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Mouse protein arrays from a TH1 cell cDNA library for antibody screening and serum profiling
Abstract
The mouse is the premier genetic model organism for the study of disease and development. We describe the establishment of a mouse T helper cell type 1 (T(H)1) protein expression library that provides direct access to thousands of recombinant mouse proteins, in particular those associated with immune responses. The advantage of a system based on the combination of large cDNA expression libraries with microarray technology is the direct connection of the DNA sequence information from a particular clone to its recombinant, expressed protein. We have generated a mouse T(H)1 expression cDNA library and used protein arrays of this library to characterize the specificity and cross-reactivity of antibodies. Additionally, we have profiled the autoantibody repertoire in serum of a mouse model for systemic lupus erythematosus on these protein arrays and validated the putative autoantigens on highly sensitive protein microarrays.
... Anti-ribosomal P antibodies are correlated with a specific clinical subtype of SLE, i.e., SLE with neuropsychiatric symptomatology (NPSLE) [27]. Although they have not yet been demonstrated in the serum of SLE patients, autoantibodies to RPS27a have been detected in a mouse model of SLE and therefore could play also a role for this disease [28]. ...
... In the present study, we used them as a model to characterize functional effects of antibodies directed towards CT and the closely related CS CPn and CPs. The results demonstrate that both α-CT and α-CS are able to interact with the ribosomal small subunit component RPS27a, a protein that has been previously demonstrated in a mouse model as a putative autoimmune target in SLE [28]. ...
... Due to the labeling of several pairs of RPS27a protein spots on the hEXselect multiprotein array, and its putative relevance as a candidate autoantigen for SLE [28], we selected this protein for further analysis. For this, we tried to confirm the interactions of α-CT and α-CS with RPS27a by an independent experimental setup, testing interactions of these antisera with recombinant samples of RPS27a and the closely related ribosomal protein RPS30 by a series of Western blots (Fig. 3). ...
Chlamydia trachomatis (CT) and the Chlamydophila species (CS) Chlamydophila pneumoniae (CPn), and Chlamydophila psittaci (CPs) are suggested to induce autoantibodies causative of several human autoimmune disorders like rheumatoid arthritis and systemic lupus erythematosus (SLE). The aim of the present study was therefore to identify cellular protein interaction partners with antisera to CT (α-CT) or CS (α-CS) and to identify functional consequences of such interaction in vitro. As detected with a commercial first trimester human prenatal brain multiprotein array (hEXselect, Engine, Germany), the most frequent interaction partner with both α-CT and α-CS was the ribosomal small subunit protein RPS27a. This could be confirmed by Western blot analysis with a recombinant RPS27a sample. In addition, immunocytochemistry with both antisera in the human choroid plexus papilloma cell line HIBCPP revealed a granular cytoplasmic staining, and Western blot analysis with whole-cell protein samples of HIBCPP cells revealed both antisera to label protein bands of different molecular weights and intensity. By 2D Western blot analysis and mass spectrometry, one of the protein spots interacting with α-CT could be identified as the RPS27a. Finally, two different methods for the detection of protein synthesis activity, the SUnSET technique and an HPG fluorescence assay revealed both antisera to cause reduced translational activity in HIBCPP cells. Together with previous findings of RPS27a as an autoimmune target in a mouse model of systemic lupus erythematosus (SLE), these results suggest that infections with CT and/or CS could induce SLE-associated immune modifications. However, direct evidence for a pathogenic role of these interactions for SLE demands further investigations.
... The amount of serum required to develop an array containing over 10,000 features can be the same as that required to develop a single feature in a well of a 96-well plate. Genetix microarrayers have been used for a range of such applications [4][5][6][7][8] . There are some cases, however, in which microwells have an advantage in that they can be easier to handle with existing instrumentation. ...
Screening tens to hundreds of proteins for enzymatic activity or protein interactions can now be performed in a quantitative and economical manner using protein microarrays. Recent validated examples include assays for human protein kinases and protein interactions with p53. Here we describe the QArray series of instruments for the printing and assaying of such arrays. Of particular note is printing of arrays into microwell plates, a methodology that combines the benefits of arrays and the convenience of a conventional assay format.
... Studies with antibodies on protein microarrays demonstrate that false positive binding to unrelated antigens can occur, not just with polyclonal antibodies, but also with some monoclonal antibodies (Michaud et al., 2003;Gutjahr et al., 2005). Indeed Keitel et al. (1997) and Kramer et al. (1997) have shown using peptide arrays and structural studies that binding can occur in unanticipated ways to completely unrelated targets. ...
Immunohistochemistry (IHC) is a powerful technique for identifying sites of protein expression in tissues at the cellular and sub-cellular level. Here we have investigated the potential of using IHC for genome-wide expression screening by measuring the success rate and specificity of a panel of 35 monoclonal antibodies recognizing 5 well characterised CD antigens. Antibodies were pre-screened on acetone fixed frozen sections of spleen, tonsil and colon tissues. 19/35 antibodies gave staining with a success rate of 0/7 for JAM-2, 1/4 for CD99, 3/6 for CD138, 5/8 for CD45 and 10/10 for MHC-class II. 16/19 of these antibodies also gave staining on formalin fixed paraffin embedded tissue sections of tonsil and colon. All antibodies that had given staining were then profiled on tissues presented in human tissue microarrays. In the frozen microarrays 216 cores from 29 normal tissue types were present and in the formalin fixed paraffin array 344 cores from 35 normal and 4 cancers were represented. Where multiple antibodies were positive, there was evidence of consistent staining of the same tissues with several antibodies. In some cases differences in staining were observed potentially due to differential splice variants, polymorphisms or protein modification. With some antibodies there was evidence of cross-reactivity to inappropriate cells or structures. In addition the staining intensity with formalin fixation was changed quantitatively for some antibodies and in a few cases qualitatively, representing differential sensitivity of specific and non-specific epitopes to fixation. Accordingly, whilst IHC has potential for describing protein expression of unknown genes, these results emphasise a need to systematically address issues of specificity and sensitivity if appropriate profiles are to be described.
... [283] This method was also used by others. [284][285][286] ...
Protein biochips are at the heart of many medical and bioanalytical applications. Increasing interest has been focused on surface activation and subsequent functionalization strategies for immobilizing these biomolecules. Different approaches using covalent and noncovalent chemistry are reviewed; particular emphasis is placed on the chemical specificity of protein attachment and on retention of protein function. Strategies for creating protein patterns (as opposed to protein arrays) are also outlined. An outlook on promising and challenging future directions for protein biochip research and applications is also offered.
... In addition, specificity of antibody staining is an important consideration and different groups verify staining patterns to different extents. For example, false positive binding to unrelated antigens can occur, not just with polyclonal antibodies, but also with monoclonal antibodies, as exemplified by previous studies with antibodies on protein microarrays [25][26][27]. In a similar way, exposing hybridoma derived monoclonal antibodies to the majority of tissue in the body has been shown to result in false positive staining [18]. ...
We have created a high quality phage display library containing over 1010 human antibodies and describe its use in the generation of antibodies on an unprecedented scale. We have selected, screened and sequenced over 38,000 recombinant antibodies to 292 antigens, yielding over 7,200 unique clones. 4,400 antibodies were characterized by specificity testing and detailed sequence analysis and the data/clones are available online. Sensitive detection was demonstrated in a bead based flow cytometry assay. Furthermore, positive staining by immunohistochemistry on tissue microarrays was found for 37% (143/381) of antibodies. Thus, we have demonstrated the potential of and illuminated the issues associated with genome-wide monoclonal antibody generation.
... Recombinant or purified proteins can be immobilized to study protein-protein interaction ( Fig. 3C) or to probe sera for the presence of specific antibodies (Fig. 3D). The latter was shown to be a suitable approach to study allergy (Kim et al. 2002) or autoimmune diseases (Gutjahr et al. 2005, Lueking et al. 2005. In so called reverse arrays, complex tissue or cell lysates (or fractions thereof) are immobilized and probed with a number of antibodies to profile the presence of antigens in many samples under identical conditions (Fig. 3E). ...
... With the development of etiological detection technology, microarrays have rapidly expanded into the area of biological research, including gene expression, signal transection, genome mismatch scanning, and protein trafficking. Among the many types of microarrays, the protein microarray offers an opportunity to study the full spectrum of protein attributes in a parallel, miniaturized, and automated fashion representing a significant shift from the traditional ''one protein at a time'' methods [58,59]. Furthermore, the method not only aids in improved diagnosis, but also identifies autoantibody signatures that may represent disease subgroups, early diagnostics [60,61] and facilitates the analysis of the outcome of vaccine trials [62]. ...
