Ryuji Kobayashi

Summary

Affiliation: The University of Texas
Country: USA

Publications

  1. pmc ISWI remodeling complexes in Xenopus egg extracts: identification as major chromosomal components that are regulated by INCENP-aurora B
    David E MacCallum
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA
    Mol Biol Cell 13:25-39. 2002
  2. ncbi request reprint Developing an understanding of proteomics: an introduction to biological mass spectrometry
    John Koomen
    Proteomics Facility, Department of Molecular Pathology, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Cancer Invest 23:47-59. 2005
  3. ncbi request reprint Insulin-like growth factor-I receptor/human epidermal growth factor receptor 2 heterodimerization contributes to trastuzumab resistance of breast cancer cells
    Rita Nahta
    Department of Breast Medical Oncology, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030 4009, USA
    Cancer Res 65:11118-28. 2005
  4. ncbi request reprint L2DTL/CDT2 and PCNA interact with p53 and regulate p53 polyubiquitination and protein stability through MDM2 and CUL4A/DDB1 complexes
    Damon Banks
    Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
    Cell Cycle 5:1719-29. 2006
  5. doi request reprint 14-3-3 zeta protein secreted by tumor associated monocytes/macrophages from ascites of epithelial ovarian cancer patients
    Ryuji Kobayashi
    Department of Molecular Pathology, Unit 951, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
    Cancer Immunol Immunother 58:247-58. 2009
  6. ncbi request reprint Monitoring autophagy in glioblastoma with antibody against isoform B of human microtubule-associated protein 1 light chain 3
    Hiroshi Aoki
    Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
    Autophagy 4:467-75. 2008
  7. pmc Phosphorylation of the proline-rich domain of Xp95 modulates Xp95 interaction with partner proteins
    Robert E Dejournett
    Department of Experimental Therapeutics, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Box 019, Houston, TX 77030, USA
    Biochem J 401:521-31. 2007
  8. pmc Phosphorylation of beta-catenin by AKT promotes beta-catenin transcriptional activity
    Dexing Fang
    Brain Tumor Center and Department of Neuro Oncology, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
    J Biol Chem 282:11221-9. 2007
  9. pmc Direct roles of the signaling kinase RSK2 in Cdc25C activation during Xenopus oocyte maturation
    Ruoning Wang
    Department of Experimental Therapeutics, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 107:19885-90. 2010
  10. pmc Proteomics-based identification of proteins secreted in apical surface fluid of squamous metaplastic human tracheobronchial epithelial cells cultured by three-dimensional organotypic air-liquid interface method
    Seung Wook Kim
    Department of Thoracic Head and Neck Medical Oncology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 4009, USA
    Cancer Res 67:6565-73. 2007

