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Beer I. Commentary: An In Silico - In Vitro Pipeline Identifying an HLA-A*02:01 + KRAS G12V + Spliced Epitope Candidate for a Broad Tumor-Immune Response in Cancer Patients. Front Immunol 2021; 12:523906. [PMID: 34326832 PMCID: PMC8315040 DOI: 10.3389/fimmu.2021.523906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/17/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ilan Beer
- Adicet Bio Inc., Menlo Park, CA, United States
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Chirurgii RV, Č R, Beer I, Job I, Janek J. Multidisciplinary surgical approach to renal cancer with vena cava invasion and pulmonary embolism. Rozhl Chir 2021; 100:88-93. [PMID: 33910342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
INTRODUCTION Renal cancer is unique for many reasons. One reason is that renal cell carcinoma can grow directly into the drainage veins of the kidney, which enter the inferior vena cava leading to the heart. This growth of tumor cells into the veins is called a tumor thrombus and is a locally aggressive renal cancer. The present article informs about the experience of our cardiac surgery department together with the transplant surgery department in successful surgical removal of a kidney with tumor, with invasion into the inferior vena cava, right atrium of the heart and pulmonary artery in two case reports. CASE REPORTS A 32 years old female without significant history, with suddenly evolving dyspnea was urgently admitted to hospital. Her condition was suspected to be caused by pulmonary artery embolisation. The diagnosis was confirmed by CT scan which revealed unknown tumor mass of the right kidney and tumor embolisation in inferior vena cava and pulmonary artery. The patient was urgently operated by a vascular surgeon and cardiothoracic surgeon. They successfully performed left radical nephrectomy and total thromboembolectomy of the tumorous masses from vena cava inferior and pulmonary artery. The postoperative course was without complications, postoperative CT revealed no residual masses, and the patient was discharged in a good condition from the hospital. A 58 years old male with arterial hypertension suffered from orchiepididymitis. CT scan showed a tumor of the left kidney with propagation of tumorous masses to inferior vena cava and pulmonary artery. In elective surgery the vascular surgeon and cardiothoracic surgeon successfully performed left radical nephrectomy with total thromboembolectomy of the tumorous masses from inferior vena cava and pulmonary artery. After surgery a temporary paralytic ileus and an episode of atrial fibrillation occurred. Both are common postoperative complications related to the given surgical procedure. Follow-up CT scan showed no residual tumor or thrombus in inferior vena cava and pulmonary artery. Echocardiography revealed persistent dilation of right compartments of the heart with good systolic functions of both ventricles. The patient was discharged from hospital in a good condition. CONCLUSION Surgical removal of renal tumor and tumor thrombus - radical nephrectomy with tumor thrombectomy - can be a curative treatment and can ensure long-term survival of the patient. Depending on the extent of the tumor thrombus, these operations can be performed in different ways - mini-invasive, robotic or open. When open surgery is used, it is possible to perform the procedure with or without extracorporeal circulation (cardiopulmonary bypass - CPB) depending on the extent of the disease.
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Hocking KM, Alvis BD, Baudenbacher F, Boyer R, Brophy CM, Beer I, Eagle S. Peripheral i.v. analysis (PIVA) of venous waveforms for volume assessment in patients undergoing haemodialysis. Br J Anaesth 2019; 119:1135-1140. [PMID: 29028929 DOI: 10.1093/bja/aex271] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2017] [Indexed: 11/13/2022] Open
Abstract
Background The assessment of intravascular volume status remains a challenge for clinicians. Peripheral i.v. analysis (PIVA) is a method for analysing the peripheral venous waveform that has been used to monitor volume status. We present a proof-of-concept study for evaluating the efficacy of PIVA in detecting changes in fluid volume. Methods We enrolled 37 hospitalized patients undergoing haemodialysis (HD) as a controlled model for intravascular volume loss. Respiratory rate (F0) and pulse rate (F1) frequencies were measured. PIVA signal was obtained by fast Fourier analysis of the venous waveform followed by weighing the magnitude of the amplitude of the pulse rate frequency. PIVA was compared with peripheral venous pressure and standard monitoring of vital signs. Results Regression analysis showed a linear correlation between volume loss and change in the PIVA signal (R2=0.77). Receiver operator curves demonstrated that the PIVA signal showed an area under the curve of 0.89 for detection of 20 ml kg-1 change in volume. There was no correlation between volume loss and peripheral venous pressure, blood pressure or pulse rate. PIVA-derived pulse rate and respiratory rate were consistent with similar numbers derived from the bio-impedance and electrical signals from the electrocardiogram. Conclusions PIVA is a minimally invasive, novel modality for detecting changes in fluid volume status, respiratory rate and pulse rate in spontaneously breathing patients with peripheral i.v. cannulas.
