Medical ProteoScope Company


Medical ProteoScope Company

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Takadate T.,Tohoku University | Onogawa T.,Tohoku University | Fujii K.,Hokkaido University | Motoi F.,Tohoku University | And 15 more authors.
Clinical Proteomics | Year: 2012

Background: Pancreatic cancer is among the most lethal malignancies worldwide. This study aimed to identify a novel prognostic biomarker, facilitating treatment selection, using mass spectrometry (MS)-based proteomic analysis with formalin-fixed paraffin-embedded (FFPE) tissue. Results: The two groups with poor prognosis (n = 4) and with better prognosis (n = 4) had been carefully chosen among 96 resected cases of pancreatic cancer during 1998 to 2007 in Tohoku University Hospital. Although those 2 groups had adjusted background (UICC-Stage IIB, Grade2, R0, gemcitabine adjuvant), there was a significant difference in postoperative mean survival time (poor 21.0 months, better 58.1 months, P = 0.0067). Cancerous epithelial cells collected from FFPE tissue sections by laser micro-dissection (LMD) were processed for liquid chromatography-tandem mass spectrometry (LC-MS/MS). In total, 1099 unique proteins were identified and 6 proteins showed different expressions in the 2 groups by semi-quantitative comparison. Among these 6 proteins, we focused on Nm23/Nucleoside Diphosphate Kinase A (NDPK-A) and immunohistochemically confirmed its expression in the cohort of 96 cases. Kaplan-Meier analysis showed high Nm23/NDPK-A expression to correlate with significantly worse overall survival (ρ = 0.0103). Moreover, in the multivariate Cox regression model, Nm23/NDPK-A over-expression remained an independent predictor of poor survival with a hazard ratio of 1.97 (95% CI 1.16-3.56, ρ = 0.0110). Conclusions: We identified 6 candidate prognostic markers for postoperative pancreatic cancer using FFPE tissues and immunohistochemically demonstrated high Nm23/NDPK-A expression to be a useful prognostic marker for pancreatic cancer. © 2012 Takadate et al.; licensee BioMed Central Ltd.

Takadate T.,Tohoku University | Onogawa T.,Tohoku University | Fukuda T.,Biosys Technologies Inc. | Motoi F.,Tohoku University | And 14 more authors.
International Journal of Cancer | Year: 2013

Pancreatic cancer is among the most lethal malignancies worldwide. We aimed to identify novel prognostic markers by applying mass spectrometry (MS)-based proteomic analysis to formalin-fixed paraffin-embedded (FFPE) tissues. Resectable, node positive pancreatic ductal adenocarcinoma (PDAC) with poor (n = 4) and better (n = 4) outcomes, based on survival duration, with essentially the same clinicopathological backgrounds, and noncancerous pancreatic ducts (n = 5) were analyzed. Cancerous and noncancerous cells collected from FFPE tissue sections by laser microdissection (LMD) were processed for liquid chromatography (LC)-tandem MS (MS/MS). Candidate proteins were identified by semiquantitative comparison and then analyzed quantitatively using selected reaction monitoring (SRM)-based MS. To confirm the associations between candidate proteins and outcomes, we immunohistochemically analyzed a cohort of 87 cases. In result, totally 1,229 proteins were identified and 170 were selected as candidate proteins for SRM-based targeted proteomics. Fourteen proteins overexpressed in cancerous as compared to noncancerous tissue showed different expressions in the poor and better outcome groups. Among these proteins, we found that three novel proteins ECH1, OLFM4 and STML2 were overexpressed in poor group than in better group, and that one known protein GTR1 was expressed reciprocally. Kaplan-Meier analysis showed high expressions of all four proteins to correlate with significantly worse overall survival (p < 0.05). In conclusion, we identified four proteins as candidates of prognostic marker of PDAC. The combination of shotgun proteomics verified by SRM and validated by immunohistochemistry resulted in the prognostic marker discovery that will contribute the understanding of PDAC biology and therapeutic development. What's new? While the search for biomarkers for particular cancers has often focused on mRNA, protein profiles may actually be more accurate. In addition, mRNA levels can't detect the activation of key signaling molecules in protein networks. In this study of pancreatic cancer, the authors used a novel strategy combining "global shotgun proteomics" using mass spectrometry (MS), and targeted "selected reaction monitoring" (SRM). They found that patients whose tumors expressed the proteins ECH1, OLFM4, STML2 and GTR1 had significantly worse outcomes. These proteins may thus have prognostic significance, and may also suggest new therapeutic targets. Copyright © 2012 UICC.

