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1
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PAT strategies and applications for cell therapy processing. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2022. [DOI: 10.1016/j.cobme.2022.100405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ogasawara T, Kuwabara R, Kozai K, Kato K. Quantitative Cell Subset Analysis Using Antibody Microarrays. ACS APPLIED BIO MATERIALS 2021; 4:7673-7681. [DOI: 10.1021/acsabm.1c00898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tomoko Ogasawara
- Department of Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
- Department of Pediatric Dentistry, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Rei Kuwabara
- Department of Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Katsuyuki Kozai
- Department of Pediatric Dentistry, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Koichi Kato
- Department of Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
- Nanomedicine Research Division, Research Institute for Nanodevice and Bio Systems, Hiroshima University, 1-4-2 Kagamiyama, Higashi-Hiroshima 739-8527, Japan
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Jin X, Xu L, Guan Y, Zhang Z, Li H. Bioinformatics Analysis of Microarray Datasets to Identify Prognostic Factors in Lung Adenocarcinoma. DNA Cell Biol 2020; 39:965-974. [PMID: 32330391 DOI: 10.1089/dna.2019.5203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Most patients with lung adenocarcinoma (LUAD) present high recurrence rate and poor prognosis after therapy. Therefore, the purpose of this study was to identify prognostic factors involved in LUAD. Five microarray datasets (including GSE75037, GSE63459, GSE43458, GSE32863, and GSE10072) were downloaded. After data preprocessing and quality control, meta-analysis was performed to screen differentially expressed genes (DEGs) using the MetaDE.ES method in MetaDE package. Subsequently, network construction and module identification were conducted by the Weighted Gene Co-expression Network Analysis method. Moreover, survival-associated genes were identified using the univariate and multivariate Cox regression method in survival package. The risk score model was constructed by prognosis associated genes, followed by the Kaplan-Meier survival analysis. Oncomine expressions analysis of several prognosis associated genes was conducted. The expression levels of key genes were detected using quantitative real-time PCR experiments. A total of 1434 DEGs between LUAD and normal samples were identified. Nine disease-associated modules were identified, in which M8 module was most correlated with LAUD phenotype. A total of 89 indicators (including T stage, M stage, and ADIPOR2) were significantly associated with LAUD prognosis, while only T stage and 9 DEGs (e.g., ARHGEF3, GTSE1, RBM15 and CD52) were retained as the potential prognostic factors following multivariate COX regression analysis. The upregulated adiponectin receptor 2 (ADIPOR2), rho guanine nucleotide exchange factor 3 (ARHGEF3), and CD52 molecule (CD52), and downregulated GTSE1 were validated in LAUD samples of Oncomine database. Importantly, ADIPOR2 and ARHGEF3 were confirmed to be down-regulated in LUAD tissues. ADIPOR2, ARHGEF3, G2 and S-phase expressed 1 (GTSE1) and CD52 might be promising prognostic factors in LUAD.
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Affiliation(s)
- Xiang Jin
- Department of Respiration, The First Hospital of Jilin University, Changchun, China
| | - Lijun Xu
- Department of Respiration, The First Hospital of Jilin University, Changchun, China
| | - Yinghui Guan
- Department of Respiration, The First Hospital of Jilin University, Changchun, China
| | - Zhen Zhang
- PICU, The First Hospital of Jilin University, Changchun, China
| | - Hongyu Li
- Department of Respiration, The First Hospital of Jilin University, Changchun, China
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Banaszek A, Bumm TGP, Nowotny B, Geis M, Jacob K, Wölfl M, Trebing J, Kucka K, Kouhestani D, Gogishvili T, Krenz B, Lutz J, Rasche L, Hönemann D, Neuweiler H, Heiby JC, Bargou RC, Wajant H, Einsele H, Riethmüller G, Stuhler G. On-target restoration of a split T cell-engaging antibody for precision immunotherapy. Nat Commun 2019; 10:5387. [PMID: 31772172 PMCID: PMC6879491 DOI: 10.1038/s41467-019-13196-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 10/02/2019] [Indexed: 12/19/2022] Open
Abstract
T cell-engaging immunotherapies are changing the landscape of current cancer care. However, suitable target antigens are scarce, restricting these strategies to very few tumor types. Here, we report on a T cell-engaging antibody derivative that comes in two complementary halves and addresses antigen combinations instead of single molecules. Each half, now coined hemibody, contains an antigen-specific single-chain variable fragment (scFv) fused to either the variable light (VL) or variable heavy (VH) chain domain of an anti-CD3 antibody. When the two hemibodies simultaneously bind their respective antigens on a single cell, they align and reconstitute the original CD3-binding site to engage T cells. Employing preclinical models for aggressive leukemia and breast cancer, we show that by the combinatorial nature of this approach, T lymphocytes exclusively eliminate dual antigen-positive cells while sparing single positive bystanders. This allows for precision targeting of cancers not amenable to current immunotherapies. The restriction of appropriate tumour-specific antigens is a current limitation for T cell-engaging immunotherapy. Here, the authors have designed a new system constituted by two halve antibodies, which engage T cells once binding to two different antigens, to specifically eliminate double positive cells in preclinical leukemia and breast cancer mouse models.
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Affiliation(s)
- Agnes Banaszek
- University Clinic Würzburg, Department of Internal Medicine II, Hematology and Oncology, Würzburg, Germany
| | - Thomas G P Bumm
- University Clinic Würzburg, Department of Internal Medicine II, Hematology and Oncology, Würzburg, Germany
| | - Boris Nowotny
- University Clinic Würzburg, Department of Internal Medicine II, Hematology and Oncology, Würzburg, Germany
| | - Maria Geis
- University Clinic Würzburg, Department of Internal Medicine II, Hematology and Oncology, Würzburg, Germany
| | - Kim Jacob
- University Clinic Würzburg, Department of Internal Medicine II, Hematology and Oncology, Würzburg, Germany
| | - Matthias Wölfl
- University Clinic Würzburg, Children's Hospital, Pediatric Oncology, Hematology and Stem Cell Transplantation, Würzburg, Germany
| | - Johannes Trebing
- University Clinic Würzburg, Department of Internal Medicine II, Division of Molecular Internal Medicine, Würzburg, Germany
| | - Kirstin Kucka
- University Clinic Würzburg, Department of Internal Medicine II, Division of Molecular Internal Medicine, Würzburg, Germany
| | - Dina Kouhestani
- University Clinic Würzburg, Department of Internal Medicine II, Hematology and Oncology, Würzburg, Germany
| | - Tea Gogishvili
- University Clinic Würzburg, Department of Internal Medicine II, Hematology and Oncology, Würzburg, Germany
| | - Bastian Krenz
- University Clinic Würzburg, Department of Internal Medicine II, Hematology and Oncology, Würzburg, Germany
| | - Justina Lutz
- University Clinic Würzburg, Department of Internal Medicine II, Hematology and Oncology, Würzburg, Germany
| | - Leo Rasche
- University Clinic Würzburg, Department of Internal Medicine II, Hematology and Oncology, Würzburg, Germany
| | - Dirk Hönemann
- University Clinic Würzburg, Department of Internal Medicine II, Hematology and Oncology, Würzburg, Germany
| | - Hannes Neuweiler
- Department of Biotechnology and Biophysics, University Würzburg, Würzburg, Germany
| | - Julia C Heiby
- Department of Biotechnology and Biophysics, University Würzburg, Würzburg, Germany
| | - Ralf C Bargou
- University Clinic Würzburg, Department of Internal Medicine II, Hematology and Oncology, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Universitätsklinikum, Würzburg, Germany
| | - Harald Wajant
- University Clinic Würzburg, Department of Internal Medicine II, Division of Molecular Internal Medicine, Würzburg, Germany
| | - Hermann Einsele
- University Clinic Würzburg, Department of Internal Medicine II, Hematology and Oncology, Würzburg, Germany
| | - Gert Riethmüller
- Ludwig-Maximilians-University, Institute for Immunology, Munich, Germany
| | - Gernot Stuhler
- University Clinic Würzburg, Department of Internal Medicine II, Hematology and Oncology, Würzburg, Germany.
