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Bracken SJ, Suthers AN, DiCioccio RA, Su H, Anand S, Poe JC, Jia W, Visentin J, Basher F, Jordan CZ, McManigle WC, Li Z, Hakim FT, Pavletic SZ, Bhuiya NS, Ho VT, Horwitz ME, Chao NJ, Sarantopoulos S. Heightened TLR7 signaling primes BCR-activated B cells in chronic graft-versus-host disease for effector functions. Blood Adv 2024; 8:667-680. [PMID: 38113462 PMCID: PMC10839617 DOI: 10.1182/bloodadvances.2023010362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 11/02/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
ABSTRACT Chronic graft-versus-host disease (cGVHD) is a debilitating, autoimmune-like syndrome that can occur after allogeneic hematopoietic stem cell transplantation. Constitutively activated B cells contribute to ongoing alloreactivity and autoreactivity in patients with cGVHD. Excessive tissue damage that occurs after transplantation exposes B cells to nucleic acids in the extracellular environment. Recognition of endogenous nucleic acids within B cells can promote pathogenic B-cell activation. Therefore, we hypothesized that cGVHD B cells aberrantly signal through RNA and DNA sensors such as Toll-like receptor 7 (TLR7) and TLR9. We found that B cells from patients and mice with cGVHD had higher expression of TLR7 than non-cGVHD B cells. Using ex vivo assays, we found that B cells from patients with cGVHD also demonstrated increased interleukin-6 production after TLR7 stimulation with R848. Low-dose B-cell receptor (BCR) stimulation augmented B-cell responses to TLR7 activation. TLR7 hyperresponsiveness in cGVHD B cells correlated with increased expression and activation of the downstream transcription factor interferon regulatory factor 5. Because RNA-containing immune complexes can activate B cells through TLR7, we used a protein microarray to identify RNA-containing antigen targets of potential pathological relevance in cGVHD. We found that many of the unique targets of active cGVHD immunoglobulin G (IgG) were nucleic acid-binding proteins. This unbiased assay identified the autoantigen and known cGVHD target Ro-52, and we found that RNA was required for IgG binding to Ro-52. Herein, we find that BCR-activated B cells have aberrant TLR7 signaling responses that promote potential effector responses in cGVHD.
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Affiliation(s)
- Sonali J. Bracken
- Division of Rheumatology and Immunology, Department of Medicine, Duke University Medical Center, Durham, NC
| | - Amy N. Suthers
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC
| | - Rachel A. DiCioccio
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC
| | - Hsuan Su
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC
| | - Sarah Anand
- Division of Hematology and Medical Oncology, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Jonathan C. Poe
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC
| | - Wei Jia
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC
| | - Jonathan Visentin
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC
- Department of Immunology and Immunogenetics, Bordeaux University Hospital, Bordeaux, France
- UMR CNRS 5164 ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Fahmin Basher
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC
| | - Collin Z. Jordan
- Division of Nephrology, Department of Medicine, Duke University Medical Center, Durham NC
| | - William C. McManigle
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University Medical Center, Durham NC
| | - Zhiguo Li
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham NC
- Duke Cancer Institute, Duke University Medical Center, Durham NC
| | - Frances T. Hakim
- Experimental Transplantation and Immunology Branch, National Cancer Institute, Bethesda, MD
| | - Steven Z. Pavletic
- Experimental Transplantation and Immunology Branch, National Cancer Institute, Bethesda, MD
| | - Nazmim S. Bhuiya
- Experimental Transplantation and Immunology Branch, National Cancer Institute, Bethesda, MD
| | - Vincent T. Ho
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Mitchell E. Horwitz
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC
- Duke Cancer Institute, Duke University Medical Center, Durham NC
| | - Nelson J. Chao
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC
- Duke Cancer Institute, Duke University Medical Center, Durham NC
- Department of Integrated Immunobiology, Duke University School of Medicine, Durham, NC
| | - Stefanie Sarantopoulos
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC
- Duke Cancer Institute, Duke University Medical Center, Durham NC
- Department of Integrated Immunobiology, Duke University School of Medicine, Durham, NC