Detail Information

Publications42

  1. pmc ISWI remodeling complexes in Xenopus egg extracts: identification as major chromosomal components that are regulated by INCENP-aurora B
    David E MacCallum
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA
    Mol Biol Cell 13:25-39. 2002
    ..Apparently contradictory to the generally accepted model, we find that neither chromosome condensation nor chromosomal targeting of condensin is compromised when H3 phosphorylation is drastically reduced by depletion of INCENP-aurora B...
  2. ncbi request reprint Developing an understanding of proteomics: an introduction to biological mass spectrometry
    John Koomen
    Proteomics Facility, Department of Molecular Pathology, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Cancer Invest 23:47-59. 2005
    ..This review article presents an introduction to mass spectrometry, a brief description of different mass spectrometry experiments, and new developments in the field...
  3. ncbi request reprint Insulin-like growth factor-I receptor/human epidermal growth factor receptor 2 heterodimerization contributes to trastuzumab resistance of breast cancer cells
    Rita Nahta
    Department of Breast Medical Oncology, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030 4009, USA
    Cancer Res 65:11118-28. 2005
    ....
  4. ncbi request reprint L2DTL/CDT2 and PCNA interact with p53 and regulate p53 polyubiquitination and protein stability through MDM2 and CUL4A/DDB1 complexes
    Damon Banks
    Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
    Cell Cycle 5:1719-29. 2006
    ..Our studies demonstrate that PCNA, L2DTL and the DDB1-CUL4A complex play critical and differential roles in regulating the protein stability of p53 and MDM2/HDM2 in unstressed and stressed cells...
  5. doi request reprint 14-3-3 zeta protein secreted by tumor associated monocytes/macrophages from ascites of epithelial ovarian cancer patients
    Ryuji Kobayashi
    Department of Molecular Pathology, Unit 951, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
    Cancer Immunol Immunother 58:247-58. 2009
    ..coli. It is demonstrated for the first time that the important adaptor protein 14-3-3 zeta is common to the secretome of ascitic MO/MA and the ascites of advanced EOC patients...
  6. ncbi request reprint Monitoring autophagy in glioblastoma with antibody against isoform B of human microtubule-associated protein 1 light chain 3
    Hiroshi Aoki
    Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
    Autophagy 4:467-75. 2008
    ..Anti-LC3B antibody provides a useful tool for monitoring the induction of autophagy in cancer cells and tissues...
  7. pmc Phosphorylation of the proline-rich domain of Xp95 modulates Xp95 interaction with partner proteins
    Robert E Dejournett
    Department of Experimental Therapeutics, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Box 019, Houston, TX 77030, USA
    Biochem J 401:521-31. 2007
    ..These findings establish that Xp95/Alix is phosphorylated within the PRD during M-phase induction, and indicate that the phosphorylation may both positively and negatively modulate their interaction with partner proteins...
  8. pmc Phosphorylation of beta-catenin by AKT promotes beta-catenin transcriptional activity
    Dexing Fang
    Brain Tumor Center and Department of Neuro Oncology, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
    J Biol Chem 282:11221-9. 2007
    ..Phosphorylation of beta-catenin by AKT increases its transcriptional activity and promotes tumor cell invasion, indicating that AKT-dependent regulation of beta-catenin plays a critical role in tumor invasion and development...
  9. pmc Direct roles of the signaling kinase RSK2 in Cdc25C activation during Xenopus oocyte maturation
    Ruoning Wang
    Department of Experimental Therapeutics, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 107:19885-90. 2010
    ..However, the phosphorylations catalyzed by MAPK, Cdc2, and RSK2 fail to fully activate Cdc25C, suggesting that additional biochemical events are required to fully activate this key cell cycle regulator...
  10. pmc Proteomics-based identification of proteins secreted in apical surface fluid of squamous metaplastic human tracheobronchial epithelial cells cultured by three-dimensional organotypic air-liquid interface method
    Seung Wook Kim
    Department of Thoracic Head and Neck Medical Oncology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 4009, USA
    Cancer Res 67:6565-73. 2007
    ..These ASF proteins may be used to detect abnormal lesions in the lung without collecting invasive biopsy specimens...
  11. ncbi request reprint Pivotal role of the cyclin-dependent kinase inhibitor p21WAF1/CIP1 in apoptosis and autophagy
    Keishi Fujiwara
    Department of Neurosurgery, University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
    J Biol Chem 283:388-97. 2008
    ..These results suggest that p21 plays an essential role in determining the type of cell death, positively for apoptosis and negatively for autophagy...
  12. ncbi request reprint Pre-analytic saliva processing affect proteomic results and biomarker screening of head and neck squamous carcinoma
    Kazufumi Ohshiro
    Department of Pathology, The University of Texas, M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
    Int J Oncol 30:743-9. 2007
    ....
  13. ncbi request reprint Tyrosine phosphorylation controls PCNA function through protein stability
    Shao Chun Wang
    Department of Molecular and Cellular Oncology, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Nat Cell Biol 8:1359-68. 2006
    ..These results identify a novel nuclear mechanism linking tyrosine kinase receptor function with the regulation of the PCNA sliding clamp...
