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Matuszewska E, Matysiak J, Bręborowicz A, Olejniczak K, Kycler Z, Kokot ZJ, Matysiak J. Proteomic features characterization of Hymenoptera venom allergy. Allergy Asthma Clin Immunol 2019; 15:77. [PMID: 31798646 PMCID: PMC6881982 DOI: 10.1186/s13223-019-0387-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 11/05/2019] [Indexed: 02/06/2023] Open
Abstract
Background Hymenoptera venom allergy is one of the most frequent causes of anaphylaxis. In its most severe form, the reaction to wasp and honey bee stings may be life-threatening. Therefore, immediate and proper diagnosis of venom allergy and implementation of suitable therapy are extremely important. Broadening the knowledge on the mechanism of the allergic reaction may contribute to the improvement of both diagnostic and treatment methods. Thus, this study aimed to discover changes in protein expression in serum of patients allergic to Hymenoptera (wasp and honeybee) venom and to point out proteins and peptides involved in the allergic inflammation. Methods Serum proteomic patterns typical to allergic patients and healthy volunteers were obtained with MALDI-TOF (matrix-assisted laser desorption/ionization-time of flight) mass spectrometer. The spectra were processed, analyzed and compared using advanced bioinformatics tools. The discriminative peaks were subjected to identification with liquid chromatography coupled with tandem mass spectrometry. Results This methodology allowed for the identification of four features differentiating between allergy and control groups. They were: fibrinogen alpha chain, coagulation factor XIII chain A, complement C4-A, and inter-alpha-trypsin inhibitor heavy chain H4. All of these proteins are involved in allergic inflammatory response. Conclusions Extending the knowledge of the Hymenoptera venom sensitization will contribute to the development of novel, sensitive and specific methods for quick and unambiguous allergy diagnosis. Understanding the basis of the allergy at the proteomic level will support the improvement of preventive and therapeutic measures.
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Affiliation(s)
- Eliza Matuszewska
- 1Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznan, Poland
| | - Joanna Matysiak
- Medical Faculty, Higher Vocational State School, 13 Kaszubska Street, 62-800 Kalisz, Poland
| | - Anna Bręborowicz
- 3Department of Pulmonology, Pediatric Allergy and Clinical Immunology, Poznan University of Medical Sciences, 27/33 Szpitalna Street, 60-572 Poznan, Poland
| | - Katarzyna Olejniczak
- 3Department of Pulmonology, Pediatric Allergy and Clinical Immunology, Poznan University of Medical Sciences, 27/33 Szpitalna Street, 60-572 Poznan, Poland
| | - Zdzisława Kycler
- 3Department of Pulmonology, Pediatric Allergy and Clinical Immunology, Poznan University of Medical Sciences, 27/33 Szpitalna Street, 60-572 Poznan, Poland
| | - Zenon J Kokot
- 1Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznan, Poland
| | - Jan Matysiak
- 1Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznan, Poland
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Uchida E, Suwa S, Yoshimoto R, Watanabe K, Kasama T, Miura O, Fukuda T. TOPK is regulated by PP2A and BCR/ABL in leukemia and enhances cell proliferation. Int J Oncol 2019; 54:1785-1796. [PMID: 30864683 DOI: 10.3892/ijo.2019.4740] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/21/2019] [Indexed: 11/06/2022] Open
Abstract
Although treatment of chronic myeloid leukemia (CML) has improved with the development of tyrosine kinase inhibitors (TKIs), patients develop fatal blast crisis (BC) whilst receiving TKI treatment. Alternative treatments for cases resistant to TKIs are required. A serine/threonine protein kinase, T‑lymphokine‑activated killer cell‑originated protein kinase (TOPK), is highly expressed in various malignant tumors. Binding of peptides to human leukocyte antigen was assessed via mass spectrometry in K562 CML cells. TOPK expression was assessed in various CML cell lines and in clinical samples obtained from patients with CML using reverse transcription‑quantitative polymerase chain reaction and western blot assays. It was observed that TOPK was expressed abundantly in BCR/ABL‑positive cell lines and at significantly higher levels in CML clinical samples compared with healthy donor samples. Overexpression of BCR/ABL or the presence of its inhibitor imatinib upregulated and downregulated TOPK expression, respectively, indicating that TOPK may be a target of BCR/ABL. TOPK inhibitor OTS514 suppressed proliferation of BCR/ABL‑positive cell lines and colony formation of CD34‑positive cells from patients with CML compared with lymphoma patients without bone marrow involvement. Furthermore, phosphorylation of TOPK was increased by protein phosphatase 2A (PP2A) inhibitor okadaic acid and was decreased in the presence of PP2A activator FTY720 compared with untreated samples. As constitutive BCR/ABL activity and inhibition of PP2A are key mechanisms of CML development, TOPK may be a crucial signaling molecule for this disease. Inhibition of TOPK may control disease status of CML, even in cases resistant to TKIs.
