Biomedical subjects

Ryuji Kobayashi

Publications and source records attributed to Ryuji Kobayashi.

At least 37 records · Page 2Linked to original sources

PubMed2005

Peritoneal and subperitoneal stroma may facilitate regional spread of ovarian cancer.

PURPOSE: Epithelial ovarian cancer (EOC) is characterized by early peritoneal involvement ultimately contributing to morbidity and mortality. To study the role of the peritoneum in fostering tumor invasion, we analyzed differences between the transcriptional repertoires of peritoneal tissue lacking detectable cancer in patients with EOC versus benign gynecologic disease. EXPERIMENTAL DESIGN: Specimens were collected at laparotomy from patients with benign disease (b) or malignant (m) ovarian pathology and comprised primary ovarian tumors, paired bilateral specimens from adjacent peritoneum and attached stroma (PE), subjacent stroma (ST), peritoneal washes, ascites, and peripheral blood mononuclear cells. Specimens were immediately frozen. RNA was amplified by in vitro transcription and cohybridized with reference RNA to a custom-made 17.5k cDNA microarray. RESULTS: Principal component analysis and unsupervised clustering did not segregate specimens from patients with benign or malignant pathology. Class comparison identified differences between benign and malignant PE and ST specimens deemed significant by permutation test (P = 0.027 and 0.012, respectively). A two-tailed Student's t test identified 402 (bPE versus mPE) and 663 (mST versus bST) genes differentially expressed at a significance level of P2 < or = 0.005 when all available paired samples from each patient were analyzed. The same comparison using one sample per patient reduced the pool of differentially expressed genes but retained permutation test significance for bST versus mST (P = 0.031) and borderline significance for bPE versus mPE (P = 0.056) differences. CONCLUSIONS: The presence of EOC may foster peritoneal implantation and growth of cancer cells by inducing factors that may represent molecular targets for disease control.

Computational Biology↗

PubMed2005

Diagnostic protein discovery using liquid chromatography/mass spectrometry for proteolytic peptide targeting.

A peptide targeting method has been developed for diagnostic protein discovery, which combines proteolytic digestion of fractionated plasma proteins and liquid chromatography coupled to electrospray time-of-flight mass spectrometry (LC/ESI-TOFMS) profiling. Proteolysis prior to profiling overcomes molecular weight limitations and compensates for the poor sensitivity of matrix-assisted laser desorption/ionization (MALDI) protein profiling. LC/MS increases the peak capacity compared to crude fractionation techniques or single sample MALDI analysis. Differentially expressed peptides are targeted in the mass chromatograms using bioinformatic techniques and subsequently sequenced with MALDI tandem MS. In a model study comparing pancreatic cancer patients to controls, 74% of the peptide targets were successfully sequenced. This profiling method was superior to previous experiments using single sample MALDI analysis for protein profiling or proteolytic peptide profiling, because more potential protein markers were identified.

Adult↗

PubMed2005

Developing an understanding of proteomics: an introduction to biological mass spectrometry.

Three components form the foundation of the rapidly growing field of proteomics research: traditional protein chemistry experiments, separations science, and biological mass spectrometry. The increasing demand for proteomics, as well as the presentation of the 2003 Nobel Prize to John Fenn and Koichi Tanaka for ion source development, has placed biological mass spectrometry in the scientific spotlight. A basic understanding of mass spectrometry is increasingly important for basic, translational, and clinical research. This review article presents an introduction to mass spectrometry, a brief description of different mass spectrometry experiments, and new developments in the field.

Mass Spectrometry↗

PubMed2005

Serum amyloid A as a tumor marker in sera of nude mice with orthotopic human pancreatic cancer and in plasma of patients with pancreatic cancer.