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Mavridou D, Psatha K, Aivaliotis M. Proteomics and Drug Repurposing in CLL towards Precision Medicine. Cancers (Basel) 2021; 13:cancers13143391. [PMID: 34298607 PMCID: PMC8303629 DOI: 10.3390/cancers13143391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Despite continued efforts, the current status of knowledge in CLL molecular pathobiology, diagnosis, prognosis and treatment remains elusive and imprecise. Proteomics approaches combined with advanced bioinformatics and drug repurposing promise to shed light on the complex proteome heterogeneity of CLL patients and mitigate, improve, or even eliminate the knowledge stagnation. In relation to this concept, this review presents a brief overview of all the available proteomics and drug repurposing studies in CLL and suggests the way such studies can be exploited to find effective therapeutic options combined with drug repurposing strategies to adopt and accost a more “precision medicine” spectrum. Abstract CLL is a hematological malignancy considered as the most frequent lymphoproliferative disease in the western world. It is characterized by high molecular heterogeneity and despite the available therapeutic options, there are many patient subgroups showing the insufficient effectiveness of disease treatment. The challenge is to investigate the individual molecular characteristics and heterogeneity of these patients. Proteomics analysis is a powerful approach that monitors the constant state of flux operators of genetic information and can unravel the proteome heterogeneity and rewiring into protein pathways in CLL patients. This review essences all the available proteomics studies in CLL and suggests the way these studies can be exploited to find effective therapeutic options combined with drug repurposing approaches. Drug repurposing utilizes all the existing knowledge of the safety and efficacy of FDA-approved or investigational drugs and anticipates drug alignment to crucial CLL therapeutic targets, leading to a better disease outcome. The drug repurposing studies in CLL are also discussed in this review. The next goal involves the integration of proteomics-based drug repurposing in precision medicine, as well as the application of this procedure into clinical practice to predict the most appropriate drugs combination that could ensure therapy and the long-term survival of each CLL patient.
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Affiliation(s)
- Dimitra Mavridou
- Laboratory of Biochemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh)—Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Konstantina Psatha
- Laboratory of Biochemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh)—Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR-70013 Heraklion, Greece
- Correspondence: (K.P.); (M.A.)
| | - Michalis Aivaliotis
- Laboratory of Biochemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh)—Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR-70013 Heraklion, Greece
- Correspondence: (K.P.); (M.A.)
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3
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Da Gama Duarte J, Goosen RW, Lawry PJ, Blackburn JM. PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization. BMC Res Notes 2018; 11:156. [PMID: 29482592 PMCID: PMC5828362 DOI: 10.1186/s13104-018-3266-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 02/22/2018] [Indexed: 12/12/2022] Open
Abstract
Objective Protein microarrays provide a high-throughput platform to measure protein interactions and associated functions, and can aid in the discovery of cancer biomarkers. The resulting protein microarray data can however be subject to systematic bias and noise, thus requiring a robust data processing, normalization and analysis pipeline to ensure high quality and robust results. To date, a comprehensive data processing pipeline is yet to be developed. Furthermore, a lack of analysis consistency is evident amongst different research groups, thereby impeding collaborative data consolidation and comparison. Thus, we sought to develop an accessible data processing tool using methods that are generalizable to the protein microarray field and which can be adapted to individual array layouts with minimal software engineering expertise. Results We developed an improved version of a previously developed pipeline of protein microarray data processing and implemented it as an open source software tool, with particular focus on widening its use and applicability. The Protein Microarray Analyser software presented here includes the following tools: (1) neighbourhood background correction, (2) net intensity correction, (3) user-defined noise threshold, (4) user-defined CV threshold amongst replicates and (5) assay controls, (6) composite ‘pin-to-pin’ normalization amongst sub-arrays, and (7) ‘array-to-array’ normalization amongst whole arrays. Electronic supplementary material The online version of this article (10.1186/s13104-018-3266-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica Da Gama Duarte
- Department of Integrative Biomedical Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. .,Tumour Immunology Laboratory, Olivia Newton-John Cancer Research Institute/School of Cancer Medicine, La Trobe University, Level 5, ONJCWC, 145 Studley Road, Heidelberg, VIC, 3084, Australia.
