytetramethylrhodamine/CTMR) that is conjugated with a short complementary DNA sequence. In the absence of adenosine, the aptamer-CTMR complexes remain closely attached to the surface of porous silicon, hence fluorescence being significantly quenched. Upon binding to adenosine, the DNA aptamer is subject to structure switching that leads to dissociation of CTMR from DNA aptamer, and consequently the CTMR fluorescence is restored, indicating a simple one-step assay of adenosine. Compared to the conventional 2D PS and ZnO nanorods-based assays, adenosine at much lower (sub-micromolar) concentration was successfully detected through the 3D macroporous silicon-based assay. The three-dimensionally and densely immobilized aptamer probes and effective fluorescence quenching on the surface of macroporous silicon enables adenosine to be detected at lower levels. Although the adenosine detection is reported here as a proof-of-concept, the developed macroporous silicon-based simple one-step assay platform can be applied in general to fluorescence quenching -based detection of many other biomolecules.

Fluorescent viral nanoparticles with stable in vitro and in vivo activity.

We synthesized fluorescent capsid nanoparticles (FCNPs) by genetically inserting fluorescent protein (FP) (DsRed or eGFP) into each of 240 surface spike tips of hepatitis B virus (HBV) capsid particles. That is, when expressed in E. coli, FCNPs formed spherical nanoparticles with uniform diameter of about 40 nm owing to the self-assembly function of HBV core protein (i.e. basic assembly unit of capsid) and were successfully purified through Ni(+2) affinity- and sucrose gradient based purification. We also added the glycine-rich fexible linker peptides in between DsRed (or eGFP) and capsid to reduce fluorescence quenching among the densely displayed DsReds (or eGFPs) on the capsid surface. As compared to cognate fluorescent monomer proteins, it is notable that FCNPs showed a significantly amplified (160-170-fold) fluorescence intensity and enhanced conformational stability even in 50% serum solutin at 37 °C. The high conformational stability of FCNPs seems to result both from the highly stable structure of HBV capsid particles and from the well oriented insertion of fluorescent protein into capsid spike tip to keep native conformation of DsRed or eGFP. When estimated with continuous exposure to strong excitation light, FCNPs also showed much higher photostability than DsRed, eGFP, and a commonly used organic fluorescent dye, which happened presumably because the enhanced conformational stability of FCNPs significantly reduced photobleaching of fluorophores. Especially, it is notable that rFCNPs stably emitted high-level fluorescence inside mouse for a prolonged period, thereby showing high in vivo stability. The developed FCNPs are likely to have a great potential to be used as an effective and non-cytotoxic tool for in vivo optical imaging as well as in vitro fluorescent reporter in various biomolecular detection assays.

Phosphatidylinositol 3'-kinase, mTOR, and glycogen synthase kinase-3ß mediated regulation of p21 in human urothelial carcinoma cells.

BACKGROUND: The PTEN/Phosphatidylinositol 3'-kinase (PI3-kinase) growth factor signaling pathway plays a critical role in epithelial tumor development in a multitude of tissue types. Deletion of the Pten tumor suppressor gene in murine urothelial cells in vivo results in upregulation of cyclin-dependent kinase inhibitor p21. We have previously shown in mice that p21 expression blocks an increase in urothelial cell proliferation due to Pten deletion. In this study, we utilized human urothelial carcinoma cells UMUC-3 and UMUC-14 to identify the signaling pathways downstream of PI3-kinase that regulate p21. METHODS: Cells were treated with a combination of PI3-kinase stimulating growth factors and kinase inhibitors, or transfected with exogenous genes in order to identify the signaling events that are necessary for p21 induction. Mice with conditional deletion of Pten in bladder urothelium were also examined for evidence of PI3-kinase pathway signaling events that affect p21 expression. RESULTS: When cells were treated with PI3-kinase activating growth factors EGF or PDGF, we found that p21 levels increased, in a manner similar to that observed in mice. We used the inhibitors LY294002, Akti-1/2, and rapamycin, to show that p21 induction is dependent upon PI3-kinase and AKT activity, and partially dependent on mTOR. We treated the cells with proteasome inhibitor MG-132 and found that p21 may be degraded in the proteasome to regulate protein levels. Importantly, our findings show that GSK-3ß plays a role in diminishing p21 levels in cells. Treatment of cells with the GSK-3ß inhibitor SB-216763 increased p21 levels, while exogenous expression of GSK-3ß caused a decrease in p21, indicating that GSK-3ß actively reduces p21 levels. We found that a combined treatment of LY294002 and SB-216763 improved the cytotoxic effect against UMUC-3 and UMUC-14 carcinoma cells over LY294002 alone, suggesting potential therapeutic uses for GSK-3ß inhibitors. Immunohistochemical staining in bladders from wild-type and Pten-deleted mice indicated that GSK-3ß inhibitory phosphorylation increases when Pten is deleted. CONCLUSION: PI3-kinase and AKT cause an upregulation of p21 by suppressing GSK-3ß activity and activating mTOR in both cultured human urothelial carcinoma cells and mouse urothelial cells in vivo.

Pten deficiency activates distinct downstream signaling pathways in a tissue-specific manner.