We screened an orthotopic nude mouse model of human pancreatic cancer for candidate serum biomarkers and examined their presence in the plasma of pancreatic cancer patients. Nude mice were injected in the pancreas with L3.9pl human pancreatic cancer cells. One week later, the mice were randomized into 4 treatment groups: i) control, saline; ii) oral STI 571; iii) intraperitoneal gemcitabine; and iv) STI 571 and gemcitabine. After 1, 2, and 3 weeks of treatment, sera and tumors were collected from mice in each group as well as uninjected mice. All sera were analyzed by surface enhanced laser desorption ionization mass spectrometry using ProteinChip technology. Protein profiles were analyzed with the Biomarker Wizard software package. The concentration of candidate proteins was evaluated in mouse sera and plasma from 135 pancreatic cancer patients, 7 pancreatitis patients, and 113 healthy volunteers. The combination therapy inhibited tumor growth. A 11.7-kDa protein peak correlating with tumor weight was purified by gel filtration, separated by SDS-PAGE, and identified as mouse serum amyloid A (SAA) by amino acid sequencing and public database searches. The expression of SAA in mouse sera was confirmed by Western blotting and correlated with tumor weight. The level of SAA in plasma of pancreatic cancer patients correlated with clinical stage and was significantly higher than in normal volunteers (mean value: 180.1 microg/ml vs 27.9 microg/ml: P<0.01) or pancreatitis patients. For SAA used as a single tumor marker with a cut-off of 75 microg/ml, the sensitivity for pancreatic cancer was 96.5% and specificity was 31.9%. Our search for specific marker proteins to identify pancreatic cancer was unsuccessful. Although SAA is not specific for pancreatic cancer and not sensitive enough to detect stage I patients, it may be a candidate biomarker for detecting and monitoring the progressive growth of pancreatic cancer.

Animals↗

PubMed2004

IkappaB kinase beta phosphorylates Dok1 serines in response to TNF, IL-1, or gamma radiation.

Dok1 is an abundant Ras-GTPase-activating protein-associated tyrosine kinase substrate that negatively regulates cell growth and promotes migration. We now find that IkappaB kinase beta (IKKbeta) associated with and phosphorylated Dok1 in human epithelial cells and B lymphocytes. IKKbeta phosphorylation of Dok1 depended on Dok1 S(439), S(443), S(446), and S(450). Recombinant IKKbeta also phosphorylated Dok1 or Dok1 amino acids 430-481 in vitro. TNF-alpha, IL-1, gamma radiation, or IKKbeta overexpression phosphorylated Dok1 S(443), S(446), and S(450) in vivo, as detected with Dok1 phospho-S site-specific antisera. Moreover, Dok1 with S(439), S(443), S(446), and S(450) mutated to A was not phosphorylated by IKKbeta in vivo. Surprisingly, mutant Dok1 A(439), A(443), A(446), and A(450) differed from wild-type Dok1 in not inhibiting platelet-derived growth factor-induced extracellular signal-regulated kinase 1/2 phosphorylation or cell growth. Mutant Dok1 A(439), A(443), A(446), and A(450) also did not promote cell motility, whereas wild-type Dok1 promoted cell motility, and Dok1 E(439), E(443), E(446), and E(450) further enhanced cell motility. These data indicate that IKKbeta phosphorylates Dok1 S(439)S(443) and S(446)S(450) after TNF-alpha, IL-1, or gamma-radiation and implicate the critical Dok1 serines in Dok1 effects after tyrosine kinase activation.

Cell Line↗

PubMed2004

Human p32, interacts with B subunit of the CCAAT-binding factor, CBF/NF-Y, and inhibits CBF-mediated transcription activation in vitro.

To understand the role of the CCAAT-binding factor, CBF, in transcription, we developed a strategy to purify the heterotrimeric CBF complex from HeLa cell extracts using two successive immunoaffinity chromatography steps. Here we show that the p32 protein, previously identified as the ASF/SF2 splicing factor-associated protein, copurified with the CBF complex. Studies of protein-protein interaction demonstrated that p32 interacts specifically with CBF-B subunit and also associates with CBF-DNA complex. Cellular localization by immunofluorescence staining revealed that p32 is present in the cell throughout the cytosol and nucleus, whereas CBF is present primarily in the nucleus. A portion of the p32 colocalizes with CBF-B in the nucleus. Interestingly, reconstitution of p32 in an in vitro transcription reaction demonstrated that p32 specifically inhibits CBF-mediated transcription activation. Altogether, our study identified p32 as a novel and specific corepressor of CBF-mediated transcription activation in vitro.