Food-borne helminthiases (FBHs) have become increasingly important due to frequent occurrence and worldwide distribution. There is increasing demand for developing more sensitive, high-throughput techniques for the simultaneous detection of multiple parasitic diseases due to limitations in differential clinical diagnosis of FBHs with similar symptoms. These infections are difficult to diagnose correctly by conventional diagnostic approaches including serological approaches.
In this study, antigens obtained from 5 parasite species, namely Cysticercus cellulosae, Angiostrongylus cantonensis, Paragonimus westermani, Trichinella spiralis and Spirometra sp., were semi-purified after immunoblotting. Sera from 365 human cases of helminthiasis and 80 healthy individuals were assayed with semi-purified antigens by both a protein microarray and the enzyme-linked immunosorbent assay (ELISA). The sensitivity, specificity and simplicity of each test for the end-user were evaluated. The specificity of the tests ranged from 97.0% (95% confidence interval (CI): 95.3-98.7%) to 100.0% (95% CI: 100.0%) in the protein microarray and from 97.7% (95% CI: 96.2-99.2%) to 100.0% (95% CI: 100.0%) in ELISA. The sensitivity varied from 85.7% (95% CI: 75.1-96.3%) to 92.1% (95% CI: 83.5-100.0%) in the protein microarray, while the corresponding values for ELISA were 82.0% (95% CI: 71.4-92.6%) to 92.1% (95% CI: 83.5-100.0%). Furthermore, the Youden index spanned from 0.83 to 0.92 in the protein microarray and from 0.80 to 0.92 in ELISA. For each parasite, the Youden index from the protein microarray was often slightly higher than the one from ELISA even though the same antigen was used.
The protein microarray platform is a convenient, versatile, high-throughput method that can easily be adapted to massive FBH screening.
Microarrays are grids of biomolecules in which each element of the grid performs a specific assay such as identification of a specific binding molecule or measuring a particular enzymatic activity. The potential of microarrays to facilitate global analysis of genes and gene products has led to its adoption in nearly every area of biological science—from basic research to clinical diagnostics. This article provides a technical overview of microarrays including information on array formats, production, and use of microarrays for interrogating various molecular species such as DNA, RNA, and proteins.
Keywords:
microarrays;
enzymatic activity;
biological science;
biomolecules
The identification and validation of disease-causing target genes is an essential first step in drug discovery and development. Genomics and proteomics technologies have already begun to uncover novel functional pathways and therapeutic targets in several human diseases such as cancers and autoimmunity. Also, bioinformatics approaches have highlighted several key targets and functional networks. In contrast to gene-profiling approaches, phenotype-oriented target identification allows direct link between the genetic alterations and a disease phenotype. Therefore, identified genes are more likely to be a cause rather than a consequence of the disease. Once a gene target or a mechanistic pathway is identified, the next step is to demonstrate that it does play a critical role in disease initiation, perpetuation, or both. A range of strategies exists for modulating gene expression in vitro and in vivo. These strategies include the use of antibodies, negative dominant controls, antisense oligonucleotides, ribozymes, and small-interfering RNAs. In contrast to in vitro assays, mouse reverse genetics such as knockout phenotypes has become a powerful approach for deciphering gene function and target validation in the context of mammalian physiology. In addition to disease-causing genes, the identification of antigens that stimulate both arms of the immune system is the major goal for effective vaccine development. The hope is that target discovery and validation processes will concurrently identify and validate therapeutic targets for drug intervention in human diseases.
The Cancer Gene Anatomy Project (CGAP) database of the National Cancer Institute has thousands of known and novel expressed sequence tags (ESTs). These ESTs, derived from diverse normal and tumor cDNA libraries, offer an attractive starting point for cancer gene discovery. Data-mining the CGAP database led to the identification of ESTs that were predicted to be specific to select solid tumors. Two genes from these efforts were taken to proof of concept for diagnostic and therapeutics indications of cancer. Microarray technology was used in conjunction with bioinformatics to understand the mechanism of one of the targets discovered. These efforts provide an example of gene discovery by using bioinformatics approaches. The strengths and weaknesses of this approach are discussed in this review.
Understanding responses of the cellular system for a dosing molecule is one of the most important problems in pharmacogenomics. In this chapter, we describe computational methods for identifying and validating drug target genes based on the gene networks estimated from microarray gene expression data. We use two types of microarray gene expression data: gene disruptant microarray data and time-course drug response microarray data. For this purpose, the information of gene networks plays an essential role and is unattainable from clustering methods, which are the standard for gene expression analysis. The gene network is estimated from disruptant microarray data by the Bayesian network model, and then the proposed method automatically identifies sets of genes or gene regulatory pathways affected by the drug. We use an actual example from analysis of Saccharomyces cerevisiae gene expression profile data to express a concrete strategy for the application of gene network information toward drug target discovery.
Identification and characterization of differentially expressed genes may be an important first step toward the understanding of both normal physiology and disease. A multitude of techniques belonging to two main categories have been developed to identify the differences in gene expression between samples from different biological origin: selection techniques and global techniques. Whereas the selection techniques strive to identify specific differentially expressed genes, the global techniques analyze the total transcriptome or a major part of the RNA population in a defined biological material. By exploiting the known sequences of the adaptors used in suppressive subtraction hybridization technique, a strategy named novel rescue-suppression-subtractive hybridization was developed. It should facilitate the discovery of differentially expressed genes.
RNA interference (RNAi) is an evolutionarily conserved phenomenon in which gene expression is silenced by double-stranded RNA (dsRNA) in a sequence-specific manner. This technology has the potential to affect all aspects of target discovery and validation. With the completion of the human genome, it is now possible to design small-interfering RNA (siRNA) libraries targeting every human gene. Specific siRNAs, libraries containing a pathway, gene family, or gene set of interest, are expected to unsecure new targets in pathways of therapeutic interest. Here, we highlight the potential of siRNA screens for target identification by using cell-based assays.
With the accumulation of vast amounts of data as a result of the sequencing of the human genome, it is necessary to identify human genes that are involved in various cellular, developmental, and disease-related processes and to clarify their functions and potential utility as targets in the treatment of disease. Identification methods based on the use of hammerhead and hairpin ribozymes have received increasing attention as possible tools for the rapid identification of key genes involved in biological processes. This chapter describes the method known as gene-discovery by a hammerhead ribozyme library for elucidation of the gene function. Use of this technology has already revealed new insights into several important biological phenomena.
In this chapter, we provide a protocol for the production of transfected cell arrays in living mammalian cells on noncoated chambered coverglass for the systematic functional analyses of human genes by high-content screening microscopy. This method should facilitate drug target validation by small-interfering RNAs.
Transgenic animals have become a key tool in functional genomics to generate models for human diseases and validate new drugs. Transgenesis includes the addition of foreign genetic information to animals and specific inhibition of endogenous gene expression. Recently, animal models provided novel insight and significantly improved our understanding of the initiation and perpetuation of human diseases. Moreover, they are an invaluable tool for target discovery, validation, and production of therapeutic proteins. However, despite the generation of several transgenic and knockout models, obtaining relevant models still faces several theoretical and technical challenges. Indeed, genes of interest are not always available and gene addition or inactivation sometimes does not allow clear conclusions because of the intrinsic complexity of living organisms or the redundancy of some metabolic pathways. In addition to homologous recombination, endogenous gene expression can be specifically inhibited using several mechanisms such as RNA interference. Here, some animal models are described to illustrate their importance in biomedical research. Moreover, guidelines for generation of these animals are presented.
The intermediate filament (IF) cytoskeleton of mammalian epithelia is generated from pairs of type I and type II keratins that are encoded by two large gene families, made up of 54 genes in humans and the mouse. These genes are expressed in a spatiotemporal and tissue-specific manner from the blastocyst stage onward. Since the discovery of keratin mutations leading to epidermolysis bullosa simplex, mutations in at least 18 keratin genes have been identified that result in keratinopathies of the epidermis and its appendages. Recently, noncanonical mutations in simple epithelial keratins were associated with pancreatic, liver, and intestinal disorders, demonstrating that keratins protect epithelia against mechanical and other forms of stress. In recent years, animal models provided novel insight and significantly improved understanding of IF function in tissue homeostasis and its role in disease. Pathological phenotypes detected in mutant mice generated so far range from embryonic lethality to tissue fragility to subtlety, which often depends on their genetic background. This range implies at least a partial influence of yet unidentified modifier genes on the phenotype after the ablation of the respective keratin. To date, nearly all available keratin mouse models were generated by taking advantage of conventional gene-targeting strategies. To reveal their cell type-specific functions and the mechanisms by which mutations lead to disease, it will be necessary to use conditional gene-targeting strategies and the introduction of point-mutated gene copies. Furthermore, conditional strategies offer the possibility to overcome embryonic or neonatal lethality in some of the keratin-deficient mice.