Nyberg F.,Astrazeneca | Nyberg F.,Karolinska Institutet | Ogiwara A.,Medical ProteoScope Company | Ogiwara A.,Tokyo Medical University | And 30 more authors.
PLoS ONE | Year: 2011

Interstitial lung disease (ILD) events have been reported in Japanese non-small-cell lung cancer (NSCLC) patients receiving EGFR tyrosine kinase inhibitors. We investigated proteomic biomarkers for mechanistic insights and improved prediction of ILD. Blood plasma was collected from 43 gefitinib-treated NSCLC patients developing acute ILD (confirmed by blinded diagnostic review) and 123 randomly selected controls in a nested case-control study within a pharmacoepidemiological cohort study in Japan. We generated ~7 million tandem mass spectrometry (MS/MS) measurements with extensive quality control and validation, producing one of the largest proteomic lung cancer datasets to date, incorporating rigorous study design, phenotype definition, and evaluation of sample processing. After alignment, scaling, and measurement batch adjustment, we identified 41 peptide peaks representing 29 proteins best predicting ILD. Multivariate peptide, protein, and pathway modeling achieved ILD prediction comparable to previously identified clinical variables; combining the two provided some improvement. The acute phase response pathway was strongly represented (17 of 29 proteins, p = 1.0×10 -25), suggesting a key role with potential utility as a marker for increased risk of acute ILD events. Validation by Western blotting showed correlation for identified proteins, confirming that robust results can be generated from an MS/MS platform implementing strict quality control. © 2011 Nyberg et al.

Nagata K.,Yokohama City University | Kawakami T.,Yokohama City University | Kawakami T.,Medical ProteoScope Company | Kurata Y.,Yokohama City University | And 6 more authors.
Journal of Proteomics | Year: 2015

Mutations in the Kit receptor tyrosine kinase gene (. KIT), which result in constitutive activation of the protein (KIT), are causally related to the development of gastrointestinal stromal tumors (GISTs). Imatinib, a targeted anticancer drug, exerts a therapeutic effect against GISTs by repressing the kinase activity of KIT. Long-term administration of this drug, however, causes the emergence of imatinib-resistant GISTs. We performed quantitative phosphoproteome analysis using a cell-based GIST model system comprising an imatinib-sensitive GIST cell line (GIST882), GIST882 under treatment with imatinib (GIST882-IM), and secondary imatinib-resistant GIST882 (GIST882-R). Phosphorylated peptides were purified from each cell line using titania-based affinity chromatography or anti-phosphotyrosine immunoprecipitation, and then subjected to LC-MS/MS based quantitative phosphoproteome analysis. Using this method we identified augmentation of the kinase activities of multiple elements of the signal transduction pathway, especially KIT and EGFR. Although, these elements were up-regulated in GIST882-R, no additionally mutated KIT mRNA was found in secondary imatinib-resistant GIST cells. Treatment of GIST882-R with imatinib in combination with gefitinib, an EGFR inhibitor, partially prevented cell growth, implying that EGFR may be involved in acquisition of secondary imatinib resistance in GIST. Biological significance: In this study, we performed a quantitative phosphoproteome analysis using a cell culture-based GIST model system. The goal of the study was to investigate the mechanism of acquired resistance in GISTs against imatinib, a molecularly targeted drug that inhibits kinase activity of the KIT protein and that has been approved for the treatment of GISTs. In imatinib-resistant GIST cells, we observed elevated expression of KIT and restoration of its kinase activity, as well as activation of multiple proliferative signaling pathways. Our results indicate that the effects of even so-called 'molecularly targeted' drugs, are broad rather than convergent, and that the mechanisms of action of such drugs during continuous administration are extremely complex. © 2014 Elsevier B.V.

