1
|
Cinquanta L, Infantino M, Bizzaro N. Detecting Autoantibodies by Multiparametric Assays: Impact on Prevention, Diagnosis, Monitoring, and Personalized Therapy in Autoimmune Diseases. J Appl Lab Med 2022; 7:137-150. [PMID: 34996071 DOI: 10.1093/jalm/jfab132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/07/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND The introduction of multiparametric autoantibody tests has been proposed to improve the accuracy of the immunological diagnosis of autoimmune diseases (AID) and to accelerate time for completing the diagnostic process. Multiplex tests are capable of detecting many autoantibodies in a single run whereas a traditional immunoassay uses a single antigen to detect only a single specificity of autoantibodies. The reasons why multiplex tests could replace conventional immunoassays lie in the evidence that they allow for more efficient handling of large numbers of samples by the laboratory, while ensuring greater diagnostic sensitivity in AID screening. CONTENT This review aims to highlight the important role that multiparametric tests could assume when designed for defined profiles they are used not only for diagnostic purposes but also to predict the onset of AID to identify clinical phenotypes and to define prognosis. Furthermore, differences in the antibody profile could identify which subjects will be responsive or not to a specific pharmacological treatment. SUMMARY The use of autoantibody profiles, when specifically requested and performed with clinically validated technologies, can represent a significant step toward personalized medicine in autoimmunology.
Collapse
Affiliation(s)
| | - Maria Infantino
- Laboratorio di Immunologia e Allergologia, Ospedale S. Giovanni di Dio, Firenze, Italy
| | - Nicola Bizzaro
- Laboratorio di Patologia Clinica, Ospedale San Antonio, Tolmezzo, Italy.,Azienda Sanitaria Universitaria Integrata di Udine, Udine, Italy
| |
Collapse
|
2
|
Meftahi GH, Bahari Z, Zarei Mahmoudabadi A, Iman M, Jangravi Z. Applications of western blot technique: From bench to bedside. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 49:509-517. [PMID: 33847452 DOI: 10.1002/bmb.21516] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
Western blot (WB) or immunoblot is a workhorse method. It is commonly used by biologists for study of different aspects of protein biomolecules. In addition, it has been widely used in disease diagnosis. Despite some limitations such as long time, different applications of WB have not been limited. In the present review, we have summarized scientific and clinical applications of WB. In addition, we described some new generation of WB techniques.
Collapse
Affiliation(s)
| | - Zahra Bahari
- Department of Physiology and Medical Physics, Faculty of Medicine, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Zarei Mahmoudabadi
- Department of Biochemistry, Faculty of Medicine, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Maryam Iman
- Department of Pharmaceutics, Faculty of Pharmacy, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Zohreh Jangravi
- Department of Biochemistry, Faculty of Medicine, Baqiyatallah University of Medical Sciences, Tehran, Iran
- Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| |
Collapse
|
3
|
Pisetsky DS, Lipsky PE. New insights into the role of antinuclear antibodies in systemic lupus erythematosus. Nat Rev Rheumatol 2020; 16:565-579. [PMID: 32884126 DOI: 10.1038/s41584-020-0480-7] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2020] [Indexed: 01/05/2023]
Abstract
Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease characterized by antinuclear antibodies (ANAs) that form immune complexes that mediate pathogenesis by tissue deposition or cytokine induction. Some ANAs bind DNA or associated nucleosome proteins, whereas other ANAs bind protein components of complexes of RNA and RNA-binding proteins (RBPs). Levels of anti-DNA antibodies can fluctuate widely, unlike those of anti-RBP antibodies, which tend to be stable. Because anti-DNA antibody levels can reflect disease activity, repeat testing is common; by contrast, a single anti-RBP antibody determination is thought to suffice for clinical purposes. Experience from clinical trials of novel therapies has provided a new perspective on ANA expression during disease, as many patients with SLE are ANA negative at screening despite previously testing positive. Because trial results suggest that patients who are ANA negative might not respond to certain agents, screening strategies now involve ANA and anti-DNA antibody testing to identify patients with so-called 'active, autoantibody-positive SLE'. Evidence suggests that ANA responses can decrease over time because of the natural history of disease or the effects of therapy. Together, these findings suggest that, during established disease, more regular serological testing could illuminate changes relevant to pathogenesis and disease status.
Collapse
Affiliation(s)
- David S Pisetsky
- Departments of Medicine and Immunology, Duke University Medical Center and Medical Research Service, Veterans Administration Medical Center, Durham, NC, USA.
| | | |
Collapse
|
4
|
Schelpe AS, Roose E, Joly BS, Pareyn I, Mancini I, Biganzoli M, Deckmyn H, Voorberg J, Fijnheer R, Peyvandi F, De Meyer SF, Coppo P, Veyradier A, Vanhoorelbeke K. Generation of anti-idiotypic antibodies to detect anti-spacer antibody idiotopes in acute thrombotic thrombocytopenic purpura patients. Haematologica 2018; 104:1268-1276. [PMID: 30523052 PMCID: PMC6545854 DOI: 10.3324/haematol.2018.205666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022] Open
Abstract
In autoantibody-mediated autoimmune diseases, autoantibody profiling allows patients to be stratified and links autoantibodies with disease severity and outcome. However, in immune-mediated thrombotic thrombocytopenic purpura (iTTP) patients, stratification according to antibody profiles and their clinical relevance has not been fully explored. We aimed to develop a new type of autoantibody profiling assay for iTTP based on the use of anti-idiotypic antibodies. Anti-idiotypic antibodies against 3 anti-spacer autoantibodies were generated in mice and were used to capture the respective anti-spacer idiotopes from 151 acute iTTP plasma samples. We next deciphered these anti-spacer idiotope profiles in iTTP patients and investigated whether these limited idiotope profiles could be linked with disease severity. We developed 3 anti-idiotypic antibodies that recognized particular idiotopes in the anti-spacer autoantibodies II-1, TTP73 or I-9, that are involved in ADAMTS13 binding; 35%, 24% and 42% of patients were positive for antibodies with the II-1, TTP73 and I-9 idiotopes, respectively. Stratifying patients according to the corresponding 8 anti-spacer idiotope profiles provided a new insight into the anti-spacer II-1, TTP73 and I-9 idiotope profiles in these patients. Finally, these limited idiotope profiles showed no association with disease severity. We successfully developed 3 anti-idiotypic antibodies that allowed us to determine the profiles of the anti-spacer II-1, TTP73 and I-9 idiotopes in iTTP patients. Increasing the number of patients and/or future development of additional anti-idiotypic antibodies against other anti-ADAMTS13 autoantibodies might allow idiotope profiles of clinical, prognostic value to be identified.
Collapse
Affiliation(s)
- An-Sofie Schelpe
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Belgium
| | - Elien Roose
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Belgium
| | - Bérangère S Joly
- Service d'Hématologie Biologique, Hôpital Lariboisière, Assistance Publique-Hôpitaux de Paris, France.,EA3518, Institut Universitaire d'Hématologie Saint-Louis, Université Paris Diderot, France
| | - Inge Pareyn
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Belgium
| | - Ilaria Mancini
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Università degli Studi di Milano, Italy.,Department of Pathophysiology and Transplantation, Fondazione Luigi Villa, Milan, Italy
| | - Marina Biganzoli
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Università degli Studi di Milano, Italy.,Department of Pathophysiology and Transplantation, Fondazione Luigi Villa, Milan, Italy
| | - Hans Deckmyn
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Belgium
| | - Jan Voorberg
- Department of Molecular and Cellular Hemostasis, Sanquin-AMC Landsteiner Laboratory, Amsterdam, the Netherlands
| | - Rob Fijnheer
- Department of Internal Medicine, Meander Medical Center, Amersfoort, the Netherlands
| | - Flora Peyvandi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Università degli Studi di Milano, Italy.,Department of Pathophysiology and Transplantation, Fondazione Luigi Villa, Milan, Italy
| | - Simon F De Meyer
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Belgium
| | - Paul Coppo
- Sorbonne Universités, Service d'Hématologie et Centre de Référence des Microangiopathies Thrombotiques (CNR-MAT), Hôpital Saint Antoine, Assistance Publique-Hôpitaux de Paris, France
| | - Agnès Veyradier
- Service d'Hématologie Biologique, Hôpital Lariboisière, Assistance Publique-Hôpitaux de Paris, France.,EA3518, Institut Universitaire d'Hématologie Saint-Louis, Université Paris Diderot, France
| | - Karen Vanhoorelbeke
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Belgium
| |
Collapse
|
5
|
Lee JR, Chan CT, Ruderman D, Chuang HY, Gaster RS, Atallah M, Mallick P, Lowe SW, Gambhir SS, Wang SX. Longitudinal Monitoring of Antibody Responses against Tumor Cells Using Magneto-nanosensors with a Nanoliter of Blood. NANO LETTERS 2017; 17:6644-6652. [PMID: 28990786 PMCID: PMC5851288 DOI: 10.1021/acs.nanolett.7b02591] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Each immunoglobulin isotype has unique immune effector functions. The contribution of these functions in the elimination of pathogens and tumors can be determined by monitoring quantitative temporal changes in isotype levels. Here, we developed a novel technique using magneto-nanosensors based on the effect of giant magnetoresistance (GMR) for longitudinal monitoring of total and antigen-specific isotype levels with high precision, using as little as 1 nL of serum. Combining in vitro serologic measurements with in vivo imaging techniques, we investigated the role of the antibody response in the regression of firefly luciferase (FL)-labeled lymphoma cells in spleen, kidney, and lymph nodes in a syngeneic Burkitt's lymphoma mouse model. Regression status was determined by whole body bioluminescent imaging (BLI). The magneto-nanosensors revealed that anti-FL IgG2a and total IgG2a were elevated and sustained in regression mice compared to non-regression mice (p < 0.05). This platform shows promise for monitoring immunotherapy, vaccination, and autoimmunity.
