PubMed Health⌕ Search

Biomedical subjects

C Yu

Publications and source records attributed to C Yu.

At least 19 recordsLinked to original sources
PubMed2026

Longitudinal ctDNA tracking in early and recurrent breast cancer using an ultrasensitive structural variant-based assay: an extended analysis from the TRACER study.

BACKGROUND: Detection of circulating tumor DNA (ctDNA) following curative-intent therapy is prognostic of disease recurrence in early-stage breast cancer (EBC). An ultrasensitive structural variant (SV)-based ctDNA assay was evaluated previously in a 100-patient EBC cohort treated with neoadjuvant therapy, demonstrating high sensitivity, specificity, and a long lead-time to relapse. The stability of primary tumor-specific SVs at and after metastatic recurrence and their utility for longer-term ctDNA monitoring had not been established. PATIENTS AND METHODS: An updated retrospective analysis of ctDNA dynamics was conducted in an expanded cohort of 121 patients with EBC treated with neoadjuvant therapy. Plasma samples were collected at key clinical timepoints and serially in several patients who experienced metastatic recurrence. Clinical variables were abstracted from medical records. Associations between ctDNA detection, dynamics, and clinical outcomes were evaluated in the early-stage and metastatic settings. RESULTS: Thirty of 121 patients experienced clinical recurrence (28 distant, 2 local) over a median follow-up of 4.2 years (range 0.5-8.8; 25 ctDNA evaluable with adjuvant timepoints). All patients with detectable ctDNA in the adjuvant setting developed metastatic recurrence (22/22). Median lead time from ctDNA detection to metastatic recurrence was 346 days (range 0-1937). Among recurrent cases, 79% of primary tumor-specific SVs (n = 17 patients, tumor fraction ≥0.1%) remained detectable in plasma [range 7% (1/14 SV)-100% (15/15); median: 92%]. ctDNA dynamics in the recurrent metastatic setting demonstrated a strong relationship with radiographic outcomes in evaluable patients (n = 9). CONCLUSION: This SV-based digital PCR assay provided ultrasensitive ctDNA detection in an expanded EBC cohort, maintaining 100% positive predictive value for metastatic recurrence. In patients with recurrence, ctDNA dynamics were concordant with radiographic outcomes. Prospective studies evaluating the clinical utility of longitudinal ctDNA monitoring are warranted.

MRD↗
PubMed2000

Impaired preneoplastic changes and liver tumor formation in tumor necrosis factor receptor type 1 knockout mice.

Hepatic stem cells (oval cells) proliferate within the liver after exposure to a variety of hepatic carcinogens and can generate both hepatocytes and bile duct cells. Oval cell proliferation is commonly seen in the preneoplastic stages of liver carcinogenesis, often accompanied by an inflammatory response. Tumor necrosis factor (TNF), an inflammatory cytokine, is also important in liver regeneration and hepatocellular growth. The experiments reported here explore the relationship among the TNF inflammatory pathway, liver stem cell activation, and tumorigenesis. We demonstrate that TNF is upregulated during oval cell proliferation induced by a choline-deficient, ethionine-supplemented diet and that it is expressed by oval cells. In TNF receptor type 1 knockout mice, oval cell proliferation is substantially impaired and tumorigenesis is reduced. Oval cell proliferation is impaired to a lesser extent in interleukin 6 knockout mice and is unchanged in TNF receptor type 2 knockout mice. These findings demonstrate that TNF signaling participates in the proliferation of oval cells during the preneoplastic phase of liver carcinogenesis and that loss of signaling through the TNF receptor type 1 reduces the incidence of tumor formation. The TNF inflammatory pathway may be a target for therapeutic intervention during the early stages of liver carcinogenesis.

Animals↗
PubMed2000

15N NMR relaxation studies of free and ligand-bound human acidic fibroblast growth factor.