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Affiliation(s)
- Emi Uchida
- Department of Hematology, Tokyo Medical and Dental University, Tokyo 113‑8519, Japan
| | - Shihoko Suwa
- Department of Hematology, Tokyo Medical and Dental University, Tokyo 113‑8519, Japan
| | - Ryoto Yoshimoto
- Department of Hematology, Tokyo Medical and Dental University, Tokyo 113‑8519, Japan
| | - Ken Watanabe
- Department of Hematology, Tokyo Medical and Dental University, Tokyo 113‑8519, Japan
| | - Takeshi Kasama
- Research Center for Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113‑8519, Japan
| | - Osamu Miura
- Department of Hematology, Tokyo Medical and Dental University, Tokyo 113‑8519, Japan
| | - Tetsuya Fukuda
- Department of Hematology, Tokyo Medical and Dental University, Tokyo 113‑8519, Japan
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Kaur G, Gras S, Mobbs JI, Vivian JP, Cortes A, Barber T, Kuttikkatte SB, Jensen LT, Attfield KE, Dendrou CA, Carrington M, McVean G, Purcell AW, Rossjohn J, Fugger L. Structural and regulatory diversity shape HLA-C protein expression levels. Nat Commun 2017; 8:15924. [PMID: 28649982 PMCID: PMC5490200 DOI: 10.1038/ncomms15924] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 05/12/2017] [Indexed: 12/14/2022] Open
Abstract
Expression of HLA-C varies widely across individuals in an allele-specific manner. This variation in expression can influence efficacy of the immune response, as shown for infectious and autoimmune diseases. MicroRNA binding partially influences differential HLA-C expression, but the additional contributing factors have remained undetermined. Here we use functional and structural analyses to demonstrate that HLA-C expression is modulated not just at the RNA level, but also at the protein level. Specifically, we show that variation in exons 2 and 3, which encode the α1/α2 domains, drives differential expression of HLA-C allomorphs at the cell surface by influencing the structure of the peptide-binding cleft and the diversity of peptides bound by the HLA-C molecules. Together with a phylogenetic analysis, these results highlight the diversity and long-term balancing selection of regulatory factors that modulate HLA-C expression.
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Affiliation(s)
- Gurman Kaur
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Stephanie Gras
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Jesse I. Mobbs
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Julian P. Vivian
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Adrian Cortes
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Thomas Barber
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Subita Balaram Kuttikkatte
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Lise Torp Jensen
- Department of Clinical Medicine, Aarhus University Hospital, 8200N Aarhus, Denmark
| | - Kathrine E. Attfield
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Calliope A. Dendrou
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7FZ, UK
| | - Anthony W. Purcell
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
- Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Lars Fugger
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Department of Clinical Medicine, Aarhus University Hospital, 8200N Aarhus, Denmark
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Pan QZ, Pan K, Wang QJ, Weng DS, Zhao JJ, Zheng HX, Zhang XF, Jiang SS, Lv L, Tang Y, Li YQ, He J, Liu Q, Chen CL, Zhang HX, Xia JC. Annexin A3 as a potential target for immunotherapy of liver cancer stem-like cells. Stem Cells 2015; 33:354-66. [PMID: 25267273 DOI: 10.1002/stem.1850] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 09/04/2014] [Indexed: 12/14/2022]
Abstract
Cancer stem-like cells/cancer-initiating cells (CSCs/CICs) are considered to represent a small population of cancer cells that is resistant to conventional cancer treatments and responsible for tumor recurrence and metastasis. The aim of this study was to establish CSC/CIC-targeting immunotherapy. In this study, we found that Annexin A3 (ANXA3) was preferentially expressed in CSCs/CICs derived from hepatocellular carcinoma (HCC) cells compared to non-CSCs/CICs. In HCC samples, high levels of ANXA3 correlated with expansion of CD133(+) tumor cells representing CSCs/CICs in HCC; the combination of high levels of ANXA3 and CD133 was associated with progression of HCC. Overexpression of ANXA3 increased the proportion of CD133(+) cells, enhancing their tumorigenicity. On the contrary, knockdown of ANXA3 decreased CD133(+) cells and inhibited tumorigenicity. The mechanistic study revealed that ANXA3-mediated maintenance of HCC CSCs/CICs activity was likely involved with the HIF1A/Notch pathway. Using ANXA3 as a target, ANXA3-transfected dendritic cells could induce more functionally active T cells and these effector T cells could superiorly kill CD133(+) HCC CSCs/CICs in vitro and in vivo. Taken together, our findings suggest that ANXA3 plays a role in HCC CSC/CIC maintenance, and that ANXA3 may represent a potential CSC/CIC-specific therapeutic target for improving the treatment of HCC.