Collapse
Affiliation(s)
- Jung-Rok Lee
- Division of Mechanical and Biomedical Engineering, Ewha Womans University, Seoul 03760, South Korea
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Carmel T. Chan
- Department of Medicine, Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Daniel Ruderman
- Ellison Institute of Transformative Medicine of USC, USC Keck School of Medicine, Los Angeles, California 90211, United States
| | - Hui-Yen Chuang
- Department of Medicine, Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Richard S. Gaster
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
- Pliant Therapeutics, Redwood City, California 94063, United States
| | - Michelle Atallah
- Cancer Biology Program, Stanford School of Medicine, Stanford, California 94305, United States
| | - Parag Mallick
- Department of Medicine, Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Scott W. Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Sanjiv S. Gambhir
- Department of Medicine, Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Shan X. Wang
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
- Department of Medicine, Department of Radiology, Stanford University, Stanford, California 94305, United States
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
6
|
Abstract
There is no serologic test that reliably measures disease activity in systemic lupus erythematosus (SLE). The ‘gold standard’ is the anti-dsDNA antibody test, which has been used as a marker of disease activity by clinicians in SLE for over 35 years. Anti-dsDNA antibodies perform best in those with lupus nephritis, specifically in the presence of a proliferative lesion [World Health Organization (WHO) class III or IV] on renal biopsy. In one recent meta-analysis, the mean positivelikelihood ratio of anti-dsDNA antibodies as a marker of disease activity in SLE was 4.14, implying the overall predictive effect was small. More recently autoantibodyassays have been developed that show greater promise in gauging SLE disease activity, specifically anti-nucleosome and anti-C1q antibodies (especially with renal disease activity). Other tests thought previously to be lacking in specificity that refinements in ELISA technology now render possibly useful include anti-heparan sulfate, anti-ssDNA and anti-Scl-70 autoantibodies. Other tests that as yet have not been shown to be as reliable (and therefore are not as useful in clinical practice for serial determinationto measure disease activity) include other anti-extractablenuclear antibodies (anti-Ro, La, Sm, RNP), anti-cardiolipinantibodies, and anti-nuclear cytoplasmic antibodies (ANCA). New technologies using proteomic determinations show promise as aids in the search for more reliable and feasible autoantibody determinations of disease activity in SLE.
Collapse
Affiliation(s)
- J D Reveille
- Division of Rheumatology, The University of Texas, Houston Health Science Center at Houston, Houston, TX 77030, USA.
| |
Collapse
|
7
|
Multiplexed autoantigen microarrays identify HLA as a key driver of anti-desmoglein and -non-desmoglein reactivities in pemphigus. Proc Natl Acad Sci U S A 2016; 113:1859-64. [PMID: 26831096 DOI: 10.1073/pnas.1525448113] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Patients with pemphigus vulgaris (PV) harbor antibodies reactive against self-antigens expressed at the surface of keratinocytes, primarily desmoglein (Dsg) 3 and, to a lesser extent, Dsg1. Conventionally, only antibodies targeting these molecules have been thought to contribute to disease pathogenesis. This notion has been challenged by a growing pool of evidence that suggests that antibodies toward additional targets may play a role in disease. The aims of this study were to (i) establish high-throughput protein microarray technology as a method to investigate traditional and putative autoantibodies (autoAbs) in PV and (ii) use multiplexed protein array technology to define the scope and specificity of the autoAb response in PV. Our analysis demonstrated significant IgG reactivity in patients with PV toward the muscarinic acetylcholine receptor subtypes 3, 4, and 5 as well as thyroid peroxidase. Furthermore, we found that healthy first- and second-degree relatives of patients with PV express autoAbs toward desmoglein and non-Dsg targets. Our analysis also identified genetic elements, particularly HLA, as key drivers of autoAb expression. Finally, we show that patients with PV exhibit significantly reduced IgM reactivity toward disease-associated antigens relative to controls. The use of protein microarrays to profile the autoAb response in PV advanced the current understanding of disease and provided insight into the complex relationship between genetics and disease development.
Collapse
|
8
|
Gebretsadik G, Menon MKC. Proteomics and Its Applications in Diagnosis of Auto Immune Diseases. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/oji.2016.61003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
9
|
Carbohydrate Microarrays. POLYSACCHARIDES 2015. [PMCID: PMC7123348 DOI: 10.1007/978-3-319-16298-0_35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Carbohydrates, like nucleic acids and proteins, are essential biological molecules. Owing to their intrinsic physicochemical properties, carbohydrates are capable of generating structural diversity in a multitude of ways and are prominently displayed on the surfaces of cell membranes or on the exposed regions of macromolecules. Recent studies highlight that carbohydrate moieties are critical for molecular recognition, cell-cell interactions, and cell signaling in many physiological and pathological processes, and for biocommunication between microbes and host species. Modern carbohydrate microarrays emerged in 2002 and brought in new high-throughput tools for “glyco code” exploration. In this section, some basic concepts of sugar chain diversity, glyco-epitope recognition, and the evolving area of glyco-epitomics and biomarker discovery are discussed. Two complementary technologies, carbohydrate antigen arrays and photogenerated glyco-chips, serve as models to illustrate how to apply carbohydrate microarrays to address biomedical questions.
Collapse
|
10
|
Wang D, Bhat R, Sobel RA, Huang W, Wang LX, Olsson T, Steinman L. Uncovering cryptic glycan markers in multiple sclerosis (MS) and experimental autoimmune encephalomyelitis (EAE). Drug Dev Res 2014; 75:172-88. [PMID: 24648292 DOI: 10.1002/ddr.21169] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 02/10/2014] [Indexed: 01/18/2023]
Abstract
Using an integrated antigen microarray approach, we observed epitope-spreading of autoantibody responses to a variety of antigenic structures in the cerebrospinal fluid (CSF) of patients with multiple sclerosis (MS) and in the serum of mice with experimental autoimmune encephalomyelitis (EAE). These included previously described protein- and lipid-based antigenic targets and newly discovered autoimmunogenic sugar moieties, notably, autoantibodies specific for the oligomannoses in both MS patient CSF and the sera of mice with EAE. These glycans are often masked by other sugar moieties and belong to a class of cryptic autoantigens. We further determined that these targets are highly expressed on multiple cell types in MS and EAE lesions. Co-immunization of SJL/J mice with a Man9-KLH conjugate at the time of EAE induction elicited highly significant levels of anti-Man9-cluster autoantibodies. Nevertheless, this anti-glycan autoantibody response was associated with a significantly reduced clinical severity of EAE. The potential of these cryptic glycan markers and targeting antibodies for diagnostic and therapeutic interventions of neurological disorders has yet to be explored.
Collapse
Affiliation(s)
- Denong Wang
- Tumor Glycomics Laboratory, SRI International Biosciences Division, Menlo Park, CA, 94025, USA
| | | | | | | | | | | | | |
Collapse
|
11
|
Lolli F, Rovero P, Chelli M, Papini AM. Toward biomarkers in multiple sclerosis: new advances. Expert Rev Neurother 2014; 6:781-94. [PMID: 16734525 DOI: 10.1586/14737175.6.5.781] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Multiple sclerosis is an autoimmune disease that commonly affects young adults. If initially characterized by acute relapses, it is later followed by only incomplete remission. Over years, progressive disability and irreversible deficit lead to chronic neurological deficits in the majority of patients. The clinical course is protracted and unpredictable, and no biological marker is useful in predicting the evolution of autoaggression and disability. It is difficult to diagnose and to monitor disease progression after the initial symptoms or even during the major clinical manifestations, and it is difficult to treat. In this review, the authors report recent advances in the field, focusing on the search of new antigens as a marker of the disease, in their relevance to the pathophysiology and diagnosis of the disease.