  14. ncbi request reprint A method for the isolation of blocked N-terminal peptides
    Gaëlle Coussot
    Department of Molecular Pathology, University of Texas, M D Anderson Cancer Center, Houston, TX 77230, USA
    Anal Biochem 361:302-4. 2007
  15. pmc High TCL1 expression and intact T-cell receptor signaling define a hyperproliferative subset of T-cell prolymphocytic leukemia
    Marco Herling
    Department of Hematopathology, University of Texas M D Anderson Cancer Center, Houston, USA
    Blood 111:328-37. 2008
    ..Experimental introduction and knockdown of TCL1 influence the kinetics and strength of TCR-mediated AKT activation. We propose that in T-PLL, TCL1 represents a highly regulated, targetable modulator of TCR-mediated AKT growth signaling...
  16. ncbi request reprint Involvement of the conserved adaptor protein Alix in actin cytoskeleton assembly
    Shujuan Pan
    Department of Experimental Therapeutics, University of Texas, M D Anderson Cancer Center, Houston, Texas 77030, USA
    J Biol Chem 281:34640-50. 2006
    ..Alix knockdown decreases the amount of alpha-actinin that associates with F-actin. These findings establish crucial involvement of Alix in actin cytoskeleton assembly...
  17. pmc Aberrant expression of katanin p60 in prostate cancer bone metastasis
    Xiangcang Ye
    Department of Cancer Biology, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
    Prostate 72:291-300. 2012
    ..Katanin p60 is a microtubule-severing protein and is involved in microtubule cytoskeleton organization in both mitotic and non-mitotic processes. Its role in cancer metastasis is unknown...
  18. ncbi request reprint Proteome analysis of isolated perfused organ effluent as a novel model for protein biomarker discovery
    John M Koomen
    Proteomics Molecular Pathology, UT MD Anderson Cancer Center, Houston, Texas 77030, USA
    J Proteome Res 5:177-82. 2006
    ..The detection of clinical markers for myocardial ischemia in this effluent was robust and analytically straightforward, validating the potential of isolated organ perfusion in diagnostic protein discovery...
  19. ncbi request reprint 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
    Kenji Yokoi
    Department of Cancer Biology, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Int J Oncol 27:1361-9. 2005
    ..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...
  20. pmc The Set1 methyltransferase opposes Ipl1 aurora kinase functions in chromosome segregation
    Ke Zhang
    Program in Genes and Development, Department of Biochemistry and Molecular Biology, M D Anderson Cancer Center, University of Texas, Houston, Texas 77030, USA
    Cell 122:723-34. 2005
    ..Moreover, our findings suggest that antagonism between lysine methylation and serine phosphorylation is a fundamental mechanism for controlling protein function...
  21. ncbi request reprint IkappaB kinase promotes tumorigenesis through inhibition of forkhead FOXO3a
    Mickey C T Hu
    Department of Molecular and Cellular Oncology, The University of Texas, Houston, TX 77030, USA
    Cell 117:225-37. 2004
    ..These results suggest the negative regulation of FOXO factors by IKK as a key mechanism for promoting cell growth and tumorigenesis...
  22. ncbi request reprint Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum
    Jeffrey S Morris
    Department of Biostatistics and Applied Mathematics, The University of Texas MD Anderson Cancer Center, Houston, USA
    Bioinformatics 21:1764-75. 2005
    ..Also, it is difficult to compare the performance of competing methods for analyzing mass spectrometry data since the true expression levels of the proteins in the population are generally not known...
  23. pmc Identification, cDNA cloning, and targeted deletion of p70, a novel, ubiquitously expressed SH3 domain-containing protein
    Nick Carpino
    Department of Biochemistry, St Jude Children s Research Hospital, and University of Tennessee Health Science Center, Memphis, Tennessee 38105, USA
    Mol Cell Biol 22:7491-500. 2002
    ..In addition, no impairment in B- and T-cell development and proliferative ability was detected...
  24. pmc IkappaB kinase beta phosphorylates Dok1 serines in response to TNF, IL-1, or gamma radiation
    Sanghoon Lee
    International Agency for Research on Cancer, 150 cours Albert Thomas, 69008 Lyon, France
    Proc Natl Acad Sci U S A 101:17416-21. 2004
    ..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...
  25. ncbi request reprint Tumor suppressor ARF degrades B23, a nucleolar protein involved in ribosome biogenesis and cell proliferation
    Koji Itahana
    Department of Molecular and Cellular Oncology, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Mol Cell 12:1151-64. 2003
    ..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...
  26. ncbi request reprint Proteomics in cancer screening and management in gynecologic cancer
    Wei Hu
    Department of Gynecologic Medical Oncology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 401, Houston, TX 77030, USA
    Curr Oncol Rep 6:456-62. 2004
    ..This article reviews proteomic techniques and their potential applications in gynecologic cancer screening and management...
  27. ncbi request reprint Comparative analyses of the three-dimensional structures and enzymatic properties of alpha, beta, gamma and delta isoforms of Ca2+-calmodulin-dependent protein kinase II
    Tara R Gaertner
    Department of Neurobiology and Anatomy, University of Texas Medical School, 6431 Fannin Street, Houston, TX 77030, USA
    J Biol Chem 279:12484-94. 2004
    ..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...
  28. ncbi request reprint SHREC, an effector complex for heterochromatic transcriptional silencing
    Tomoyasu Sugiyama