| | - Ryan W Goosen
- Department of Integrative Biomedical Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Peter J Lawry
- Olivia Newton-John Cancer Research Institute/School of Cancer Medicine, La Trobe University, Level 5, ONJCWC, 145 Studley Road, Heidelberg, VIC, 3084, Australia
| | - Jonathan M Blackburn
- Department of Integrative Biomedical Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Blackburn Laboratory, N3.03, Wernher & Beit Building North, Institute of Infectious Disease & Molecular Medicine, UCT Faculty of Health Sciences, Observatory, Cape Town, 7925, South Africa
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Díez P, Góngora R, Orfao A, Fuentes M. Functional proteomic insights in B-cell chronic lymphocytic leukemia. Expert Rev Proteomics 2016; 14:137-146. [DOI: 10.1080/14789450.2017.1275967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
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Novel myeloma-associated antigens revealed in the context of syngeneic hematopoietic stem cell transplantation. Blood 2012; 119:3142-50. [PMID: 22267603 DOI: 10.1182/blood-2011-11-388926] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Targets of curative donor-derived graft-versus-myeloma (GVM) responses after allogeneic hematopoietic stem cell transplantation (HSCT) remain poorly defined, partly because immunity against minor histocompatibility Ags (mHAgs) complicates the elucidation of multiple myeloma (MM)-specific targets. We hypothesized that syngeneic HSCT would facilitate the identification of GVM-associated Ags because donor immune responses in this setting should exclusively target unique tumor Ags in the absence of donor-host genetic disparities. Therefore, in the present study, we investigated the development of tumor immunity in an HLA-A0201(+) MM patient who achieved durable remission after myeloablative syngeneic HSCT. Using high-density protein microarrays to screen post-HSCT plasma, we identified 6 Ags that elicited high-titer (1:5000-1:10 000) Abs that correlated with clinical tumor regression. Two Ags (DAPK2 and PIM1) had enriched expression in primary MM tissues. Both elicited Ab responses in other MM patients after chemotherapy or HSCT (11 and 6 of 32 patients for DAPK2 and PIM1, respectively). The index patient also developed specific CD8(+) T-cell responses to HLA-A2-restricted peptides derived from DAPK2 and PIM1. Peptide-specific T cells recognized HLA-A2(+) MM-derived cell lines and primary MM tumor cells. Coordinated T- and B-cell immunity develops against MM-associated Ags after syngeneic HSCT. DAPK1 and PIM1 are promising target Ags for MM-directed immunotherapy.
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Miersch S, LaBaer J. Nucleic Acid programmable protein arrays: versatile tools for array-based functional protein studies. ACTA ACUST UNITED AC 2011; Chapter 27:Unit27.2. [PMID: 21488044 DOI: 10.1002/0471140864.ps2702s64] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Protein microarrays offer a global perspective on the function of expressed gene products. However, technical issues related to the stability and dynamic range of microarrays printed with purified protein have hampered their widespread adoption. Taking an alternate approach, the Nucleic Acid Programmable Protein Array (NAPPA) is constructed by spotting protein-encoding plasmid DNA at high density, in addressable fashion, on an array surface. Proteins are subsequently generated in situ just prior to experimentation using cell-free expression systems. As such, the NAPPA platform offers a unique and viable alternative that circumvents many of the inherent limitations of spotted protein arrays, enabling diverse functional protein studies including protein-small molecule, protein-protein, antigen-antibody, and protein-nucleic acid interactions. It further offers a versatile and adaptable platform amenable to a variety of capture modalities and expression systems, and, most importantly, construction of the array is accessible to any lab with an array printer and laser slide scanner. This unit is intended to provide a reference for investigators wishing to generate arrays based on this platform, and details (1) the basic construction of cDNA-based protein microarrays from DNA isolation to printing and development, (2) quality-control efforts taken to ensure the usefulness and integrity of microarray data, and (3) a particular example of the application of self-assembling protein arrays to screen for blood-borne antibody biomarkers.