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Affiliation(s)
- K M Hocking
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | | | - F Baudenbacher
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - R Boyer
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - C M Brophy
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - I Beer
- Medical Affairs, Baxter International Inc., Deerfield, IL, USA
| | - S Eagle
- Department of Anesthesiology
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Mylonas R, Beer I, Iseli C, Chong C, Pak HS, Gfeller D, Coukos G, Xenarios I, Müller M, Bassani-Sternberg M. Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome. Mol Cell Proteomics 2018; 17:2347-2357. [PMID: 30171158 PMCID: PMC6283289 DOI: 10.1074/mcp.ra118.000877] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/27/2018] [Indexed: 12/21/2022] Open
Abstract
It has been reported that about 30% of the HLA-I ligands are produced by proteasomal splicing of two noncontiguous fragments of a parental protein. We report that the identification of many of those spliced peptides is ambiguous. With an alternative workflow, based on de novo sequencing and subsequent verification with multiple search tools, we estimate that the upper bound for the proportion of cis-spliced peptides is 2–6%. Nevertheless, the true contribution of spliced peptides to the ligandome may be much smaller. Spliced peptides are short protein fragments spliced together in the proteasome by peptide bond formation. True estimation of the contribution of proteasome-spliced peptides (PSPs) to the global human leukocyte antigen (HLA) ligandome is critical. A recent study suggested that PSPs contribute up to 30% of the HLA ligandome. We performed a thorough reanalysis of the reported results using multiple computational tools and various validation steps and concluded that only a fraction of the proposed PSPs passes the quality filters. To better estimate the actual number of PSPs, we present an alternative workflow. We performed de novo sequencing of the HLA-peptide spectra and discarded all de novo sequences found in the UniProt database. We checked whether the remaining de novo sequences could match spliced peptides from human proteins. The spliced sequences were appended to the UniProt fasta file, which was searched by two search tools at a false discovery rate (FDR) of 1%. We find that 2–6% of the HLA ligandome could be explained as spliced protein fragments. The majority of these potential PSPs have good peptide-spectrum match properties and are predicted to bind the respective HLA molecules. However, it remains to be shown how many of these potential PSPs actually originate from proteasomal splicing events.
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Affiliation(s)
- Roman Mylonas
- Vital-IT, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ilan Beer
- Adicet Bio Israel, Ltd., Technion City, 32000, Haifa, Israel
| | - Christian Iseli
- Vital-IT, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Chloe Chong
- Ludwig Cancer Research Center, University of Lausanne, 1066 Epalinges, Switzerland; Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Hui-Song Pak
- Ludwig Cancer Research Center, University of Lausanne, 1066 Epalinges, Switzerland; Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - David Gfeller
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Ludwig Cancer Research Center, University of Lausanne, 1066 Epalinges, Switzerland
| | - George Coukos
- Ludwig Cancer Research Center, University of Lausanne, 1066 Epalinges, Switzerland; Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Ioannis Xenarios
- Vital-IT, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Markus Müller
- Vital-IT, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Michal Bassani-Sternberg
- Vital-IT, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
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Makhija D, Laplante S, Beer I, Schermer C, Perrault L. Evaluation of the cost-effectiveness of the high-chloride vs. low-chloride crystalloid fluids in hospitalized patients from the us third-party provider perspective. Intensive Care Med Exp 2015. [PMCID: PMC4798375 DOI: 10.1186/2197-425x-3-s1-a156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Bar-Dayan Y, Beer I, Boaz M, Landau Z, Jakubowicz D, Wainstein J. Hyperglycaemia in patients with no history of diabetes presenting to Internal Medicine Departments. Int J Clin Pract 2015; 69:1289-95. [PMID: 26178790 DOI: 10.1111/ijcp.12690] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/30/2015] [Indexed: 01/08/2023] Open
Abstract
AIMS Stress hyperglycaemia during hospitalisation may be the first sign of diabetes mellitus (DM). Most hospitals routinely measure blood glucose, which may enable early diagnosis. This study measured the prevalence of hyperglycaemia in hospitalised adults with no history of diabetes, and whether the discharge summary recommended work-up. METHODS Files with at least one random blood glucose (RBG) sample were included and reviewed for specific discharge recommendations concerning elevated blood glucose. Hyperglycaemia was defined as serum glucose > 200 mg/dl. Length of stay, in-hospital mortality and 3-year mortality were examined. RESULTS Among 5274 discharged patients, 1479 had DM. They were older and had a higher incidence of cerebrovascular risk factors. Among 3714 patients without known DM, 211 (5.7%) had at least one RBG > 200 mg/dl. Of these patients, 31 died and 24 left against medical advice. Of the remaining 156, 25(16%) files included instructions to the family physician. These patients were younger, more overweight and less frequently diagnosed with dementia or other mental illness. Patients with RBG > 200 mg/dl had prolonged hospital stay (6.5 ± 5.3 vs. 4.0 ± 4.8; p < 0.001). In-hospital mortality and 3-year mortality were increased by 5.1 and 1.89, respectively (p < 0.001 for both parameters) compared to those without RBG ≤ 200 mg/dl. RBG > 200 mg/dl emerged as a significant, independent predictor of prolonged hospital stay and death. CONCLUSIONS Random blood glucose > 200 mg/dl is common in medical departments and is associated with increased in-hospital and 3-year out-hospital mortality.