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Affiliation(s)
- Qiu-Zhong Pan
- Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China; Department of Biotherapy, Sun Yat-Sen University Cancer Center, Guangzhou, People's Republic of China
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Kim HS, Kang D, Moon MH, Kim HJ. Identification of pancreatic cancer-associated tumor antigen from HSP-enriched tumor lysate-pulsed human dendritic cells. Yonsei Med J 2014; 55:1014-27. [PMID: 24954332 PMCID: PMC4075362 DOI: 10.3349/ymj.2014.55.4.1014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 10/23/2013] [Accepted: 11/04/2013] [Indexed: 11/27/2022] Open
Abstract
PURPOSE Vaccine strategies utilizing dendritic cells (DCs) to elicit anti-tumor immunity are the subject of intense research. Although we have shown that DCs pulsed with heat-treated tumor lysate (HTL) induced more potent anti-tumor immunity than DCs pulsed with conventional tumor lysate (TL), the underlying molecular mechanism is unclear. In order to explore the molecular basis of this approach and to identify potential antigenic peptides from pancreatic cancer, we analyzed and compared the major histocompatibility complex (MHC) ligands derived from TL- and HTL-pulsed dendritic cells by mass spectrophotometry. MATERIALS AND METHODS Human monocyte-derived dendritic cells were pulsed with TL or HTL prior to maturation induction. To delineate differences of MHC-bound peptide repertoire eluted from DCs pulsed with TL or HTL, nanoflow liquid chromatography-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS-MS) was employed. RESULTS HTL, but not TL, significantly induced DC function, assessed by phenotypic maturation, allostimulation capacity and IFN-γ secretion by stimulated allogeneic T cells. DCs pulsed with TL or HTL displayed pancreas or pancreatic cancer-related peptides in context of MHC class I and II molecules. Some of the identified peptides had not been previously reported as expressed in pancreatic cancer or cancer of other tissue types. CONCLUSION Our partial lists of MHC-associated peptides revealed the differences between peptide profiles eluted from HTL-and TL-loaded DCs, implying that induced heat shock proteins in HTL chaperone tumor-derived peptides enhanced their delivery to DCs and promoted cross-presentation by DC. These findings may aid in identifying novel tumor antigens or biomarkers and in designing future vaccination strategies.
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Affiliation(s)
- Han-Soo Kim
- Innovative Cell and Gene Therapy Center, International St. Mary's Hospital, Incheon, Korea
| | - Dukjin Kang
- Center for Bioanalysis, Division of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon, Korea
| | | | - Hyung Jik Kim
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon, Korea.
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Leng J, Zhu D, Wu D, Zhu T, Zhao N, Guo Y. Analysis of the differentially expressed low molecular weight peptides in human serum via an N-terminal isotope labeling technique combining nano-liquid chromatography/matrix-assisted laser desorption/ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:2555-2562. [PMID: 23008073 DOI: 10.1002/rcm.6369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RATIONALE Peptidomics analysis of human serum is challenging due to the low abundance of serum peptides and interference from the complex matrix. This study analyzed the differentially expressed (DE) low molecular weight peptides in human serum integrating a DMPITC-based N-terminal isotope labeling technique with nano-liquid chromatography and matrix-assisted laser desorption/ionization mass spectrometry (nano-LC/MALDI-MS). METHODS The workflow introduced a [d(6)]-4,6-dimethoxypyrimidine-2-isothiocyanate (DMPITC)-labeled mixture of aliquots from test samples as the internal standard. The spiked [d(0)]-DMPITC-labeled samples were separated by nano-LC then spotted on the MALDI target. Both quantitative and qualitative studies for serum peptides were achieved based on the isotope-labeled peaks. RESULTS The DMPITC labeling technique combined with nano-LC/MALDI-MS not only minimized the errors in peptide quantitation, but also allowed convenient recognition of the labeled peptides due to the 6 Da mass difference. The data showed that the entire research procedure as well as the subsequent data analysis method were effective, reproducible, and sensitive for the analysis of DE serum peptides. CONCLUSIONS This study successfully established a research model for DE serum peptides using DMPITC-based N-terminal isotope labeling and nano-LC/MALDI-MS. Application of the DMPITC-based N-terminal labeling technique is expected to provide a promising tool for the investigation of peptides in vivo, especially for the analysis of DE peptides under different biological conditions.
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Affiliation(s)
- Jiapeng Leng
- Shanghai Mass Spectrometry Center, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
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Application of on-line nanoLC-IT-TOF in the identification of serum β-catenin complex in mice scald model. PLoS One 2012; 7:e46530. [PMID: 23056334 PMCID: PMC3467219 DOI: 10.1371/journal.pone.0046530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 09/04/2012] [Indexed: 11/19/2022] Open
Abstract
Severe burn shock remains an unresolved clinical problem with an urgent need to explore novel therapeutic treatments. Intracellular β-catenin, through interaction with other proteins, has been reported to be able to regulate the size of cutaneous wounds. Higher expression of β-catenin is associated with larger sized wounds. However, the identification of serum β-catenin complex is difficult and has been rarely reported. The exploitation of more binding partners can contribute to uncovering the exact mechanisms behind serum β-catenin mediated biological effects. Here, we describe a method that consists of immunoprecipitation, SDS-PAGE, in-gel digestion, and nanoLC coupled to LCMS-IT-TOF for the investigation of serum β-catenin complex in mice scald model. Among selected gel bands obtained from the protein gels, a total of 31 peptides were identified and sequenced with high statistical significance (p<0.01). Three proteins (alpha-2-marcoglobulin, serine protease inhibitor A3K, and serine protease inhibitor A1A) were identified and validated with high reliability and high reproducibility. It was inferred that these proteins might interact with serum β-catenin, which could affect the wound healing resulting from burn shock. Our study demonstrated that the on-line coupling of nano-LC with a LCMS-IT-TOF mass spectrometer was capable of sensitive and automated characterization of the serum β-catenin complex in mice scald model.