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Affiliation(s)
- Shane Miersch
- Biodesign Institute at Arizona State University, Tempe, Arizona
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7
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DeLuca DS, Marina O, Ray S, Zhang GL, Wu CJ, Brusic V. Data processing and analysis for protein microarrays. Methods Mol Biol 2011; 723:337-47. [PMID: 21370075 DOI: 10.1007/978-1-61779-043-0_21] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein microarrays are a high-throughput technology capable of generating large quantities of proteomics data. They can be used for general research or for clinical diagnostics. Bioinformatics and statistical analysis techniques are required for interpretation and reaching biologically relevant conclusions from raw data. We describe essential algorithms for processing protein microarray data, including spot-finding on slide images, Z score, and significance analysis of microarrays (SAM) calculations, as well as the concentration dependent analysis (CDA). We also describe available tools for protein microarray analysis, and provide a template for a step-by-step approach to performing an analysis centered on the CDA method. We conclude with a discussion of fundamental and practical issues and considerations.
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Affiliation(s)
- David S DeLuca
- Cancer Vaccine Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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Abstract
Recombinant antigen arrays represent a new frontier in parallel analysis of multiple immune response profiles requiring only minute blood samples. In this article, we review the benefits and pitfalls of recombinant antigen microarrays developed for multiplexed antibody quantification. In particular, we describe the development of antigen arrays presenting a set of Y chromosome-encoded antigens, called H-Y antigens. These H-Y antigens are immunologically recognized as minor histocompatibility antigens (mHA) following allogeneic blood and organ transplantation. Clinically relevant B-cell responses against H-Y antigens have been demonstrated in male patients receiving female hematopoietic stem cell grafts and are associated with chronic graft versus host development. This chapter discusses our recombinant antigen microarray methods to measure these clinically relevant allo-antibodies.
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9
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Protein microarrays and biomarkers of infectious disease. Int J Mol Sci 2010; 11:5165-83. [PMID: 21614200 PMCID: PMC3100839 DOI: 10.3390/ijms11125165] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 12/11/2010] [Accepted: 12/15/2010] [Indexed: 01/11/2023] Open
Abstract
Protein microarrays are powerful tools that are widely used in systems biology research. For infectious diseases, proteome microarrays assembled from proteins of pathogens will play an increasingly important role in discovery of diagnostic markers, vaccines, and therapeutics. Distinct formats of protein microarrays have been developed for different applications, including abundance-based and function-based methods. Depending on the application, design issues should be considered, such as the need for multiplexing and label or label free detection methods. New developments, challenges, and future demands in infectious disease research will impact the application of protein microarrays for discovery and validation of biomarkers.
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Reverse phase protein microarray technology in traumatic brain injury. J Neurosci Methods 2010; 192:96-101. [DOI: 10.1016/j.jneumeth.2010.07.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2010] [Revised: 07/12/2010] [Accepted: 07/21/2010] [Indexed: 11/17/2022]
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Chronic humoral rejection of human kidney allografts associates with broad autoantibody responses. Transplantation 2010; 89:1239-46. [PMID: 20445487 DOI: 10.1097/tp.0b013e3181d72091] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Chronic humoral rejection (CHR) is a major complication after kidney transplantation. The cause of CHR is currently unknown. Autoantibodies have often been reported in kidney transplant recipients alongside antidonor human leukocyte antigen antibodies. Yet, the lack of comprehensive studies has limited our understanding of this autoimmune component in the pathophysiology of CHR. METHODS By using a series of ELISA and immunocytochemistry assays, we assessed the development of autoantibodies in 25 kidney transplant recipients with CHR and 25 patients with stable graft function. We also compared the reactivity of five CHR and five non-CHR patient sera with 8027 recombinant human proteins using protein microarrays. RESULTS We observed that a majority of CHR patients, but not non-CHR control patients, had developed antibody responses to one or several autoantigens at the time of rejection. Protein microarray assays revealed a burst of autoimmunity at the time of CHR. Remarkably, microarray analysis showed minimal overlap between profiles, indicating that each CHR patient had developed autoantibodies to a unique set of antigenic targets. CONCLUSION The breadth of autoantibody responses, together with the absence of consensual targets, suggests that these antibody responses result from systemic B-cell deregulation.