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Chakraborty A, Debnath GH, Mukherjee P. Assessing inter lanthanide photophysical interactions in co-doped titanium dioxide nanoparticles for multiplex assays. RSC Adv 2017. [DOI: 10.1039/c7ra07120e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
This work assesses inter lanthanide photophysical interactions in titanium dioxide nanoparticles towards the development of multiplex assays.
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Affiliation(s)
- Arijita Chakraborty
- Centre for Research in Nanoscience and Nanotechnology
- University of Calcutta
- Kolkata-700106
- India
| | - Gouranga H. Debnath
- Centre for Research in Nanoscience and Nanotechnology
- University of Calcutta
- Kolkata-700106
- India
| | - Prasun Mukherjee
- Centre for Research in Nanoscience and Nanotechnology
- University of Calcutta
- Kolkata-700106
- India
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Belov L, Hallal S, Matic K, Zhou J, Wissmueller S, Ahmed N, Tanjil S, Mulligan SP, Best OG, Simpson RJ, Christopherson RI. Surface Profiling of Extracellular Vesicles from Plasma or Ascites Fluid Using DotScan Antibody Microarrays. Methods Mol Biol 2017; 1619:263-301. [PMID: 28674892 DOI: 10.1007/978-1-4939-7057-5_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DotScan antibody microarrays were initially developed for the extensive surface profiling of live leukemia and lymphoma cells. DotScan's diagnostic capability was validated with an extensive clinical trial using mononuclear cells from the blood or bone marrow of leukemia or lymphoma patients. DotScan has also been used for the profiling of surface proteins on peripheral blood mononuclear cells (PBMC) from patients with HIV, liver disease, and stable and progressive B-cell chronic lymphocytic leukemia (CLL). Fluorescence multiplexing allowed the simultaneous profiling of cancer cells and leukocytes from disaggregated colorectal and melanoma tumor biopsies after capture on DotScan. In this chapter, we have used DotScan for the surface profiling of extracellular vesicles (EV) recovered from conditioned growth medium of cancer cell lines and the blood of patients with CLL. The detection of captured EV was performed by enhanced chemiluminescence (ECL) using biotinylated antibodies that recognized antigens expressed on the surface of the EV subset of interest. DotScan was also used to profile EV from the blood of healthy individuals and the ascites fluid of ovarian cancer patients. DotScan binding patterns of EV from human plasma and other body fluids may yield diagnostic or prognostic signatures for monitoring the incidence, treatment, and progression of cancers.
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Affiliation(s)
- Larissa Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Susannah Hallal
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Kieran Matic
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Jerry Zhou
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Sandra Wissmueller
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Nuzhat Ahmed
- Fiona Elsey Cancer Research Institute, Ballarat, VIC, 3350, Australia
- Federation University, Ballarat, VIC, 3355, Australia
| | - Sumaiya Tanjil
- Department of Obstetrics & Gynaecology, Women's Cancer Research Centre, Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | - Stephen P Mulligan
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
- Kolling Institute of Medical Research, Royal North Shore Hospital, St. Leonards, NSW, 2065, Australia
| | - O Giles Best
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
- Kolling Institute of Medical Research, Royal North Shore Hospital, St. Leonards, NSW, 2065, Australia
| | - Richard J Simpson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
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Belov L, Matic KJ, Hallal S, Best OG, Mulligan SP, Christopherson RI. Extensive surface protein profiles of extracellular vesicles from cancer cells may provide diagnostic signatures from blood samples. J Extracell Vesicles 2016; 5:25355. [PMID: 27086589 PMCID: PMC4834364 DOI: 10.3402/jev.v5.25355] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 02/25/2016] [Accepted: 03/15/2016] [Indexed: 12/20/2022] Open
Abstract
Extracellular vesicles (EV) are membranous particles (30–1,000 nm in diameter) secreted by cells. Important biological functions have been attributed to 2 subsets of EV, the exosomes (bud from endosomal membranes) and the microvesicles (MV; bud from plasma membranes). Since both types of particles contain surface proteins derived from their cell of origin, their detection in blood may enable diagnosis and prognosis of disease. We have used an antibody microarray (DotScan) to compare the surface protein profiles of live cancer cells with those of their EV, based on their binding patterns to immobilized antibodies. Initially, EV derived from the cancer cell lines, LIM1215 (colorectal cancer) and MEC1 (B-cell chronic lymphocytic leukaemia; CLL), were used for assay optimization. Biotinylated antibodies specific for EpCAM (CD326) and CD19, respectively, were used to detect captured particles by enhanced chemiluminescence. Subsequently, this approach was used to profile CD19+ EV from the plasma of CLL patients. These EV expressed a subset (~40%) of the proteins detected on CLL cells from the same patients: moderate or high levels of CD5, CD19, CD31, CD44, CD55, CD62L, CD82, HLA-A,B,C, HLA-DR; low levels of CD21, CD49c, CD63. None of these proteins was detected on EV from the plasma of age- and gender-matched healthy individuals.