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Affiliation(s)
- Y Bar-Dayan
- Diabetes Unit, Wolfson Medical Center, Holon, Israel
- Sackler Faculty of Medicine, Tel Aviv, Israel
| | - I Beer
- Department of Medicine, Wolfson Medical Center, Holon, Israel
| | - M Boaz
- Epidemiology and Research Unit, Wolfson Medical Center, Holon, Israel
- Ariel University, Ariel, Israel
| | - Z Landau
- Sackler Faculty of Medicine, Tel Aviv, Israel
- Pediatric Diabetes Unit, Wolfson Medical Center, Holon, Israel
| | - D Jakubowicz
- Diabetes Unit, Wolfson Medical Center, Holon, Israel
- Sackler Faculty of Medicine, Tel Aviv, Israel
| | - J Wainstein
- Diabetes Unit, Wolfson Medical Center, Holon, Israel
- Sackler Faculty of Medicine, Tel Aviv, Israel
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Milner E, Gutter-Kapon L, Bassani-Strenberg M, Barnea E, Beer I, Admon A. The effect of proteasome inhibition on the generation of the human leukocyte antigen (HLA) peptidome. Mol Cell Proteomics 2013; 12:1853-64. [PMID: 23538226 DOI: 10.1074/mcp.m112.026013] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Major histocompatibility complex (MHC) class I peptidome is thought to be generated mostly through proteasomal degradation of cellular proteins, a notion that is based on the alterations in presentation of selected peptides following proteasome inhibition. We evaluated the effects of proteasome inhibitors, epoxomicin and bortezomib, on human cultured cancer cells. Because the inhibitors did not reduce the level of presentation of the cell surface human leukocyte antigen (HLA) molecules, we followed their effects on the rates of synthesis of both HLA peptidome and proteome of the cells, using dynamic stable isotope labeling in tissue culture (dynamic-SILAC). The inhibitors reduced the rates of synthesis of most cellular proteins and HLA peptides, yet the synthesis rates of some of the proteins and HLA peptides was not decreased by the inhibitors and of some even increased. Therefore, we concluded that the inhibitors affected the production of the HLA peptidome in a complex manner, including modulation of the synthesis rates of the source proteins of the HLA peptides, in addition to their effect on their degradation. The collected data may suggest that the current reliance on proteasome inhibition may overestimate the centrality of the proteasome in the generation of the MHC peptidome. It is therefore suggested that the relative contribution of the proteasomal and nonproteasomal pathways to the production of the MHC peptidome should be revaluated in accordance with the inhibitors effects on the synthesis rates of the source proteins of the MHC peptides.
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Affiliation(s)
- Elena Milner
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
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Lorente E, Infantes S, Barnea E, Beer I, Barriga A, García-Medel N, Lasala F, Jiménez M, Admon A, López D. Diversity of natural self-derived ligands presented by different HLA class I molecules in transporter antigen processing-deficient cells. PLoS One 2013; 8:e59118. [PMID: 23555621 PMCID: PMC3608615 DOI: 10.1371/journal.pone.0059118] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 02/11/2013] [Indexed: 12/16/2022] Open
Abstract
The transporter associated with antigen processing (TAP) translocates the cytosol-derived proteolytic peptides to the endoplasmic reticulum lumen where they complex with nascent human leukocyte antigen (HLA) class I molecules. Non-functional TAP complexes and viral or tumoral blocking of these transporters leads to reduced HLA class I surface expression and a drastic change in the available peptide repertoire. Using mass spectrometry to analyze complex human leukocyte antigen HLA-bound peptide pools isolated from large numbers of TAP-deficient cells, we identified 334 TAP-independent ligands naturally presented by four different HLA-A, -B, and -C class I molecules with very different TAP dependency from the same cell line. The repertoire of TAP-independent peptides examined favored increased peptide lengths and a lack of strict binding motifs for all four HLA class I molecules studied. The TAP-independent peptidome arose from 182 parental proteins, the majority of which yielded one HLA ligand. In contrast, TAP-independent antigen processing of very few cellular proteins generated multiple HLA ligands. Comparison between TAP-independent peptidome and proteome of several subcellular locations suggests that the secretory vesicle-like organelles could be a relevant source of parental proteins for TAP-independent HLA ligands. Finally, a predominant endoproteolytic peptidase specificity for Arg/Lys or Leu/Phe residues in the P(1) position of the scissile bond was found for the TAP-independent ligands. These data draw a new and intricate picture of TAP-independent pathways.