Collapse
Affiliation(s)
- Francesco Lolli
- Laboratorio Interdipartimentale di Chimica & Biologia dei Peptidi & Proteine, Polo Scientifico e Tecnologico, Università degli Studi di Firenze, via Ugo Schiff 6, I-50019 Sesto Fiorentino, Italy.
| | | | | | | |
Collapse
|
12
|
Wang D, Tang J, Wolfinger RD, Carroll GT. Carbohydrate Microarrays. POLYSACCHARIDES 2014. [DOI: 10.1007/978-3-319-03751-6_35-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
13
|
Wang J, Barker K, Steel J, Park J, Saul J, Festa F, Wallstrom G, Yu X, Bian X, Anderson KS, Figueroa JD, LaBaer J, Qiu J. A versatile protein microarray platform enabling antibody profiling against denatured proteins. Proteomics Clin Appl 2013; 7:378-83. [PMID: 23027520 DOI: 10.1002/prca.201200062] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/21/2012] [Accepted: 08/23/2012] [Indexed: 11/10/2022]
Abstract
PURPOSE We aim to develop a protein microarray platform capable of presenting both natural and denatured forms of proteins for antibody biomarker discovery. We will further optimize plasma screening protocols to improve detection. EXPERIMENTAL DESIGN We developed a new covalent capture protein microarray chemistry using HaloTag fusion proteins and ligand. To enhance protein yield, we used HeLa cell lysate as an in vitro transcription translation (IVTT) system. Escherichia coli lysates were added to the plasma blocking buffer to reduce nonspecific background. These protein microarrays were probed with plasma samples and autoantibody responses were quantified and compared with or without denaturing buffer treatment. RESULTS We demonstrated that protein microarrays using the covalent attachment chemistry endured denaturing conditions. Blocking with E. coli lysates greatly reduced the background signals and expression with IVTT based on HeLa cell lysates significantly improved the antibody signals on protein microarrays probed with plasma samples. Plasma samples probed on denatured protein arrays produced autoantibody profiles distinct from those probed on natively displayed proteins. CONCLUSIONS AND CLINICAL RELEVANCE This versatile protein microarray platform allows the display of both natural and denatured proteins, offers a new dimension to search for disease-specific antibodies, broadens the repertoire of potential biomarkers, and will potentially yield clinical diagnostics with greater performance.
Collapse
Affiliation(s)
- Jie Wang
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287-6401, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Pemphigus vulgaris autoantibody profiling by proteomic technique. PLoS One 2013; 8:e57587. [PMID: 23505434 PMCID: PMC3591405 DOI: 10.1371/journal.pone.0057587] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 01/23/2013] [Indexed: 11/24/2022] Open
Abstract
Pemphigus vulgaris (PV) is a mucocutaneous blistering disease characterized by IgG autoantibodies against the stratified squamous epithelium. Current understanding of PV pathophysiology does not explain the mechanism of acantholysis in patients lacking desmoglein antibodies, which justifies a search for novel targets of pemphigus autoimmunity. We tested 264 pemphigus and 138 normal control sera on the multiplexed protein array platform containing 701 human genes encompassing many known keratinocyte cell-surface molecules and members of protein families targeted by organ-non-specific PV antibodies. The top 10 antigens recognized by the majority of test patients’ sera were proteins encoded by the DSC1, DSC3, ATP2C1, PKP3, CHRM3, COL21A1, ANXA8L1, CD88 and CHRNE genes. The most common combinations of target antigens included at least one of the adhesion molecules DSC1, DSC3 or PKP3 and/or the acetylcholine receptor CHRM3 or CHRNE with or without the MHC class II antigen DRA. To identify the PV antibodies most specific to the disease process, we sorted the data based on the ratio of patient to control frequencies of antigen recognition. The frequency of antigen recognition by patients that exceeded that of control by 10 and more times were the molecules encoded by the CD33, GP1BA, CHRND, SLC36A4, CD1B, CD32, CDH8, CDH9, PMP22 and HLA-E genes as well as mitochondrial proteins encoded by the NDUFS1, CYB5B, SOD2, PDHA1 and FH genes. The highest specificity to PV showed combinations of autoantibodies to the calcium pump encoded by ATP2C1 with C5a receptor plus DSC1 or DSC3 or HLA-DRA. The results identified new targets of pemphigus autoimmunity. Novel autoantibody signatures may help explain individual variations in disease severity and treatment response, and serve as sensitive and specific biomarkers for new diagnostic assays in PV patients.
Collapse
|
15
|
Dhandha MM, Seiffert-Sinha K, Sinha AA. Specific immunoglobulin isotypes correlate with disease activity, morphology, duration and HLA association in Pemphigus vulgaris. Autoimmunity 2012; 45:516-26. [PMID: 22779708 DOI: 10.3109/08916934.2012.702811] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The molecular basis of disease heterogeneity in autoimmune conditions such as Pemphigus vulgaris is poorly understood. Although desmoglein 3 (Dsg3) has been well established as a primary target of immunoglobulin (Ig) autoantibodies in PV, there remain several questions regarding the overall distribution of anti-Dsg3 Ig subtypes among patient subsets and considerable controversy regarding whether an isotype switch can be observed between phases of disease activity. To systematically address the outstanding questions related to Ig-isotype specificity in PV, we analyzed IgA, IgM, IgG1, 2, 3 and 4 anti-Dsg3 levels by ELISA in 202 serum samples obtained from 92 patients with distinct clinical profiles based on a set of defined variable (activity, morphology, age, duration) and constant (HLA-type, gender, age of onset) clinical parameters, and 47 serum samples from HLA-matched and -unmatched controls. Our findings provide support for earlier studies identifying IgG4 and IgG1 as the predominant antibodies in PV with significantly higher levels in active than remittent patients. We do not see evidence for an isotype switch between phases of disease activity and remission, and both IgG4 and IgG1 subtypes remain elevated in remittent patients relative to controls. We do, however, find IgG4 to be the sole subtype that further distinguishes PV patient subgroups based on different disease morphologies, disease duration, and HLA-types. These data provide further insight into the immune mechanisms responsible for phenotypic expression of disease, and contribute to the broader effort to establish comprehensive immunoprofiles underlying disease heterogeneity to facilitate increasingly specific and individualized therapeutic interventions.
Collapse
Affiliation(s)
- Maulik M Dhandha
- Division of Dermatology and Cutaneous Sciences, Michigan State University, East Lansing, Michigan, USA
| | | | | |
Collapse
|
16
|
|
17
|
Beyer NH, Lueking A, Kowald A, Frederiksen JL, Heegaard NHH. Investigation of autoantibody profiles for cerebrospinal fluid biomarker discovery in patients with relapsing-remitting multiple sclerosis. J Neuroimmunol 2011; 242:26-32. [PMID: 22177943 DOI: 10.1016/j.jneuroim.2011.08.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 08/12/2011] [Accepted: 08/16/2011] [Indexed: 12/23/2022]
Abstract
Using the UNIarray® marker technology platform, cerebrospinal fluid immunoglobulin G reactivities of 15 controls and 17 RRMS patients against human recombinant proteins were investigated. Patient cerebrospinal fluids were oligoclonal band positive and reactivities were compared to that of sex- and age-matched controls. We hereby aimed at the characterization of autoreactivity in patients with RRMS. Differences in autoreactivities between control and RRMS samples were identified comprising autoantigens identified in this study only and previously reported autoantigens as well. A combination of the 10-15 most significant proteins may be investigated further as autoantigens for diagnostic purposes. Additional investigations may include minimizing the number of proteins used in such diagnostic tests.
Collapse
Affiliation(s)
- Natascha Helena Beyer
- Department of Clinical Biochemistry and Immunology, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark.
| | | | | | | | | |
Collapse
|
18
|
Farinazzo A, Gini B, Milli A, Ruffini F, Marconi S, Turano E, Anghileri E, Barbieri F, Cecconi D, Furlan R, Bonetti B. 2D immunomic approach for the study of IgG autoantibodies in the experimental model of multiple sclerosis. J Neuroimmunol 2011; 232:63-7. [DOI: 10.1016/j.jneuroim.2010.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Revised: 09/14/2010] [Accepted: 10/04/2010] [Indexed: 10/18/2022]
|
19
|
Abstract
Systemic lupus erythematosus (SLE) and related diseases are characterized by circulating autoantibodies to defined intracellular targets. Among the earliest identified autoantibodies were those directed to components of U2-U6 small nuclear ribonucleoproteins (snRNPs) known as Smith (Sm) antigen, which are highly specific for SLE. The Sm-antigen is composed of at least nine different polypeptides with molecular weights ranging from 9 to 29.5 kDa (B (B1, 28 kDa), B' (B2, 29 kDa), N (B3, 29.5 kDa), D1 (16 kDa), D2 (16.5 kDa), D3 (18 kDa), E (12 kDa), F (11 kDa), and G (9 kDa)). All of the nine core proteins, but most frequently the B and D polypeptides, are targets of the anti-Sm autoimmune response. However, since SmBB' and U1 specific RNPs share the cross-reactive epitope motif PPPGMRPP, SmD is regarded as the most SLE specific Sm-antigen. It has been shown that the polypeptides D1, D3, and BB' contain symmetrical dimethylarginine, constituting a major autoepitope within the C-terminus of SmD1 and SmD3. Several synthetic peptides have been used for the detection of anti-Sm antibodies and thus for the diagnosis of SLE. Anti-Sm antibodies have been reported to occur later than other SLE associated autoantibodies and, on average, around 1 year before the clinical onset of SLE. The present review provides a comprehensive summary on the history of anti-Sm antibodies and their use as biochemical tools to study cellular processes and as biomarker in the diagnosis of SLE. Additionally, a meta-analysis focused on recent data analyzes the prevalence of anti-Sm antibodies in SLE.