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Affiliation(s)
- Larissa Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia;
| | - Kieran J Matic
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Susannah Hallal
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - O Giles Best
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.,Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Stephen P Mulligan
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.,Kolling Institute of Medical Research, Royal North Shore Hospital, St Leonards, NSW, Australia
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Hu B, Niu X, Cheng L, Yang LN, Li Q, Wang Y, Tao SC, Zhou SM. Discovering cancer biomarkers from clinical samples by protein microarrays. Proteomics Clin Appl 2015; 9:98-110. [PMID: 25523829 DOI: 10.1002/prca.201400094] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/26/2014] [Accepted: 12/15/2014] [Indexed: 12/25/2022]
Abstract
Cancer biomarkers are of potential use in early cancer diagnosis, anticancer therapy development, and monitoring the responses to treatments. Protein-based cancer biomarkers are major forms in use, as they are much easier to be monitored in body fluids or tissues. For cancer biomarker discovery, high-throughput techniques such as protein microarrays hold great promises, because they are capable of global unbiased monitoring but with a miniaturized format. In doing so, novel and cancer type specific biomarkers can be systematically discovered at an affordable cost. In this review, we give a relatively complete picture on protein microarrays applied to clinical samples for cancer biomarker discovery, and conclude this review with the future perspectives.
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Affiliation(s)
- Bin Hu
- Institute for Microsurgery of Limbs, Shanghai Sixth Hospital, Shanghai Jiao Tong University, Shanghai, China
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Wold ED, McBride R, Axup JY, Kazane SA, Smider VV. Antibody microarrays utilizing site-specific antibody-oligonucleotide conjugates. Bioconjug Chem 2015; 26:807-11. [PMID: 25884500 DOI: 10.1021/acs.bioconjchem.5b00111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein arrays are typically made by random absorption of proteins to the array surface, potentially limiting the amount of properly oriented and functional molecules. We report the development of a DNA encoded antibody microarray utilizing site-specific antibody-oligonucleotide conjugates that can be used for cell immobilization as well as the detection of genes and proteins. This technology allows for the facile generation of antibody microarrays while circumventing many of the drawbacks of conventionally produced antibody arrays. We demonstrate that this method can be used to capture and detect SK-BR-3 cells (Her2+ breast cancer cells) at concentrations as low as 10(2) cells/mL (which is equivalent to 10 cells per 100 μL array) without the use of microfluidics, which is 100- to 10(5)-fold more sensitive than comparable techniques. Additionally, the method was shown to be able to detect cells in a complex mixture, effectively immobilizing and specifically detecting Her2+ cells at a concentration of 10(2) SK-BR-3 cells/mL in 4 × 10(6) white blood cells/mL. Patients with a variety of cancers can have circulating tumor cell counts of between 1 and 10(3) cells/mL in whole blood, well within the range of this technology.
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Affiliation(s)
| | | | | | - Stephanie A Kazane
- ‡California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, La Jolla, California 92037, United States
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Álvarez-Chaver P, Otero-Estévez O, Páez de la Cadena M, Rodríguez-Berrocal FJ, Martínez-Zorzano VS. Proteomics for discovery of candidate colorectal cancer biomarkers. World J Gastroenterol 2014; 20:3804-3824. [PMID: 24744574 PMCID: PMC3983438 DOI: 10.3748/wjg.v20.i14.3804] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/24/2014] [Accepted: 03/10/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the second most common cause of cancer-related deaths in Europe and other Western countries, mainly due to the lack of well-validated clinically useful biomarkers with enough sensitivity and specificity to detect this disease at early stages. Although it is well known that the pathogenesis of CRC is a progressive accumulation of mutations in multiple genes, much less is known at the proteome level. Therefore, in the last years many proteomic studies have been conducted to find new candidate protein biomarkers for diagnosis, prognosis and as therapeutic targets for this malignancy, as well as to elucidate the molecular mechanisms of colorectal carcinogenesis. An important advantage of the proteomic approaches is the capacity to look for multiple differentially expressed proteins in a single study. This review provides an overview of the recent reports describing the different proteomic tools used for the discovery of new protein markers for CRC such as two-dimensional electrophoresis methods, quantitative mass spectrometry-based techniques or protein microarrays. Additionally, we will also focus on the diverse biological samples used for CRC biomarker discovery such as tissue, serum and faeces, besides cell lines and murine models, discussing their advantages and disadvantages, and summarize the most frequently identified candidate CRC markers.
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Williams MWY, Guiffre AK, Fletcher JP. Platelets and smooth muscle cells affecting the differentiation of monocytes. PLoS One 2014; 9:e88172. [PMID: 24551082 PMCID: PMC3925135 DOI: 10.1371/journal.pone.0088172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 01/06/2014] [Indexed: 11/30/2022] Open
Abstract
Background Atherosclerosis is characterised by the formation of plaques. Monocytes play a pivotal role in plaque development as they differentiate into foam cells, a component of the lipid core whilst smooth muscle cells (SMC) are the principal cell identified in the cap. Recently, the ability of monocytes to differentiate into a myriad of other cell types has been reported. In lieu of these findings the ability of monocytes to differentiate into SMCs/smooth muscle (SM)-like cells was investigated. Method and Results Human monocytes were co-cultured with platelets or human coronary aortic SMCs and then analysed to assess their differentiation into SMCs/SM-like cells. The differentiated cells expressed a number of SMC markers and genes as determined by immunofluorescence staining and quantitative polymerase chain reaction (qPCR). CD array analysis identified marker expression profiles that discriminated them from monocytes, macrophages and foam cells as well as the expression of markers which overlapped with fibroblast and mesenchymal cells. Electron microscopy studies identified microfilaments and increased amounts of rough endoplasmic reticulum indicative of the SM- like cells, fibroblasts. Conclusions In the appropriate environmental conditions, monocytes can differentiate into SM-like cells potentially contributing to cap formation and plaque stability. Thus, monocytes may play a dual role in the development of plaque formation and ultimately atherosclerosis.
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Affiliation(s)
- Michelle W. Y. Williams
- Department of Surgery, University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia
- * E-mail:
| | - Ann K. Guiffre
- Department of Surgery, University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia
| | - John P. Fletcher
- Department of Surgery, University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia
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González-González M, Bartolome R, Jara-Acevedo R, Casado-Vela J, Dasilva N, Matarraz S, García J, Alcazar JA, Sayagues JM, Orfao A, Fuentes M. Evaluation of homo- and hetero-functionally activated glass surfaces for optimized antibody arrays. Anal Biochem 2014; 450:37-45. [PMID: 24440232 DOI: 10.1016/j.ab.2014.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 01/07/2014] [Indexed: 11/17/2022]
Abstract
Antibody arrays hold great promise for biomedical applications, but they are typically manufactured using chemically functionalized surfaces that still require optimization. Here, we describe novel hetero-functionally activated glass surfaces favoring oriented antibody binding for improved performance in protein microarray applications. Antibody arrays manufactured in our facility using the functionalization chemistries described here proved to be reproducible and stable and also showed good signal intensities. As a proof-of-principle of the glass surface functionalization protocols described in this article, we built antibody-based arrays functionalized with different chemistries that enabled the simultaneous detection of 71 human leukocyte membrane differentiation antigens commonly found in peripheral blood mononuclear cells. Such detection is specific and semi-quantitative and can be performed in a single assay under native conditions. In summary, the protocol described here, based on the use of antibody array technology, enabled the concurrent detection of a set of membrane proteins under native conditions in a specific, selective, and semi-quantitative manner and in a single assay.