Recent epidemiological research indicates that a coexistent anemia among patients with heart failure might worsen their prognosis. However, whether the reduced synthesis of red blood cells is a contributing factor to the development and progression to overt heart failure, or whether it simply is a mere consequence of a dysfunctional heart, remains to be elucidated. Studies in mice with experimentally induced acute myocardial infarction leading to subsequent development of a postinfarction congestive heart failure have shed some light on this problem. Careful analyses of the number and of the functions of various hematopoietic cells residing in either blood or bone marrow point to a possible inhibitory role of cytokines, such tumor necrosis factor alpha, on hematopoiesis. The present protocols will hopefully encourage further studies of hematopoiesis and immunity in heart failure by using a combination of animal models with state-of-the-art techniques in molecular biology to define and validate possible targets for therapy.
The ability of the immune system to distinguish between self- and nonself antigens is controlled by mechanisms of central and peripheral tolerance. Although the induction and maintenance of tolerance is important for preventing autoimmunity, breaking self-tolerance is a crucial constituent for combating cancers. Cancer patients are able to develop spontaneous immune responses to tumors that they bear, however these responses are not suboptimal for eradicating tumors. Moreover, none of the current immune strategies is able to activate the immune system to respond against tumor cells as it responds against infectious agents. These observations have raised the question of how to activate immunity in cancer patients to a threshold required for tumor rejection. Because tolerance is emerging as a central obstacle for immune recognition of human tumor antigens, this chapter describes how T- and B-cells are generated and activated in the periphery. It also outlines the technical advances in tumor antigen discovery and validation.
The recent progress of proteomics has opened new avenues for tumor-associated antigen discovery. Here, I describe a two-dimensional (2D), gel-based Western blot approach for screening and identification of proteins eliciting a humoral response in cancer. Sera from patients are used in 2D Western blot experiments for screening of autoantibodies, and the immunoreactive target proteins are subsequently identified by mass spectrometry. Applied to several types of cancer, this proteomic-based approach has revealed a high frequency of autoantibodies in sera from cancer patients and has led to the identification of novel tumor antigens. Relevant examples are described.
Functional proteomics is a promising technique for the rational identification of novel therapeutic targets and biological markers. The studies of protein-protein interactions have been gained from the development of high-throughput technologies such as the yeast two-hybrid system, protein arrays, phage display, and systematic analysis of interaction maps for the prediction of protein functions. Because antibodies are used extensively as diagnostic and clinical tools, the characterization of their antigen specificity is of prime importance. Indeed, screening protein arrays with sera from patients with either cancer or autoimmune diseases would facilitate the identification of autoantibody signatures that can be used for diagnosis and/or prognosis of patients. The usefulness of multiplexed measurements lies not only in the ability to screen many individual marker candidates but also in evaluating the use of multiple markers in combination. Here, we review the advantage of protein and serum screening of peptides and cDNA repertoires displayed on phages as well as the fabrication of protein microarrays for probing immune responses in patients.
Protein microarrays with immobilised proteins on their surface are new analytical tools to overcome the current limits with respect to sample volume and throughput. They have a great potential as well with respect to multiplexing of complex samples, as a research tool and in diagnostics. Based on recent advances in this technology, new applications for protein microarrays in studying autoimmune diseases were described. Required tools for bioinformatical analysis of protein microarrays concerning normalisation, clustering and classification methods are discussed. The huge potential of this technology as well as future requirements such as protein microarray based diagnostics are presented.
Protein array technology is becoming an increasingly important tool in the drive toward proteome-scale analysis of protein activity and interactions. Presently, this technology compliments the more traditional methods for proteomic analysis, including two-dimensional gel electrophoresis/chromatography and mass spectrometry. While the task of producing a “whole-proteome” chip, containing active proteins, is a daunting one, current protein and antibody arrays represent the first steps toward that goal. In this review, we discuss current approaches for the generation of protein arrays, and their applications, including their use in the study of protein–protein, protein–nucleic acid, enzyme–substrate, and so on, interactions. Potential applications of protein arrays in interaction screening, such as compound–protein interactions are also discussed.
RNA interference (RNAi) refers to post-transcriptional silencing of gene expression as a result of the introduction of double-stranded RNA into cells. The application of RNAi in experimental systems has significantly accelerated elucidation of gene functions. In order to facilitate large-scale functional genomics studies using RNAi, several high-throughput approaches have been developed based on microarray or microwell assays. The recent establishment of large libraries of RNAi reagents combined with a variety of detection assays has further improved the performance of functional genome-wide screens in mammalian cells.
Protein microarrays represent an important new tool in proteomic systems biology. This review focuses on the contributions of protein microarrays to the discovery of novel disease biomarkers through antibody-based assays. Of particular interest is the use of protein microarrays for immune response profiling, through which a disease-specific antibody repertoire may be defined. The antigens and antibodies revealed by these studies are useful for clinical assay development, with enormous potential to aid in diagnosis, prognosis, disease staging and treatment selection. The discovery and characterization of novel biomarkers specifically tailored to disease type and stage are expected to enable personalized medicine by facilitating preventative medicine, predictive diagnostics and individualized curative therapies.
For the development and production of protein biochips for antibody characterization and biomarker discovery, Protagen AG relies on two Tecan HS 4800™ Pro hybridization stations for automated processing.
The human genome has been sequenced and the challenges of understanding the function of the newly discovered genes have been addressed. High-throughput technologies such as DNA microarrays have been developed for the profiling of gene expression patterns in whole organisms or tissues. Protein arrays are emerging to follow DNA chips as possible screening tools. Here, we review the generation and application of microarray technology to obtain more information on the regulation of proteins, their biochemical functions and their potential interaction partners. Already, a large variety of assays based on antibody-antigen interactions exists. In addition, the medical relevance of protein arrays will be discussed.
Modern tools in proteomics require access to large arrays of specific binders for use in multiplex array formats, such as microarrays, to decipher complex biological processes. Combinatorial protein libraries offer a solution to the generation of collections of specific binders, but unit operations in the process to isolate binders from such libraries must be automatable to ensure an efficient procedure. In the present study, we show how a microfluidic concept that utilizes particle separation in an acoustic force field can be used to efficiently separate antigen-bound from unbound members of such libraries in a continuous flow format. Such a technology has the hallmarks for incorporation in a fully automated selection system for the isolation of specific binders.
Protein array technology has begun to play a significant role in the study of protein-protein interactions and in the identification of antigenic targets of serum autoantibodies in a variety of autoimmune disorders. More recently, this technology has been applied to the identification of autoantibody signatures in cancer. The identification of tumour-associated antigens (TAAs) recognised by the patient's immune response represents an exciting approach to identify novel diagnostic cancer biomarkers and may contribute towards a better understanding of the molecular mechanisms involved. Circulating autoantibodies have not only been used to identify TAAs as diagnostic/prognostic markers and potential therapeutic targets, they also represent excellent biomarkers for the early detection of tumours and potential markers for monitoring the efficacy of treatment. Protein array technology offers the ability to screen the humoral immune response in cancer against thousands of proteins in a high throughput technique, thus readily identifying new panels of TAAs. Such an approach should not only aid in improved diagnostics, but has already contributed to the identification of complex autoantibody signatures that may represent disease subgroups, early diagnostics and facilitated the analysis of vaccine trials.
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.
Autoantibodies against autologous tumor-associated antigens have been detected in the asymptomatic stage of cancer and can thus serve as biomarkers for early cancer diagnosis. Moreover, because autoantibodies are found in sera, they can be screened easily using a noninvasive approach. Consequently, many studies have been initiated to identify novel autoantibodies relevant to various cancer types. To facilitate autoantibody discovery, approaches that allow the simultaneous identification of multiple autoantibodies are preferred. Five such techniques--SEREX, phage display, protein microarray, SERPA and MAPPing--are discussed here. In the second part of this review, we discussed autoantibodies found in the five most common cancers (lung, breast, colorectal, stomach and liver). The discovery of panels of tumor-associated antigens and autoantibody signatures with high sensitivity and specificity would aid in the development of diagnostics, prognostics and therapeutics for cancer patients.