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Vigil A, Davies DH, Felgner PL. Defining the humoral immune response to infectious agents using high-density protein microarrays. Future Microbiol 2010; 5:241-51. [PMID: 20143947 DOI: 10.2217/fmb.09.127] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A major component of the adaptive immune response to infection is the generation of protective and long-lasting humoral immunity. Traditional approaches to understanding the host's humoral immune response are unable to provide an integrated understanding of the antibody repertoire generated in response to infection. By studying multiple antigenic responses in parallel, we can learn more about the breadth and dynamics of the antibody response to infection. Measurement of antibody production following vaccination is also a gauge for efficacy, as generation of antibodies can protect from future infections and limit disease. Protein microarrays are well suited to identify, quantify and compare individual antigenic responses following exposure to infectious agents. This technology can be applied to the development of improved serodiagnostic tests, discovery of subunit vaccine antigen candidates, epidemiologic research and vaccine development, as well as providing novel insights into infectious disease and the immune system. In this review, we will discuss the use of protein microarrays as a powerful tool to define the humoral immune response to bacteria and viruses.
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Affiliation(s)
- Adam Vigil
- University of California Irvine, Department of Medicine, Division of Infectious Diseases, 3501 Hewitt Hall, Irvine, CA 92697, USA.
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13
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Marina O, Hainz U, Biernacki MA, Zhang W, Cai A, Duke-Cohan JS, Liu F, Brusic V, Neuberg D, Kutok JL, Alyea EP, Canning CM, Soiffer RJ, Ritz J, Wu CJ. Serologic markers of effective tumor immunity against chronic lymphocytic leukemia include nonmutated B-cell antigens. Cancer Res 2010; 70:1344-55. [PMID: 20124481 PMCID: PMC2852266 DOI: 10.1158/0008-5472.can-09-3143] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Patients with chronic lymphocytic leukemia (CLL) who relapse after allogeneic transplant may achieve durable remission following donor lymphocyte infusion (DLI), showing the potency of donor-derived immunity in eradicating tumors. We sought to elucidate the antigenic basis of the effective graft-versus-leukemia (GvL) responses associated with DLI for the treatment of CLL by analyzing the specificity of plasma antibody responses developing in two DLI-treated patients who achieved long-term remission without graft-versus-host disease. By probing high-density protein microarrays with patient plasma, we discovered 35 predominantly intracellular antigens that elicited high-titer antibody reactivity greater in post-DLI than in pre-DLI plasma. Three antigens-C6orf130, MDS032, and ZFYVE19-were identified by both patients. Along with additional candidate antigens DAPK3, SERBP1, and OGFOD1, these proteins showed higher transcript and protein expression in B cells and CLL cells compared with normal peripheral blood mononuclear cells. DAPK3 and the shared antigens do not represent minor histocompatibility antigens, as their sequences are identical in both donor and tumor. Although ZFYVE19, DAPK3, and OGFOD1 elicited minimal antibody reactivity in 12 normal subjects and 12 chemotherapy-treated CLL patients, 5 of 12 CLL patients with clinical GvL responses were serologically reactive to these antigens. Moreover, antibody reactivity against these antigens was temporally correlated with clinical disease regression. These B-cell antigens represent promising biomarkers of effective anti-CLL immunity.