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Affiliation(s)
- María González-González
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Raquel Bartolome
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | | | - Juan Casado-Vela
- Spanish National Research Council (CSIC)-Spanish National Biotechnology Centre (CNB), 28049 Madrid, Spain
| | - Noelia Dasilva
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Sergio Matarraz
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Jacinto García
- Servicio de Cirugía, Hospital Clínico Universitario de Salamanca-IBSAL, 37007 Salamanca, Spain
| | - J A Alcazar
- Servicio de Cirugía, Hospital Clínico Universitario de Salamanca-IBSAL, 37007 Salamanca, Spain
| | - J M Sayagues
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Alberto Orfao
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain.
| | - Manuel Fuentes
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain.
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Borrebaeck CAK, Wingren C. High-throughput proteomics using antibody microarrays: an update. Expert Rev Mol Diagn 2014; 7:673-86. [PMID: 17892372 DOI: 10.1586/14737159.7.5.673] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Antibody-based microarrays are a rapidly emerging technology that has advanced from the first proof-of-concept studies to demanding serum protein profiling applications during recent years, displaying great promise within disease proteomics. Miniaturized micro- and nanoarrays can be fabricated with an almost infinite number of antibodies carrying the desired specificities. While consuming only minute amounts of reagents, multiplexed and ultrasensitive assays can be performed targeting high- as well as low-abundance analytes in complex nonfractionated proteomes. The microarray images generated can then be converted into protein expression profiles or protein atlases, revealing a detailed composition of the sample. The technology will provide unique opportunities for fields such as disease diagnostics, biomarker discovery, patient stratification, predicting disease recurrence and drug target discovery. This review describes an update of high-throughput proteomics, using antibody-based microarrays, focusing on key technological advances and novel applications that have emerged over the last 3 years.
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Affiliation(s)
- Carl A K Borrebaeck
- Lund University, Department of Immunotechnology & CREATE Health, BMC D13, SE-221 84 Lund, Sweden.
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Casado-Vela J, Fuentes M, Franco-Zorrilla JM. Screening of Protein–Protein and Protein–DNA Interactions Using Microarrays. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:231-81. [DOI: 10.1016/b978-0-12-800453-1.00008-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Multiplex flow cytometry barcoding and antibody arrays identify surface antigen profiles of primary and metastatic colon cancer cell lines. PLoS One 2013; 8:e53015. [PMID: 23308131 PMCID: PMC3538639 DOI: 10.1371/journal.pone.0053015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 11/22/2012] [Indexed: 01/06/2023] Open
Abstract
Colon cancer is a deadly disease affecting millions of people worldwide. Current treatment challenges include management of disease burden as well as improvements in detection and targeting of tumor cells. To identify disease state-specific surface antigen signatures, we combined fluorescent cell barcoding with high-throughput flow cytometric profiling of primary and metastatic colon cancer lines (SW480, SW620, and HCT116). Our multiplexed technique offers improvements over conventional methods by permitting the simultaneous and rapid screening of cancer cells with reduced effort and cost. The method uses a protein-level analysis with commercially available antibodies on live cells with intact epitopes to detect potential tumor-specific targets that can be further investigated for their clinical utility. Multiplexed antibody arrays can easily be applied to other tumor types or pathologies for discovery-based approaches to target identification.
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Perenkov AD, Novikov DV, Sakharnov NA, Alyasova AV, Utkin OV, Baryshnikov AY, Novikov VV. Heterogeneous CD38 expression in tumor tissues of patients with colorectal cancer. Mol Biol 2012. [DOI: 10.1134/s002689331205010x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Revzin A, Maverakis E, Chang HC. Biosensors for immune cell analysis-A perspective. BIOMICROFLUIDICS 2012; 6:21301-2130113. [PMID: 22655003 PMCID: PMC3360707 DOI: 10.1063/1.4706845] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 04/10/2012] [Indexed: 05/14/2023]
Abstract
Massively parallel analysis of single immune cells or small immune cell colonies for disease detection, drug screening, and antibody production represents a "killer app" for the rapidly maturing microfabrication and microfluidic technologies. In our view, microfabricated solid-phase and flow cytometry platforms of the future will be complete with biosensors and electrical/mechanical/optical actuators and will enable multi-parametric analysis of cell function, real-time detection of secreted signals, and facile retrieval of cells deemed interesting.
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Zhou J, Belov L, Solomon MJ, Chan C, Clarke SJ, Christopherson RI. Colorectal cancer cell surface protein profiling using an antibody microarray and fluorescence multiplexing. J Vis Exp 2011:3322. [PMID: 21968569 DOI: 10.3791/3322] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The current prognosis and classification of CRC relies on staging systems that integrate histopathologic and clinical findings. However, in the majority of CRC cases, cell dysfunction is the result of numerous mutations that modify protein expression and post-translational modification(1). A number of cell surface antigens, including cluster of differentiation (CD) antigens, have been identified as potential prognostic or metastatic biomarkers in CRC. These antigens make ideal biomarkers as their expression often changes with tumour progression or interactions with other cell types, such as tumour-infiltrating lymphocytes (TILs) and tumour-associated macrophages (TAMs). The use of immunohistochemistry (IHC) for cancer sub-classification and prognostication is well established for some tumour types(2,3). However, no single 'marker' has shown prognostic significance greater than clinico-pathological staging or gained wide acceptance for use in routine pathology reporting of all CRC cases. A more recent approach to prognostic stratification of disease phenotypes relies on surface protein profiles using multiple 'markers'. While expression profiling of tumours using proteomic techniques such as iTRAQ is a powerful tool for the discovery of biomarkers4, it is not optimal for routine use in diagnostic laboratories and cannot distinguish different cell types in a mixed population. In addition, large amounts of tumour tissue are required for the profiling of purified plasma membrane glycoproteins by these methods. In this video we described a simple method for surface proteome profiling of viable cells from disaggregated CRC samples using a DotScan CRC antibody microarray. The 122-antibody microarray consists of a standard 82-antibody region recognizing a range of lineage-specific leukocyte markers, adhesion molecules, receptors and markers of inflammation and immune response(5), together with a satellite region for detection of 40 potentially prognostic markers for CRC. Cells are captured only on antibodies for which they express the corresponding antigen. The cell density per dot, determined by optical scanning, reflects the proportion of cells expressing that antigen, the level of expression of the antigen and affinity of the antibody(6). For CRC tissue or normal intestinal mucosa, optical scans reflect the immunophenotype of mixed populations of cells. Fluorescence multiplexing can then be used to profile selected sub-populations of cells of interest captured on the array. For example, Alexa 647-anti-epithelial cell adhesion molecule (EpCAM; CD326), is a pan-epithelial differentiation antigen that was used to detect CRC cells and also epithelial cells of normal intestinal mucosa, while Phycoerythrin-anti-CD3, was used to detect infiltrating T-cells(7). The DotScan CRC microarray should be the prototype for a diagnostic alternative to the anatomically-based CRC staging system.