Sato K.,Central Institute for Experimental Animals | Oiwa R.,Central Institute for Experimental Animals | Kumita W.,Central Institute for Experimental Animals | Henry R.,Horizon Discovery | And 23 more authors.
Cell Stem Cell | Year: 2016

Recent advances in genome editing have facilitated the generation of nonhuman primate (NHP) models, with potential to unmask the complex biology of human disease not revealed by rodent models. However, their broader use is hindered by the challenges associated with generation of adult NHP models as well as the cost of their production. Here, we describe the generation of a marmoset model of severe combined immunodeficiency (SCID). This study optimized zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) to target interleukin-2 receptor subunit gamma (IL2RG) in pronuclear stage marmoset embryos. Nine of 21 neonates exhibited mutations in the . IL2RG gene, concomitant with immunodeficiency, and three neonates have currently survived from 240 days to 1.8 years. Our approach demonstrates highly efficient production of founder NHP with SCID phenotypes, with promises of multiple pre-clinical and translational applications. In this article, Sato and colleagues describe the generation of an immunodeficient nonhuman primate model. By optimizing ZFN and TALEN targeting of the . IL2RG gene in marmoset fibroblasts and embryos, and using blastomere splitting as a proxy for rapid genome editing to reduce mosaicism, the authors generated founder animals with an immunodeficient phenotype similar to that of human patients with X-SCID. © 2016 Elsevier Inc.

Guo R.,Tokyo Medical University | Hirano T.,Toda Chuo General Hospital | Kawakami T.,Tokyo Medical University | Kawakami T.,Medical ProteoScope Company | And 7 more authors.
Japanese Journal of Lung Cancer | Year: 2010

Objective. There is a need to establish clinically useful serum biomarkers for effective lung cancer screening. We investigated extracellular proteins secreted or shed from surgically resected lung adenocarcinoma tissue into its primary culture medium. Methods. In 12 lung adenocarcinoma cases, protein specimens from both culture supernatants of adenocarcinoma tissue and the normal peripheral lung (NPL) tissue were labeled with different fluorescent dyes (CyDye™: Cy2, Cy3 and Cy5) and co-resolved in single two-dimensional (2-D) gels. Quantitative protein profiles were obtained by differential fluorescence imaging of the gels. Results. The twelve pairs of 2-D gel images of both adenocarcinoma and NPL specimens revealed 34 distinct protein spots, detected in at least 5 gel images and highly concentrated in the adenocarcinoma cultures, on average more than double the concentration of analysis identified all of these protein spots, including napsin A and pulmonary surfactant-associated protein A which are responsible for the development of type II pneumocytes, and are the proteins commonly upregulated in tumor cells. Conclusion. These results suggest the usefulness of the tissue culture method to identify potential serum biomarkers to enable the early detection of lung adenocarcinoma. © 2010 The Japan Lung Cancer Society.

Nishiyama T.,Tokyo University of Science | Kuroda S.,Tokyo University of Science | Takiguchi E.,Tokyo University of Science | Nakamura T.,Tokyo University of Science | And 7 more authors.
Biochemical and Biophysical Research Communications | Year: 2012