The development of autoantibodies is observed in autoimmune disorders and numerous cancers. Consequently, autoantibodies form the basis of potential diagnostic and prognostic assays, as well as approaches for monitoring disease progression and treatment response. The effective use of autoantigen biomarkers for these applications, however, is contingent upon the identification of not one but multiple biomarkers. This is a consequence of the observation that the development of autoantibodies to any given protein is typically seen only in a fraction of patients. We have previously demonstrated the utility of functional protein microarrays containing thousands of different human proteins (ProtoArrays) for discovering novel autoimmune biomarkers in serum and plasma. Here, we describe a protocol for detecting autoantibodies in urine.
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.
The future ability to manipulate the growth of new blood vessels (angiogenesis) holds great promise for treating ischemic
disease and cancer. Several models of human in vivo angiogenesis have been described, but they seem to depend on transgenic
support and have not been validated in a therapeutic context. Here, we describe an in vivo assay that mimics human angiogenesis
in which native human umbilical vein-derived endothelial cells are suspended in a liquid laminin/collagen gel (Matrigel),
injected into immunodeficient mice, and develop into mature, functional vessels that vascularize the Matrigel plug in the
course of 30 d. Moreover, we demonstrate how to target this process therapeutically by sustained delivery of the angiogenesis
inhibitor endostatin from subcutaneously implanted microosmotic pumps.
Key WordsAdoptive transfer–angiogenesis–endostatin–human umbilical vein-derived endothelial cells–HUVECs–Matrigel–RAG2 mice
Microarray formatted assays have become well established for the global analysis of nucleic acids, but are only beginning
to be adopted for proteomic analysis. This chapter reviews the current status of protein microarray assays and highlights
efforts using cells and tissues on microarrays. These ‘other’ microarrays have the potential to yield highly parallel miniaturized
assays that will accelerate drug discovery efforts and facilitate understanding of biological complexity.
Key WordsProtein microarray-proteomics-immobilized-kinase assay-binding assay-microarray-reverse phase microarray-antibody array-cell microarray-tissue microarray-reverse transfection
Proteinbiochips sind integrale Bestandteile einer wachsenden Zahl medizinischer und bioanalytischer Anwendungen, weshalb das Interesse an Methoden zur Proteinimmobilisierung für die Herstellung solcher Chips in den letzten Jahren stark gestiegen ist. Dieser Aufsatz gibt einen Überblick über chemische Verfahren zur kovalenten und nichtkovalenten Anbindung von Proteinen auf Oberflächen, wobei ein spezielles Augenmerk auf chemische Selektivität und die Erhaltung der Proteinfunktion bei der Immobilisierung gelegt wird. Ferner werden Strategien zur Herstellung strukturierter Proteinoberflächen umrissen. Abschließend wird ein Ausblick auf mögliche Entwicklungsrichtungen im Bereich der Proteinbiochipforschung und -anwendung gegeben.
Protein biochips have a great potential in future parallel processing of complex samples as a research tool and in diagnostics. For the generation of protein biochips, highly automated technologies have been developed for cDNA expression library production, high throughput protein expression, large scale analysis of proteins, and protein microarray generation. Using this technology, we present here a strategy to identify potential autoantigens involved in the pathogenesis of alopecia areata, an often chronic disease leading to the rapid loss of scalp hair. Only little is known about the putative autoantigen(s) involved in this process. By combining protein microarray technology with the use of large cDNA expression libraries, we profiled the autoantibody repertoire of sera from alopecia areata patients against a human protein array consisting of 37,200 redundant, recombinant human proteins. The data sets obtained from incubations with patient sera were compared with control sera from clinically healthy persons and to background incubations with anti-human IgG antibodies. From these results, a smaller protein subset was generated and subjected to qualitative and quantitative validation on highly sensitive protein microarrays to identify novel alopecia areata-associated autoantigens. Eight autoantigens were identified by protein chip technology and were successfully confirmed by Western blot analysis. These autoantigens were arrayed on protein microarrays to generate a disease-associated protein chip. To confirm the specificity of the results obtained, sera from patients with psoriasis or hand and foot eczema as well as skin allergy were additionally examined on the disease-associated protein chip. By using alopecia areata as a model for an autoimmune disease, our investigations show that the protein microarray technology has potential for the identification and evaluation of autoantigens as well as in diagnosis such as to differentiate alopecia areata from other skin diseases.
Sera from patients with systemic lupus erythematosus contain specific autoantibodies directed against different polypeptide components of the multicatalytic proteinase (also known as proteasome or prosome). These human autoantibodies, in contrast to polyclonal antibodies obtained in rabbits against the purified enzyme, recognize highly conserved epitopes of the multicatalytic proteinase polypeptides from yeast to human.
Sera from patients with systemic lupus erythematosus contain specific autoantibodies directed against different polypeptide components of the multicatalytic proteinase (also known as proteasome or prosome). These human autoantibodies, in contrast to polyclonal antibodies obtained in rabbits against the purified enzyme, recognize highly conserved epitopes of the multicatalytic proteinase polypeptides from yeast to human.
In order to examine the mechanisms by which clonal deletion of autoreactive T cells occurs, a peptide antigen was used to
induce deletion of antigen-reactive thymocytes in vivo. Mice transgenic for a T cell receptor (TCR) that reacts to this peptide
contain thymocytes that progress from the immature to the mature phenotype. Intraperitoneal administration of the peptide
antigen to transgenic mice results in a rapid deletion of the immature CD4+ CD8+ TCRlo thymocytes. Apoptosis of cortical thymocytes
can be seen within 20 hours of treatment. These results provide direct evidence for the in vivo role of apoptosis in the development
of antigen-induced tolerance.
Monoclonal antibodies against murine immune interferon (IFN-gamma) were produced by fusing the murine nonsecreting myeloma cell line P3.X63.Ag8.653 with spleen cells from rats immunized with IFN-gamma-containing supernatants obtained by stimulating a T-cell lymphoma, L12-R4, with phorbol 12-myristate 13-acetate. Supernatants from a twice-cloned hybridoma (AN-18.17.24) were found to neutralize and to adsorb in depletion experiments up to 27 units of mouse IFN-gamma but not equivalent amounts of mouse leukocyte or fibroblast IFNs. The AN-18.17.24 monoclonal antibody neutralized to the same extent mouse IFN-gamma from different sources--namely, (i) concanavalin A-stimulated spleen cells, (ii) alloantigen-stimulated spleen cells, and (iii) monkey fibroblasts transfected with the cloned gene of murine IFN-gamma. Moreover, the monoclonal antibody displayed species specificity, since it did not neutralize IFN-gamma of human origin. Binding inhibition experiments with murine IFN-gamma preparations exposed to enzymatic or physicochemical degradation demonstrated that the protein moiety and not the carbohydrate residues were responsible for the binding to the AN-18.17.24 monoclonal antibody. Finally, this monoclonal antibody immunoprecipitated two molecular species of IFN-gamma of about 16.8 and 17.8 kilodaltons, respectively, from [35S]methionine- or [3H]glucosamine-labeled supernatants of stimulated L12-R4 cells.
The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons,
a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST
programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering
the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program
that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining
statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using
this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration
as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST
is used to uncover several new and interesting members of the BRCT superfamily.
We have developed a technique to establish catalogues of protein products of arrayed cDNA clones identified by DNA hybridisation
or sequencing. A human fetal brain cDNA library was directionally cloned in a bacterial vector that allows IPTG-inducible
expression of His6-tagged fusion proteins. Using robot technology, the library was arrayed in microtitre plates and gridded
onto high-density in situ filters. A monoclonal antibody recognising the N-terminal RGSH6 sequence of expressed proteins (RGS·His antibody, Qiagen) detected 20% of the library as putative expression clones. Two
example genes, GAPDH and HSP90α, were identified on high-density filters using DNA probes and antibodies against their proteins.
The in vitro cloning of DNA molecules traditionally uses PCR amplification or site-specific restriction endonucleases to generate linear DNA inserts with defined termini and requires DNA ligase to covalently join those inserts to vectors with the corresponding ends. We have used the properties of Vaccinia DNA topoisomerase I to develop a ligase-free technology for the covalent joining of DNA fragments to suitable plasmid vectors. This system is much more efficient than cloning methods that require ligase because the rapid DNA rejoining activity of Vaccinia topoisomerase I allows ligation in only 5 min at room temperature, whereas the enzyme's high substrate specificity ensures a low rate of vector-alone transformants. We have used this topoisomerase I-mediated cloning technology to develop a process for accelerated cloning and expression of individual ORFs. Its suitability for genome-scale molecular cloning and expression is demonstrated in this report.