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Affiliation(s)
- Jerry Zhou
- School of Molecular Bioscience, University of Sydney.
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20
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Rucevic M, Hixson D, Josic D. Mammalian plasma membrane proteins as potential biomarkers and drug targets. Electrophoresis 2011; 32:1549-64. [PMID: 21706493 DOI: 10.1002/elps.201100212] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Defining the plasma membrane proteome is crucial to understand the role of plasma membrane in fundamental biological processes. Change in membrane proteins is one of the first events that take place under pathological conditions, making plasma membrane proteins a likely source of potential disease biomarkers with prognostic or diagnostic potential. Membrane proteins are also potential targets for monoclonal antibodies and other drugs that block receptors or inhibit enzymes essential to the disease progress. Despite several advanced methods recently developed for the analysis of hydrophobic proteins and proteins with posttranslational modifications, integral membrane proteins are still under-represented in plasma membrane proteome. Recent advances in proteomic investigation of plasma membrane proteins, defining their roles as diagnostic and prognostic disease biomarkers and as target molecules in disease treatment, are presented.
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Affiliation(s)
- Marijana Rucevic
- COBRE Center for Cancer Research Development, Rhode Island Hospital, Providence, RI, USA
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Hatanaka H, Yasukawa T, Mizutani F. Detection of Surface Antigens on Living Cells through Incorporation of Immunorecognition into the Distinct Positioning of Cells with Positive and Negative Dielectrophoresis. Anal Chem 2011; 83:7207-12. [DOI: 10.1021/ac201789m] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Hironobu Hatanaka
- Graduate School of Material Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Tomoyuki Yasukawa
- Graduate School of Material Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- JST-CREST, 5, Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Fumio Mizutani
- Graduate School of Material Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
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Belov L, Zhou J, Christopherson RI. Cell surface markers in colorectal cancer prognosis. Int J Mol Sci 2010; 12:78-113. [PMID: 21339979 PMCID: PMC3039945 DOI: 10.3390/ijms12010078] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 12/16/2010] [Accepted: 12/20/2010] [Indexed: 12/14/2022] Open
Abstract
The classification of colorectal cancers (CRC) is currently based largely on histologically determined tumour characteristics, such as differentiation status and tumour stage, i.e., depth of tumour invasion, involvement of regional lymph nodes and the occurrence of metastatic spread to other organs. These are the conventional prognostic factors for patient survival and often determine the requirement for adjuvant therapy after surgical resection of the primary tumour. However, patients with the same CRC stage can have very different disease-related outcomes. For some, surgical removal of early-stage tumours leads to full recovery, while for others, disease recurrence and metastasis may occur regardless of adjuvant therapy. It is therefore important to understand the molecular processes that lead to disease progression and metastasis and to find more reliable prognostic markers and novel targets for therapy. This review focuses on cell surface proteins that correlate with tumour progression, metastasis and patient outcome, and discusses some of the challenges in finding prognostic protein markers in CRC.
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Affiliation(s)
- Larissa Belov
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; E-Mails: (J.Z.); (R.I.C.)
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23
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An extended antibody microarray for surface profiling metastatic melanoma. J Immunol Methods 2010; 358:23-34. [PMID: 20363224 DOI: 10.1016/j.jim.2010.03.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 03/24/2010] [Accepted: 03/25/2010] [Indexed: 11/24/2022]
Abstract
An antibody microarray was developed for profiling the surface proteome of melanoma cells, which may facilitate melanoma sub-classification and provide important prognostic information useful in predicting the clinical behavior of the melanoma (e.g., likely sites of metastatic spread), patient outcome and treatment response. Forty-eight antibodies were selected based on their correlation with melanoma development, progression and/or prognosis and printed on nitrocellulose slides. The immobilised antibodies capture live cells expressing corresponding antigens to produce a cell binding dot pattern representing the surface antigen profile (immunophenotype) of the melanoma. Surface antigen signatures were determined for a normal melanocyte and 6 melanoma cell lines and cell suspensions prepared from 10 surgically excised melanoma lymph node metastases. A procedure for obtaining separate surface antigen profiles for melanoma cells and leukocytes from clinical lymph node samples was also developed using anti-CD45 magnetic beads. The capture of live, bead-bound leukocytes on these antibody microarrays provides a significant enhancement of this microarray technology. The antibody microarray will be used to profile panels of surgically excised melanoma lymph node metastases (melanoma and leukocyte fractions) to determine whether the immunophenotypes correlate with clinicopathological characteristics, disease progression and clinical outcome.
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Zhou J, Belov L, Huang PY, Shin JS, Solomon MJ, Chapuis PH, Bokey L, Chan C, Clarke C, Clarke SJ, Christopherson RI. Surface antigen profiling of colorectal cancer using antibody microarrays with fluorescence multiplexing. J Immunol Methods 2010; 355:40-51. [DOI: 10.1016/j.jim.2010.01.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 01/27/2010] [Accepted: 01/29/2010] [Indexed: 01/05/2023]
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Shi CJ, Qin RY, Wang M, Tian R, Zhang ZF, Gong WQ. Identification of tumor spheres from human gallbladder carcinoma GBC-SD cells cultured in serum-free medium. Shijie Huaren Xiaohua Zazhi 2010; 18:865-870. [DOI: 10.11569/wcjd.v18.i9.865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To isolate and expand cancer stem cells in human gallbladder carcinoma cell line GBC-SD and to identify their biological properties.
METHODS: GBC-SD cells were cultured in serum-free conditions to derive tumor spheres. Tumor spheres were then expanded and cultured in serum-containing medium to permit their differentiation. The proliferative capacity of tumor sphere-forming cells was tested by methyl thiazoly tetrazolium (MTT) assay. The tumorigenicity of tumor sphere-forming cells was evaluated using animal experiments. The expression of CD15s and CD24 on the surface of tumor sphere-forming cells was detected by flow cytometry.
RESULTS: Small number of floating tumor spheres were isolated and expanded in serum-free conditions. These tumor spheres attached to the bottom of culture plates and began to differentiate in serum-containing medium. The proliferation and xenograft tumorigenicity of tumor sphere-forming cells (80.00% vs 10.00%, P < 0.05) significantly increased compared with those cultured in serum-containing conditions. The percentage of CD15s-bearing cell population was significantly higher in tumor spheres than in the common GBC-SD cells (2.56% ± 0.38% vs 10.77% ± 0.93%, t = 18.25, P < 0.05).