Collapse
|
20
|
El Khoury G, Laurenceau E, Chevolot Y, Mérieux Y, Desbos A, Fabien N, Rigal D, Souteyrand E, Cloarec JP. Development of miniaturized immunoassay: Influence of surface chemistry and comparison with enzyme-linked immunosorbent assay and Western blot. Anal Biochem 2010; 400:10-8. [DOI: 10.1016/j.ab.2010.01.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 01/06/2010] [Accepted: 01/10/2010] [Indexed: 10/19/2022]
|
21
|
Song Q, Liu G, Hu S, Zhang Y, Tao Y, Han Y, Zeng H, Huang W, Li F, Chen P, Zhu J, Hu C, Zhang S, Li Y, Zhu H, Wu L. Novel autoimmune hepatitis-specific autoantigens identified using protein microarray technology. J Proteome Res 2010; 9:30-9. [PMID: 19545157 DOI: 10.1021/pr900131e] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Autoimmune hepatitis (AIH) is a chronic necroinflammatory disease of the liver with a poorly understood etiology. Detection of nonorgan-specific and liver-related autoantibodies using immunoserological approaches has been widely used for diagnosis and prognosis. However, unambiguous and accurate detection of the disease requires the identification and characterization of disease-specific autoantigens. In the present study, we have profiled the autoantigen repertoire of patients with AIH versus those with other liver diseases, identifying and validating three novel and highly specific biomarkers for AIH. In phase I, we fabricated a human protein chip of 5011 nonredundant proteins and used it to quickly identify 11 candidate autoantigens with relative small serum collection. In phase II, we fabricated an AIH-specific protein chip and obtained autoimmunogenic profiles of serum samples from 44 AIH patients, 50 healthy controls, and 184 additional patients suffering from hepatitis B, hepatitis C, systemic lupus erythematosus, primary Sjogren's syndrome, rheumatoid arthritis, or primary biliary cirrhosis. With this two-phase approach, we identified three new antigens, RPS20, Alba-like, and dUTPase, as highly AIH-specific biomarkers, with sensitivities of 47.5% (RPS20), 45.5% (Alba-like), and 22.7% (dUTPase). These potential biomarkers were further validated with additional AIH samples in a double-blind design. Finally, we demonstrated that these new biomarkers could be readily applied to ELISA-based assays for use in clinical diagnosis/prognosis.
Collapse
Affiliation(s)
- Qifeng Song
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
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
| |
Collapse
|
23
|
Bizzaro N, Tampoia M. Diagnostic accuracy of immunoassays for the detection of antibodies to citrullinated proteins. Clin Rev Allergy Immunol 2009; 34:16-20. [PMID: 18270852 DOI: 10.1007/s12016-007-8027-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anticitrullinated protein/peptide antibodies (ACPA) are highly specific for rheumatoid arthritis (RA). They can be found early in the disease course and are associated with more severe joint destruction and disease activity. In the last 4 years, important progress has been made in the detection and identification of ACPA, improving antigenic composition and epitope recognition. Consequently, many ACPA-ELISA kits have been developed by several manufacturers and are now commercially available. However, albeit their widespread use in clinical laboratories, the use of some kits has not been accompanied by a clinical validation nor by a comparative evaluation of their diagnostic accuracy. In addition, full automation of ACPA assays featuring ease of use, rapid response, and high productivity is just beginning to appear on the market and also deserves clinical and analytical validation. This review will consider the most relevant characteristics of the ACPA-ELISA assays and will describe the results of a comparative study performed with all the currently available second- and third-generation commercial methods.
Collapse
Affiliation(s)
- Nicola Bizzaro
- Laboratorio di Patologia Clinica, Ospedale Civile, Via Morgagni, 18, 33028, Tolmezzo, UD, Italy.
| | | |
Collapse
|
24
|
Disis ML, Wallace DR, Gooley TA, Dang Y, Slota M, Lu H, Coveler AL, Childs JS, Higgins DM, Fintak PA, dela Rosa C, Tietje K, Link J, Waisman J, Salazar LG. Concurrent trastuzumab and HER2/neu-specific vaccination in patients with metastatic breast cancer. J Clin Oncol 2009; 27:4685-92. [PMID: 19720923 DOI: 10.1200/jco.2008.20.6789] [Citation(s) in RCA: 217] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
PURPOSE The primary objectives of this phase I/II study were to evaluate the safety and immunogenicity of combination therapy consisting of concurrent trastuzumab and human epidermal growth factor receptor 2 (HER2)/neu-specific vaccination in patients with HER2/neu-overexpressing metastatic breast cancer. PATIENTS AND METHODS Twenty-two patients with stage IV HER2/neu-positive breast cancer receiving trastuzumab therapy were vaccinated with an HER2/neu T-helper peptide-based vaccine. Toxicity was graded according to National Cancer Institute criteria, and antigen specific T-cell immunity was assessed by interferon gamma enzyme-linked immunosorbent spot assay. Data on progression-free and overall survival were collected. RESULTS Concurrent trastuzumab and HER2/neu vaccinations were well tolerated, with 15% of patients experiencing an asymptomatic decline in left ventricular ejection fraction below the normal range during combination therapy. Although many patients had pre-existing immunity specific for HER2/neu and other breast cancer antigens while treated with trastuzumab alone, that immunity could be significantly boosted and maintained with vaccination. Epitope spreading within HER2/neu and to additional tumor-related proteins was stimulated by immunization, and the magnitude of the T-cell response generated was significantly inversely correlated with serum transforming growth factor beta levels. At a median follow-up of 36 months from the first vaccine, the median overall survival in the study population has not been reached. CONCLUSION Combination therapy with trastuzumab and a HER2/neu vaccine is associated with minimal toxicity and results in prolonged, robust, antigen-specific immune responses in treated patients.
Collapse
Affiliation(s)
- Mary L Disis
- Tumor Vaccine Group, Center for Translational Medicine in Women's Health, University of Washington, Seattle, WA 98195-8050, USa.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Bansard C, Lequerre T, Daveau M, Boyer O, Tron F, Salier JP, Vittecoq O, Le-Loet X. Can rheumatoid arthritis responsiveness to methotrexate and biologics be predicted? Rheumatology (Oxford) 2009; 48:1021-8. [DOI: 10.1093/rheumatology/kep112] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
|
26
|
Caiazzo RJ, Maher AJ, Drummond MP, Lander CI, Tassinari OW, Nelson BP, Liu BCS. Protein microarrays as an application for disease biomarkers. Proteomics Clin Appl 2009; 3:138-47. [DOI: 10.1002/prca.200800149] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Indexed: 12/23/2022]
|
27
|
El-Kased RF, Koy C, Deierling T, Lorenz P, Qian Z, Li Y, Thiesen HJ, Glocker MO. Mass spectrometric and peptide chip epitope mapping of rheumatoid arthritis autoantigen RA33. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2009; 15:747-759. [PMID: 19940341 DOI: 10.1255/ejms.1040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The protein termed RA33 was determined to be one major autoantigen in rheumatoid arthritis (RA) patients and antiRA33 auto-antibodies were found to appear shortly after onset of RA. They are often detectable before a final diagnosis can be made in the clinic. The aim of our study is to characterise the epitope of a monoclonal antiRA33 antibody on recombinant RA33 using mass spectrometric epitope mapping. Recombinant RA33 has been subjected to BrCN cleavage and fragments were separated by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). Subsequent in-gel proteolytic digestion and mass spectrometric analysis determined the partial sequences in the protein bands. Western blotting of SDS-PAGE-separated protein fragments revealed immuno-positive, i.e. epitope-containing bands. BrCN-derived RA33 fragments were also separated by high- performance liquid chromatography (HPLC) and immuno-reactivity of peptides was measured by dot-blot analysis with the individual HPLC fractions after partial amino acid sequences were determined. The epitope region identified herewith was compared to data from peptide chip analysis with 15-meric synthetic peptides attached to a glass surface. Results from all three analyses consistently showed that the epitope of the monoclonal antiRA33 antibody is located in the aa79-84 region on recombinant RA33; the epitope sequence is MAARPHSIDGRVVEP. Sequence comparisons of the 15 best scoring peptides from the peptide chip analysis revealed that the epitope can be separated into two adjacent binding parts. The N-terminal binding parts comprise the amino acid residues "DGR", resembling the general physico-chemical properties "acidic/polar-small-basic". The C-terminal binding parts contain the amino acid residues "VVE", with the motif "hydrophobic-gap-acidic". The matching epitope region that emerged from our analysis on both the full-length protein and the 15-meric surface bound peptides suggests that peptide chips are indeed suitable tools for screening patterns of autoantibodies in patients suffering from autoimmune diseases.