CCAAT-Binding Factor↗

PubMed2004

IkappaB kinase promotes tumorigenesis through inhibition of forkhead FOXO3a.

Nuclear exclusion of the forkhead transcription factor FOXO3a by protein kinase Akt contributes to cell survival. We investigated the pathological relationship between phosphoylated-Akt (Akt-p) and FOXO3a in primary tumors. Surprisingly, FOXO3a was found to be excluded from the nuclei of some tumors lacking Akt-p, suggesting an Akt-independent mechanism of regulating FOXO3a localization. We provide evidence for such a mechanism by showing that IkappaB kinase (IKK) physically interacts with, phosphorylates, and inhibits FOXO3a independent of Akt and causes proteolysis of FOXO3a via the Ub-dependent proteasome pathway. Cytoplasmic FOXO3a correlates with expression of IKKbeta or Akt-p in many tumors and associates with poor survival in breast cancer. Further, constitutive expression of IKKbeta promotes cell proliferation and tumorigenesis that can be overridden by FOXO3a. These results suggest the negative regulation of FOXO factors by IKK as a key mechanism for promoting cell growth and tumorigenesis.

Active Transport, Cell Nucleus↗

PubMed2004

Comparative analyses of the three-dimensional structures and enzymatic properties of alpha, beta, gamma and delta isoforms of Ca2+-calmodulin-dependent protein kinase II.

Ca(2+)-calmodulin-dependent protein kinase II (CaM-kinase II) is a ubiquitous Ser/Thr-directed protein kinase that is expressed from a family of four genes (alpha, beta, gamma, and delta) in mammalian cells. We have documented the three-dimensional structures and the biophysical and enzymatic properties of the four gene products. Biophysical analyses showed that each isoform assembles into oligomeric forms and their three-dimensional structures at 21-25 A revealed that all four isoforms were dodecamers with similar but highly unusual architecture. A gear-shaped core comprising the association domain has the catalytic domains tethered on appendages, six of which extend from both ends of the core. At this level of resolution, we can discern no isoform-dependent differences in ultrastructure of the holoenzymes. Enzymatic analyses showed that the isoforms were similar in their K(m) for ATP and the peptide substrate syntide, but showed significant differences in their interactions with Ca(2+)-calmodulin as assessed by binding, substrate phosphorylation, and autophosphorylation. Interestingly, the rank order of CaM binding affinity (gamma > beta > delta > alpha) does not directly correlate with the rank order of their CaM dependence for autophosphorylation (beta > gamma > delta > alpha). Simulations utilizing this data revealed that the measured differences in CaM binding affinities play a minor role in the autophosphorylation of the enzyme, which is largely dictated by the rate of autophosphorylation for each isoform.

Adenosine Triphosphate↗

PubMed2004

Diagnostic protein discovery using proteolytic peptide targeting and identification.

Plasma protein profiling with mass spectrometry is currently being evaluated as a diagnostic tool for cancer and other diseases. These experiments consist of three steps: plasma protein fractionation, analysis with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS), and comparisons of the MALDI profiles to develop diagnostic fingerprints using bioinformatic techniques. While preliminary results appear promising in small sample groups, the method is limited by the sensitivity of MALDI-MS for intact proteins, the limited mass range of MALDI-MS, and difficulties associated with isolating individual proteins for identification to validate the diagnostic fingerprint. Here we present an alternative and improved method directed toward diagnostic protein discovery, which incorporates proteolytic peptide profiling, bioinformatic targeting of ion signals, and MALDI tandem mass spectrometry (MS/MS) peptide sequencing, rather than fingerprinting. Pancreatic cancer patients, pancreatitis patients, and controls are used as the model system. Profiling peptides after enzymatic digestion improves sensitivity and extends the accessible protein molecular weight range when compared to intact protein profiling. The first step is to extract and fractionate the proteins from plasma. Each fraction is digested with trypsin and subsequently analyzed by MALDI-MS. Rather than using bioinformatic analysis as a pattern-matching technique, peptides are targeted based on the disease to control peak intensity ratios measured in the averages of all mass spectra in each group and t-tests of the intensity of each individual peak. The targeted peptide ion signals are subsequently identified using MALDI-MS/MS in quadrupole-TOF and tandem-TOF instruments. This study found not only the proteins targeted and identified by a previous protein profiling experiment, but also detected additional proteins. These initial results are consistent with the known biology of pancreatic cancer or pancreatitis, but are not specific to those diseases.