We have developed a novel protein chip technology that allows the high-throughput analysis of biochemical activities, and used this approach to analyse nearly all of the protein kinases from Saccharomyces cerevisiae. Protein chips are disposable arrays of microwells in silicone elastomer sheets placed on top of microscope slides. The high density and small size of the wells allows for high-throughput batch processing and simultaneous analysis of many individual samples. Only small amounts of protein are required. Of 122 known and predicted yeast protein kinases, 119 were overexpressed and analysed using 17 different substrates and protein chips. We found many novel activities and that a large number of protein kinases are capable of phosphorylating tyrosine. The tyrosine phosphorylating enzymes often share common amino acid residues that lie near the catalytic region. Thus, our study identified a number of novel features of protein kinases and demonstrates that protein chip technology is useful for high-throughput screening of protein biochemical activity.
To facilitate studies of the yeast proteome, we cloned 5800 open reading frames and overexpressed and purified their corresponding proteins. The proteins were printed onto slides at high spatial density to form a yeast proteome microarray and screened for their ability to interact with proteins and phospholipids. We identified many new calmodulin- and phospholipid-interacting proteins; a common potential binding motif was identified for many of the calmodulin-binding proteins. Thus, microarrays of an entire eukaryotic proteome can be prepared and screened for diverse biochemical activities. The microarrays can also be used to screen protein-drug interactions and to detect posttranslational modifications.
We developed a high-throughput technique for the generation of cDNA libraries in the yeast Saccharomyces cerevisiae which enables the selection of cloned cDNA inserts containing open reading frames (ORFs). For direct screening of random-primed cDNA libraries, we have constructed a yeast shuttle/expression vector, the so-called ORF vector pYEXTSH3, which allows the enriched growth of protein expression clones. The selection system is based on the HIS3 marker gene fused to the C terminus of the cDNA insert. The cDNAs cloned in-frame result in histidine prototrophic yeast cells growing on minimal medium, whereas clones bearing the vector without insert or out-of-frame inserts should not grow on this medium. A randomly primed cDNA library from human fetal brain tissue was cloned in this novel vector, and using robot technology the selected clones were arrayed in microtiter plates and were analyzed by sequencing and for protein expression. In the constructed cDNA expression library, about 60% of clones bear an insert in the correct reading frame. In comparison to unselected libraries it was possible to increase the clones with inserts in the correct reading frame more than fourfold, from 14% to 60%. With the expression system described here, we could avoid time-consuming and costly techniques for identification of clones expressing protein by using antibody screening on high-density filters and subsequently rearraying the selected clones in a new "daughter" library. The advantage of this ORF vector is that, in a one-step screening procedure, it allows the generation of expression libraries enriched for clones with correct reading frames as sources of recombinant proteins.
We constructed miniaturized autoantigen arrays to perform large-scale multiplex characterization of autoantibody responses directed against structurally diverse autoantigens, using submicroliter quantities of clinical samples. Autoantigen microarrays were produced by attaching hundreds of proteins, peptides and other biomolecules to the surface of derivatized glass slides using a robotic arrayer. Arrays were incubated with patient serum, and spectrally resolvable fluorescent labels were used to detect autoantibody binding to specific autoantigens on the array. We describe and characterize arrays containing the major autoantigens in eight distinct human autoimmune diseases, including systemic lupus erythematosus and rheumatoid arthritis. This represents the first report of application of such technology to multiple human disease sera, and will enable validated detection of antibodies recognizing autoantigens including proteins, peptides, enzyme complexes, ribonucleoprotein complexes, DNA and post-translationally modified antigens. Autoantigen microarrays represent a powerful tool to study the specificity and pathogenesis of autoantibody responses, and to identify and define relevant autoantigens in human autoimmune diseases.
Systemic lupus erythematosus (SLE) is inherited as a complex polygenic trait. (New Zealand Black (NZB) x New Zealand White (NZW)) F(1) hybrid mice develop symptoms that remarkably resemble human SLE, but (NZB x PL/J)F(1) hybrids do not develop lupus. Our study was conducted using (NZW x PL/J)F(1) x NZB (BWP) mice to determine the effects of the PL/J and the NZW genome on disease. Forty-five percent of BWP female mice had significant proteinuria and 25% died before 12 mo of age compared with (NZB x NZW)F(1) mice in which >90% developed severe renal disease and died before 12 mo. The analysis of BWP mice revealed a novel locus (chi(2) = 25.0; p < 1 x 10(-6); log of likelihood = 6.6 for mortality) designated Wbw1 on chromosome 2, which apparently plays an important role in the development of the disease. We also observed that both H-2 class II (the u haplotype) and TNF-alpha (TNF(z) allele) appear to contribute to the disease. A suggestive linkage to proteinuria and death was found for an NZW allele (designated Wbw2) telomeric to the H-2 locus. The NZW allele that overlaps with the previously described locus Sle1c at the telomeric part of chromosome 1 was associated with antinuclear autoantibody production in the present study. Furthermore, the previously identified Sle and Lbw susceptibility loci were associated with an increased incidence of disease. Thus, multiple NZW alleles including the Wbw1 allele discovered in this study contribute to disease induction, in conjunction with the NZB genome, and the PL/J genome appears to be protective.
The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.
Molecular cloning, sequencing of the human genome, and other major advances in biomedical research have contributed substantially to our understanding of autoimmune disease. Nevertheless, to date, such advances have failed to reveal the etiology of or yield curative therapies for autoimmune disease. New approaches are needed. Proteomics, the large-scale study of expression and function of proteins that compose our tissues and mediate disease, represents a powerful and promising strategy. We developed protein and peptide arrays to profile autoantibody responses in autoimmune disease. Protein and peptide array analysis of autoimmune samples is revealing human and pathogen proteins involved in initiation and perpetuation of autoimmunity. Proteomic determination of autoantibody profiles can be utilized for diagnosis, prognostication, and guiding tolerizing therapy for autoimmune disease.
To verify the genome annotation and to create a resource to functionally characterize the proteome, we attempted to Gateway-clone all predicted protein-encoding open reading frames (ORFs), or the 'ORFeome,' of Caenorhabditis elegans. We successfully cloned approximately 12,000 ORFs (ORFeome 1.1), of which roughly 4,000 correspond to genes that are untouched by any cDNA or expressed-sequence tag (EST). More than 50% of predicted genes needed corrections in their intron-exon structures. Notably, approximately 11,000 C. elegans proteins can now be expressed under many conditions and characterized using various high-throughput strategies, including large-scale interactome mapping. We suggest that similar ORFeome projects will be valuable for other organisms, including humans.
There is burgeoning interest in protein microarrays, but a source of thousands of nonredundant, purified proteins was not previously available. Here we show a glass chip containing 2413 nonredundant purified human fusion proteins on a polymer surface, where densities up to 1600 proteins/cm(2) on a microscope slide can be realized. In addition, the polymer coating of the glass slide enables screening of protein interactions under nondenaturing conditions. Such screenings require only 200-microl sample volumes, illustrating their potential for high-throughput applications. Here we demonstrate two applications: the characterization of antibody binding, specificity, and cross-reactivity; and profiling the antibody repertoire in body fluids, such as serum from patients with autoimmune diseases. For the first application, we have incubated these protein chips with anti-RGSHis(6), anti-GAPDH, and anti-HSP90beta antibodies. In an initial proof of principle study for the second application, we have screened serum from alopecia and arthritis patients. With analysis of large sample numbers, identification of disease-associated proteins to generate novel diagnostic markers may be possible.
A critical role for the conserved alpha-integrin cytoplasmic motif, KVGFFKR, is recognized in the regulation of activation of the platelet integrin alpha(IIb)beta(3). To understand the molecular mechanisms of this regulation, we sought to determine the nature of the protein interactions with this cytoplasmic motif. We used a tagged synthetic peptide, biotin-KVGFFKR, to probe a high density protein expression array (37,200 recombinant human proteins) for high affinity interactions. A number of potential integrin-binding proteins were identified. One such protein, a chloride channel regulatory protein, ICln, was characterized further because its affinity for the integrin peptide was highest as was its expression in platelets. We verified the presence of ICln in human platelets by PCR, Western blots, immunohistochemistry, and its co-association with alpha(IIb)beta(3) by surface plasmon resonance. The affinity of this interaction was 82.2 +/- 24.4 nm in a cell free assay. ICln co-immunoprecipitates with alpha(IIb)beta(3) in platelet lysates demonstrating that this interaction is physiologically relevant. Furthermore, immobilized KVGFFKR peptides, but not control KAAAAAR peptides, specifically extract ICln from platelet lysates. Acyclovir (100 microm to 5 mm), a pharmacological inhibitor of the ICln chloride channel, specifically inhibits integrin activation (PAC-1 expression) and platelet aggregation without affecting CD62 P expression confirming a specific role for ICln in integrin activation. In parallel, a cell-permeable peptide corresponding to the potential integrin-recognition domain on ICln (AKFEEE, 10-100 microm) also inhibits platelet function. Thus, we have identified, verified, and characterized a novel functional interaction between the platelet integrin and ICln, in the platelet membrane.