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Affiliation(s)
- Elena Lorente
- Unidad de Procesamiento Antigénico-Inmunología Viral, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Susana Infantes
- Unidad de Procesamiento Antigénico-Inmunología Viral, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Eilon Barnea
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ilan Beer
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Alejandro Barriga
- Unidad de Procesamiento Antigénico-Inmunología Viral, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Noel García-Medel
- Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, Madrid, Spain
| | - Fátima Lasala
- Unidad de Proteómica, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Mercedes Jiménez
- Unidad de Proteómica, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Arie Admon
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Daniel López
- Unidad de Procesamiento Antigénico-Inmunología Viral, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- * E-mail:
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Infantes S, Lorente E, Barnea E, Beer I, Barriga A, Lasala F, Jiménez M, Admon A, López D. Natural HLA-B*2705 protein ligands with glutamine as anchor motif: implications for HLA-B27 association with spondyloarthropathy. J Biol Chem 2013; 288:10882-9. [PMID: 23430249 DOI: 10.1074/jbc.m113.455352] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The presentation of short viral peptide antigens by human leukocyte antigen (HLA) class I molecules on cell surfaces is a key step in the activation of cytotoxic T lymphocytes, which mediate the killing of pathogen-infected cells or initiate autoimmune tissue damage. HLA-B27 is a well known class I molecule that is used to study both facets of the cellular immune response. Using mass spectrometry analysis of complex HLA-bound peptide pools isolated from large amounts of HLA-B*2705(+) cells, we identified 200 naturally processed HLA-B*2705 ligands. Our analyses revealed that a change in the position (P) 2 anchor motif was detected in the 3% of HLA-B*2705 ligands identified. B*2705 class I molecules were able to bind these six GlnP2 peptides, which showed significant homology to pathogenic bacterial sequences, with a broad range of affinities. One of these ligands was able to bind with distinct conformations to HLA-B27 subtypes differentially associated with ankylosing spondylitis. These conformational differences could be sufficient to initiate autoimmune damage in patients with ankylosing spondylitis-associated subtypes. Therefore, these kinds of peptides (short, with GlnP2, and similar low affinity to all HLA-B27 subtypes tested but with unlike conformations in differentially ankylosing spondylitis-associated subtypes) must not be excluded from future researches involving potential arthritogenic peptides.
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Affiliation(s)
- Susana Infantes
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda (Madrid), Spain
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Lorente E, Infantes S, Abia D, Barnea E, Beer I, García R, Lasala F, Jiménez M, Mir C, Morreale A, Admon A, López D. A viral, transporter associated with antigen processing (TAP)-independent, high affinity ligand with alternative interactions endogenously presented by the nonclassical human leukocyte antigen E class I molecule. J Biol Chem 2012; 287:34895-34903. [PMID: 22927436 PMCID: PMC3471699 DOI: 10.1074/jbc.m112.362293] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 08/10/2012] [Indexed: 01/05/2023] Open
Abstract
The transporter associated with antigen processing (TAP) enables the flow of viral peptides generated in the cytosol by the proteasome and other proteases to the endoplasmic reticulum, where they complex with nascent human leukocyte antigen (HLA) class I. Later, these peptide-HLA class I complexes can be recognized by CD8(+) lymphocytes. Cancerous cells and infected cells in which TAP is blocked, as well as individuals with unusable TAP complexes, are able to present peptides on HLA class I by generating them through TAP-independent processing pathways. Here, we identify a physiologically processed HLA-E ligand derived from the D8L protein in TAP-deficient vaccinia virus-infected cells. This natural high affinity HLA-E class I ligand uses alternative interactions to the anchor motifs previously described to be presented on nonclassical HLA class I molecules. This octameric peptide was also presented on HLA-Cw1 with similar binding affinity on both classical and nonclassical class I molecules. In addition, this viral peptide inhibits HLA-E-mediated cytolysis by natural killer cells. Comparison between the amino acid sequences of the presenting HLA-E and HLA-Cw1 alleles revealed a shared structural motif in both HLA class molecules, which could be related to their observed similar cross-reactivity affinities. This motif consists of several residues located on the floor of the peptide-binding site. These data expand the role of HLA-E as an antigen-presenting molecule.
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Affiliation(s)
- Elena Lorente
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - Susana Infantes
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - David Abia
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Eilon Barnea
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ilan Beer
- IBM Haifa Research Lab, Haifa 31905, Israel
| | - Ruth García
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - Fátima Lasala
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - Mercedes Jiménez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - Carmen Mir
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - Antonio Morreale
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Arie Admon
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Daniel López
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain.
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Admon A, Milner E, Gutter L, Barnea E, Beer I. Quantitating the role of the proteasome in generating the HLA peptidome. Mol Immunol 2012. [DOI: 10.1016/j.molimm.2012.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Ulrich M, Beer I, Braitmaier P, Dierkes M, Kummer F, Krismer B, Schumacher U, Grapler-Mainka U, Riethmuller J, Jensen PO, Bjarnsholt T, Hoiby N, Bellon G, Doring G. Relative contribution of Prevotella intermedia and Pseudomonas aeruginosa to lung pathology in airways of patients with cystic fibrosis. Thorax 2010; 65:978-84. [DOI: 10.1136/thx.2010.137745] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abstract
OBJECTIVE The HLA-B27 allele is strongly associated with the group of inflammatory diseases known as the spondylarthritides (SpA). The aim of this study was to perform a large-scale, direct biochemical analysis of the HLA-B*2705 peptidome in order to identify candidates for mimicry between HLA-B27 peptides derived from cartilage proteins and arthritogenic bacterial sequences and to refine the consensus binding motif of this important allele. METHODS The peptides were recovered by recombinant expression of soluble HLA-B27 molecules secreted from cultured chondrocytic cells or HeLa cells. Analysis was based on capillary chromatography and tandem mass spectrometry in combination with stable isotope labeling with amino acids in cell culture or chemical labeling with iTRAQ to enhance the validity of the data. RESULTS Over 1,268 B27 peptides were identified, with 569 of them at high certainty, thus enabling better refinement of the B27 motif. This enabled the prediction of both short peptides and long peptides whose middle residues likely bulge out of the binding groove. Moreover, we identified a number of human B27 peptide sequences derived from human cartilage proteins, some of which are similar to common bacterial sequences. CONCLUSION The peptides we identified may provide the missing link between bacterial infections and the resulting SpA.