15N NMR relaxation data have been used to characterize the backbone dynamics of the human acidic fibroblast growth factor (hFGF-1) in its free and sucrose octasulfate (SOS)-bound states. (15)N longitudinal (R(1)), transverse (R(2)) relaxation rates and (1H)-(15)N steady-state nuclear Overhauser effects were obtained at 500 and 600 MHz (at 25 degrees C) for all resolved backbone amide groups using (1)H- detected two-dimensional NMR experiments. Relaxation data were fit to the extended model free dynamics for each NH group. The overall correlation time (tau(m)) for the free and SOS-bound forms were estimated to be 10.4 +/- 1.07 and 11.1 +/- 1.35 ns, respectively. Titration experiments with SOS reveals that the ligand binds specifically to the C-terminal domain of the protein in a 1:1 ratio. Binding of SOS to hFGF-1 is found to induce a subtle conformational change in the protein. Significant conformational exchange (R(ex)) is observed for several residues in the free form of the protein. However, in the SOS-bound form only three residues exhibit significant R(ex) values, suggesting that the dynamics on the micro- to millisecond time scale in the free form is coupled to the cis-trans-proline isomerization. hFGF-1 is a rigid molecule with an average generalized parameter (S(2)) value of 0.89 +/- 0.03. Upon binding to SOS, there is a marked decrease in the overall flexibility (S(2) = 0.94 +/- 0.02) of the hFGF-1 molecule. However, the segment comprising residues 103-111 shows increased flexibility in the presence of SOS. Significant correlation is found between residues that show high flexibility and the putative receptor binding sites on the protein.

Binding Sites↗
PubMed2000

Functional expression of NAD(P)H oxidase p47 in lung microvascular endothelial cells.

Vascular endothelial cell superoxide (O(*)(2)) has an important role in intracellular signaling, in interaction with other reactive species such as nitric oxide, and in vascular dysfunction. Little is known regarding the source and function of O(*)(2) from microvascular endothelial cells from specific tissues. Mouse lung microvascular endothelial cells stimulated with phorbol ester (PMA) or NADPH generated significant O(*)(2), which was inhibited by diphenyleneiodonium (DPI) but not by allopurinol, rotenone, indomethacin, or quinacrine. Optimal O(*)(2) generation required cytosolic as well as particulate cell fractions of cells. In parallel studies, PMA induced increased expression of the p47 component of the NAD(P)H oxidase in the particulate fraction, which was inhibited by staurosporine and calphostin. These data demonstrate that NAD(P)H oxidase is an important source of O(*)(2) generation in lung microvascular endothelial cells.

Allopurinol↗
PubMed2000

Rapid staining of proteins on polyacrylamide gels and nitrocellulose membranes using a mixture of fluorescent dyes.

The present work describes a novel, fluorescence-based method for staining proteins on SDS-PAGE and membrane(s). In this method, proteins are stained using a mixed-dye (sulfo-rhodamine B and 1-anilino-8-naphthalene sulfonic acid (NH(4)(+))) solution. The mixed-dye staining protocol can detect proteins up to a concentration of 15 ng. This method is generally applicable to all proteins and is more sensitive than the conventional Coomassie blue method. The staining method is rapid and efficient. Staining-destaining of proteins using the mixed-dye protocol takes less than half an hour. Another interesting feature of the staining protocol described here is the applicability to the staining of proteins on nitrocellulose membranes.

Anilino Naphthalenesulfonates↗
PubMed2000

Identification and characterization of an equilibrium intermediate in the unfolding pathway of an all beta-barrel protein.

The guanidinium hydrochloride (GdnHCl)-induced unfolding of an all beta-sheet protein, the human acidic fibroblast growth factor (hFGF-1), is studied using a variety of biophysical techniques including multidimensional NMR spectroscopy. The unfolding of hFGF-1 in GdnHCl is shown to involve the formation of a stable equilibrium intermediate. Size exclusion chromotagraphy using fast protein liquid chromatography shows that the intermediate accumulates maximally at 0.96 m GdnHCl. 1-Anilinonapthalene 8-sulfonate binding, one-dimensional (1)H NMR, and limited proteolytic digestion experiments suggest that the intermediate has characteristics resembling a molten globule state. Chemical shift perturbation and hydrogen-deuterium exchange monitored by (1)H-(15)N heteronuclear single quantum coherence spectra reveal that profound structural changes in the intermediate state (in 0.96 m GdnHCl) occur in the C-terminal, heparin binding region of the protein molecule. Additionally, results of the stopped flow fluorescence experiments suggest that the kinetic refolding of hFGF-1 proceeds through the accumulation of an intermediate at low concentrations of the denaturant. To our knowledge, the present study is the first report wherein an equilibrium intermediate is characterized in detail in an all beta-barrel protein.