Adult↗

PubMed2004

Proteomics in cancer screening and management in gynecologic cancer.

Biomarkers are used routinely for population screening, disease diagnosis and prognosis, monitoring of therapy, and prediction of therapeutic response. Unfortunately, most biomarkers have low sensitivity and specificity and little predictive value. Novel techniques for better screening and early diagnosis of ovarian cancer are urgently needed. Proteomics, the study of the cellular proteins and their activation states, integrates some fundamental techniques, including high-throughput protein purification and profiling, genomic and proteomic databases, and mass spectrometry. In oncology, proteomics will contribute greatly to our understanding of gene functions in tumor development and provide information in clinical applications. This article reviews proteomic techniques and their potential applications in gynecologic cancer screening and management.

Biomarkers, Tumor↗

PubMed2003

Protein components of mitochondrial DNA nucleoids in higher eukaryotes.

Mitochondrial DNA (mtDNA) is not packaged in nucleosomal particles, but has been reported to associate with the mitochondrial inner membrane. Gentle lysis of Xenopus oocyte mitochondria with nonionic detergent liberates a nucleoprotein complex containing mtDNA associated with a previously characterized DNA binding partner, mitochondrial transcription factor A (mtTFA), as well as a series of inner membrane proteins identified by sequencing. More extensive detergent treatment stripped most of these proteins from the DNA, leaving a limited number of proteins in a nucleoid core. Sequencing of the major proteins retained in association with mtDNA revealed the expected mtDNA binding proteins, mtTFA and mitochondrial single-stranded DNA binding protein (mtSSB), as well as four proteins not previously reported to associate with mtDNA. These include adenine nucleotide translocator 1, the lipoyl-containing E2 subunits of pyruvate dehydrogenase and branched chain alpha-ketoacid dehydrogenase and prohibitin 2. The association of several of these proteins with mtTFA-containing mtDNA nucleoids was confirmed by immunoprecipitation.

3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)↗

PubMed2003

Alp13, an MRG family protein, is a component of fission yeast Clr6 histone deacetylase required for genomic integrity.

The post-translational modifications of histones are key to the modulation of chromatin structure. Distinct patterns of modifications established by histone-modifying enzymes control diverse chromosomal processes. Here, we report the purification and molecular characterization of the fission yeast Clr6 histone deacetyl ase involved in higher order chromatin assembly. We show that a chromodomain protein Alp13, which belongs to the conserved MRG protein family linked to cellular senescence in humans, is associated with Clr6. In addition, Clr6 interacts with homologs of the mammalian transcriptional co-repressors Sin3, Pst1 and Pst2, and a WD40 repeat-containing protein, Prw1. Alp13, Pst2 and Prw1 form a stable complex with Clr6 in the nucleus. Deletion of any of these factors causes progressive loss of viability and sensitivity to DNA-damaging agents, and impairs condensation/resolution of chromosomes during mitosis. This is accompanied by hyperacetylation of histones and a reduction in histone H3 Ser10 phosphorylation, which correlates with chromosome condensation during mitosis. These results link the MRG family protein Alp13 to histone deacetylation, and suggest that Clr6 and its associated factors are essential for fundamental chromosomal events.

Acetylation↗

PubMed2003

Expression and purification of the angiogenesis inhibitor 16-kDa prolactin fragment from insect cells.