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Infantes S, Lorente E, Barnea E, Beer I, Cragnolini JJ, García R, Lasala F, Jiménez M, Admon A, López D. Multiple, non-conserved, internal viral ligands naturally presented by HLA-B27 in human respiratory syncytial virus-infected cells. Mol Cell Proteomics 2010; 9:1533-9. [PMID: 20081153 DOI: 10.1074/mcp.m900508-mcp200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytotoxic T lymphocyte (CTL)-mediated death of virus-infected cells requires prior recognition of short viral peptide antigens that are presented by human leukocyte antigen (HLA) class I molecules on the surface of infected cells. The CTL response is critical for the clearance of human respiratory syncytial virus (HRSV) infection. Using mass spectrometry analysis of complex HLA-bound peptide pools isolated from large amounts of HRSV-infected cells, we identified nine naturally processed HLA-B27 ligands. The isolated peptides are derived from six internal, not envelope, proteins of the infective virus. The sequences of most of these ligands are not conserved between different HRSV strains, suggesting a mechanism to explain recurrent infection with virus of different HRSV antigenic subgroups. In addition, these nine ligands represent a significant fraction of the proteome of this virus, which is monitored by the same HLA class I allele. These data have implications for vaccine development as well as for analysis of the CTL response.
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Affiliation(s)
- Susana Infantes
- Unidad de Protemica, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
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Abstract
Small cell lung carcinoma (SCLC) is an aggressive, highly metastatic cancer with a strong tendency for chemotherapy resistance. Identification of proteins uniquely expressed in SCLC cells, can facilitate the development of new diagnostic tools, improve immunotherapy, and deepen our understanding of the underlying mechanisms of the disease. Here we describe a comparative proteomics analysis of ten SCLC cell lines and three controls lines, while searching for proteins preferentially expressed in SCLC cells as potential disease markers. Total protein extracts were compared by two-dimensional gel electrophoresis and by two-dimensional liquid chromatography resulting in the identification of 1093 proteins, 202 of which were detected only in the SCLC cells. These include proteins of different cellular functions, including cellular proliferation and known tumor antigens. Since SCLC has a neuroendocrine origin, of major interest are the identified proteins involved in nerve and brain embryonic development. These proteins are potentially valuable as both tumor markers and as antigens for immunotherapy.
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Affiliation(s)
- Tamar Ziv
- Department of Biology, The Smoler Proteomics Center, Technion, Haifa, Israel
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Abstract
Peptides presented by the major histocompatibility complex (MHC) are derived from the degradation of cellular proteins. Thus, the repertoire of these peptides (the MHC peptidome) should correlate better with the cellular protein degradation scheme (the degradome) than with the cellular proteome. To test the validity of this statement and to determine whether the majority of MHC peptides are derived from short lived proteins, from defective ribosome products, or from regular long lived cellular proteins we analyzed in parallel the turnover kinetics of both MHC peptides and cellular proteins in the same cancer cells. The analysis was performed by pulse-chase experiments based on stable isotope labeling in tissue culture followed by capillary chromatography and tandem mass spectrometry. Indeed only a limited correlation was observed between the proteome and the MHC peptidome observed in the same cells. Moreover a detailed analysis of the turnover kinetics of the MHC peptides helped to assign their origin to normal, to short lived or long lived proteins, or to the defective ribosome products. Furthermore the analysis of the MHC peptides turnover kinetics helped to direct attention to abnormalities in the degradation schemes of their source proteins. These observations can be extended to search for cancer-related abnormalities in protein degradation, including those that lead to loss of tumor suppressors and cell cycle regulatory proteins.
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Affiliation(s)
- Elena Milner
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
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17
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Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS, Kapp EA, Moritz RL, Chan DW, Rai AJ, Admon A, Aebersold R, Eng J, Hancock WS, Hefta SA, Meyer H, Paik YK, Yoo JS, Ping P, Pounds J, Adkins J, Qian X, Wang R, Wasinger V, Wu CY, Zhao X, Zeng R, Archakov A, Tsugita A, Beer I, Pandey A, Pisano M, Andrews P, Tammen H, Speicher DW, Hanash SM. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 2005; 5:3226-45. [PMID: 16104056 DOI: 10.1002/pmic.200500358] [Citation(s) in RCA: 592] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anti-coagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics.med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay-based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.