Protein array technology has emerged as a new tool to enable ordered screening of proteins for expression and molecular interactions in high throughput. Besides classical solid-phase substrates, such as micro-titre plates and membrane filters, protein arrays have recently been devised with chip-sized supports. Several applications on protein chips have been described, but to our knowledge no studies using plant protein chips were published so far.
The aim of this study was to generate Arabidopsis protein chips and to demonstrate the feasibility of the protein chip technology for the investigation of antigen-antibody interactions. Therefore, Arabidopsis cDNAs encoding 95 different proteins were cloned into a GATEWAY-compatible Escherichia coli expression vector. RGS-His6-tagged recombinant proteins were purified in high throughput and robotically arrayed onto glass slides coated either with a nitrocellulose based polymer (FAST slides) or polyacrylamide (PAA slides). Using an anti-RGS-His6 antibody all proteins were detected on the chips. The detection limit was ca. 2–3.6 fmol per spot on FAST slides or 0.1–1.8 fmol per spot on PAA slides. The Arabidopsis protein chips were used for the characterisation of monoclonal antibodies or polyclonal sera. We were able to show that a monoclonal anti-TCP1 antibody and anti-MYB6 and anti-DOF11 sera bound specifically to their respective antigens and did not cross-react with the other 94 proteins including other DOF and MYB transcription factors on the chips. To enable screening of antibodies or other interacting molecules against thousands of Arabidopsis proteins in future, we generated an ordered cDNA expression library and started with high-throughput cloning of full-length cDNAs with GATEWAY technology.
Autoantibodies occur in low frequencies among patients with myositis characterizing only distinct subsets of this disease. Most of these known antibodies are directed to enzymatically active complexes. The 20S proteasome represents an essential cytoplasmatic protein complex for intracellular nonlysosomal protein degradation, and is involved in major histocompatibility complex class I restricted antigen processing. In this study we investigated whether the 20S proteasome complex is an antibody target in myositis and in other autoimmune diseases. 34 sera of poly/dermatomyositis patients were assayed for antiproteasomal antibodies using enzyme-linked immunosorbent assay, immunoblot, and two-dimensional non-equilibrium pH gradient electrophoresis (NEPHGE). Sera was from patients with systemic lupus erythematosus (SLE), mixed connective tissue disease, and rheumatoid arthritis; healthy volunteers served as controls. In 62% (21/34) of the cases sera from patients with myositis and in 58% (30/52) of the cases sera from patients with SLE reacted with the 20S proteasome. These frequencies exceeded those of sera from patients with mixed connective tissue disease, rheumatoid arthritis, and healthy controls. The alpha-type subunit C9 of the 20S proteasome was determined to be the predominant target of the autoimmune sera in myositis and SLE. Lacking other frequent autoantibodies in myositis, the antiproteasome antibodies are the most common humoral immune response so far detected in this disease entity.
A staggering amount of genetic information is contained within the DNA of complex organisms such as humans. Of these vast tracts of DNA code, only very small regions actually constitute the 'genes'; with the information ultimately translated into proteins, the basic machinery of cells. However, a complex organism has a cell or tissue type and developmental specific pattern of gene expression which interact in complex networks within and between these cells or tissues. Such a combination of vast tracts of genomic DNA, tissue and developmental specific transcription of small subsets of this information, plus complex interactions between gene products provides a daunting scientific and logistical challenge if a global picture of gene function within complex organisms is to be obtained. This objective can be achieved only through an interdisciplinary combination of biology, computer image analysis, and robotic engineering. The development of a global approach to the understanding of complex genomes is not just an academic challenge. For example, the ability to understand the complex network of gene interactions, or to be able rapidly to screen many genetic samples in parallel, would have enormous consequences for the pharmaceutical and diagnostic industries. The systems described are used in several genetic screening or drug discovery centres that require rapid, reliable, high density screening of small quantities of biological or biologically active material.
A simple method for generating cDNA libraries from submicrogram quantities of mRNA is describe. It combines classical first-stand synthesis with the novel RNase H-DNA polymerase I-mediated second-strand synthesis [Okayama, H., and Berg, P., Mol. Cell. Biol. 2 (1982) 161–170]. Neiher the elaborate vector-primer system nor the classical hairpin loop cleavage by S1 nuclease are used. cDNA thus made can be tailed and cloned without further purification or sizing. Cloning efficiencies can be as high as 106 recombinants generated per μg mRNA, a considerable improvement over earlier methods. Using the fully sequenced1300 nucleotide-long bovine preproenkephalin mRNA, we have established by sequencing that the method yields faithful full-length transcripts. This procedure considerably simplifies the establishment of cDNA libraries and thus the cloning of low-abundance mRNAs.
Protein interaction mapping using large-scale two-hybrid analysis has been proposed as a way to functionally annotate large numbers of uncharacterized proteins predicted by complete genome sequences. This approach was examined in Caenorhabditis elegans, starting with 27 proteins involved in vulval development. The resulting map reveals both known and new potential interactions and provides a functional annotation for approximately 100 uncharacterized gene products. A protein interaction mapping project is now feasible for C. elegans on a genome-wide scale and should contribute to the understanding of molecular mechanisms in this organism and in human diseases.
We have observed that proteins, such as human tissue-type plasminogen activator, pro-urokinase or gp41 of human immunodeficiency virus, which have a high content of rare codons in their respective genes, are not readily expressed in Escherichia coli. Furthermore induction of these heterologous genes leads to growth inhibition and plasmid instability. Supplementation with tRNA(AGA/AGG(Arg)) by cotransfection with the dnaY gene, which supplies this minor tRNA, resulted in high-level production with greatly improved cell viability and plasmid stability.
B-cell stimulatory factor-1 (BSF-1), formerly designated B-cell growth factor, is a T-cell-derived factor required for entry into the S phase of the cell cycle by B cells stimulated with low concentrations of anti-IgM antibodies. BSF-1 acts directly on resting B cells to prepare them to synthesize DNA more promptly on subsequent exposure to competent stimuli and to strikingly enhance their expression of class II molecules of the major histocompatibility complex. Previous studies have shown that murine BSF-1 can be separated physically from interleukin-2 (IL-2) and that the molecule has an apparent relative molecular mass (Mr) of approximately 15,000 and pI values of 6.4-6.7 and 7.4. Here, we report the production of a monoclonal antibody to BSF-1, its use in characterizing BSF-1, and functional studies demonstrating that this molecule is distinct from IL-1, IL-2 and IL-3.
SLE is a syndrome characterized by diverse clinical signs and symptoms, including rash, serositis, nephritis, central nervous system disease, thrombocytopenia, and leukopenia. These and other manifestations are present in patients with immune abnormalities indicative of B cell hyperactivity: hypergammaglobulinemia, increased amounts of antibodies reactive with self-determinants (characteristically including nuclear antigens), and increased numbers of circulating antibody-producing cells. It is this immune hyperactivity, inclusive of anti-self responses, which groups the patients with diverse clinical manifestations into a single syndrome called lupus.
A novel nitrilotriacetic acid adsorbent has been prepared for metal chelate affinity chromatography. The new resin is a quadridentate chelate former and specially suitable for metal ions with coordination numbers of six, since two valencies remain for the reversible binding of biopolymers. It has been found to chelate Cu2+ and Ni2+ strongly and to be superior to the known iminodiacetic acid adsorbent. Charged with Ni2+, it was evaluated for the ability to bind peptides and proteins containing neighbouring histidine residues. The remarkable specificity found makes it an attractive addition to the range of adsorbents for metal chelate affinity chromatography.