Anilino Naphthalenesulfonates↗
PubMed2000

The nonsense-mediated decay pathway and mutually exclusive expression of alternatively spliced FGFR2IIIb and -IIIc mRNAs.

Exons IIIb and IIIc of the FGFR2 gene are alternatively spliced in a mutually exclusive manner in different cell types. A switch from expression of FGFR2IIIb to FGFR2IIIc accompanies the transition of nonmalignant rat prostate tumor epithelial cells (DTE) to cells comprising malignant AT3 tumors. Here we used transfection of minigenes with and without alterations in reading frame and with and without introns to examine how translation affects observed FGFR2 splice products. We observed that nonsense mutations in other than the last exon led to a dramatic reduction in mRNA that is abrogated by removal of downstream introns in both DTE and AT3 cells. The mRNA, devoid of both IIIb and IIIc exons (C1-C2), is a major splice product from minigenes lacking an intron downstream of the second common exon C2. From these observations, we suggest that repression of exon IIIc and activation of exon IIIb inclusion in DTE cells lead to the generation of both C1-IIIb-C2 and C1-C2 products. However, the C1-C2 product from the native gene is degraded due to a frameshift and a premature termination codon caused by splicing C1 and C2 together. Derepression of exon IIIc and repression of exon IIIb lead to the generation of both C1-IIIc-C2 and C1-C2 products in AT3 cells, but the C1-C2 product is degraded. The C1-IIIb-IIIc-C2 mRNA containing a premature termination codon in exon IIIc was present, but at apparently trace levels in both cell types. The nonsense-mediated mRNA decay pathway and cell type-dependent rates of inclusion of exons IIIb and IIIc result in the mutually exclusive expression of FGFR2IIIb and IIIc.

Alternative Splicing↗
PubMed2000

Structural events during the refolding of an all beta-sheet protein.

The refolding kinetics of the 140-residue, all beta-sheet, human fibroblast growth factor (hFGF-1) is studied using a variety of biophysical techniques such as stopped-flow fluorescence, stopped-flow circular dichroism, and quenched-flow hydrogen exchange in conjunction with multidimensional NMR spectroscopy. Urea-induced unfolding of hFGF-1 under equilibrium conditions reveals that the protein folds via a two-state (native <--> unfolded) mechanism without the accumulation of stable intermediates. However, measurement of the unfolding and refolding rates in various concentrations of urea shows that the refolding of hFGF-1 proceeds through accumulation of kinetic intermediates. Results of the quenched-flow hydrogen exchange experiments reveal that the hydrogen bonds linking the N- and C-terminal ends are the first to form during the refolding of hFGF-1. The basic beta-trefoil framework is provided by the simultaneous formation of beta-strands I, IV, IX, and X. The other beta-strands comprising the beta-barrel structure of hFGF-1 are formed relatively slowly with time constants ranging from 4 to 13 s.

Fibroblast Growth Factor 1↗
PubMed2000

Intersubunit interactions in human X,K-ATPases: role of membrane domains M9 and M10 in the assembly process and association efficiency of human, nongastric H,K-ATPase alpha subunits (ATP1al1) with known beta subunits.

Na,K- and H,K-ATPase (X,K-ATPase) alpha subunits need association with a beta subunit for their maturation, but the authentic beta subunit of nongastric H,K-ATPase alpha subunits has not been identified. To better define alpha-beta interactions in these ATPases, we coexpressed human, nongastric H,K-ATPase alpha (AL1) and Na,K-ATPase alpha1 (alpha1NK) as well as AL1-alpha1 and alpha1-AL1 chimeras, which contain exchanged M9 and M10 membrane domains, together with each of the known beta subunits in Xenopus oocytes and followed their resistance to cellular and proteolytic degradation and their ER exit. We show that all beta subunits (gastric betaHK, beta1NK, beta2NK, beta3NK, or Bufo bladder beta) can associate efficiently with alpha1NK, but only gastric betaHK, beta2NK, and Bufo bladder beta can form stably expressed AL1-beta complexes that can leave the ER. The trypsin resistance and the forces of subunit interaction, probed by detergent resistance, are lower for AL1-beta complexes than for alpha1NK-beta complexes. Furthermore, chimeric alpha1-AL1 can be stabilized by beta subunits, but alpha1-AL1-gastric betaHK complexes are retained in the ER. On the other hand, chimeric AL1-alpha1 cannot be stabilized by any beta subunit. In conclusion, these results indicate that (1) none of the known beta subunits is the real partner subunit of AL1 but an as yet unidentified, authentic beta should have structural features resembling gastric betaHK, beta2NK, or Bufo bladder beta and (2) beta-mediated maturation of alpha subunits is a multistep process which depends on the membrane insertion properties of alpha subunits as well as on several discrete events of intersubunit interactions.