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Arikata M, Itoh Y, Okamatsu M, Maeda T, Shiina T, Tanaka K, Suzuki S, Nakayama M, Sakoda Y, Ishigaki H, Takada A, Ishida H, Soda K, Pham VL, Tsuchiya H, Nakamura S, Torii R, Shimizu T, Inoko H, Ohkubo I, Kida H, Ogasawara K. Memory immune responses against pandemic (H1N1) 2009 influenza virus induced by a whole particle vaccine in cynomolgus monkeys carrying Mafa-A1*052:02. PLoS One 2012; 7:e37220. [PMID: 22623997 PMCID: PMC3356377 DOI: 10.1371/journal.pone.0037220] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Accepted: 04/15/2012] [Indexed: 11/18/2022] Open
Abstract
We made an H1N1 vaccine candidate from a virus library consisting of 144 ( = 16 HA×9 NA) non-pathogenic influenza A viruses and examined its protective effects against a pandemic (2009) H1N1 strain using immunologically naïve cynomolgus macaques to exclude preexisting immunity and to employ a preclinical study since preexisting immunity in humans previously vaccinated or infected with influenza virus might make comparison of vaccine efficacy difficult. Furthermore, macaques carrying a major histocompatibility complex class I molecule, Mafa-A1*052:02, were used to analyze peptide-specific CD8(+) T cell responses. Sera of macaques immunized with an inactivated whole particle formulation without addition of an adjuvant showed higher neutralization titers against the vaccine strain A/Hokkaido/2/1981 (H1N1) than did sera of macaques immunized with a split formulation. Neutralization activities against the pandemic strain A/Narita/1/2009 (H1N1) in sera of macaques immunized twice with the split vaccine reached levels similar to those in sera of macaques immunized once with the whole particle vaccine. After inoculation with the pandemic virus, the virus was detected in nasal samples of unvaccinated macaques for 6 days after infection and for 2.67 days and 5.33 days on average in macaques vaccinated with the whole particle vaccine and the split vaccine, respectively. After the challenge infection, recall neutralizing antibody responses against the pandemic virus and CD8(+) T cell responses specific for nucleoprotein peptide NP262-270 bound to Mafa-A1*052:02 in macaques vaccinated with the whole particle vaccine were observed more promptly or more vigorously than those in macaques vaccinated with the split vaccine. These findings demonstrated that the vaccine derived from our virus library was effective for pandemic virus infection in macaques and that the whole particle vaccine conferred more effective memory and broader cross-reactive immune responses to macaques against pandemic influenza virus infection than did the split vaccine.
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Affiliation(s)
- Masahiko Arikata
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
- Department of Otorhinolaryngology-Head and Neck Surgery, Shiga University of Medical Science, Otsu, Japan
| | - Yasushi Itoh
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
- * E-mail:
| | - Masatoshi Okamatsu
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Toshinaga Maeda
- Division of Molecular Medical Biochemistry, Shiga University of Medical Science, Otsu, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Keiko Tanaka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Shingo Suzuki
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Misako Nakayama
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Hirohito Ishigaki
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Ayato Takada
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hideaki Ishida
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Kosuke Soda
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Van Loi Pham
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Hideaki Tsuchiya
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Shinichiro Nakamura
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Ryuzo Torii
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Takeshi Shimizu
- Department of Otorhinolaryngology-Head and Neck Surgery, Shiga University of Medical Science, Otsu, Japan
| | - Hidetoshi Inoko
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Iwao Ohkubo
- Division of Molecular Medical Biochemistry, Shiga University of Medical Science, Otsu, Japan
| | - Hiroshi Kida
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kazumasa Ogasawara
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
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Qian K, Gu W, Yuan P, Liu F, Wang Y, Monteiro M, Yu C. Enrichment and detection of peptides from biological systems using designed periodic mesoporous organosilica microspheres. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:231-236. [PMID: 22135224 DOI: 10.1002/smll.201101770] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 09/26/2011] [Indexed: 05/31/2023]
Abstract
Periodic mesoporous organosilica microspheres (PMOMs) are designed with integrated structural features, including a cubic mesostructure, hydrophobic wall composition, a uniform pore size of ≈3 nm, and a spherical morphology in micrometers, all advantageous for size-selective and highly efficient enrichment of peptides from mixtures. Consequently, PMOMs can be used to capture peptides in a range of complex biological systems.
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Affiliation(s)
- Kun Qian
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia Fax: (+)61-7-33463973
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Agrawal GK, Bourguignon J, Rolland N, Ephritikhine G, Ferro M, Jaquinod M, Alexiou KG, Chardot T, Chakraborty N, Jolivet P, Doonan JH, Rakwal R. Plant organelle proteomics: collaborating for optimal cell function. MASS SPECTROMETRY REVIEWS 2011; 30:772-853. [PMID: 21038434 DOI: 10.1002/mas.20301] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 02/02/2010] [Accepted: 02/02/2010] [Indexed: 05/10/2023]
Abstract
Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), P.O. Box 13265, Sanepa, Kathmandu, Nepal.