CONCLUSION: The cancer stem cells in GBC-SD cell line can be isolated and expanded in serum-free conditions. CD15s may be a cell surface marker for these cancer stem cells.
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26
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Ellmark P, Ghatnekar-Nilsson S, Meister A, Heinzelmann H, Montelius L, Wingren C, Borrebaeck CAK. Attovial-based antibody nanoarrays. Proteomics 2010; 9:5406-13. [PMID: 19798667 DOI: 10.1002/pmic.200800962] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Antibody array-based technology is a powerful emerging tool in proteomics, but to enable global proteome analysis, antibody array layouts with even higher density has to be developed. To this end, we have further developed the first generation of a nanoarray platform, based on attoliter-sized vials, attovials, which we have characterized and used for the detection of complement factor C1q in human serum samples. Finally, we demonstrated proof-of-concept for individual functionalization of the attovials with a recombinant antibody.
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Affiliation(s)
- Peter Ellmark
- Department of Immunotechnology, Lund University, Lund, Sweden
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Abstract
The incidence of cancer and its associated mortality are increasing globally, indicating an urgent need to develop even more effective and sensitive sets of biomarkers that could help in early diagnosis and consequent intervention. Given that many cellular processes are carried out by proteins, cancer research has recently shifted toward an exploration of the full proteome for such discovery. Among the advanced methodologies that are being developed for analyzing the proteome, antibody microarrays have become a prominent tool for gathering the information required for a better understanding of disease biology, early detection, discrimination of tumors and monitoring of disease progression. Here, we review the technical aspects and challenges in the development and use of antibody microarray assays and examine recently reported applications in oncoproteomics.
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Affiliation(s)
- Mohamed Ss Alhamdani
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany.
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28
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Wang K, Solis-Wever X, Aguas C, Liu Y, Li P, Pappas D. Differential Mobility Cytometry. Anal Chem 2009; 81:3334-43. [DOI: 10.1021/ac900277y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Kelong Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061
| | - Ximena Solis-Wever
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061
| | - Charmaine Aguas
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061
| | - Yan Liu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061
| | - Peng Li
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061
| | - Dimitri Pappas
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061
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29
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Profiling CD antigens on leukaemias with an antibody microarray. FEBS Lett 2009; 583:1785-91. [PMID: 19298816 DOI: 10.1016/j.febslet.2009.03.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 03/10/2009] [Accepted: 03/11/2009] [Indexed: 01/01/2023]
Abstract
Cluster of differentiation (CD) antigens are defined when a surface molecule found on some members of a standard panel of human cells reacts with at least one novel antibody, and there is good accompanying molecular data. Monoclonal antibodies to surface CD antigens on leukocytes have been used for flow cytometry, and more recently to construct microarrays that capture live cells. These DotScan microarrays enable the rapid and highly parallel characterization of repertoires of CD antigens whose expression patterns may be correlated with discrete leukaemia subtypes, or used to define biomarker 'signatures' for non-hematological diseases. DotScan with fluorescence multiplexing enables profiling of CD antigens for minor subsets of cells, such as colorectal cancer cells and tumour-infiltrating lymphocytes from a surgical sample.
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Abstract
Antibody-based microarrays are a new powerful proteomic technology that can be used to generate rapid and detailed expression profiles of defined sets of protein analytes in complex samples as well as high-resolution portraits of entire proteomes. Miniaturized micro- and nanoarrays can be printed with numerous antibodies carrying the desired specificities. Multiplexed and ultra-sensitive assays, specifically targeting several analytes in a single experiment, can be performed, while consuming only minute amounts of the sample. The array images generated can then be converted into protein expression profiles, or maps, revealing the detailed composition of the sample. This promising proteomic research tool will thus provide unique opportunities for e.g. disease proteomics, biomarker discovery, disease diagnostics, and patient stratification. This review describes the antibody-based microarray technology and applications thereof.
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31
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Shishkin AV, Shmyrev II, Kuznetsova SA, Ovchinina NG, Butylin AA, Ataullakhanov FI, Vorob’ev AI. Immunological biochips for parallel detection of surface antigens and morphological analysis of cells. BIOCHEMISTRY (MOSCOW) SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2008. [DOI: 10.1134/s1990747808030057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Shishkin AV, Shmyrev II, Kuznetsova SA, Ovchinina NG, Butylin AA, Ataullakhanov FI, Vorob’ev AI. Immunological biochips for studies of human erythrocytes. BIOCHEMISTRY MOSCOW SUPPLEMENT SERIES A-MEMBRANE AND CELL BIOLOGY 2008. [DOI: 10.1134/s1990747808030045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
The application of protein biomarkers as an aid for the detection and treatment of diseases has been subject to intensified interest in recent years. The quantitative assaying of protein biomarkers in easily obtainable biological fluids such as serum and urine offers the opportunity to improve patient care via earlier and more accurate diagnoses in a convenient, non-invasive manner as well as providing a potential route towards more individually targeted treatment. Essential to achieving progress in biomarker technology is the ability to screen large numbers of proteins simultaneously in a single experiment with high sensitivity and selectivity. In this article, we highlight recent progress in the use of microarrays for high-throughput biomarker profiling and discuss some of the challenges associated with these efforts.
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Affiliation(s)
- Hye Jin Lee
- Department of Chemistry, Kyungpook National University, Daegu 702-701, South Korea.
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34
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Phenotypic protein profiling of different B cell sub-populations using antibody CD-microarrays. Cancer Lett 2008; 265:98-106. [DOI: 10.1016/j.canlet.2008.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 01/28/2008] [Accepted: 02/03/2008] [Indexed: 11/22/2022]
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35
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36
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Lui R, Brown A, Wu B, Lin MW, Thompson J, Braet F, Dyer W, Lattimore J, Macdonald P, Adelstein S, dos Remedios CG. Use of Antibody Microarrays in the Analysis of Inflammation, Autoimmunity, Viral Infection, and Cancer Metastases. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch31] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
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37
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Wang K, Marshall MK, Garza G, Pappas D. Open-tubular capillary cell affinity chromatography: single and tandem blood cell separation. Anal Chem 2008; 80:2118-24. [PMID: 18288818 DOI: 10.1021/ac702553w] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this paper, an open-tubular capillary cell affinity chromatography (OT-CAC) method to enrich and separate target cells is described. Open tubular capillaries coated with anti-CD4, anti-CD14, or anti-CD19 antibodies were used as affinity chromatography columns to separate target blood cells. Cells were eluted using either shear force or bubbles. Bubbles were used to elute the captured cells without diluting the captured cells appreciably, while maintaining viability (the viability of the recovered cells was 85.83 +/- 7.34%; the viability of the cells was 90.41 +/- 3.49% before separation). Several aspects of the OT-CAC method were studied, such as the affinity of one antibody between two different cell lines, the effect of shear force, and the recovery of captured cells. Single- and multicell type separations were demonstrated by isolating CD4+ cells with antiCD4 coated capillary and isolating CD4+ and CD19+ cells with two capillaries in tandem from blood samples. In the one cell type isolation test, an average of 87.7% of the recovered cells from antiCD4 capillary were lymphocytes and an average of 97.7% of those lymphocytes were CD4+ cells. In the original blood sample, only 14.2% of the leukocytes were CD4+ cells. Two capillary columns were also run in tandem, separating two blood cell types from a single sample with high purity. The use of different elution shear forces was demonstrated to selectively elute one cell type. This method is an inexpensive, rapid, and effective method to separate target cells from blood samples.