Animals↗
PubMed2000

PU.1 inhibits GATA-1 function and erythroid differentiation by blocking GATA-1 DNA binding.

The lineage-specific transcription factors GATA-1 and PU.1 can physically interact to inhibit each other's function, but the mechanism of repression of GATA-1 function by PU.1 has not been elucidated. Both the N terminus and the C terminus of PU.1 can physically interact with the C-terminal zinc finger of GATA-1. It is demonstrated that the PU.1 N terminus, but not the C terminus, is required for inhibiting GATA-1 function. Induced overexpression of PU.1 in K562 erythroleukemia cells blocks hemin-induced erythroid differentiation. In this system, PU.1 does not affect the expression of GATA-1 messenger RNA, protein, or nuclear localization. However, GATA-1 DNA binding decreases dramatically. By means of electrophoretic mobility shift assays with purified proteins, it is demonstrated that the N-terminal 70 amino acids of PU.1 can specifically block GATA-1 DNA binding. In addition, PU.1 had a similar effect in the G1ER cell line, in which the GATA-1 null erythroid cell line G1E has been transduced with a GATA-1-estrogen receptor fusion gene, which is directly dependent on induction of the GATA-1 fusion protein to effect erythroid maturation. Consistent with in vitro binding assays, overexpression of PU.1 blocked DNA binding of the GATA-1 fusion protein as well as GATA-1-mediated erythroid differentiation of these G1ER cells. These results demonstrate a novel mechanism by which function of a lineage-specific transcription factor is inhibited by another lineage-restricted factor through direct protein-protein interactions. These findings contribute to understanding how protein-protein interactions participate in hematopoietic differentiation and leukemogenesis. (Blood. 2000;96:2641-2648)

Biological Transport↗
PubMed2000

Chiral monolithic columns for enantioselective capillary electrochromatography prepared by copolymerization of a monomer with quinidine functionality. 1. Optimization of polymerization conditions, porous properties, and chemistry of the stationary phase.

Monolithic columns for chiral capillary electrochromatography have been prepared within the confines of untreated fused-silica capillaries in a single step by a simple copolymerization of mixtures of O-[2-(methacryloyloxy)ethylcarbamoyl]-10,11-dihydroquinidine , ethylene dimethacrylate, and glycidyl methacrylate or 2-hydroxyethyl methacrylate in the presence of mixture of cyclohexanol and 1-dodecanol as a porogenic solvent. The porous properties of the monolithic columns can easily be controlled through changes in the composition of the binary porogenic solvent. Although both thermal- and UV light-initiated polymerizations afford useful capillary columns, monoliths prepared using the former approach exhibit better chromatographic properties. The ability to control pore size independently of the polymerization mixture composition enables the preparation of monoliths with varying percentages of the chiral monomer and cross-linker, as well as the optimization of their separation properties. Very good separations of model racemate (R,S)-N-3,5-dinitrobenzoylleucine were achieved using an optimized monolithic CEC column, with high efficiencies of up to 74000 plates/m for the retained peaks.

Chromatography, Liquid↗
PubMed2000

Influence of mobile phase composition and cross-linking density on the enantiomeric recognition properties of molecularly imprinted polymers.