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Affiliation(s)
- Gilbert S Omenn
- Internal Medicine, University of Michigan, Ann Arbor, MI 48109-0656, USA.
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18
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Abstract
The human Plasma Proteome Project (PPP) is a large-scale collaboration between many laboratories. One of the most demanding tasks in the PPP involved the analysis of very large amounts of raw MS/MS data produced by the participants. The main approach for managing this task was letting the participants analyze their own data and submit the results to the central PPP repository as lists of identified proteins and peptides. To complement this distributed approach, we also performed centralized analysis of the raw MS/MS data provided by the participants. Due to the data redundancy inherent in such a project, centralized analysis has the potential to reduce the computational effort by reducing redundancy before the analysis. Centralized analysis can also unify the process and take advantage of data sharing among laboratories to improve protein identification and validation. The process we employed included removing low-quality spectra, clustering spectra by mutual similarity, and applying uniform peptide and protein identification procedures. To demonstrate the process, we analyzed 5.28 million MS/MS spectra derived by eight laboratories from tryptic peptides of serum and plasma proteins.
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Affiliation(s)
- Ilan Beer
- IBM Research Laboratory, Haifa, Israel.
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Barnea E, Sorkin R, Ziv T, Beer I, Admon A. Evaluation of prefractionation methods as a preparatory step for multidimensional based chromatography of serum proteins. Proteomics 2005; 5:3367-75. [PMID: 16047308 DOI: 10.1002/pmic.200401221] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Prefractionations of proteins prior to their proteolysis, chromatography, and MS/MS analyses help reduce complexity and increase the yield of protein identifications. A number of methods were evaluated here for prefractionating serum samples distributed to the participating laboratories as part of the human Plasma Proteome Project. These methods include strong cation exchange (SCX) chromatography, slicing of SDS-PAGE gel bands, and liquid-phase IEF of the proteins. The fractionated proteins were trypsinized and the resulting peptides were resolved and analyzed by multidimensional protein identification technology coupled to IT MS/MS. The MS/MS spectra were clustered, combined, and searched against the IPI protein databank using Pep-Miner. The identification results were evaluated for the efficacy of the different prefractionation methodologies to identify larger numbers of proteins at higher confidence and to achieve the best coverage of the proteins with the identified peptides. Prefractionation based on SCX resulted in the largest number of identified proteins, followed by gel slices and then the liquid-phase IEF. An important observation was that each of the methods revealed a set of unique proteins, some identified with high confidence. Therefore, for comprehensive identification of the serum proteins, several different prefractionation approaches should be used in parallel.
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Affiliation(s)
- Eilon Barnea
- Department of Biology, The Smoler Proteomics Center, Technion, Haifa, Israel
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Sogayar AMCB, Silva E, Cal RGR, Beer I, Safi J, Kayath M, Akamine N. Costs of sepsis treatment between survivors and nonsurvivors in Brazilian ICUs: does it matter? Crit Care 2005. [PMCID: PMC4097514 DOI: 10.1186/cc3607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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21
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Sogayar AMCB, Silva E, Cal RGR, Beer I, Akamine N, Safi J, Kayath M. What are the direct costs of sepsis treatment in Brazilian ICUs? Crit Care 2005. [PMCID: PMC4097563 DOI: 10.1186/cc3656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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22
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Pizzo VRP, Beer I, de Cleva R, Zilberstein B. Intermittent left bundle branch block (LBBB) as a clinical manifestation of myocardial contusion after blunt chest trauma. Emerg Med J 2005; 22:300-1. [PMID: 15788845 PMCID: PMC1726743 DOI: 10.1136/emj.2003.012518] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Injury to the heart in blunt chest trauma is dependent on a number of factors. Symptoms are often non-specific, and there is no gold standard test for diagnosis. Injuries to small areas of the myocardium may only be identified at autopsy. We report a 38 year old man who sustained a number of injuries in a road traffic accident, and in whom the single clinical or ECG abnormality was a left bundle branch block (LBBB); he had a myocardial injury rated as grade II. The patient was treated for his injuries and later discharged. As this is a difficult diagnosis, algorithms of blunt chest trauma may save time and money by avoiding misleading diagnosis and unnecessary monitoring and admissions.