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Affiliation(s)
- Kelong Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Box 41061, Lubbock, Texas 79409-1061, USA
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38
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Narasimhan K, Changqing Z, Choolani M. Ovarian cancer proteomics: Many technologies one goal. Proteomics Clin Appl 2008; 2:195-218. [DOI: 10.1002/prca.200780003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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39
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The applicability of a cluster of differentiation monoclonal antibody microarray to the diagnosis of human disease. Methods Mol Biol 2008; 439:199-209. [PMID: 18370105 DOI: 10.1007/978-1-59745-188-8_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Recent advances in antibody microarray technology have facilitated the development of multiplexed diagnostic platforms. Highly parallel antigen expression data obtained from these arrays allow disease states to be characterized using protein patterns rather than individual protein markers. The development of an antibody microarray platform of general applicability requires careful consideration of the array content. The human cluster of differentiation (CD) antigens constitute a promising candidate set, being united by their common expression at the leukocyte cell surface and the fact that the majority perform critical functions in the human immune response. The diagnostic potential of a microarray, containing 82 cluster of differentiation monoclonal antibodies (DotScan microarrays) has been demonstrated for a variety of infectious and neoplastic disease states, including HIV, many acute and chronic leukemias, and colorectal cancer. It is likely that these microarrays will have more general utility that extends to other pathological categories, including autoimmune, metabolic, and degenerative diseases.
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40
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Brown A, Lattimore JD, McGrady M, Sullivan D, Dyer W, Braet F, dos Remedios C. Stable and unstable angina: Identifying novel markers on circulating leukocytes. Proteomics Clin Appl 2007; 2:90-8. [DOI: 10.1002/prca.200780090] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Indexed: 11/11/2022]
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41
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Starkuviene V, Pepperkok R, Erfle H. Transfected cell microarrays: an efficient tool for high-throughput functional analysis. Expert Rev Proteomics 2007; 4:479-89. [PMID: 17705706 DOI: 10.1586/14789450.4.4.479] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Transfected cell microarrays are considered to be a breakthrough methodology for high-throughput and high-content functional genomics. Here, recent advances in the cell microarray field are reviewed, along with its potential to increase the speed of determining gene function. These advances, combined with an increasing number and diversity of gene perturbing systems, such as RNAi and ectopic gene expression, provide tools for expanding our understanding of biology at the systems level.
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Affiliation(s)
- Vytaute Starkuviene
- European Molecular Biology Laboratory, Cell Biology & Cell Biophysics Unit, Heidelberg, Germany.
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42
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Kato K, Ishimuro T, Arima Y, Hirata I, Iwata H. High-Throughput Immunophenotyping by Surface Plasmon Resonance Imaging. Anal Chem 2007; 79:8616-23. [DOI: 10.1021/ac071548s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Koichi Kato
- Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan, Faculty of Medical Engineering, Suzuka University of Medical Science, 1001-1 Kishioka-cho, Suzuka 510-0293, Japan, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan, and Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation
| | - Toshinari Ishimuro
- Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan, Faculty of Medical Engineering, Suzuka University of Medical Science, 1001-1 Kishioka-cho, Suzuka 510-0293, Japan, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan, and Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation
| | - Yusuke Arima
- Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan, Faculty of Medical Engineering, Suzuka University of Medical Science, 1001-1 Kishioka-cho, Suzuka 510-0293, Japan, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan, and Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation
| | - Isao Hirata
- Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan, Faculty of Medical Engineering, Suzuka University of Medical Science, 1001-1 Kishioka-cho, Suzuka 510-0293, Japan, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan, and Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation
| | - Hiroo Iwata
- Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan, Faculty of Medical Engineering, Suzuka University of Medical Science, 1001-1 Kishioka-cho, Suzuka 510-0293, Japan, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan, and Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation
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Pappas D, Wang K. Cellular separations: A review of new challenges in analytical chemistry. Anal Chim Acta 2007; 601:26-35. [PMID: 17904469 DOI: 10.1016/j.aca.2007.08.033] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 08/03/2007] [Accepted: 08/20/2007] [Indexed: 11/15/2022]
Abstract
The ability to generate a sample of cells of a given phenotype is a prerequisite for many cellular assays. In response to this growing need, numerous methods for cell separation have been developed in recent years. This Review covers recent progress in the field of cell separations and cell chromatography. Cell separation principles-such as size and affinity capture-are discussed, as well as conventional methods such as fluorescence-activated cell sorting and magnetic sorting. Planar flow cell arrays, dielectrophoresis, field-flow methods, and column separation devices are reviewed, as well as applications of these methods to medicine and biotechnology. Cell attachment and adhesion strategies and a comparison of techniques are also presented.
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Affiliation(s)
- Dimitri Pappas
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
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Wang K, Cometti B, Pappas D. Isolation and counting of multiple cell types using an affinity separation device. Anal Chim Acta 2007; 601:1-9. [PMID: 17904467 DOI: 10.1016/j.aca.2007.08.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 08/14/2007] [Accepted: 08/18/2007] [Indexed: 11/24/2022]
Abstract
A simple device for the separation of cells by phenotype is described. Cells are separated/isolated using capture antibodies on a glass chip. Unlike other "sandwich" type assays, the readout is performed without labels using transmission microscopy, simplifying cell enumeration. T and B lymphocytes from cell culture or whole blood were separated using antibodies for the CD4, CD19, and CD71 antigens. The separation slides were found to reproducibly bind cells by antigen expression, allowing for accurate enumeration of mixed cell samples. Inter- and intra-device variability was evaluated, and the issue of nonspecific binding is addressed. We envision that this type of cell separation technique could be used in remote settings, as sample preparation is minimal and the analysis time is rapid (20 min from sample acquisition to final readout).