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MESH Headings
- Antigens, Surface/analysis
- Antigens, Surface/blood
- Antigens, Surface/genetics
- Antigens, Surface/metabolism
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Bone Marrow Transplantation/immunology
- Cell Lineage/immunology
- Female
- Humans
- Immunity, Innate/genetics
- Immunity, Innate/immunology
- Immunodominant Epitopes/analysis
- Immunodominant Epitopes/blood
- Leukemia, Lymphocytic, Chronic, B-Cell/blood
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Male
- Middle Aged
- Mutation/physiology
- Prognosis
- Protein Array Analysis
- Treatment Outcome
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Affiliation(s)
- Ovidiu Marina
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston MA
- William Beaumont Hospital, Transitional Year Program, Royal Oak, MI
| | - Ursula Hainz
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston MA
| | - Melinda A. Biernacki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston MA
- University of Connecticut School of Medicine, Farmington, CT
| | - Wandi Zhang
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston MA
| | - Ann Cai
- Harvard Medical School, Boston MA
| | - Jonathan S. Duke-Cohan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston MA
- Harvard Medical School, Boston MA
| | - Fenglong Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston MA
| | - Vladimir Brusic
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston MA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston MA
| | - Jeffery L. Kutok
- Harvard Medical School, Boston MA
- Department of Pathology, Brigham and Women’s Hospital, Boston MA
| | - Edwin P. Alyea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston MA
- Harvard Medical School, Boston MA
- Department of Medicine, Brigham and Women's Hospital, Boston MA
| | - Christine M. Canning
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston MA
| | - Robert J. Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston MA
- Harvard Medical School, Boston MA
- Department of Medicine, Brigham and Women's Hospital, Boston MA
| | - Jerome Ritz
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston MA
- Harvard Medical School, Boston MA
- Department of Medicine, Brigham and Women's Hospital, Boston MA
| | - Catherine J. Wu
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston MA
- Harvard Medical School, Boston MA
- Department of Medicine, Brigham and Women's Hospital, Boston MA
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14
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Biernacki MA, Marina O, Zhang W, Liu F, Bruns I, Cai A, Neuberg D, Canning CM, Alyea EP, Soiffer RJ, Brusic V, Ritz J, Wu CJ. Efficacious immune therapy in chronic myelogenous leukemia (CML) recognizes antigens that are expressed on CML progenitor cells. Cancer Res 2010; 70:906-15. [PMID: 20103624 DOI: 10.1158/0008-5472.can-09-2303] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Curative effects of graft-versus-leukemia-based therapies such as donor lymphocyte infusion (DLI) for chronic myelogenous leukemia (CML) may result from immunologic ablation of self-renewing CML progenitor cells. Patients who achieved durable remissions after DLI developed a significant B-cell lymphocytosis after treatment, which did not occur in patients who were unresponsive to DLI. In this study, we identified antigen targets of this B-cell response by probing two immunoproteomic platforms with plasma immunoglobulins from seven CML patients with clinically apparent graft-versus-leukemia responses after DLI. In total, 62 antigens elicited greater reactivity from post-DLI versus pre-DLI plasma. Microarray analysis revealed that >70% of the antigens were expressed in CML CD34(+) cells, suggesting that expression in malignant progenitor cells is a feature common to antibody targets of DLI. We confirmed elevated expression of three target antigens (RAB38, TBCE, and DUSP12) in CML that together consistently elicited antibody responses in 18 of 21 of an additional cohort of CML patients with therapeutic responses, but not in normal donors and rarely in non-CML patients. In summary, immunologic targets of curative DLI responses include multiple antigens on CML progenitor cells, identifying them as potential immunogens for vaccination and/or monitoring of immunotherapeutics designed to eliminate myeloid leukemia stem cells.