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Seliger B, Dressler SP, Massa C, Recktenwald CV, Altenberend F, Bukur J, Marincola FM, Wang E, Stevanovic S, Lichtenfels R. Identification and characterization of human leukocyte antigen class I ligands in renal cell carcinoma cells. Proteomics 2011; 11:2528-41. [PMID: 21595034 DOI: 10.1002/pmic.201000486] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 03/07/2011] [Accepted: 03/28/2011] [Indexed: 02/01/2023]
Abstract
The presentation of tumor antigen-derived peptides by human leukocyte antigen (HLA) class I surface antigens on tumor cells is a key prerequisite to trigger effective T-cell responses in cancer patients. Multiple complementary strategies like cDNA and serological expression cloning, reverse immunology and different 'ome'-based methods have been employed to identify potential T-cell targets. This report focuses on a ligandomic profiling approach leading to the identification of 49 naturally processed HLA class I peptide ligands presented on the cell surface of renal cell carcinoma (RCC) cells. The source proteins of the defined HLA ligands are classified according to their biological function and subcellular localization. Previously established cDNA microarray data of paired tissue specimen of RCC and renal epithelium assessed the transcriptional regulation for 28 source proteins. In addition, HLA-A2-restricted, peptide-specific T cells directed against a HLA ligand derived from sulfiredoxin-1 (SRXN1) were generated, which were able to recognize and lyse ligand-presenting target cells in a HLA class I-restricted manner. Furthermore, tumor-infiltrating T cells isolated from a RCC patient were also able to kill SRXN1 expressing tumor cells. Thus, this experimental strategy might be suited to define potential candidate biomarkers and novel targets for T-cell-based immunotherapies of this disease.
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Affiliation(s)
- Barbara Seliger
- Institute of Medical Immunology, Martin-Luther University Halle-Wittenberg, Halle, Germany.
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12
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Condina MR, Gustafsson JOR, Klingler-Hoffmann M, Bagley CJ, McColl SR, Hoffmann P. EZYprep LC-coupled MALDI-TOF/TOF MS: an improved matrix spray application for phosphopeptide characterisation. Proteomics 2010; 10:2516-30. [PMID: 20432483 DOI: 10.1002/pmic.200900800] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The quality of MALDI-TOF mass spectrometric analysis is highly dependent on the matrix and its deposition strategy. Although different matrix-deposition methods have specific advantages, one major problem in the field of proteomics, particularly with respect to quantitation, is reproducibility between users or laboratories. Compounding this is the varying crystal homogeneity of matrices depending on the deposition strategy used. Here, we describe a novel optimised matrix-deposition strategy for LC-MALDI-TOF/TOF MS using an automated instrument that produces a nebulised matrix "mist" under controlled atmospheric conditions. Comparisons of this with previously reported strategies showed the method to be advantageous for the atypical matrix, 2,5-DHB, and improved phosphopeptide ionisation when compared with deposition strategies for CHCA. This optimised DHB matrix-deposition strategy with LC-MALDI-TOF/TOF MS, termed EZYprep LC, was subsequently optimised for phosphoproteome analysis and compared to LC-ESI-IT-MS and a previously reported approach for phosphotyrosine identification and characterisation. These methods were used to map phosphorylation on epidermal growth factor-stimulated epidermal growth factor receptor to gauge the sensitivity of the proposed method. EZYprep DHB LC-MALDI-TOF/TOF MS was able to identify more phosphopeptides and characterise more phosphorylation sites than the other two proteomic strategies, thus proving to be a sensitive approach for phosphoproteome analysis.
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Affiliation(s)
- Mark R Condina
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA, Australia
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13
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Abstract
Modulation of the immune system for therapeutic ends has a long history, stretching back to Edward Jenner's use of cowpox to induce immunity to smallpox in 1796. Since then, immunotherapy, in the form of prophylactic and therapeutic vaccines, has enabled doctors to treat and prevent a variety of infectious diseases, including cholera, poliomyelitis, diphtheria, measles and mumps. Immunotherapy is now increasingly being applied to oncology. Cancer immunotherapy attempts to harness the power and specificity of the immune system for the treatment of malignancy. Although cancer cells are less immunogenic than pathogens, the immune system is capable of recognizing and eliminating tumor cells. However, tumors frequently interfere with the development and function of immune responses. Thus, the challenge for cancer immunotherapy is to apply advances in cellular and molecular immunology and develop strategies that effectively and safely augment antitumor responses.