In an immune response, effector functions are controlled by T helper (Th) 1 cytokines [interferon-gamma (IFN-gamma), interleukin (IL)-2 and tumor necrosis factor-beta] and Th2 cytokines (IL-4, IL-5 and IL-10). Here we analyze by multiparameter immunofluorescence to what extent IL-2, IL-4, IL-5, IL-10 and IFN-gamma are co-expressed in individual normal murine Th cells upon activation in vitro with the bacterial superantigen Staphylococcus aureus enterotoxin B, presented in the context of major histocompatibility complex class II. IL-2 and IFN-gamma are co-expressed by some, but not by other Th cells. Expression of IL-4 and IFN-gamma is exclusive. IL-10 is co-expressed in individual cells either with IL-4 or with IFN-gamma. No IL-5-expressing cells are detected. While IL-10- and IL-4-co-expressing Th cells correspond to classical Th 2 cells, cells co-expressing IL-10 and IFN-gamma could be involved in negative-feedback regulation of a Th1 response. Apart from such functional implications, our results show that IL-2, IL-4, IL-5, IL-10 and IFN-gamma are expressed independently of each other in individual murine Th cells.
Proteins translate genomic sequence information into function, enabling biological processes. As a complementary approach to gene expression profiling on cDNA microarrays, we have developed a technique for high-throughput gene expression and antibody screening on chip-size protein microarrays. Using a picking/spotting robot equipped with a new transfer stamp, protein solutions were gridded onto polyvinylidene difluoride filters at high density. Specific purified protein was detected on the filters with high sensitivity (250 amol or 10 pg of a test protein). On a microarray made from bacterial lysates of 92 human cDNA clones expressed in a microtiter plate, putative protein expressors could be reliably identified. The rate of false-positive clones, expressing proteins in incorrect reading frames, was low. Product specificity of selected clones was confirmed on identical microarrays using monoclonal antibodies. Cross-reactivities of some antibodies with unrelated proteins imply the use of protein microarrays for antibody specificity screening against whole libraries of proteins. Because this application would not be restricted to antigen-antibody systems, protein microarrays should provide a general resource for high-throughput screens of gene expression and receptor-ligand interactions.
For any attempt to understand the biology of an organism the incorporation of a cDNA-based approach is unavoidable, because it is a major approach to studying gene function. The complete sequence of the genome alone is not sufficient to understand any organism; its gene regulation, expression, splice variation, posttranslational modifications, and proteinprotein interactions all need to be addressed. Because the majority of vertebrate genes have probably been identified as ESTs44,52 the next stage of the Human Genome Project is attributing functional information to these sequences. In most cases hybridization-based approaches on arrayed pieces of DNA represent the most efficient way to study the expression level and splicing of a gene in a given tissue. Similar technology, now being applied at the protein level using protein expression libraries, high-density protein membranes, and antibody screening, should allow studies of protein localization and modifications.
We have constructed a human fetal brain cDNA library in an Escherichia coli expression vector for high-throughput screening of recombinant human proteins. Using robot technology, the library was arrayed in microtiter plates and gridded onto high-density filter membranes. Putative expression clones were detected on the filters using an antibody against the N-terminal sequence RGS-His(6) of fusion proteins. Positive clones were rearrayed into a new sublibrary, and 96 randomly chosen clones were analyzed. Expression products were analyzed by SDS-PAGE, affinity purification, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry, and the determined protein masses were compared to masses predicted from DNA sequencing data. It was found that 66% of these clones contained inserts in a correct reading frame. Sixty-four percent of the correct reading frame clones comprised the complete coding sequence of a human protein. High-throughput microtiter plate methods were developed for protein expression, extraction, purification, and mass spectrometric analyses. An enzyme assay for glyceraldehyde-3-phosphate dehydrogenase activity in native extracts was adapted to the microtiter plate format. Our data indicate that high-throughput screening of an arrayed protein expression library is an economical way of generating large numbers of clones producing recombinant human proteins for structural and functional analyses.
Antibodies are used extensively as diagnostic tools in a wide array of different analyses. Monoclonal and recombinant antibodies provide a never ending source of molecules and can produce endless possibilities for novel genetic constructs. Antibodies are still very much in vogue and are now also being used in microarray analysis of the proteome using protein chips. Here, recent opportunities presented by antibodies as diagnostic tools are reviewed.
We have constructed a novel Pichia pastoris/Escherichia coli dual expression vector for the production of recombinant proteins in both host systems. In this vector, an E. coli T7 promoter region, including the ribosome binding site from the phage T7 major capsid protein for efficient translation is placed downstream from the yeast alcohol oxidase promoter (AOX). For detection and purification of the target protein, the vector contains an amino-terminal oligohistidine domain (His6) followed by the hemaglutinine epitope (HA) adjacent to the cloning sites. A P. pastoris autonomous replicating sequence (PARS) was integrated enabling simple propagation and recovery of plasmids from yeast and bacteria (1). In the present study, the expression of human proteins in P. pastoris and E. coli was compared using this single expression vector. For this purpose we have subcloned a cDNA expression library deriving from human fetal brain (2) into our dual expression T7 vector and investigated 96 randomly picked clones. After sequencing, 29 clones in the correct reading frame have been identified, their plasmids isolated and shuttled from yeast to bacteria. All proteins were expressed soluble in P. pastoris, whereas in E. coli only 31% could be purified under native conditions. Our data indicates that this dual expression vector allows the economic expression and purification of proteins in different hosts without subcloning.
Identification of immunogenic leukemia-associated antigens as target structures is mandatory for specific immunotherapy of leukemia. Here, we define acute myeloid leukemia (AML) antigens eliciting a humoral immune response in the autologous host. We applied the method of serologic screening of cDNA expression libraries with autologous serum (SEREX). To date, this technique has been used to characterize antigen structures in solid tumors. The mRNA expression pattern of these newly in AML isolated antigens and previously described leukemia antigens (PRAME, MAGE-1, and Wt-1) was evaluated by reverse transcriptase polymerase chain reaction. For Wt-1, Western blotting also was performed. Screening of a cDNA expression library prepared from a patient with AML FAB M2 using autologous and allogeneic sera, followed by sequencing of positive clones, yielded three autoantigens (Prp1p/Zer1p, L19H1, and one without homology to previously described genes) and two antigens reactive with allogeneic sera (MAZ, PINCH). PRAME mRNA was expressed in 47% of 34 AML patients, but not in 13 CD34(+) cell samples or in peripheral blood mononuclear cells of 13 healthy volunteers. mRNA expression of MAZ was detected in 44% of AML patients, but only in 8% of healthy donors. Humoral responses to MAZ were detected in 35%. More than 80% of the screened AML patients showed simultaneous expression of two or more of these antigens.Differential expression in AML patients vs healthy volunteers suggests that the immunogenic antigens PRAME and MAZ are potential candidates for immunotherapy in AML.
We describe the technical feasibility and methodology to characterize a protein by a minimal set of structural information generated by matrix assisted laser desorption/ionization (MALDI)-mass spectrometry, termed a "minimal protein Identifier" (MPI). MPIs can be determined for proteins from two-dimensional gels and recombinant proteins and can be used to compare and identify proteins from these sources.
Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by the presence of antinuclear antibodies. We performed serological analysis of cDNA expression library (SEREX) to identify autoantibodies associated with SLE. The screening of three different cDNA expression libraries with pooled sera of patients with SLE yielded 11 independent clones that reacted with pooled sera of patients with SLE. In this screening, autoantibodies to poly(ADP-ribose) polymerase (PARP), U1snRNP, and galectin-3 were prevalent in the sera of patients with SLE (26/68, 25/68, 12/63, respectively). The frequency of autoantibody to PARP was significantly higher in SLE than that of healthy donors (0/76) (38.2% vs 0%, p<0.00001). The autoantibody to PARP was infrequently detected in the serum of patients with RA (1/50). However, autoantibody to PARP was not found in the sera of patients with other rheumatic diseases including Sjogren's syndrome (0/19), systemic sclerosis (0/18), and polymyositis/myositis (0/37). The frequency of autoantibody to human galectin-3 (12/63) was significantly higher in SLE than that of healthy donors (0/56) (19% vs 0%, p=0.0006). Autoantibody to galectin-3 was not found in the sera of patients with rheumatoid arthritis (0/50), Sjogren's syndrome (0/18), and systemic sclerosis (0/19). Interestingly, autoantibody to galectin-3 was also prevalent in the sera of patients with polymyositis/dermatomyositis (16/37, 43.2%). Further functional characterization of these autoantibodies would be necessary to determine their value as diagnostic markers or to define clinical subsets of patients with SLE. Statistical analysis revealed that the presence of autoantibody to PARP was inversely related with pleurisy, and the presence of autoantibody to galectin-3 related with renal disease.