Collapse
Affiliation(s)
- R F El-Kased
- Proteome Center Rostock, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies. BMC Bioinformatics 2008; 9 Suppl 12:S20. [PMID: 19091020 PMCID: PMC2638160 DOI: 10.1186/1471-2105-9-s12-s20] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the adaptive immune system, variable regions of immunoglobulin (IG) are encoded by random recombination of variable (V), diversity (D), and joining (J) gene segments in the germline. Partitioning the functional antibody sequences to their sourcing germline gene segments is vital not only for understanding antibody maturation but also for promoting the potential engineering of the therapeutic antibodies. To date, several tools have been developed to perform such "trace-back" calculations. Yet, the predicting ability and processing volume of those tools vary significantly for different sets of data. Moreover, none of them give a confidence for immunoglobulin heavy diversity (IGHD) identification. Developing fast, efficient and enhanced tools is always needed with the booming of immunological data. RESULTS Here, a program named Ab-origin is presented. It is designed by batch query against germline databases based on empirical knowledge, optimized scoring scheme and appropriate parameters. Special efforts have been paid to improve the identification accuracy of the short and volatile region, IGHD. In particular, a threshold score for certain sensitivity and specificity is provided to give the confidence level of the IGHD identification. CONCLUSION When evaluated using different sets of both simulated data and experimental data, Ab-origin outperformed all the other five popular tools in terms of prediction accuracy. The features of batch query and confidence indication of IGHD identification would provide extra help to users. The program is freely available at http://mpsq.biosino.org/ab-origin/supplementary.html.
Collapse
|
29
|
López-Pedrera C, Barbarroja N, Aguirre MA, Torres LA, Velasco F, Cuadrado MJ. Genomics and proteomics: a new approach for assessing thrombotic risk in autoimmune diseases. Lupus 2008; 17:904-15. [DOI: 10.1177/0961203308095285] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Several systemic autoimmune conditions, including rheumatoid arthritis, systemic lupus erythematosus and antiphospholipid syndrome, are characterised by enhanced atherosclerosis and, consequently, higher cardiovascular morbidity and mortality rates. The association of these diseases with atherosclerosis suggests a common pathogenic mechanism. Genomic and proteomic studies performed on atherosclerotic plaques have further confirmed the presence of a gene and protein profile similar to that observed in autoimmune diseases with cardiovascular risks. Human sera and body fluids have been analysed and have resulted in the identification of auto-antibodies that can be used as diagnostic markers in specific autoimmune diseases, and proteomic fingerprints of blood cells, tissues and body fluids have resulted in the identification of individual proteins or patterns of protein expression that are deregulated. The information provided by these proteomic studies is of diagnostic and therapeutic potential. In this review, we discuss new approaches available for assessing thrombotic risk in autoimmune diseases, focusing in the genomic and proteomic methods now available to deep into the origin of the mechanisms associated with vascular involvement in systemic autoimmune diseases. The increasing data available suggests that when treating patients with these autoimmune disorders, paying attention to the increased risk of cardiovascular disease is essential.
Collapse
Affiliation(s)
- C López-Pedrera
- Unidad de Investigación, Hospital Universitario Reina Sofía, Cordoba, Spain
| | - N Barbarroja
- Unidad de Investigación, Hospital Universitario Reina Sofía, Cordoba, Spain
| | - MA Aguirre
- Unidad de Investigación, Hospital Universitario Reina Sofía, Cordoba, Spain
| | - LA Torres
- Unidad de Investigación, Hospital Universitario Reina Sofía, Cordoba, Spain
| | - F Velasco
- Unidad de Investigación, Hospital Universitario Reina Sofía, Cordoba, Spain
| | - MJ Cuadrado
- Lupus Research Unit, St Thomas Hospital, London, UK
| |
Collapse
|
30
|
Plebani M, Pittoni M, Celadin M, Bernardi D, Mion MM. Recent advances in diagnostic technologies for autoimmune diseases. Autoimmun Rev 2008; 8:238-43. [PMID: 18718878 DOI: 10.1016/j.autrev.2008.07.032] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2008] [Indexed: 12/11/2022]
Abstract
The investigation of autoimmunity provides an interest challenge in "omics" research and, particularly, proteome research, as autoimmune diseases are common disorders of unsolved etiology that occur in a wide range of manifestations, in all of which tissues and organs are attacked by the body's own immune system. Autoantibodies are a hallmark of many autoimmune diseases and the presence of autoantibodies is a distinctive and key characteristic of autoimmune diseases. Conventionally, the study of autoimmune response has always been conducted by analysing the presence and/or concentration of individual antibodies in biological fluids. New proteomic techniques allow the simultaneous identification/measurement of different autoantibodies in sera of patients suffering from autoimmune diseases. The possibility of simultaneously measuring a number of correlated analytes appears to be very interesting for analytical reasons (reduced volumes of biological samples, reagents and low costs), logistical/managerial reasons, and pathophysiological reasons (combination of markers in disease-oriented or organ-oriented profiling). In particular, we describe data collected by using high-throughput techniques such as antigen microarrays and mass spectrometry for antibody profiling. While recently collected data demonstrate satisfactory analytical sensitivity and reproducibility, some issues such as standardization and data interpretation have to be solved before the introduction of these new and promising techniques into clinical practice.
Collapse
Affiliation(s)
- Mario Plebani
- Department of Laboratory Medicine, University-Hospital of Padova, Italy.
| | | | | | | | | |
Collapse
|
31
|
Fritzler MJ. Advances in understanding newer autoantibodies and their role as biomarkers in systemic lupus erythematosus. ACTA ACUST UNITED AC 2007; 1:393-408. [DOI: 10.1517/17530059.1.3.393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
32
|
Sukhanova A, Susha AS, Bek A, Mayilo S, Rogach AL, Feldmann J, Oleinikov V, Reveil B, Donvito B, Cohen JHM, Nabiev I. Nanocrystal-encoded fluorescent microbeads for proteomics: antibody profiling and diagnostics of autoimmune diseases. NANO LETTERS 2007; 7:2322-7. [PMID: 17645364 DOI: 10.1021/nl070966+] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The first application of nanocrystal (NC)-encoded microbeads to clinical proteomics is demonstrated by multiplexed detection of circulating autoantibodies, markers of systemic sclerosis. Two-color complexes, consisting of NC-encoded, antigen-covered beads, anti-antigen antibody or clinical serum samples, and dye-tagged detecting antibodies, were observed using flow cytometry assays and on the surface of single beads. The results of flow cytometry assays correlated with the ELISA technique and provided clear discrimination between the sera samples of healthy donors and patients with autoimmune disease. Microbead fluorescence signals exhibited narrow distribution regardless of their surface antigen staining, without the need of any fluorescence compensation-a parameter determining the limit of sensitivity of flow cytometry assays. In single bead measurements, less than 30 dye-labeled antibodies interacting with the topoI-specific antibodies at the surface of a bead have been detected by the emission of dye excited through the FRET from NCs. In this format, the antibody-bead interaction reaction turns specifically the fluorescence signal from dye label off and on, additionally increasing autoantibody detection sensitivity.
Collapse
Affiliation(s)
- Alyona Sukhanova
- EA No. 3798 Détection et Approches Thérapeutiques Nanotechnologiques dans les Mécanismes Biologiques de Défense, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Caiazzo RJ, Tassinari OW, Ehrlich JR, Liu BCS. Autoantibody microarrays for biomarker discovery. Expert Rev Proteomics 2007; 4:261-72. [PMID: 17425461 DOI: 10.1586/14789450.4.2.261] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Identification of autoantigens and the detection of autoantibody reactivity are useful in biomarker discovery and for explaining the role of important biochemical pathways in disease. Despite all of their potential advantages, the main challenge to working with autoantibodies is their sensitivity. Nevertheless, proteomics may hold the key to overcoming this limitation by providing the means to multiplex. Clearly, the ability to detect multiple autoantigens using a platform such as a high-density antigen microarray would improve sensitivity and specificity of detection for autoantibody profiling. The aims of this review are to: briefly describe the current status of antigen-autoantibody microarrays; provide examples of their use in biomarker discoveries; address current limitations; and provide examples and strategies to facilitate their implementation in the clinical setting.