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Affiliation(s)
- Joseph F. Murphy
- Department of Surgery, Trinity Centre for Health Sciences, Adelaide and Meath incorporating the National Children’s Hospital, Tallaght, Dublin 24, Ireland
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14
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Liepe J, Mishto M, Textoris-Taube K, Janek K, Keller C, Henklein P, Kloetzel PM, Zaikin A. The 20S proteasome splicing activity discovered by SpliceMet. PLoS Comput Biol 2010; 6:e1000830. [PMID: 20613855 PMCID: PMC2891702 DOI: 10.1371/journal.pcbi.1000830] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 05/24/2010] [Indexed: 01/18/2023] Open
Abstract
The identification of proteasome-generated spliced peptides (PSP) revealed a new unpredicted activity of the major cellular protease. However, so far characterization of PSP was entirely dependent on the availability of patient-derived cytotoxic CD8+ T lymphocytes (CTL) thus preventing a systematic investigation of proteasome-catalyzed peptide splicing (PCPS). For an unrestricted PSP identification we here developed SpliceMet, combining the computer-based algorithm ProteaJ with in vitro proteasomal degradation assays and mass spectrometry. By applying SpliceMet for the analysis of proteasomal processing products of four different substrate polypeptides, derived from human tumor as well as viral antigens, we identified fifteen new spliced peptides generated by PCPS either by cis or from two separate substrate molecules, i.e., by trans splicing. Our data suggest that 20S proteasomes represent a molecular machine that, due to its catalytic and structural properties, facilitates the generation of spliced peptides, thereby providing a pool of qualitatively new peptides from which functionally relevant products may be selected.
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Affiliation(s)
- Juliane Liepe
- Institut für Biochemie, Charité, Universitätsmedizin Berlin, Berlin, Germany
- Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College London, London, United Kingdom
| | - Michele Mishto
- Institut für Biochemie, Charité, Universitätsmedizin Berlin, Berlin, Germany
- Interdepartmental Center for Studies on Biophysics, Bioinformatics and Biocomplexity ‘L. Galvani’ (CIG), University of Bologna, Bologna, Italy
| | | | - Katharina Janek
- Institut für Biochemie, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Christin Keller
- Institut für Biochemie, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Petra Henklein
- Institut für Biochemie, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | | | - Alexey Zaikin
- Institute for Women's Health and Department of Mathematics, University College London, London, United Kingdom
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15
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Peš O, Preisler J. Off-line coupling of microcolumn separations to desorption mass spectrometry. J Chromatogr A 2010; 1217:3966-77. [DOI: 10.1016/j.chroma.2010.02.058] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 02/22/2010] [Accepted: 02/24/2010] [Indexed: 01/13/2023]
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16
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Deng M, Li F, Ballif BA, Li S, Chen X, Guo L, Ye X. Identification and functional analysis of a novel cyclin e/cdk2 substrate ankrd17. J Biol Chem 2009; 284:7875-88. [PMID: 19150984 DOI: 10.1074/jbc.m807827200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cyclin E/Cdk2 is a key regulator in G(1)-S transition. We have identified a novel cyclin E/Cdk2 substrate called Ankrd17 (ankyrin repeat protein 17) using the TAP tag purification technique. Ankrd17 protein contains two clusters of a total 25 ankyrin repeats at its N terminus, one NES (nuclear exporting signal) and one NLS (nuclear localization signal) in the middle, and one RXL motif at its C terminus. Ankrd17 is expressed in various tissues and associates with cyclin E/Cdk2 in an RXL-dependent manner. It can be phosphorylated by cyclin E/Cdk2 at 3 phosphorylation sites (Ser(1791), Ser(1794), and Ser(2150)). Overexpression of Ankrd17 promotes S phase entry, whereas depletion of Ankrd17 expression by small interfering RNA inhibits DNA replication and blocks cell cycle progression as well as up-regulates the expression of p53 and p21. Ankrd17 is localized to the nucleus and interacts with DNA replication factors including MCM family members, Cdc6 and PCNA. Depletion of Ankrd17 results in decreased loading of Cdc6 and PCNA onto DNA suggesting that Ankrd17 may be directly involved in the DNA replication process. Taken together, these data indicate that Ankrd17 is an important downstream effector of cyclin E/Cdk2 and positively regulates G(1)/S transition.
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Affiliation(s)
- Min Deng
- Department of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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17
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Linscheid MW, Ahrends R, Pieper S, Kühn A. Liquid chromatography-mass spectrometry-based quantitative proteomics. Methods Mol Biol 2009; 564:189-205. [PMID: 19544024 DOI: 10.1007/978-1-60761-157-8_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
During the last decades, molecular sciences revolutionized biomedical research and gave rise to the biotechnology industry. During the next decades, the application of the quantitative sciences--informatics, physics, chemistry, and engineering--to biomedical research brings about the next revolution that will improve human healthcare and certainly create new technologies, since there is no doubt that small changes can have great effects. It is not a question of "yes" or "no," but of "how much," to make best use of the medical options we will have. In this context, the development of accurate analytical methods must be considered a cornerstone, since the understanding of biological processes will be impossible without information about the minute changes induced in cells by interactions of cell constituents with all sorts of endogenous and exogenous influences and disturbances. The first quantitative techniques, which were developed, allowed monitoring relative changes only, but they clearly showed the significance of the information obtained. The recent advent of techniques claiming to quantify proteins and peptides not only relative to each other, but also in an absolute fashion, promised another quantum leap, since knowing the absolute amount will allow comparing even unrelated species and the definition of parameters will permit to model biological systems much more accurate than before. To bring these promises to life, several approaches are under development at this point in time and this review is focused on those developments.