The 16-kDa fragment of prolactin (16-kDa PRL), derived from proteolytic cleavage of 23-kDa PRL, was shown to have antiangiogenic activity. Previous studies have shown that recombinant 16-kDa PRL produced from bacteria often contained endotoxins, which are cytotoxic to endothelial cells, and varied in its biological activity due to changes in its refolding from inclusion bodies. These problems limited the use of recombinant 16-kDa PRL. To improve the generation of recombinant 16-kDa PRL, we expressed 16-kDa PRL in Sf9 insect cells using a baculoviral expression system. The signal sequence of the human PRL gene and codons for seven histidines were added to the N- and C-termini, respectively, of the 16-kDa PRL cDNA construct. Recombinant 16-kDa PRL was detected in both the cell pellet and the medium. About 0.28 mg purified protein was isolated from the cell pellet of 4 x 10(7) infected cells using nickel affinity chromatography. Sixteen kilodalton PRL was posttranslationally modified with apparent molecular weights of 16 and 18 kDa on SDS-PAGE. The level of 18-kDa protein was significantly reduced after digestion with peptidyl-N-glycosidase, suggesting that the heterogeneity was due to glycosylation of 16-kDa PRL. N-terminal sequence analysis confirmed the fact that both proteins were human 16-kDa PRL and the signal sequences were cleaved at the same position as that of human PRL. Consistent with its role as an angiogenesis inhibitor, purified recombinant 16-kDa PRL inhibits the proliferation of endothelial cells with a potency similar to that previously reported for the protein generated in Escherichia coli. This 16-kDa PRL expressed in Sf9 cells is a useful reagent for functional studies and for the purification and identification of its receptor.

Angiogenesis Inhibitors↗

PubMed2003

Tumor suppressor ARF degrades B23, a nucleolar protein involved in ribosome biogenesis and cell proliferation.

The tumor suppressor ARF induces a p53-dependent and -independent cell cycle arrest. Unlike the nucleoplasmic MDM2 and p53, ARF localizes in the nucleolus. The role of ARF in the nucleolus, the molecular target, and the mechanism of its p53-independent function remains unclear. Here we show that ARF interacts with B23, a multifunctional nucleolar protein involved in ribosome biogenesis, and promotes its polyubiquitination and degradation. Overexpression of B23 induces a cell cycle arrest in normal fibroblasts, whereas in cells lacking p53 it promotes S phase entry. Conversely, knocking down B23 inhibits the processing of preribosomal RNA and induces cell death. Further, oncogenic Ras induces B23 only in ARF null cells, but not in cells that retain wild-type ARF. Together, our results reveal a molecular mechanism of ARF in regulating ribosome biogenesis and cell proliferation via inhibiting B23, and suggest a nucleolar role of ARF in surveillance of oncogenic insults.

Cell Division↗

PubMed2003

[Developmental consideration on the loss of self-evidence (natürlichen Selbstverständlichkeit) in pervasive developmental disorders].

The "loss of self-evidence" has been noted by many, particularly in our country, as a fundamental dysfunction in schizophrenia. Recent recognition of this "loss of self-evidence" in personality disorders such as borderline cases, and developmental disorders such as autism and Asperger's syndrome is focusing renewed interest on this perspective. It is possible that investigation into this "loss of self-evidence" noted in the pervasive developmental disorders may provide clues into the process of its development and acquisition. This paper takes up the issue of "loss of self-evidence" illustrated through the treatment process of 2 patients (female, adulthood autism, adolescent Asperger's syndrome) the author has treated. The psychopathology of the "loss of self-evidence" seen in the pervasive developmental disorders is discussed through these cases in terms of development from the standpoint of clinical intervention for relationship disturbance. The conclusions are as follows. First, the grave psychopathology pertaining to "self-evidence" in the adult autism and adolescent Asperger's syndrome cases is discussed, wherein difficulty in controlling one's action by one's own will giving rise to serious estrangement between experience and consciousness is noted as the pathology held in common by the two. Next, through examination of the normal acquisition process of words and language, it is shown that the essence of the language disorder seen in pervasive developmental disorders lies in the acquisition of meanings of objects being based upon the absence of common experience between subject and caregiver. As such, words representing meaning and content as we see them are imprinted on such individuals, never harmonizing with their own experiential world, giving rise to serious estrangement between their experience and consciousness. Third, sharing what the child is focusing upon in the outer world and how he/she is relating to it in their experiential world, and approaching them with words appropriate to their interpretation, is pointed out as being of critical importance in the self-evidence. In support of this, it is asserted that the establishment of affective communication characterized by mutual resonance of body and affect, and the development of communication upon this basis will, for the first time, enable transmission of culture to such individuals in favorable form, emphasizing the exceptional importance of attachment formation (amae) as being the key to this process.