A series of experiments were conducted to investigate elements which affect the enantiomeric recognition properties of molecularly imprinted polymers (MIPs) in the HPLC mode. Our results show that the recognition properties of MIPs are greatly influenced by the mobile phase used. For a polymer prepared in acetonitrile, a good enantiomeric separation was observed when acetonitrile-based mobile phase was used, when the mobile phase was changed to chloroform-based, no enantiomeric recognition was observed although the sample molecule was retarded. This indicates that the specific co-operative binding interactions between the functional groups at the imprinted polymer's recognition sites and the sample molecule were considerably disrupted and only non-specific interactions remained. When the mobile phase was changed back to acetonitrile-based, the recognition was regained. In contrast, for polymers prepared in chloroform, chloroform-based mobile phase gave much better separation than acetonitrile-based mobile phase. When other solvents were tested, significant solvent effects were generally observed. Based on these observations, the recognition properties of the methacrylic acid (MAA)-co-ethylene glycol dimethacrylate (EGDMA) polymers were reinvestigated, and the results show that by simply using an optimised mobile phase system, significantly improved recognition over previously reported results was observed. For a polymer made against Cbz-L-Trp, 100 microg of Cbz-D,L-Trp was separated with a separation factor (alpha) of 4.23 and a resolution (Rs) of 3.87, whereas in the previous report, 10 microg of Cbz-D,L-Trp was only separated with alpha = 1.67 and Rs = 0.1. It is generally realised that the imprinted polymer's recognition property is also very much influenced by the nature of the polymer network. It was shown that the recognition decreased with a decrease in the apparent degree of cross-linking (molar percentage of cross-linker in the polymerisation mixture). Nonetheless, our results show that in our optimised assay system a significant separation could still be obtained on a polymer which was only 22% cross-linked. We consider this to be of importance, since it may suggest a way of imprinting larger molecules because of the possibly improved mass transfer in low cross-linking density polymers. It was reported that when trifunctional cross-linkers [for example: trimethylolpropane trimethacrylate (TRIM)] were used as the cross-linker instead of EGDMA, considerably improved enantiomeric separation and resolving capability were observed. Our results show that the improved performance of the MAA-co-EGDMA MIPs is actually comparable to the performance of the MIPs prepared with those trifunctional cross-linkers. The combination of a hydrogen bonding functional monomer (acrylamide) with TRIM also did not give improved recognition. The results suggest that although the three-dimensional network of these two kinds of polymer may be quite different, the observed recognition improvements were probably largely due to solvent effect.

Chromatography, High Pressure Liquid↗
PubMed2000

Regulation of cell cycle proteins by TNF-alpha and TGF-beta in cells of oligodendroglial lineage.

Proliferation and apoptosis are two dynamic, interrelated processes that are regulated by growth factors and cytokines. We investigated the effects of tumor necrosis factor-alpha (TNF-alpha) and transforming growth factor-beta (TGF-beta) on apoptosis and regulation of cell cycle proteins in OLG lineage cells. We found that: (1) both cytokines enhanced apoptosis in neonatal pre-OLGs but only TNFalpha-mediated apoptosis persisted in the presence of a mitogen, fibroblast growth factor (FGF); (2) cell cycle proteins such as p21(waf1/cip1), p27(kip1), cyclin D1 and PCNA were differentially regulated by TNF-alpha and TGF-beta. We conclude that differential modulation of cell cycle proteins by TNF-alpha and TGF-beta contributes to the diversity of their biological effects in OLG lineage cells.

Aging↗
PubMed2000

Comparison of the structural stability of two homologous toxins isolated from the Taiwan cobra (Naja naja atra) venom.

Cardiotoxin analogue III (CTX III) and cobrotoxin (CBTX) isolated from the Taiwan cobra venom (Naja naja atra) are structurally homologous, small molecular weight, all-beta-sheet proteins, cross-linked by four disulfide bonds at identical positions. The conformational stabilities of these toxins are compared based on temperature-dependent chemical shifts and amide proton exchange kinetics using two-dimensional NMR spectroscopy. The structure of CTX III is found to be significantly more stable than that of CBTX. In both the toxins, beta-strand III appears to constitute the stability core. In CTX III, the stability of the triple-stranded beta-sheet domain is observed to be markedly higher than the double-stranded beta-sheet segment. In contrast, in CBTX, both structural domains (double- and triple-stranded beta-sheet domains) appear to contribute equally to the stability of the protein. Estimation of the free energy of exchange (Delta G(ex)) of residues in CBTX and CTX III reveals that the enhanced stability of the structure of CTX III stems from the strong interactions among the beta-strands constituting the triple-stranded beta-sheet domain and also the molecular forces bridging the residues at the N- and C-terminal ends of the molecule.