Collapse
Affiliation(s)
- Robert J Caiazzo
- Harvard Medical School, Molecular Urology Laboratory, Brigham & Women's Hospital, Boston, MA 02115, USA.
| | | | | | | |
Collapse
|
34
|
Li QZ, Zhou J, Wandstrat AE, Carr-Johnson F, Branch V, Karp DR, Mohan C, Wakeland EK, Olsen NJ. Protein array autoantibody profiles for insights into systemic lupus erythematosus and incomplete lupus syndromes. Clin Exp Immunol 2007; 147:60-70. [PMID: 17177964 PMCID: PMC1810453 DOI: 10.1111/j.1365-2249.2006.03251.x] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The objective of this study was to investigate the prevalence and clinical significance of a spectrum of autoantibodies in systemic lupus erythematosus and incomplete lupus syndromes using a proteome microarray bearing 70 autoantigens. Microarrays containing candidate autoantigens or control proteins were printed on 16-section slides. These arrays were used to profile 93 serum samples from patients with systemic lupus erythematosus (SLE (n = 33), incomplete LE (ILE; n = 23), first-degree relatives (FDRs) of SLE patients (n = 20) and non-autoimmune controls (NC; n = 17). Data were analysed using the significance analysis of microarray (SAM) and clustering algorithms. Correlations with disease features were determined. Serum from ILE and SLE patients contained high levels of IgG autoantibodies to 50 autoantigens and IgM autoantibodies to 12 autoantigens. Elevated levels of at least one IgG autoantibody were detected in 26% of SLE and 19% of ILE samples; elevated IgM autoantibodies were present in 13% of SLE and 17% of ILE samples. IgG autoantibodies segregated into seven clusters including two specific for DNA and RNA autoantigens that were correlated with the number of lupus criteria. Three IgG autoantibody clusters specific for collagens, DNA and histones, were correlated with renal involvement. Of the four IgM autoantibody clusters, two were correlated negatively with the number of lupus criteria; none were correlated with renal disease. The IgG : IgM autoantibody ratios generally showed a stepwise increase in the groups following disease burden from NC to SLE. Insights derived from the expanded autoantibody profiling made possible with the antigen array suggest differences in autoreactivity in ILE and SLE. Determining whether the IgM aurotreactivity that predominates in ILE represents an early stage prior to IgG switching or is persistent and relatively protective will require further longitudinal studies.
Collapse
Affiliation(s)
- Q-Z Li
- Center for Immunology, University of Texas Southwestern Medical Center, Dalls, TX, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Villalta D, Tozzoli R, Tonutti E, Bizzaro N. The laboratory approach to the diagnosis of autoimmune diseases: is it time to change? Autoimmun Rev 2007; 6:359-65. [PMID: 17537381 DOI: 10.1016/j.autrev.2007.01.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2006] [Accepted: 01/01/2007] [Indexed: 12/20/2022]
Abstract
Array technology and proteomics are about to launch the era of multiplexed analysis, which allows simultaneous detection of numerous autoantibody specificities and the possibility of defining broad autoantibody profiles. This will probably improve disease staging, risk stratification, prognosis and treatment. However, although these technologies are very promising, they are still in their infancy, and therefore need to undergo strict analytical and clinical validation processes. The latter should involve clinicians and pathologists in prospective, multicentric studies conducted on large numbers of patients to define the specific significance of the various autoantibody profiles. Establishing common standards for the publication and sharing of microarray-generated data will be important for this purpose. Only when these studies have been completed will these new technologies find a place in clinical laboratories. Although we are entering a decade which will probably see a radical change in the diagnostic approach to autoimmune diseases, we do not yet have sufficient knowledge to apply proteomic technologies on a large scale. For the time being, therefore, it is advisable to continue using well-established approaches and diagnostic algorithms such as those reported in the international guidelines, which have been prepared in accordance with the principles of appropriateness and evidence-based medicine.
Collapse
Affiliation(s)
- Danilo Villalta
- Immunologia Clinica e Virologia, Azienda Ospedaliera S. Maria degli Angeli, via Montereale 24, 33170 Pordenone, Italy.
| | | | | | | |
Collapse
|
36
|
Ling MM, Ricks C, Lea P. Multiplexing molecular diagnostics and immunoassays using emerging microarray technologies. Expert Rev Mol Diagn 2007; 7:87-98. [PMID: 17187487 DOI: 10.1586/14737159.7.1.87] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Enzyme-linked immunosorbent assays (ELISA) are frequently used for quantitative measurement of the presence of protein, for single-analyte testing, in a sample. The application of ELISA in a microarray format has the potential to simultaneously measure the presence and/or concentrations of numerous proteins, in multiplex testing, all contained in a small drop of test fluid. Microspot microarray technology, in combination with protein biomarkers and nucleic acid diagnostics, appears to be the future high-performance analytical platform of choice. Validation of a large number of disease markers in both molecular and protein diagnostics has paved the way for the emergence of the multiplex assay. Initially, simple low-throughput multiplex assays were tested using the immunoassay format. These were followed by low-level multiplexing and high-throughput array-based immunoassays. More recently, two types of high-level multiplexing and high-throughput diagnostic methods using microspot arrays and bead arrays have been successfully developed to complement single-analyte assays. The value in rapid diagnostic evaluation for high-throughput multiplex, diagnostic test systems based on sound assay design must take into account data screening, normalization and statistical evaluation of possible concentration measurement, data errors and automated operation. Benefits of using multiplex array platforms include improved-quality patient care, as well as cost effectiveness and time saving. These multiplex methods also set the stage for future protein/nucleic acid codetection. Currently, the one analyte at a time test scheme is still dominant; nonetheless, the multiplex microspot microarray tests evaluated in a single multiassay analyzer are expected to become a significant part of clinical diagnostic testing within the next 5-10 years. This review is focused on microspot array and bead array methods for providing high throughput and a high degree of multiplexing in diagnostic testing.
Collapse
Affiliation(s)
- Michael M Ling
- umedik Inc., 36 Meteor Drive, Toronto, Ontario M9W 1A4, Canada.
| | | | | |
Collapse
|
37
|
Ichihara T, Akada JK, Kamei S, Ohshiro S, Sato D, Fujimoto M, Kuramitsu Y, Nakamura K. A novel approach of protein immobilization for protein chips using an oligo-cysteine tag. J Proteome Res 2006; 5:2144-51. [PMID: 16944925 DOI: 10.1021/pr0504889] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein chip technology is essential for high-throughput functional proteomics. We developed a novel protein tag consisting of five tandem cysteine repeats (Cys-tag) at termini of proteins. The Cys-tag was designed to allow covalent attachment of proteins to the surface of a maleimide-modified, diamond-like, carbon-coated silicon substrate. As model proteins, we created an enhanced green fluorescent protein (EGFP) and an EGFP-stathmin fusion protein, both of which contained a Cys-tag. We also included an oligo-histidine tag to allow its purification by the use of Ni beads, and we expressed the protein in Escherichia coli. The purified Cys-tagged EGFP could be captured on the maleimide-coated substrate efficiently so that 50 pg of the fusion protein was detected by fluorescence, and as little as 5 pg was immunodetected by combination with enhanced chemiluminescence. This highly sensitive immunodetection may be due to the strong covalent binding of the Cys-tag to the substrate combined with efficient exposure of the protein to the surrounding solution. Thus, the Cys-tag should be useful for developing a novel protein printing method for protein chips that requires very low amounts of protein and can be used for high-performance analysis of protein-ligand interactions.
Collapse
Affiliation(s)
- Teruhisa Ichihara
- Technical Research Laboratory, Toyo Kohan Company, Ltd., Higashi-toyoi, 1296, Kudamatsu, Yamaguchi 733-8611,Japan
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Balboni I, Chan SM, Kattah M, Tenenbaum JD, Butte AJ, Utz PJ. Multiplexed protein array platforms for analysis of autoimmune diseases. Annu Rev Immunol 2006; 24:391-418. [PMID: 16551254 DOI: 10.1146/annurev.immunol.24.021605.090709] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Several proteomics platforms have emerged in the past decade that show great promise for filling in the many gaps that remain from earlier studies of the genome and from the sequencing of the human genome itself. This review describes applications of proteomics technologies to the study of autoimmune diseases. We focus largely on biased technology platforms that are capable of analyzing a large panel of known analytes, as opposed to techniques such as two-dimensional gel electrophoresis (2DIGE) or mass spectroscopy that represent unbiased approaches (as reviewed in 1). At present, the main analytes that can be systematically studied in autoimmunity include autoantibodies, cytokines and chemokines, components of signaling pathways, and cell-surface receptors. We review the most commonly used platforms for such studies, citing important discoveries and limitations that exist. We conclude by reviewing advances in biomedical informatics that will eventually allow the human proteome to be deciphered.
Collapse
Affiliation(s)
- Imelda Balboni
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | | | | | | | | |
Collapse
|
39
|
Kingsmore SF. Multiplexed protein measurement: technologies and applications of protein and antibody arrays. Nat Rev Drug Discov 2006; 5:310-20. [PMID: 16582876 PMCID: PMC1780251 DOI: 10.1038/nrd2006] [Citation(s) in RCA: 508] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The ability to measure the abundance of many proteins precisely and simultaneously in experimental samples is an important, recent advance for static and dynamic, as well as descriptive and predictive, biological research. The value of multiplexed protein measurement is being established in applications such as comprehensive proteomic surveys, studies of protein networks and pathways, validation of genomic discoveries and clinical biomarker development. As standards do not yet exist that bridge all of these applications, the current recommended best practice for validation of results is to approach study design in an iterative process and to integrate data from several measurement technologies. This review describes current and emerging multiplexed protein measurement technologies and their applications, and discusses the remaining challenges in this field.