Adolescent↗

PubMed2003

[Motivational conflict, attachment "amae" and emotional communication between infants with autistic spectrum disorders and their caregivers].

To date, many researchers in Japan have been working on the assumption that the cause of autistic spectrum disorders is attributable to some disorder in the ability of the child. We have been working on the premise that the autistic spectrum disorders are brought about by some form of relationship disturbances in early infancy, and have been attempting to validate this hypothesis through early intervention. We have been examining the developmental process of affective communication in infants with autistic spectrum disorders. We postulated approach-avoidance motivational conflict (Richer, 1993) as the primary factor impeding development of affective communication, focusing therapeutic intervention on this perspective. As a result, attachment behavior was remarkably improved in the children. Through a clinical course of an example, the problem pertaining to the process of acquiring the function of language cognition is discussed. Starting with the concept that the meaning of any given object is not stipulated as a unique existence, but by context, it is pointed out that in order to relate the meaning of some object to a child, sharing with the child "which" attributes of the object the child should focus upon and "how" it should be dealt with are indispensable. This is then followed by discussion of how this cannot be accomplished without deepening of affective communication upon the basis of attachment formation.

Adult↗

PubMed2002

CAND1 binds to unneddylated CUL1 and regulates the formation of SCF ubiquitin E3 ligase complex.

The SCF ubiquitin E3 ligase regulates ubiquitin-dependent proteolysis of many regulatory proteins such as p27(Kip1), IkappaB, and beta-catenin. We report the isolation of a CUL1 binding protein, p120(CAND1). We found the majority of CUL1 is in a complex with CAND1 and ROC1 independent of SKP1 and F box protein SKP2. Both in vivo and in vitro, CAND1 prevents the binding of SKP1 and SKP2 to CUL1 while dissociation of CAND1 from CUL1 promotes the reverse reaction. Neddylation of CUL1 or the presence of SKP1 and ATP causes CAND1 dissociation. Our data suggest that CAND1 regulates the formation of the SCF complex, and its dissociation from CUL1 is coupled with the incorporation of F box proteins into the SCF complex, causing their destabilization.

Adenosine Triphosphate↗

PubMed2002

Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD.

The carboxyl-terminal domain (CTD) of the largest subunit of eukaryotic RNA polymerase II (pol II) plays an important role in promoting steps of pre-mRNA processing. To identify proteins in human cells that bind to the CTD and that could mediate its functions in pre-mRNA processing, we used the mouse CTD expressed in bacterial cells in affinity chromatography experiments. Two proteins present in HeLa cell extract, the splicing and transcription-associated factors, PSF and p54nrb/NonO, bound specifically and could be purified to virtual homogeneity by chromatography on immobilized CTD matrices. Both hypo- and hyperphosphorylated CTD matrices bound these proteins with similar selectivity. PSF and p54nrb/NonO also copurified with a holoenzyme form of pol II containing hypophosphorylated CTD and could be coimmunoprecipitated with antibodies specific for this and the hyperphosphorylated form of pol II. That PSF and p54nrb/NonO promoted the binding of RNA to immobilized CTD matrices suggested these proteins can interact with the CTD and RNA simultaneously. PSF and p54nrb/NonO may therefore provide a direct physical link between the pol II CTD and pre-mRNA processing components, at both the initiation and elongation phases of transcription.

Amino Acid Sequence↗