    Laboratory of Molecular Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Cell 128:491-504. 2007
    ..Our analyses suggest that SHREC regulates nucleosome positioning to assemble higher-order chromatin structures critical for heterochromatin functions...
  29. ncbi request reprint Expression and purification of the angiogenesis inhibitor 16-kDa prolactin fragment from insect cells
    Matthew Galfione
    Department of Molecular Pathology, University of Texas, M D Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
    Protein Expr Purif 28:252-8. 2003
    ..This 16-kDa PRL expressed in Sf9 cells is a useful reagent for functional studies and for the purification and identification of its receptor...
  30. ncbi request reprint Protein components of mitochondrial DNA nucleoids in higher eukaryotes
    Daniel F Bogenhagen
    Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
    Mol Cell Proteomics 2:1205-16. 2003
    ..The association of several of these proteins with mtTFA-containing mtDNA nucleoids was confirmed by immunoprecipitation...
  31. ncbi request reprint CAND1 binds to unneddylated CUL1 and regulates the formation of SCF ubiquitin E3 ligase complex
    Jianyu Zheng
    Department of Genetics, Yale University School of Medicine, 333 Cedar Street, Yale University, New Haven, CT 06520, USA
    Mol Cell 10:1519-26. 2002
    ..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...
  32. pmc Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD
    Andrew Emili
    Banting and Best Department of Medical Research, C H Best Institute, University of Toronto, Ontario, Canada
    RNA 8:1102-11. 2002
    ..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...
  33. ncbi request reprint Diagnostic protein discovery using liquid chromatography/mass spectrometry for proteolytic peptide targeting
    John M Koomen
    Molecular Pathology, University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
    Rapid Commun Mass Spectrom 19:1624-36. 2005
    ..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...
  34. pmc Human p32, interacts with B subunit of the CCAAT-binding factor, CBF/NF-Y, and inhibits CBF-mediated transcription activation in vitro
    Chandrani Chattopadhyay
    Department of Molecular Genetics, M D Anderson Cancer Center and Genes, Graduate School of Biomedical Sciences, The University of Texas, Houston, TX 77030, USA
    Nucleic Acids Res 32:3632-41. 2004
    ..Altogether, our study identified p32 as a novel and specific corepressor of CBF-mediated transcription activation in vitro...
  35. ncbi request reprint Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery
    John M Koomen
    Department of Molecular Pathology, University of Texas, M D Anderson Cancer Center, 0089, UT M D, 1515 Holcombe Blvd, Houston, Texas 77030, USA
    J Proteome Res 4:972-81. 2005
    ..On the basis of these data, we discuss limitations in biomarker discovery in the low molecular weight plasma or serum proteome using crude fractionation coupled to MALDI-MS profiling...
  36. ncbi request reprint Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins
    John M Koomen
    Department of Molecular Pathology, University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
    Clin Cancer Res 11:1110-8. 2005
    ..The identifications reveal only common serum proteins and components of the acute phase response, including serum amyloid A, alpha-1-antitrypsin, alpha-1-antichymotrypsin, and inter-alpha-trypsin inhibitor...
  37. ncbi request reprint Peritoneal and subperitoneal stroma may facilitate regional spread of ovarian cancer
    Ena Wang
    Immunogenetics Section, Department of Transfusion Medicine, NIH, Bethesda, Maryland 20892, USA
    Clin Cancer Res 11:113-22. 2005
    ..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...
  38. ncbi request reprint L2DTL/CDT2 interacts with the CUL4/DDB1 complex and PCNA and regulates CDT1 proteolysis in response to DNA damage
    Leigh Ann Higa
    Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
    Cell Cycle 5:1675-80. 2006
    ..Our studies suggest that L2DTL and PCNA interact with CUL4/DDB1 complexes and are involved in CDT1 degradation after DNA damage...
  39. ncbi request reprint Induction of p21 by p53 following DNA damage inhibits both Cdk4 and Cdk2 activities
    Guangan He
    Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Box 019, 1515 Holcombe Blvd, Houston, TX 77030, USA
    Oncogene 24:2929-43. 2005
    ....
  40. ncbi request reprint CUL4-DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation
    Leigh Ann Higa
    Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
    Nat Cell Biol 8:1277-83. 2006
    ..Our studies suggest that CUL4-DDB1 ligases use WDR proteins as molecular adaptors for substrate recognition, and modulate multiple biological processes through ubiquitin-dependent proteolysis...
  41. ncbi request reprint Diagnostic protein discovery using proteolytic peptide targeting and identification
    John M Koomen
    Molecular Pathology, University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
    Rapid Commun Mass Spectrom 18:2537-48. 2004
    ..These initial results are consistent with the known biology of pancreatic cancer or pancreatitis, but are not specific to those diseases...
  42. pmc ALY is a common coactivator of RUNX1 and c-Myb on the type B leukemogenic virus enhancer
    Jennifer A Mertz
    Section of Molecular Genetics and Microbiology, University of Texas at Austin, One University Station, A5000 24th Street and Speedway, ESB 226, Austin, TX 78712 0162, USA
    J Virol 81:3503-13. 2007
    ..ALY also synergized with c-Myb, and coimmunoprecipitation experiments demonstrated an interaction between ALY and c-Myb. These experiments suggest a central role for ALY in T-cell enhancer function and oncogene activation...