The 6th International Conference of Immunotherapy of the Rheumatic Diseases was held in Limassol, Cyprus, May 15–18 2002.
The mouse is the premier genetic model organism for the study of human disease and development. With the recent advances in sequencing of the human and mouse genomes, there is strong interest now in large-scale approaches to decipher the function of mouse genes using various mutagenesis technologies. This review discusses what tools are currently available for manipulating and mutagenizing the mouse genome, such as ethylnitrosourea and gene trap mutagenesis, engineered inversions and deletions using the cre-lox system, and proviral insertional mutagenesis in somatic cells, and how these are being used to uncover gene function.
We compared the clinical sensitivity and specificity of three different methods for the detection of serum antiribosomal P protein (anti-P) antibodies in systemic lupus erythematosus (SLE). Sera from 60 unselected SLE patients, 100 healthy subjects and 100 patients with other rheumatic inflammatory diseases were screened for anti-P antibodies by immunoblotting (IB) on P proteins from Raji cells and by two ELISA assays, one using the C-terminal 22 aminoacid long synthetic peptide (C-22) of P proteins, the other using a multiple antigen peptide (MAP) carrying four copies of the C-terminal 13 aminoacid long P peptide.Anti-P antibodies were found in 20% lupus sera by IB, 16.7% by MAP ELISA and 11.7% by C-22 ELISA. The specificity for SLE diagnosis of the three tests in healthy subjects and other rheumatic diseases was: 100% by IB, 100% (vs healthy subjects) and 97% (vs rheumatic diseases) by C-22 ELISA, 100% by MAP ELISA. The agreement between methods was good; differences in concordance rates were restricted to weak positivities. We observed a high concordance in the results of IB and ELISA methods for anti-P antibody detection. IB on P proteins extracted from human lymphoid cells is more sensitive than both ELISAs; IB and MAP ELISA perform better than the C-22 ELISA in determining weakly positive sera.
The 20S proteasome plays a leading immunologic role in the cytosolic generation of MHC class I restricted antigens, and it represents an abundant antigen in several autoimmune diseases. To investigate the effects of autoimmune inflammatory and perioperative traumatic cellular damage, we determined qualitative and quantitative properties of released proteasomes (circulating proteasomes, cProteasomes) from serum samples of patients with a variety of autoimmune diseases.
cProteasomes were analyzed from serum samples of 314 patients with several systemic and organ-specific autoimmune diseases and 85 healthy controls. The concentrations of cProteasomes were determined by sandwich ELISA using a monoclonal and a polyclonal proteasome-specific antibody. Followup analyses were performed in patients with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) as well as in patients with myasthenia gravis undergoing thoracoscopic thymectomy.
Strongly increased levels of cProteasomes (> 1000 ng/ml) were detected in samples obtained from patients with autoimmune myositis, SLE, primary Sjögren's syndrome, RA, and autoimmune hepatitis. Significant differences were observed in the mean values of cProteasomes comparing systemic with organ-specific autoimmune diseases. Followup analyses revealed a close correlation of cProteasome with the autoimmune process as well as cellular damage. Moreover, cProteasomes were isolated in intact and native as well as in degraded or dissociated forms from the serum samples. The immuno-subunit LMP7 was found to be incorporated in the circulating protease complex.
Levels of cProteasomes are markedly elevated in patients with systemic autoimmune diseases, apparently correlating with disease activity. The cProteasomes represent novel sensitive markers of the autoimmune inflammatory processes and/or reflect the magnitude of cellular damage.
Antibodies specific for ribosomal P proteins (anti-P) are a hallmark of systemic lupus as anti-DNA antibodies are. It has been reported that anti-P antibodies are more frequently detected in anti-dsDNA positive sera. The aim of the present study was to verify the binding ability of anti-P antibodies towards polynucleotides and nucleosomes. We purified anti-P antibodies from 8 SLE patients' sera and we analysed them by ELISA on plates coated with DNA or nucleosomes. We performed also inhibition experiments in order to verify the specificity of the binding. All the purified anti-P antibodies bound DNA, but some anti-DNA binding activity remained among the non-anti-P antibodies in the flow through. Only half of the purified antibodies bound to nucleosomes, and anti-nucleosomal activity was demonstrated also in non anti-P antibody fraction. The inhibition experiments performed on two anti-P antibodies pointed out that only the homologous antigen inhibited the binding to either P peptide or DNA coated onto the solid phase. These results show that sera in which the two specificities coexist contain antibodies endowed with a double binding ability for DNA and the P peptide.
To assess the specificity of autoantibodies (aAbs) directed against the ribosomal P-proteins (RPPaAbs) in patients with systemic lupus erythematosus (SLE) and to investigate aAbs directed to other ribosomal proteins, 100 SLE, 100 rheumatoid arthritis (RA), 25 thyroiditis and 20 blood-donors were analyzed in a comparative study using an immunoblotting technique. Forty-eight percent of SLB sera contained aAbs directed against the ribosomal proteins of the 60 S subunit compared to 9% for RA, 5% for blood donors and 0% for thyroiditis. RPPaAbs were only found in SLE (25%) and aAbs directed to a 31 kDa and/or a 28 kDa protein of the 60 S subunit were found with a statistically higher frequency for SLE compared to RA (p < 0.0001). aAbs directed to proteins of the 40 S subunit were present in 63% of the SLE sera compared to 42% for RA, 4% for thyroiditis and 5% for blood donors. The number of positive sera was not statistically different between SLE and RA but a much more intense reactivity was observed for SLE sera. These data shows that the aAbs against the ribosomal proteins, especially the P-proteins along with the 28 and 31 kDa proteins of the 60 S subunit proteins, can be considered as useful biological markers for t he diagnosis of SLE inclinical practice.
We previously reported that autoantibodies (autoAbs) to the main epitope on CD69 reacted to its homologous amino acid sequence in low-density-lipoprotein-receptor-related protein 2 (LPR2), a multiligand receptor for protein reabsorption. In this study, we have investigated the prevalence, autoepitope distribution, and clinical significance of the autoAbs to LRP2 in patients with systemic autoimmune diseases. Using six recombinant proteins (F2-F7) for LRP2 and one for CD69, we detected autoAbs to LRP2 in sera of patients with rheumatoid arthritis (RA), systemic lupus erythematosus, Behçet's disease, systemic sclerosis, and osteoarthritis and then mapped autoepitopes by Western blotting. The autoAbs to LRP2 were detected in 87% of the patients with rheumatoid arthritis, 40% of those with systemic lupus erythematosus, 35% of those with systemic sclerosis, 15% of those with osteoarthritis, and 3% of those with Behçet's disease. Multiple epitopes on LRP2 were recognized by most of the anti-LRP2+ serum samples. All of the tested anti-CD69 autoAb+ samples reacted to LRP2-F3 containing the homologous sequence to the main epitope of CD69; however, only 38% of the anti-LRP2-F3+ samples reacted to CD69. Clinically, the existence of the autoAbs to LRP2-F4, -F5, and -F6 correlated with the presence of proteinuria in RA. This study revealed that LRP2 is a major autoantigen in RA. The autoAbs to LRP2 are probably produced by the antigen-driven mechanism and the autoimmunity to LRP2 may spread to include CD69. The anti-LRP2 autoAbs may play pathological roles by inhibiting the reabsorbing function of LRP2.
Protein arrays provide a powerful approach to study autoimmune disease. Autoimmune responses activate B cells to produce autoantibodies that recognize self-molecules termed autoantigens, many of which are proteins or protein complexes. Protein arrays enable profiling of the specificity of autoantibody responses against panels of peptides and proteins representing known autoantigens as well as candidate autoantigens. In addition to identifying autoantigens and mapping immunodominant epitopes, proteomic analysis of autoantibody responses will further enable diagnosis, prognosis, and tailoring of antigen-specific tolerizing therapy.
To functionally characterize numerous novel proteins encoded by cDNAs sequenced by the German Consortium, 800 were tagged with green fluorescent protein. The subcellular localizations of the fusion proteins were examined in living cells, enabling their classification in subcellular groups. Their activity in cell growth, cell death, and protein transport was screened in high throughput using robotic liquid handling and reading stations. The resulting information is integrated with functional genomics and proteomics data for further understanding of protein functions in the cellular context.
Colony blot procedure
- Anon
Anon, Colony blot procedure, The QIAexpressionist, 3rd ed., Qiagen, Hilden, Germany, 1997, pp. 31 – 35.
Bridging genomics and proteomics
- Cahill
Robotics, computing, and biology
- Lehrach