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Affiliation(s)
- Melinda A Biernacki
- Cancer Vaccine Center and Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
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15
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Sboner A, Karpikov A, Chen G, Smith M, Dawn M, Freeman-Cook L, Schweitzer B, Gerstein MB. Robust-Linear-Model Normalization To Reduce Technical Variability in Functional Protein Microarrays. J Proteome Res 2009; 8:5451-64. [DOI: 10.1021/pr900412k] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrea Sboner
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, Invitrogen, part of Life Technologies, 5791 Van Allen Way, Carlsbad, California 92008, Invitrogen, part of Life Technologies, 29851 Willow Creek Road, Eugene, Oregon 97402, Invitrogen, part of Life Technologies, 5781 Van Allen Way, Carlsbad, California 92008, Program in Computational Biology and Biochemistry, Yale University, New Haven, Connecticut 06520, and Department of Computer Science, Yale University
| | - Alexander Karpikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, Invitrogen, part of Life Technologies, 5791 Van Allen Way, Carlsbad, California 92008, Invitrogen, part of Life Technologies, 29851 Willow Creek Road, Eugene, Oregon 97402, Invitrogen, part of Life Technologies, 5781 Van Allen Way, Carlsbad, California 92008, Program in Computational Biology and Biochemistry, Yale University, New Haven, Connecticut 06520, and Department of Computer Science, Yale University
| | - Gengxin Chen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, Invitrogen, part of Life Technologies, 5791 Van Allen Way, Carlsbad, California 92008, Invitrogen, part of Life Technologies, 29851 Willow Creek Road, Eugene, Oregon 97402, Invitrogen, part of Life Technologies, 5781 Van Allen Way, Carlsbad, California 92008, Program in Computational Biology and Biochemistry, Yale University, New Haven, Connecticut 06520, and Department of Computer Science, Yale University
| | - Michael Smith
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, Invitrogen, part of Life Technologies, 5791 Van Allen Way, Carlsbad, California 92008, Invitrogen, part of Life Technologies, 29851 Willow Creek Road, Eugene, Oregon 97402, Invitrogen, part of Life Technologies, 5781 Van Allen Way, Carlsbad, California 92008, Program in Computational Biology and Biochemistry, Yale University, New Haven, Connecticut 06520, and Department of Computer Science, Yale University
| | - Mattoon Dawn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, Invitrogen, part of Life Technologies, 5791 Van Allen Way, Carlsbad, California 92008, Invitrogen, part of Life Technologies, 29851 Willow Creek Road, Eugene, Oregon 97402, Invitrogen, part of Life Technologies, 5781 Van Allen Way, Carlsbad, California 92008, Program in Computational Biology and Biochemistry, Yale University, New Haven, Connecticut 06520, and Department of Computer Science, Yale University
| | - Lisa Freeman-Cook
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, Invitrogen, part of Life Technologies, 5791 Van Allen Way, Carlsbad, California 92008, Invitrogen, part of Life Technologies, 29851 Willow Creek Road, Eugene, Oregon 97402, Invitrogen, part of Life Technologies, 5781 Van Allen Way, Carlsbad, California 92008, Program in Computational Biology and Biochemistry, Yale University, New Haven, Connecticut 06520, and Department of Computer Science, Yale University
| | - Barry Schweitzer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, Invitrogen, part of Life Technologies, 5791 Van Allen Way, Carlsbad, California 92008, Invitrogen, part of Life Technologies, 29851 Willow Creek Road, Eugene, Oregon 97402, Invitrogen, part of Life Technologies, 5781 Van Allen Way, Carlsbad, California 92008, Program in Computational Biology and Biochemistry, Yale University, New Haven, Connecticut 06520, and Department of Computer Science, Yale University
| | - Mark B. Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, Invitrogen, part of Life Technologies, 5791 Van Allen Way, Carlsbad, California 92008, Invitrogen, part of Life Technologies, 29851 Willow Creek Road, Eugene, Oregon 97402, Invitrogen, part of Life Technologies, 5781 Van Allen Way, Carlsbad, California 92008, Program in Computational Biology and Biochemistry, Yale University, New Haven, Connecticut 06520, and Department of Computer Science, Yale University
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16