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Affiliation(s)
- V R P Pizzo
- Department of Clinical Emergencies, Hospital das Clínicas, University of São Paulo Medical School, São Paulo, Brazil
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23
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Beer I, de Cleva R, Faintuch J, Matsuda M, Zilberstein B, Gama-rodrigues J. Crit Care 2005; 9:P121. [DOI: 10.1186/cc3665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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24
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Beer I, Maciel A, Coelho J, de Cleva R. Crit Care 2005; 9:P116. [DOI: 10.1186/cc3660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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26
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Abstract
Tandem mass spectrometry (MS/MS), coupled with liquid chromatography (LC), is a powerful tool for the analysis and comparison of complex protein and peptide mixtures. However, the extremely large amounts of data that result from the process are very complex and difficult to analyze. We show how the clustering of similar spectra from multiple LC-MS/MS runs can help in data management and improve the analysis of complex peptide mixtures. The major effect of spectrum clustering is the reduction of the huge amounts of data to a manageable size. As a result, analysis time is shorter and more data can be stored for further analysis. Furthermore, spectrum quality improvement allows the identification of more peptides with greater confidence, the comparison of complex peptide mixtures is facilitated, and the entire proteomics project is presented in concise form. Pep-Miner is an advanced software tool that implements these clustering-based applications. It proved useful in several comparative proteomics projects involving lung cancer cells and various other cell types. In one of these projects, Pep-Miner reduced 517 000 spectra to 20 900 clusters and identified 2518 peptides derived from 830 proteins. Clustering and identification lasted less than two hours on an IBM Thinkpad T23 computer (laptop). Pep-Miner's unique properties make it a very useful tool for large-scale shotgun proteomics projects.
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Affiliation(s)
- Ilan Beer
- IBM Haifa Research Lab, Haifa, Israel.
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27
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Buchsbaum S, Barnea E, Dassau L, Beer I, Milner E, Admon A. Large-scale analysis of HLA peptides presented by HLA-Cw4. Immunogenetics 2003; 55:172-176. [PMID: 12750860 DOI: 10.1007/s00251-003-0570-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2003] [Revised: 03/17/2003] [Indexed: 10/26/2022]
Abstract
A large number of HLA-Cw4 (Cw *0402) peptides were purified, sequenced, and identified from breast and ovarian carcinoma cell lines. HLA-Cw4 molecules were expressed in these cells as soluble, secreted HLA (sHLA) and recovered from the growth medium. The peptides were separated by capillary reversed-phase HPLC and analyzed by tandem mass-spectrometry. The resulting peptides fit to some extent, but not completely, the known consensus of the Cw4 peptide-binding motif. Among the identified peptides, there are a few that originate from proteins of possible interest for cancer immunotherapy or diagnostics, including mucin-5B, ART-1, fatty acid synthase, putative prostate cancer tumor suppressor, DNA topoisomerase-1, and Rac1. This work demonstrates that large-scale identification of HLA peptides recovered from sHLA is an advantageous approach for establishing the HLA peptide consensus of different haplotypes and the identification of useful peptides for treatment of diseases such as cancer, viral, and autoimmune diseases.
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Affiliation(s)
- Samuel Buchsbaum
- Department of Biology, Technion, Israel Institute of Technology, 32000, Haifa , Israel
| | - Eilon Barnea
- Department of Biology, Technion, Israel Institute of Technology, 32000, Haifa , Israel
| | - Lior Dassau
- Department of Biology, Technion, Israel Institute of Technology, 32000, Haifa , Israel
| | - Ilan Beer
- IBM Research Laboratory, Haifa, Israel
| | - Elena Milner
- Department of Biology, Technion, Israel Institute of Technology, 32000, Haifa , Israel
| | - Arie Admon
- Department of Biology, Technion, Israel Institute of Technology, 32000, Haifa , Israel.
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28
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Vrsanský D, Valach B, Beer I, Pekar F. [Should fiber gastroscopy be standard in preoperative examinations for cardiac surgery?]. Rozhl Chir 2003; 82:170-6. [PMID: 12728568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
UNLABELLED We introduced a gastrofibroscopy into a standard preoperative protocol for all patients indicated to the cardiac surgery. AIM OF THE STUDY Validation of our protocol. MATERIAL AND METHODS 957 consecutive patients operated on from May 1995 to January 2002 were divided to group A--gastrofibroscopy only for patients with positive history or clinical signs of peptic ulcer (151 pts.) and group B--patients with gastrofibroscopy as a standard procedure (806 pts). RESULTS Significant difference in incidence of peptic ulcer complications between groups (A--5.9% versus B--1.1%, p < 0.05). Related mortality was 1.3% in-group A versus 0% in-group B. Positive history of peptic ulcer had only two patients (11% of 18) with postoperative complication. In-group B we found high incidence of peptic defects (B--35% versus A--9%, p < 0.01) requiring treatment by gastroenterologist. Majority (230 of 281-82%) of pts. with preoperative positive defect had negative history of a peptic ulcer. CONCLUSIONS Current tendency to perform gastrofibroscopic examination only in patients with positive history of peptic ulcer is not able to detect "silent" lesions. Perioperative treatment with H2 blockers fails to prevent the manifestation of peptic ulcer complication. Gastrofibroscopy should be a routine part of the preoperative protocol in cardiac surgery.