Collapse
|
40
|
González-Buitrago JM, González C. Present and future of the autoimmunity laboratory. Clin Chim Acta 2006; 365:50-7. [PMID: 16126186 DOI: 10.1016/j.cca.2005.07.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2005] [Revised: 07/04/2005] [Accepted: 07/05/2005] [Indexed: 11/20/2022]
Abstract
At present, autoimmunity laboratories are very dynamic owing to the constant and increasing availability of new tests, mainly due to the detection of new autoantibodies. The main characteristic of the autoimmunity laboratory and the one that differentiates it from other laboratories that use immunoassays as basic techniques is that it determines antibodies (autoantibodies) and not antigens. For this reason, immunoassay techniques must employ antigens as reagents. Indirect immunofluorescence has and continues to be a basic technique in autoimmunity studies. However, over the last few years, a significant trend at autoimmunity laboratories has been the gradual replacement of immunofluorescence microscopy by immunoassay. Of the several different forms of immunoassay, the enzyme-linked immunosorbent assay (ELISA) format is the one most used in autoimmunity laboratories. Recombinant DNA technology has allowed the production of large quantities of antigens for autoantibody analysis. Flow cytometry for the analysis of microsphere-based immunoassays allows the simultaneous measurement of several autoantibodies. Likewise, autoantigen microarrays provide a practical means to analyse biological fluids in the search for a high number of autoantibodies. We are now at the beginning of an era of multiplexed analysis, with a high capacity of autoantibody specificities. Future trends in this field include immunoassays with greater analytical sensitivity, simultaneous multiplexed capability, the use of protein microarrays, and the use of other technologies such as microfluidics.
Collapse
Affiliation(s)
- José M González-Buitrago
- Servicio de Bioquímica, Hospital Universitario, Salamanca, Spain and Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, 37007 Salamanca, Spain.
| | | |
Collapse
|
41
|
Glocker MO, Guthke R, Kekow J, Thiesen HJ. Rheumatoid arthritis, a complex multifactorial disease: on the way toward individualized medicine. Med Res Rev 2006; 26:63-87. [PMID: 16283676 DOI: 10.1002/med.20045] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
With the availability of the human genome sequence and those of related species like chimpanzee, mouse, and rat, data driven research for tackling the molecular grounds of rheumatoid arthritis (RA), a multifactorial polygenic disease, can be considered a realistic challenge to the scientific community. A comprehensive research strategy is presented enabling the integration of multiple research efforts on studying autoimmunity by so called systems biology approaches. An integrative scientific concept is discussed of how to unravel molecular mechanisms of complex diseases by making use of state-of-the-art methodologies in functional and comparative genomics. A continuous interchange of data-driven and hypothesis-driven research is adjoined to determine the nature of rheumatic diseases with autoimmune background. Instead of studying single genes and proteins, RNA and protein microarray profiles are currently obtained in numerous research projects producing read-outs termed gene signatures rather than DNA and/or protein markers. A comprehensive study of the RNA, protein, and metabolite regimes is undertaken that eventually will lead to a "holistic" view of how all respective molecules, pathways and cells themselves interact with each other. Some of the above mentioned research aspects have already been studied by the authors, hopefully leading to new diagnostics and therapeutics in the future.
Collapse
|
42
|
Tozzoli R, Villalta D, Kodermaz G, Bagnasco M, Tonutti E, Bizzaro N. Autoantibody profiling of patients with autoimmune thyroid disease using a new multiplexed immunoassay method. Clin Chem Lab Med 2006; 44:837-42. [PMID: 16776630 DOI: 10.1515/cclm.2006.137] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractClin Chem Lab Med 2006;44:837–42.
Collapse
Affiliation(s)
- Renato Tozzoli
- Laboratorio di Chimica-clinica e Microbiologia, Ospedale di Latisana, Latisana, Italy
| | | | | | | | | | | |
Collapse
|
43
|
Abstract
AbstractA variety of technologies for autoantibody profiling have been developed. The main techniques are line-blot immunoassays, bar-coded nanoparticle immunoassays, and bead-based assays with flow cytometry detection and antigen microarrays. Some of these technologies are only able to measure a limited number of autoantibodies, while others can detect elevated numbers. Assays for antinuclear antibody specificities using line-blot immunoassays and bead-based assays with flow cytometry detection are already commercialised. Antigen microarrays for autoantibody measurement are only in the development phase, although in the not too distant future these assays will probably appear on the market. Multiplexed testing in the autoimmunity laboratory appears to have a promising future, since this technique permits a reduction in analytical time, with a shorter turnaround time.Clin Chem Lab Med 2006;44:1169–74.
Collapse
Affiliation(s)
- José M González-Buitrago
- Laboratorio de Autoinmunidad, Servicio de Bioquímica Clínica, Hospital Universitario de Salamanca, y Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Salamanca, Spain.
| |
Collapse
|
44
|
Kappos L, Achtnichts L, Dahlke F, Kuhle J, Naegelin Y, Sandbrink R, Lindberg RLP. Genomics and proteomics: role in the management of multiple sclerosis. J Neurol 2005; 252 Suppl 3:iii21-iii27. [PMID: 16170496 DOI: 10.1007/s00415-005-2013-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Epidemiological studies and neuro-imaging have provided important insights into the natural course and prognostic factors of multiple sclerosis (MS), but our ability to predict different courses of the disease, and especially its response to treatment, is still very limited. Pharmacogenetic, pharmacogenomic and proteomic studies aim to assess gene and protein function in disease and promise to help to fill this important gap in our knowledge. Such studies may increase our understanding of disease mechanisms and responses to therapeutic compounds. Large-scale transcriptional expression profiling can be performed using gene chip microarrays; this technology allows screening for differentially expressed genes without having well-defined underlying hypotheses ("discovery-driven research"). To complement the technique, real time reverse transcription and polymerase chain reaction (RT-PCR) can be used for more targeted profiling and provides quantitative data on pre-selected genes. However, to maximise their clinical utility, expression profiling results need to be combined with well-documented clinical and imaging data. Two forthcoming studies will investigate the long-term effects of early treatment with interferon beta-1b (IFNbeta) on the course of MS. The BENEFIT (BEtaseron/Betaferon in Newly Emerging MS for Initial Treatment) study will incorporate pharmacogenetic and pharmacogenomic analyses to determine the genetic elements controlling treatment response. BEST-PGx (Betaferon/Betaseron in Early relapsing-remitting MS Surveillance Trial-Pharmacogenomics) is an exploratory 2-year study that will investigate the value of RNA expression profiling and pharmacogenetics in predicting treatment response to IFNbeta in patients with early relapsing MS. The main goal of BEST-PGx is the identification of differences in gene expression profiles of patients showing differential treatment responses. In addition, this study may reveal new information relevant to the mechanism of action of interferon treatment in MS and also to differences in the underlying pathology of the immune system. These data may help us approach the goal of a really "individualised therapy" with increased efficacy, reduced adverse drug reactions and more efficient use of health care resources.
Collapse
Affiliation(s)
- Ludwig Kappos
- Outpatient Clinic Neurology-Neurosurgery, University Hospital, Petersgraben 4, 4031 Basel, Switzerland.
| | | | | | | | | | | | | |
Collapse
|
45
|
Perez OD. Appreciating the Heterogeneity in Autoimmune Disease: Multiparameter Assessment of Intracellular Signaling Mechanisms. Ann N Y Acad Sci 2005; 1062:155-64. [PMID: 16461798 DOI: 10.1196/annals.1358.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Autoimmune disease pathologies are multifactorial with complex interactive networks of cells and chemical messengers that initiate cascades of aberrant cellular activity. Rheumatoid arthritis (RA) is a chronic inflammatory disease that is characterized by systemic inflammation, destruction of the joints, and production of autoantibodies recognizing dozens of putative autoantigens. The presence of autoreactive T cells in individuals leads to pathological autoimmunity by activating additional cellular constituents to mediate inflammation and joint destruction. The etiology of RA is unknown, and knowledge is lacking of the molecular mechanisms underlying the production and subsequent regulation of autoreactive T cells and predicting patient responses to treatments. Biochemical investigations into mechanisms of the disease have relied on animal models that are helpful in dissecting elements of the disease but that are not necessarily reflective of human RA development. The study of multiple activated signaling pathways in complex populations of cells, such as peripheral blood, at the single-cell level has not previously been possible. This article describes how intracellular phosphoepitope staining methodology in conjunction with surface-cell immunophenotyping can be used to deconvolute cellular subsets and allow functional characterization of patient-derived material. Multiparameter flow cytometric analysis allows for small subpopulations-representing different cellular subsets and differentiation or activation states-to be discerned and simultaneously assessed for intracellular biochemical activities. This article also describes how single-cell signal network analysis can be used to stratify patients and may be useful for understanding mechanisms of disease progression, treatment resistance, and development of diagnostic indicators.