PTEN deficiency predisposes to a subset of human cancers, but the mechanism that underlies such selectivity is unknown. We have generated a mouse line that conditionally deletes Pten in urogenital epithelium. These mice develop carcinomas at high frequency in the prostate but at relatively low frequency in the bladder, despite early and complete penetrance of hyperplasia in both organs. Cell proliferation is initially high in the bladder of newborn Pten-deficient mice but within days is inhibited by p21 induction. In contrast, proliferation remains elevated in Pten-deficient prostate, where p21 is never induced, suggesting that p21 induction is a bladder-specific compensatory mechanism to inhibit proliferation caused by Pten deletion. Furthermore, the AKT/mammalian target of rapamycin growth pathway, which is highly activated in Pten-deficient prostate, is not activated in bladder epithelium. Our results reveal alternative downstream signaling pathways activated by Pten deficiency that lead to tissue-specific susceptibilities to tumorigenesis.

Variable methylation of the Epstein-Barr virus Wp EBNA gene promoter in B-lymphoblastoid cell lines.

During the initial stages of Epstein-Barr virus (EBV) infection of peripheral resting B cells, transcription of the six genes encoding the EBV latency-associated nuclear antigens (EBNAs) is driven from Wp, a promoter that is present in multiple copies within the EBV major internal repeat. As infection progresses, transcription from Wp is downregulated following upregulation of EBNA gene transcription driven from a promoter, Cp, located ca. 3 kb upstream of the first copy of Wp. Recently published data have provided evidence that, concomitant with the switch in EBNA gene promoter usage, Wp becomes heavily methylated (R. J. Tierney et al., J. Virol. 74:10468-10479, 2000). Based on this observation, it has been argued that methylation of Wp plays a pivotal role in suppressing Wp activity in EBV-immortalized B-lymphoblastoid cell lines (LCLs). Here we present data compiled from analyses of Wp methylation in eight randomly selected low-passage-number B-LCLs. These data demonstrate that there is considerable variability in Wp methylation, both between different cell lines and within clonal LCLs. Overall, less methylation of Wp was noted in established, low-passage-number LCLs than was previously observed in bulk cultures of infected B cells at days 18 and 21 postinfection. Importantly, the majority of LCLs examined harbored both unmethylated and methylated copies of Wp. In addition, all low-passage-number LCLs examined contained both Cp- and Wp-initiated EBNA transcripts, arguing for the presence of some transcriptionally active copies of Wp. Taken together, these data argue that other factors, perhaps in conjunction with Wp methylation, play a role in suppressing Wp activity in LCLs.

Deletion of Epstein-Barr virus regulatory sequences upstream of the EBNA gene promoter Wp1 is unfavorable for B-Cell immortalization.

Transcription of the six Epstein-Barr virus (EBV) EBNA genes is coordinately regulated, being driven by either the Cp promoter, which is encoded within the unique region just upstream of the EBV major internal repeat (IR-1), or by the Wp promoter, which is encoded within the IR-1 repeat and thus present in multiple copies. Previous analyses of Cp- and Wp-initiated transcription have identified a shared cis-regulatory element mapping to the region extending from -169 to -369 bp upstream of the Wp transcription initiation site (M. T. Puglielli, N. Desai, and S. H. Speck, J. Virol. 71:120-128, 1997). To assess the impact of this regulatory region on Cp and Wp activity in the context of the viral genome, we attempted to delete this regulatory region upstream of the first copy of Wp (Wp1). While 10 recombinant viruses were obtained in which this deletion was incorporated in the interior of the IR-1 repeat, only a single lymphoblastoid cell line (LCL) immortalized by a recombinant EBV harboring the deletion upstream of Wp1 was recovered. In contrast, using a control targeting vector in which the Wp regulatory sequences were intact but which contained a sequence tag within the W0 exon, we demonstrated that of the five recombinant viruses analyzed in which the crossover event had occurred upstream of the Wp sequence tag, four had incorporated the tagged sequences into Wp1 of the virus. Taken together, these results indicate that deletion of the regulatory sequences from -369 to -169 bp upstream of Wp1 is unfavorable for EBV-driven B-cell immortalization but is tolerated within the interior of the IR-1 repeat. Analysis of promoter usage in the clone 9-60 LCL, in which the W enhancer sequences were deleted upstream of Wp1, revealed the following: (i) the level of Cp-initiated transcription was significantly diminished compared to that of wild-type LCLs; (ii) the decreased Cp-initiated transcription was not efficiently compensated by transcription initiation from Wp1; and (iii) transcription initiation from downstream Wp promoters was detectable. This is the first report of an LCL in which transcription initiation from a Wp downstream of Wp1 has been documented.

Life and death in paradise.

Over 500 researchers participated in a recent American Association for Cancer Research special conference, entitled "Apoptosis and Cancer: Basic Mechanisms and Therapeutic Opportunities in the Post-Genomic Era" (February 13-17, 2002) in sunny Hawaii (Hilton Waikoloa village, Kona, Hawaii). The meeting participants presented the most recent findings on the mechanisms regulating cell death in cancer. In the past decade, apoptosis research has undergone a quantum leap, metamorphosing from a descriptive, phenomenological discipline into a molecularly defined, highly complex signalling field. This transformation was highlighted in the conference's opening talk by meeting co-organizer, John Reed (The Burnham Institute, La Jolla, CA). Reed and colleagues used published protein functional information and bio-informatic mining of the available human genome databases to tabulate the number of human proteins predicted to be involved in regulating apoptosis. The list includes 11 catalytically active caspases, 26 CARD (caspase associated recruitment domain)-, 32 DD (death domain)-, 12 DED (death effector domain)-, 8 BIR (baculovirus inhibitor of apoptosis protein region)-, 24 BH (Bcl-2 homology)-, and 34 PAAD/PYD (pyrin/PAAD)-containing sequences.