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Affiliation(s)
- D Vrsanský
- Kardiochirurgické oddelenie Kardiocentra NsP F.D. Roosevelta, Banská Bystrica, Slovenská republika
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29
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Martins-Fadiga HCM, Trabarch M, Beer I, Costa MC, Chiamolera M. Use of Acute Physiology and Chronic Health Evaluation II in nontraumatic neurological intensive care patients: calibration and discrimination analysis. Crit Care 2003; 7. [PMCID: PMC3301095 DOI: 10.1186/cc2293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
| | - M Trabarch
- Hospital de Beneficência Portuguesa, São Paulo, SP, Brazil
| | - I Beer
- Hospital de Beneficência Portuguesa, São Paulo, SP, Brazil
| | - MC Costa
- Hospital de Beneficência Portuguesa, São Paulo, SP, Brazil
| | - M Chiamolera
- Hospital de Beneficência Portuguesa, São Paulo, SP, Brazil
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30
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Beer I, Bielik E, Kollárik V. [Intrapericardial rupture of the inferior vena cava caused by blunt trauma]. Rozhl Chir 2002; 81:398-400. [PMID: 12238258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
A thirty-years-old man with pectus excavatum was unconscious, in shock and with a history of blunt trauma of the chest and epigastrium admitted to hospital. After a short time he developed signs of pericardial and peritoneal effusion with tamponade and circulatory failure. Urgent laparotomy and sternotomy was performed. We found approximately a 5 cm long rupture of the right atrium, anterior wall of the intrapericardial part of the vena cava inferior with short extension to the infradiaphragmatic part of the vena cava inferior. We controlled bleeding by hand and by application of a Satinsky partial vascular clamp. Final plastic correction of the rupture was performed by implantation of a native autologous pericardial flap. After a complicated postoperative course the patient was discharged on the 37th postoperative day. Seven months after surgery the patient is in a good condition and has no signs of stenosis at the place of correction.
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Affiliation(s)
- I Beer
- Kardiochirurgické oddelenie NsP F. D. Roosevelta, Banská Bystrica, Slovenská republika
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31
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Barnea E, Beer I, Patoka R, Ziv T, Kessler O, Tzehoval E, Eisenbach L, Zavazava N, Admon A. Analysis of endogenous peptides bound by soluble MHC class I molecules: a novel approach for identifying tumor-specific antigens. Eur J Immunol 2002; 32:213-22. [PMID: 11782012 DOI: 10.1002/1521-4141(200201)32:1<213::aid-immu213>3.0.co;2-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The Human MHC Project aims at comprehensive cataloging of peptides presented within the context of different human leukocyte antigens (HLA) expressed by cells of various tissue origins, both in health and in disease. Of major interest are peptides presented on cancer cells, which include peptides derived from tumor antigens that are of interest for immunotherapy. Here, HLA-restricted tumor-specific antigens were identified by transfecting human breast, ovarian and prostate tumor cell lines with truncated genes of HLA-A2 and HLA-B7. Soluble HLA secreted by these cell lines were purified by affinity chromatography and analyzed by nano-capillary electrospray ionization-tandem mass spectrometry. Typically, a large peptide pool was recovered and sequenced including peptides derived from MAGE-B2 and mucin and other new tumor-derived antigens that may serve as potential candidates for immunotherapy.
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Affiliation(s)
- Eilon Barnea
- The Smoler Protein Center, Department of Biology, Technion, Haifa, Israel
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Abstract
Kombucha tea is an alternative therapy that is gaining popularity as a remedy for a diverse range of ailments. We report two cases of symptomatic lead poisoning requiring chelation therapy in a married couple who had been drinking Kombucha tea for six months, brewing the tea in a ceramic pot. We postulate that acids in the tea eluted lead from the glaze pigment used in the ceramic pot, in a manner analogous to elution of lead from crystal decanters by wine and spirits.
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Affiliation(s)
- T G Phan
- Royal Prince Alfred Hospital, Camperdown, NSW.
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35
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Chaib E, Bertevello P, Pinto FC, Ferreira CE, Nagahama CI, Cahali RB, Beer I, Perini MV, Xavier AC, Costa LJ. [Main variations of the extrahepatic biliary system and their application to the so-called "split-liver" transplantation technique]. Rev Hosp Clin Fac Med Sao Paulo 1995; 50:311-3. [PMID: 8731250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Sixty fresh adult livers were obtained from cadavers together with celiac trunk, head of the pancreas and superior mesenteric artery. We have found a single right hepatic duct in 13(21.6%) of the cases and a multiple right hepatic duct in 47(78.3%). A single left hepatic duct was found in 3(5%) of the cases and a multiple left hepatic duct in 57(95%). A median hepatic duct was found in 18(30%) of the cases, out of this 2(3.3%) was multiple median hepatic duct.
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Affiliation(s)
- E Chaib
- Faculdade de Medicina da Universidade de São Paulo
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36
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37
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Elischerová K, Beer I, Gálik L, Patka O, Havelková E. [Listeriosis of the central nervous system]. BRATISL MED J 1972; 58:615-23. [PMID: 4651579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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38
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Bianca S, Climescu E, Beer I, Tautu C. [Retinitis punctata albescens and heredo-ataxia]. Ann Ocul (Paris) 1970; 203:661-8. [PMID: 5455259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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39
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Palade M, Dacian I, Beer I. [Considerations on cystic tumors of the frontal sinus]. Otorinolaringologie 1965; 10:359-62. [PMID: 5886552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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