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Affiliation(s)
- Michael W Linscheid
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor Str. 2, 12489 Berlin, Germany
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18
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Lasaosa M, Delmotte N, Huber CG, Melchior K, Heinzle E, Tholey A. A 2D reversed-phase × ion-pair reversed-phase HPLC-MALDI TOF/TOF-MS approach for shotgun proteome analysis. Anal Bioanal Chem 2008; 393:1245-56. [DOI: 10.1007/s00216-008-2539-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 11/13/2008] [Accepted: 11/21/2008] [Indexed: 10/21/2022]
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19
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Saz JM, Marina ML. Application of micro- and nano-HPLC to the determination and characterization of bioactive and biomarker peptides. J Sep Sci 2008; 31:446-58. [PMID: 18266259 DOI: 10.1002/jssc.200700589] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This article reviews the works published since 2001 (included) on the micro/nano-HPLC analysis of bioactive and biomarker peptides. The main achievements related to the improvement of the detection sensitivity, quantitation repeatability and reproducibility, and separation selectivity are highlighted. A wide attention is paid to the application of micro/nano-HPLC to the analysis of bioactive peptides in biological matrices. The uses of micro/nano-HPLC in peptidomics to discover new endogenous bioactive peptides and to develop quantitation procedures to compare the levels of peptides of interest in two different biological samples are also considered. Finally, the application of micro/nano-HPLC to the analysis of biomarker peptides for various diseases is also included in this review.
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Affiliation(s)
- José María Saz
- Department of Analytical Chemistry, Faculty of Chemistry, University of Alcalá, Alcalá de Henares, Madrid, Spain
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20
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LC MALDI-TOF MS/MS and LC ESI FTMS analyses of HLA-B27 associated peptides isolated from peripheral blood cells. Immunol Lett 2008; 116:79-85. [DOI: 10.1016/j.imlet.2007.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 11/12/2007] [Accepted: 11/13/2007] [Indexed: 11/19/2022]
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21
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Seliger B, Dressler SP, Lichtenfels R, Kellner R. Candidate biomarkers in renal cell carcinoma. Proteomics 2007; 7:4601-12. [DOI: 10.1002/pmic.200700415] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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22
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Millo E, Pietra G, Armirotti A, Vacca P, Mingari MC, Moretta L, Damonte G. Purification and HPLC-MS analysis of a naturally processed HCMV-derived peptide isolated from the HEK-293T/HLA-E+/Ul40+ cell transfectants and presented at the cell surface in the context of HLA-E. J Immunol Methods 2007; 322:128-36. [PMID: 17331531 DOI: 10.1016/j.jim.2007.01.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Revised: 01/16/2007] [Accepted: 01/18/2007] [Indexed: 11/20/2022]
Abstract
A new method for isolation and characterization of peptides presented in the context of the nonclassical human leukocytes antigen (HLA) class I molecule HLA-E was developed. A combination of different chromatographic steps coupled with electrospray mass spectrometry allowed us to detect the presence of small amounts of a naturally processed human Cytomegalovirus (HCMV)-derived peptide isolated from the HEK-293T/HLA-E+/UL40+ transfected cells of from HELA cell line. The peptide sequence was confirmed by tandem mass spectrometry (MS/MS). This approach provides a versatile and sensitive method for direct identification of MHC class I-binding peptides that might be derive from different pathogen or tumor-associated proteins.
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Affiliation(s)
- E Millo
- Dipartimento di Medicina Sperimentale, Sezione di Biochimica, c/o CEBR, Università degli Studi di Genova, Genova, Italy.
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23
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Wahl A, Weidanz J, Hildebrand W. Direct class I HLA antigen discovery to distinguish virus-infected and cancerous cells. Expert Rev Proteomics 2007; 3:641-52. [PMID: 17181478 DOI: 10.1586/14789450.3.6.641] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Class I human leukocyte antigen molecules are nature's proteome-scanning chips, presenting thousands of endogenously loaded peptides on the surface of virtually every cell in the body. Cytotoxic T cells survey the class I human leukocyte antigen peptide cargo presented, recognize peptides unique to unhealthy cells and destroy diseased cells. A precise understanding of how class I molecules distinguish diseased cells is positioned to drive immune-based diagnostics, therapies and vaccines. When identifying epitopes unique to unhealthy cells, the most experimentally direct approach is to examine the class I-presented peptides of infected/cancerous cells. Here we discuss the strategies adapted for protein production, protein/peptide purification, peptide separation and for maintaining experimental reproducibility during the direct characterization of class I human leukocyte antigen peptides.
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Affiliation(s)
- Angela Wahl
- University of Oklahoma, Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 975 NE, 10 Street, BRC Room 317, Oklahoma City, OK 73104, USA.