Collapse
Affiliation(s)
- Omar D Perez
- The Baxter Laboratory for Genetic Pharmacology, Department of Microbiology & Immunology, Stanford University, 269 Campus Dr., CCSR 4225, Stanford, CA 94305, USA.
| |
Collapse
|
46
|
Chu KH, Tang CY, Wu A, Leung PSC. Seafood allergy: lessons from clinical symptoms, immunological mechanisms and molecular biology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2005; 97:205-35. [PMID: 16261809 DOI: 10.1007/b135827] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Food allergy consists of a wide range of disorders that result from adverse immune responses to dietary antigens. Manifestations of allergic response includes acute, potentially fatal anaphylactic reactions and a variety of chronic diseases that mainly affect the gastrointestinal tract, skin, and respiratory tract. Tools for clinical diagnosis and management, which have not changed much in the past two decades, include the clinical history, tests for specific IgE antibody to suspected foods, elimination diets, oral food challenges, and provision of medications such as epinephrine for emergency treatment. On the other hand, recent immunological and molecular biological research have enhanced our understanding of the mechanisms of these disorders and revealed the identities of many food allergens. Here, we will discuss seafood allergies with respect to the clinical manifestations, diagnosis, immunological mechanisms, and molecular biology of seafood allergens. Furthermore, potential applications and future directions in the clinical management of seafood allergies are discussed.
Collapse
Affiliation(s)
- Ka Hou Chu
- Department of Biology, The Chinese University of Hong Kong, Hong Kong, China
| | | | | | | |
Collapse
|
47
|
Knutson KL, Disis ML. Tumor antigen-specific T helper cells in cancer immunity and immunotherapy. Cancer Immunol Immunother 2005; 54:721-8. [PMID: 16010587 PMCID: PMC11032889 DOI: 10.1007/s00262-004-0653-2] [Citation(s) in RCA: 488] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2004] [Accepted: 11/11/2004] [Indexed: 10/25/2022]
Abstract
Historically, cancer-directed immune-based therapies have focused on eliciting a cytotoxic T cell (CTL) response, primarily due to the fact that CTL can directly kill tumors. In addition, many putative tumor antigens are intracellular proteins, and CTL respond to peptides presented in the context of MHC class I which are most often derived from intracellular proteins. Recently, increasing importance is being given to the stimulation of a CD4+ T helper cell (Th) response in cancer immunotherapy. Th cells are central to the development of an immune response by activating antigen-specific effector cells and recruiting cells of the innate immune system such as macrophages and mast cells. Two predominant Th cell subtypes exist, Th1 and Th2. Th1 cells, characterized by secretion of IFN-gamma and TNF-alpha, are primarily responsible for activating and regulating the development and persistence of CTL. In addition, Th1 cells activate antigen-presenting cells (APC) and induce limited production of the type of antibodies that can enhance the uptake of infected cells or tumor cells into APC. Th2 cells favor a predominantly humoral response. Particularly important during Th differentiation is the cytokine environment at the site of antigen deposition or in the local lymph node. Th1 commitment relies on the local production of IL-12, and Th2 development is promoted by IL-4 in the absence of IL-12. Specifically modulating the Th1 cell response against a tumor antigen may lead to effective immune-based therapies. Th1 cells are already widely implicated in the tissue-specific destruction that occurs during the pathogenesis of autoimmune diseases, such as diabetes mellitus and multiple sclerosis. Th1 cells directly kill tumor cells via release of cytokines that activate death receptors on the tumor cell surface. We now know that cross-priming of the tumor-specific response by potent APC is a major mechanism of the developing endogenous immune response; therefore, even intracellular proteins can be presented in the context of MHC class II. Indeed, recent studies demonstrate the importance of cross-priming in eliciting CTL. Many vaccine strategies aim to stimulate the Th response specific for a tumor antigen. Early clinical trials have shown that focus on the Th effector arm of the immune system can result in significant levels of both antigen-specific Th cells and CTL, the generation of long lasting immunity, and a Th1 phenotype resulting in the development of epitope spreading.
Collapse
Affiliation(s)
- K L Knutson
- Department of Immunology, Mayo Clinic College of Medicine, 342C Guggenheim Bldg., 200 First St. SW, Rochester, MN 55906, USA.
| | | |
Collapse
|
48
|
Wakui M, Morel L, Butfiloski EJ, Kim C, Sobel ES. Genetic Dissection of Systemic Lupus Erythematosus Pathogenesis: Partial Functional Complementation betweenSle1andSle3/5Demonstrates Requirement for Intracellular Coexpression for Full Phenotypic Expression of Lupus. THE JOURNAL OF IMMUNOLOGY 2005; 175:1337-45. [PMID: 16002739 DOI: 10.4049/jimmunol.175.2.1337] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Sle1 on chromosome 1 and Sle3/5 on chromosome 7 are two of the most critical lupus susceptibility loci of the New Zealand Black/White-derived NZM2410 mouse strain. In contrast to C57BL/6 mice congenic for either Sle1 (B6.Sle1) or Sle3/5 (B6.Sle3/5), strains that express only a modest lupus-related phenotype, the bicongenic B6.Sle1.Sle3/5 strain has a robust phenotype, suggesting a critical role for epistatic interactions in lupus pathogenesis. Mixed chimera experiments indicated that the two loci are functionally expressed by different cell populations and predicted that phenotypic expression of the phenotypic features of the B6.Sle1.Sle3/5 strain could be fully reproduced with a combination of B6.Sle1 and B6.Sle3/5 bone marrow. Contrary to our expectations, there was only a partial functional complementation in these mixed chimeras. Spleen enlargement, CD4:CD8 ratio elevation, and epitope spreading of autoantibodies were fully developed in B6+B6.Sle1.Sle3/5 but not in B6.Sle1+B6.Sle3/5 mixed chimeras. This study is the first to present evidence that the pathways mediated by two critical lupus susceptibility loci derived from the New Zealand White strain must be integrated intracellularly for epistatic interactions to occur. Our mixed chimera approach continues to provide novel insights into the functional genetic pathways underlying this important murine model of systemic autoimmunity.
Collapse
Affiliation(s)
- Masatoshi Wakui
- Department of Medicine and Division of Rheumatology and Clinical Immunology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | | | | | | | | |
Collapse
|
49
|
Tampoia M, Brescia V, Fontana A, Maggiolini P, Zucano A, Pansini N. Proteomic: New advances in the diagnosis of rheumatoid arthritis. Clin Chim Acta 2005; 357:219-25. [PMID: 15896730 DOI: 10.1016/j.cccn.2005.03.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Accepted: 03/09/2005] [Indexed: 11/28/2022]
Abstract
BACKGROUND Rheumatoid arthritis (RA) is a chronic autoimmune disease affecting the joints. A number of novel treatment modalities have been introduced over the past years, and rheumatologists are now attempting to institute optimal treatment in recent-onset arthritis. To facilitate diagnosis during the early stages of disease, when often not all clinical symptoms are manifest, a good serological marker is needed. METHODS Antibodies directed to citrullinated proteins provide this ability. The most sensitive assay for detecting these antibodies is the so-called anti-cyclic citrullinated peptide, second generation (CCP II) enzyme-linked immunosorbent assay (ELISA). RESULTS The diagnostic and prognostic potential of anti-CCP antibodies and the availability of a fully automated assay method lead us to conclude that the test is satisfactory for routine use as a serological marker of RA. In addition, we consider the potential of multiplex autoantibody assays, including miniaturized, high-throughput microarray technology, to improve diagnosis and prognostication in early onset arthritis patients.
Collapse
Affiliation(s)
- M Tampoia
- Laboratorio di Patologia Clinica I, Azienda Ospedaliera Policlinico, 70124 Bari, Italy.
| | | | | | | | | | | |
Collapse
|
50
|
Abstract
Protein microarrays have been developed and partially validated for studying blood cells, which play a role in many human diseases. Arrays of capture antibodies are commercially available for analyzing cytokines and intracellular signaling proteins. Several academic laboratories have developed antigen microarrays for characterizing autoimmune and allergic diseases, with a goal toward using such arrays to profile antibodies found in blood or other biological fluids. Arrays composed of major histocompatibility complex tetramers have been constructed and validated for analysis of immune responses in mice, paving the way toward studying antigen-specific T-lymphocyte responses. Finally, reverse-phase protein lysate microarray technology, first developed for analyzing cancer cells from tissue sections, has now been demonstrated for studying living cells, including knockout cells, cells treated with drugs such as kinase inhibitors, and rare populations of lymphocytes such as regulatory T cells. The goal of this review is to focus on advances in and future uses of arrays of proteins that can be printed on glass microscope slides using traditional microarray robots that are commonly found at academic medical centers. Dissemination of protein array technology will occur in the next decade and will markedly change how immunology research, particularly in the fields of autoimmunity and inflammation, is conducted.
Collapse
Affiliation(s)
- Paul J Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|