Animals↗
PubMed2000

Conformational study of a custom antibacterial peptide cecropin B1: implications of the lytic activity.

Cecropin B1 (CB1) with two amphipathic alpha-helical segments is a derivative of the natural antibacterial peptide, cecropin B. The assays of cell lysis show that, compared with cecropin A (CA), CB1 has a similar ability to lyse bacteria with a higher potency (two- to six-fold higher) in killing cancer cells. The difference may be due to the fact that the peptides possess different structures and sequences. In this study, the solution structure of CB1 in 20% hexafluoroisopropanol was determined by two-dimensional nuclear magnetic resonance (NMR) spectroscopy. The (1)H NMR resonances were assigned. A total of 350 inter-proton distances were used to calculate the solution structure of CB1. The final ensemble structures were well converged, showing the minimum root mean square deviation. The results indicate that CB1 has two stretches of helices spanning from residues 3 to 22 and from residues 26 to 33, which are connected by a hinge section formed by Gly-23 and Pro-24. Lys-25 is partially incorporated in the hinge region. The bent angle between two helical segments located in two planes was between 100 and 110 degrees. With comparisons of the known NMR structure of CA and its activities on bacteria and cancer cells, the structure-function relationship of the peptides is discussed.

Amino Acid Sequence↗
PubMed2000

ABC-me: a novel mitochondrial transporter induced by GATA-1 during erythroid differentiation.

Transcription factor GATA-1 is essential for normal erythropoiesis. GATA-binding sites are consistently found in promoters or enhancers of genes expressed selectively in erythroid cells. To discover novel GATA-1-regulated genes, we searched for GATA-1-activated transcripts in G1E cells, an erythroid line derived from GATA-1(-) embryonic stem cells. By subtractive analysis, we identified a new ATP-binding cassette (ABC) transporter that is strongly and rapidly induced by GATA-1. This protein, named ABC-me (for ABC-mitochondrial erythroid), localizes to the mitochondrial inner membrane and is expressed at particularly high levels in erythroid tissues of embryos and adults. ABC-me is induced during erythroid maturation in cell lines and primary hematopoietic cells, and its overexpression enhances hemoglobin synthesis in erythroleukemia cells. The ABC proteins participate in diverse physiological processes by coupling ATP hydrolysis to the transport of a variety of substrates across cell membranes. We speculate that ABC-me, a newly identified erythroid-expressed ABC superfamily member, may mediate critical mitochondrial transport functions related to heme biosynthesis.

ATP-Binding Cassette Transporters↗
PubMed2000

Elevated cholesterol metabolism and bile acid synthesis in mice lacking membrane tyrosine kinase receptor FGFR4.

Heparan sulfate-regulated transmembrane tyrosine kinase receptor FGFR4 is the major FGFR isotype in mature hepatocytes. Fibroblast growth factor has been implicated in the definition of liver from foregut endoderm where FGFR4 is expressed and stimulation of hepatocyte DNA synthesis in vitro. Here we show that livers of mice lacking FGFR4 exhibited normal morphology and regenerated normally in response to partial hepatectomy. However, the FGFR4 (-/-) mice exhibited depleted gallbladders, an elevated bile acid pool and elevated excretion of bile acids. Cholesterol- and bile acid-controlled liver cholesterol 7alpha-hydroxylase, the limiting enzyme for bile acid synthesis, was elevated, unresponsive to dietary cholesterol, but repressed normally by dietary cholate. Expression pattern and cholate-dependent, cholesterol-induced hepatomegaly in the FGFR4 (-/-) mice suggested that activation of receptor interacting protein 140, a co-repressor of feed-forward activator liver X receptor alpha, may mediate the negative regulation of cholesterol- and bile acid-controlled liver cholesterol 7alpha-hydroxylase transcription by FGFR4 and cholate. The results demonstrate that transmembrane sensors interface with metabolite-controlled transcription networks and suggest that pericellular matrix-controlled liver FGFR4 in particular may ensure adequate cholesterol for cell structures and signal transduction.

Animals↗