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Affiliation(s)
- Kelong Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
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Pollard HB, Srivastava M, Eidelman O, Jozwik C, Rothwell SW, Mueller GP, Jacobowitz DM, Darling T, Guggino WB, Wright J, Zeitlin PL, Paweletz CP. Protein microarray platforms for clinical proteomics. Proteomics Clin Appl 2007; 1:934-52. [PMID: 21136748 DOI: 10.1002/prca.200700154] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Indexed: 11/12/2022]
Abstract
Proteomics for clinical applications is presently in a state of transition. It has become clear that the classical approaches based on 2-DE and/or MS need to be complemented by different kinds of technologies. The well-known problems include sample complexity, sensitivity, quantitation, reproducibility, and analysis time. We suggest that the new technologies for clinical proteomics can be supported by antibody-centric protein microarray platforms. These platforms presently include antibody microarrays and lysate, or reverse capture/reverse phase protein microarrays. Other forms of these arrays are in less mature developmental stages, including ORF and self assembling protein microarrays. Bioinformatic support for interpreting these arrays is becoming more available as the whole field of systems biology begins to mature. The present set of applications for these platforms is profoundly focused on certain common cancers, immunology, and cystic fibrosis. However, we predict that many more disease entities will become studied as knowledge of the power and availability of these platforms becomes more widely established. We anticipate that these platforms will eventually evolve to accommodate label-free detection technologies, human genome-scale numbers of analytes, and increases in analytic and bioinformatic speeds.
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Affiliation(s)
- Harvey B Pollard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, USUHS, Bethesda, MD, USA.
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Kato K, Toda M, Iwata H. Antibody arrays for quantitative immunophenotyping. Biomaterials 2007; 28:1289-97. [PMID: 17126397 DOI: 10.1016/j.biomaterials.2006.11.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2006] [Accepted: 11/03/2006] [Indexed: 11/25/2022]
Abstract
Detection of multiple surface antigens expressed on living cell is an important step for cell processing and clinical diagnosis. Here we describe the preparation of antibody arrays that allow parallel detection of multiple surface antigens through affinity binding of living cells. An antibody array was fabricated by photo-assisted patterning of an alkanethiol monolayer formed on a gold-coated glass plate and subsequent immobilization of antibodies specific for cell surface antigens in an array format. We demonstrate here that rapid phenotyping can be performed on the array for both adhesion-dependent and non-dependent cells by direct cell binding assays. The density of bound cells on each antibody spot was in accordance with their contents in an original suspension. This result suggests the feasibility of the array-based method for quantitative assessment of multiple antigen expression. These findings will serve to extend the range of fundamental and clinical applications of antibody arrays.
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Affiliation(s)
- Koichi Kato
- Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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Sun L, Sung KB, Dentinger C, Lutz B, Nguyen L, Zhang J, Qin H, Yamakawa M, Cao M, Lu Y, Chmura AJ, Zhu J, Su X, Berlin AA, Chan S, Knudsen B. Composite organic-inorganic nanoparticles as Raman labels for tissue analysis. NANO LETTERS 2007; 7:351-6. [PMID: 17298000 DOI: 10.1021/nl062453t] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Composite organic-inorganic nanoparticles (COINs) are novel optical labels for detection of biomolecules. We have previously developed methods to encapsulate COINs and to functionalize them with antibodies. Here we report the first steps toward application of COINs to the detection of proteins in human tissues. Two analytes, PSA and CK18, are detected simultaneously using two different COINs in a direct binding assay, and two different COINs are shown to simultaneously label PSA in tissue samples.
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Affiliation(s)
- Lei Sun
- Biomedical/Life Sciences, Digital Health Group, Intel Corporation, SC3-41, 2200 Mission College Boulevard, Santa Clara, California 95054, USA
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Wingren C, Borrebaeck CAK. Antibody microarrays: current status and key technological advances. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2006; 10:411-27. [PMID: 17069517 DOI: 10.1089/omi.2006.10.411] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Antibody-based microarrays are among the novel classes of rapidly evolving proteomic technologies that holds great promise in biomedicine. Miniaturized microarrays (< 1 cm2) can be printed with thousands of individual antibodies carrying the desired specificities, and with biological sample (e.g., an entire proteome) added, virtually any specifically bound analytes can be detected. While consuming only minute amounts (< microL scale) of reagents, ultra- sensitive assays (zeptomol range) can readily be performed in a highly multiplexed manner. The microarray patterns generated can then be transformed into proteomic maps, or detailed molecular fingerprints, revealing the composition of the proteome. Thus, protein expression profiling and global proteome analysis using this tool will offer new opportunities for drug target and biomarker discovery, disease diagnostics, and insights into disease biology. Adopting the antibody microarray technology platform, several biomedical applications, ranging from focused assays to proteome-scale analysis will be rapidly emerging in the coming years. This review will discuss the current status of the antibody microarray technology focusing on recent technological advances and key issues in the process of evolving the methodology into a high-performing proteomic research tool.
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Ellmark P, Ingvarsson J, Carlsson A, Lundin BS, Wingren C, Borrebaeck CAK. Identification of protein expression signatures associated with Helicobacter pylori infection and gastric adenocarcinoma using recombinant antibody microarrays. Mol Cell Proteomics 2006; 5:1638-46. [PMID: 16844680 DOI: 10.1074/mcp.m600170-mcp200] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Antibody microarray based technology is a powerful emerging tool in proteomics, target discovery, and differential analysis. Here, we report the first study where recombinant antibody fragments have been used to construct large scale antibody microarrays, composed of 127 different antibodies against mostly immunoregulatory antigens. The arrays were based on single framework recombinant antibody fragments (SinFabs) designed for high on-chip stability and functionality and were used for the analysis of malignant and normal stomach tissue samples from Helicobacter pylori-positive and -negative patients. Our results demonstrate that distinct tumor- as well as infection-associated protein expression signatures could be identified from these complex tissue proteomes, as well as biomarkers such as IL-9, IL-11, and MCP-4, previously not found in these diseases. In a longer perspective, this study may improve the understanding of H. pylori-induced stomach cancer and lead to development of improved diagnostics.
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Affiliation(s)
- Peter Ellmark
- Department of Immunotechnology, Lund University, BMC D13, SE-22184 Lund, Sweden
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Haab BB. Applications of antibody array platforms. Curr Opin Biotechnol 2006; 17:415-21. [PMID: 16837184 DOI: 10.1016/j.copbio.2006.06.013] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Revised: 06/02/2006] [Accepted: 06/30/2006] [Indexed: 12/20/2022]
Abstract
Antibody arrays are valuable for the parallel analysis of multiple proteins in small sample volumes. The earliest and most widely used application of antibody arrays has been to measure multiple protein abundances, using sandwich assays and label-based assays, for biomarker discovery and biological studies. Modifications to these assays have led to studies profiling specific protein post-translational modifications. Additional novel uses include profiling enzyme activities and protein cell-surface expression. Finally, array-based antibody platforms are being used to assist the development and characterization of antibodies. Continued progress in the technology will surely lead to extensions of these applications and the development of new ways of using the methods.
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Affiliation(s)
- Brian B Haab
- Van Andel Research Institute, Grand Rapids, MI 49503, USA.
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