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Cretich M, di Carlo G, Longhi R, Gotti C, Spinella N, Coffa S, Galati C, Renna L, Chiari M. High sensitivity protein assays on microarray silicon slides. Anal Chem 2009; 81:5197-203. [PMID: 19485342 DOI: 10.1021/ac900658c] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In this work, we report on the improvement of microarray sensitivity provided by a crystalline silicon substrate coated with thermal silicon oxide functionalized by a polymeric coating. The improvement is intended for experimental procedures and instrumentations typically involved in microarray technology, such as fluorescence labeling and a confocal laser scanning apparatus. The optimized layer of thermally grown silicon oxide (SiO(2)) of a highly reproducible thickness, low roughness, and fluorescence background provides fluorescence intensification due to the constructive interference between the incident and reflected waves of the fluorescence radiation. The oxide surface is coated by a copolymer of N,N-dimethylacrylamide, N-acryloyloxysuccinimide, and 3-(trimethoxysilyl)propyl methacrylate, copoly(DMA-NAS-MAPS), which forms, by a simple and robust procedure, a functional nanometric film. The polymeric coating with a thickness that does not appreciably alter the optical properties of the silicon oxide confers to the slides optimal binding specificity leading to a high signal-to-noise ratio. The present work aims to demonstrate the great potential that exists by combining an optimized reflective substrate with a high performance surface chemistry. Moreover, the techniques chosen for both the substrate and surface chemistry are simple, inexpensive, and amenable to mass production. The present application highlights their potential use for diagnostic applications of real clinical relevance. The coated silicon slides, tested in protein and peptide microarrays for detection of specific antibodies, lead to a 5-10-fold enhancement of the fluorescence signals in comparison to glass slides.
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Affiliation(s)
- Marina Cretich
- Istituto di Chimica del Riconoscimento Molecolare, CNR, 20131 Milano, Italy
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Porcheray F, Wong W, Saidman SL, De Vito J, Girouard TC, Chittenden M, Shaffer J, Tolkoff-Rubin N, Dey BR, Spitzer TR, Colvin RB, Cosimi AB, Kawai T, Sachs DH, Sykes M, Zorn E. B-cell immunity in the context of T-cell tolerance after combined kidney and bone marrow transplantation in humans. Am J Transplant 2009; 9:2126-35. [PMID: 19624570 PMCID: PMC2837587 DOI: 10.1111/j.1600-6143.2009.02738.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Five patients with end-stage kidney disease received combined kidney and bone marrow transplants from HLA haploidentical donors following nonmyeloablative conditioning to induce renal allograft tolerance. Immunosuppressive therapy was successfully discontinued in four patients with subsequent follow-up of 3 to more than 6 years. This allograft acceptance was accompanied by specific T-cell unresponsiveness to donor antigens. However, two of these four patients showed evidence of de novo antibodies reactive to donor antigens between 1 and 2 years posttransplant. These humoral responses were characterized by the presence of donor HLA-specific antibodies in the serum with or without the deposition of the complement molecule C4d in the graft. Immunofluorescence staining, ELISA assays and antibody profiling using protein microarrays demonstrated the co-development of auto- and alloantibodies in these two patients. These responses were preceded by elevated serum BAFF levels and coincided with B-cell reconstitution as revealed by a high frequency of transitional B cells in the periphery. To date, these B cell responses have not been associated with evidence of humoral rejection and their clinical significance is still unclear. Overall, our findings showed the development of B-cell allo- and autoimmunity in patients with T-cell tolerance to the donor graft.
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Affiliation(s)
- F. Porcheray
- Transplantation Biology Research Center, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - W. Wong
- Renal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - S. L Saidman
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - J. De Vito
- Transplantation Biology Research Center, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - T. C. Girouard
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - M. Chittenden
- Transplantation Biology Research Center, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - J. Shaffer
- Transplantation Biology Research Center, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - N. Tolkoff-Rubin
- Renal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - B. R. Dey
- Division of Bone Marrow Transplantation, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - T. R. Spitzer
- Division of Bone Marrow Transplantation, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - R. B. Colvin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - A. B. Cosimi
- Transplant Unit, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - T. Kawai
- Transplant Unit, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - D. H. Sachs
- Transplantation Biology Research Center, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - M. Sykes
- Transplantation Biology Research Center, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - E. Zorn
- Transplantation Biology Research Center, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA,Corresponding author: Emmanuel Zorn,
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