ASB2 proteins are E3 ubiquitin (Ub) ligases that ubiquitinate filamins. There are two ASB2 splice variants, ASB2α and ASB2β. ASB2β has a ubiquitin-binding motif (UIM) at the N-terminal region but ASB2α does not. Here, we provide the first evidence that ASB2β but not ASB2α is monoubiquitinated and that this monoubiquitination involves the UIM. Myc-tagged ASB2β and hemagglutinin (HA)-tagged Ub were co-expressed in HEK293 cells using the pCMV expression vector. Immunoprecipitation with an anti-Myc antibody followed by immunoblotting with anti-Myc and anti-HA antibodies showed an additional ASB2β protein band that had both a Myc and a HA tag. The molecular weight of this protein was larger than that of ASB2β, and the difference in molecular weight between these two proteins corresponded to the molecular weight of monoubiquitin, strongly implying that monoubiquitinated ASB2β is produced in cells. ASB2β with mutations in the UIM motif; either Glu·Asp·Glu27-29Ala·Ala·Ala mutations (ASB2β M1) or a Ser38Ala mutation, (ASB2β M2) were not monoubiquitinated, suggesting the importance of the UIM for ASB2β monoubiquitination. Furthermore, an ASB2β mutant that lacked a SOCS box (ASB2β ΔC) and did not show E3 Ub ligase activity was monoubiquitinated to the same extent as the wild-type ASB2β. In contrast, an ASB2β mutant that lacked the UIM-containing domain (ASB2β ΔN) was not monoubiquitinated. These results suggest that ASB2β but not ASB2α might be monoubiquitinated and that the ASB2β UIM motif, but not its E3 Ub ligase activity, plays a pivotal role in this monoubiquitination. © 2012.

Kanamori H.,Keio University | Kawakami T.,Tokyo Medical University | Kawakami T.,Medical ProteoScope Company | Effendi K.,Keio University | And 12 more authors.
Oncology | Year: 2011

Objective: Hepatocellular carcinoma (HCC) is characterized by a multistage process of tumor progression. This study addressed its molecular features to identify novel protein candidates involved in HCC progression. Methods: Using liquid chromatography-tandem mass spectrometry, proteomes of 4 early HCCs and 4 non-HCC tissues derived from 2 cases of liver transplant surgery were compared with respect to the separation profiles of their tryptic peptides. Immunohistochemistry was performed on 106 HCC nodules to confirm the results of the proteomic analysis. Results: Statistical analysis of the profiles selected the peptide peaks differentiating HCC from non-HCC. A database search of the tandem mass spectrometry data from those peptide peaks identified 61 proteins, including a cytoskeletal protein, talin-1, as upregulated in HCC. Talin-1 expression levels in HCC nodules were significantly associated with the dedifferentiation of HCC (p = 0.001). A follow-up survey of the examined clinical cases revealed a correlation between talin-1 upregulation and a shorter time to recurrence after resection (p = 0.039), which may be related to the higher rate of portal vein invasion in HCCs with talin-1 up-regulation (p = 0.029). Conclusions: Proteomic analysis led to identification of talin-1 as a promising HCC marker. Talin-1 upregulation is associated with HCC progression and may serve as a prognostic marker. Copyright © 2011 S. Karger AG, Basel.

Kohroki J.,Tokyo University of Science | Kuroda S.,Tokyo University of Science | Takiguchi E.,Tokyo University of Science | Nakamura T.,Tokyo University of Science | And 5 more authors.
Biochemical and Biophysical Research Communications | Year: 2011

An alternative splicing variant of E3 ubiquitin ligase ASB2, termed ASB2a, has a distinct N-terminal sequence containing a ubiquitin-interacting motif (UIM) consensus sequence. Examination of the minimal essential region for binding to polyubiquitinated proteins indicated that the UIM consensus sequence (residues 26-41) alone is not enough, and that amino acids 12-41 from the N-terminus of ASB2a is essential for binding. ASB2a(12-41) peptide was chemically synthesized and coupled to Sepharose 4B via disulfide bonds. This ASB2a(12-41) peptide-coupled affinity resin bound both K48- and K63-linked polyubiquitinated proteins in cell lysates and comprehensively captured polyubiquitinated proteins, including polyubiquitinated β-catenin, I-κB, and EGF receptor, which were eluted with 2-mercaptoethanol under non-denaturing conditions. These results indicate that this UIM affinity purification (designated as ubiquitin-trapping) is a useful method to discover polyubiquitinated proteins and their associated proteins. © 2011 Elsevier Inc.

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