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24
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Hillen N, Stevanovic S. Contribution of mass spectrometry-based proteomics to immunology. Expert Rev Proteomics 2007; 3:653-64. [PMID: 17181480 DOI: 10.1586/14789450.3.6.653] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Antigen processing forwards various information about the cellular status and the proteome to the cell surface for scrutiny by the cellular immune system. Thus the repertoire of major histocompatibility complex (MHC)-bound peptides and the MHC ligandome, indirectly mirrors the proteome in order to make alterations instantly detectable and, if necessary, to oppose them. Mass spectrometry is the core technology for analysis of both proteome and MHC ligandome and has evoked several strategies to gain qualitative and quantitative insight into the MHC-presented peptide repertoire. After immunoaffinity purification of detergent-solubilized peptide-MHC complexes followed by acid elution of peptides, liquid chromatography-mass spectrometry is applied to determine individual peptide sequences and, thus, allow qualitative characterization of the MHC-bound repertoire. Differential quantification based on stable isotope labeling enables the relative comparison of two samples, such as diseased and healthy tissue. Targeted searches for certain natural ligands, such as the 'predict-calibrate-detect' strategy, include motif-based epitope prediction and calibration with reference peptides. Thus, various approaches are now available for exposing and understanding the intricacies of the MHC ligand repertoire. Analysis of differences in the MHC ligandome under distinct conditions contributes to our understanding of basic cellular processes, but also enables the formulation of immunodiagnostic or immunotherapeutic strategies.
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Affiliation(s)
- Nina Hillen
- University of Tübingen, Department of Immunology, Institute for Cell Biology, 72076 Tübingen, Germany.
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25
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Abstract
Liquid chromatography-matrix-assisted laser desorption/ionization mass spectrometry represents a sensitive, hyphenated MS- and MS/MS-technique with a broad range of applications in all areas ofproteome analysis. Whereas a number of interface types have been developed for coupling MALDI MS and liquid chromatography, in this chapter selected on-line and off-line types and techniques will be discussed with respect to their individual properties and performance. The technique is especially attractive in off-line mode where LC-separation and MS analyses are decoupled and each step can be performed at its individual optimum. Different speed of chromatographic separation and achievement of S/N criteria in MS or MS/MS mode can be optimized independently by individual adjustment of specific operating parameters. This flexibility makes LC-MALDI MS attractive for the analysis of peptide mixtures from low to medium complexity. Using sequential MS analysis of parallel LC runs (multiplexing), even highly complex samples can be handled. Quantitation at the MS and MS/MS level can be accomplished by a variety of labeling techniques, where the predominant formation of singly charged ions in MALDI alleviates the assignment of isotopomers. After discussing the level of complementarity between LC-MALDI and LC-ESI MS, selected applications of LC-MALDI MS are presented. Examples of membrane protein analysis applying 1D SDS PAGE are discussed in detail as well as applications in protein interaction analysis. These application examples clearly show that in all respects LC-MALDI MS and MS/MS are flexible and sensitive techniques which can be adapted to a wide range of different workflows.
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26
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Gouttefangeas C, Stenzl A, Stevanović S, Rammensee HG. Immunotherapy of renal cell carcinoma. Cancer Immunol Immunother 2007; 56:117-28. [PMID: 16676181 PMCID: PMC11030119 DOI: 10.1007/s00262-006-0172-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2006] [Accepted: 04/10/2006] [Indexed: 01/02/2023]
Abstract
Carcinomas of the kidney generally have a poor prognosis and respond minimally to classical radiotherapy or chemotherapy. Immunotherapy constitutes an interesting alternative to these established forms of treatment, and indeed, cytokine-based therapies have been used for many years, leading to favorable clinical responses in a small subset of patients. During the past few years, immunotherapeutical trials targeting renal cell tumor-associated antigens have also been reported, with diverse passive or active approaches using antibodies or aimed at activating tumor-directed T lymphocytes. The following review presents the results and the progress made in the field, including classical cytokine treatments, non-myeloablative stem cell transplantation and antigen specific-based trials, with special focus on T-cell studies. In consideration of the few specific molecular targets described so far for this tumor entity, current strategies which can lead to the identification of new relevant antigens will be discussed. Hopefully these will very soon contribute to an improvement in renal cell carcinoma specific immunotherapy and its evaluation.
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Affiliation(s)
- Cécile Gouttefangeas
- Institute for Cell Biology, Department of Immunology, Eberhard Karls University, Auf der Morgenstelle 15, 72076, Tubingen, Germany.
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27
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Tabi Z, Man S. Challenges for cancer vaccine development. Adv Drug Deliv Rev 2006; 58:902-15. [PMID: 16979786 DOI: 10.1016/j.addr.2006.05.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2006] [Revised: 05/01/2006] [Accepted: 07/10/2006] [Indexed: 11/19/2022]
Abstract
The first generation of human cancer vaccines has been tested in phase III clinical trials, but only a few of these have demonstrated sufficient efficacy to be licensed for clinical use. This article reviews some of the mechanisms that could contribute to these limited clinical responses, and highlights the challenges faced for development of future vaccines.
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Affiliation(s)
- Z Tabi
- Department of Oncology and Palliative Medicine, Velindre Hospital, Whitchurch, Cardiff CF14 2TL, UK.
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