Proteomics technologies for the study of autoimmune disease

Proteomics in support of immunotherapy: contribution to model-based precision medicine

INTRODUCTION

Proteomics encompasses a wide and expanding range of methods to identify, characterize, and quantify thousands of proteins from a variety of biological samples, including blood samples, tumors, and tissues. Such methods are supportive of various forms of immunotherapy applied to chronic conditions such as allergies, autoimmune diseases, cancers, and infectious diseases.

AREAS COVERED

In support of immunotherapy, proteomics based on mass spectrometry has multiple specific applications related to (i) disease modeling and patient stratification, (ii) antigen/ autoantigen/neoantigen/ allergen identification, (iii) characterization of proteins and monoclonal antibodies used for immunotherapeutic or diagnostic purposes, (iv) identification of biomarkers and companion diagnostics and (v) monitoring by immunoproteomics of immune responses elicited in the course of the disease or following immunotherapy.

EXPERT OPINION

Proteomics contributes as an enabling technology to an evolution of immunotherapy toward a precision medicine approach aiming to better tailor treatments to patients' specificities in multiple disease areas. This trend is favored by a better understanding through multi-omics profiling of both the patient's characteristics, his/her immune status as well as of the features of the immunotherapeutic drug.

Predictive value of autoantibodies for activity of systemic lupus erythematosus

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.

Role of autoimmune responses in periodontal disease

Periodontal diseases are characterized by localized infections and inflammatory conditions that directly affect teeth supporting structures which are the major cause of tooth loss. Several studies have demonstrated the involvement of autoimmune responses in periodontal disease. Evidences of involvement of immunopathology have been reported in periodontal disease. Bacteria in the dental plaque induce antibody formation. Autoreactive T cells, natural killer cells, ANCA, heat shock proteins, autoantibodies, and genetic factors are reported to have an important role in the autoimmune component of periodontal disease. The present review describes the involvement of autoimmune responses in periodontal diseases and also the mechanisms underlying these responses. This review is an attempt to throw light on the etiopathogenesis of periodontal disease highlighting the autoimmunity aspect of the etiopathogenesis involved in the initiation and progression of the disease. However, further clinical trials are required to strengthen the role of autoimmunity as a cause of periodontal disease.

Advances in systems biology approaches for autoimmune diseases

Because autoimmune diseases (AIDs) result from a complex combination of genetic and epigenetic factors, as well as an altered immune response to endogenous or exogenous antigens, systems biology approaches have been widely applied. The use of multi-omics approaches, including blood transcriptomics, genomics, epigenetics, proteomics, and metabolomics, not only allow for the discovery of a number of biomarkers but also will provide new directions for further translational AIDs applications. Systems biology approaches rely on high-throughput techniques with data analysis platforms that leverage the assessment of genes, proteins, metabolites, and network analysis of complex biologic or pathways implicated in specific AID conditions. To facilitate the discovery of validated and qualified biomarkers, better-coordinated multi-omics approaches and standardized translational research, in combination with the skills of biologists, clinicians, engineers, and bioinformaticians, are required.

Current state of diagnostic technologies in the autoimmunology laboratory

The methods for detecting and measuring autoantibodies have evolved markedly in recent years, encompassing three generations of analytical technologies. Many different immunoassay methods have been developed and used for research and laboratory practice purposes, from the early conventional (or monoplex) analytical methods able to detect single autoantibodies to the more recent multiplex platforms that can quantify tens of molecules. Although it has been in use for over 50 years, indirect immunofluorescence remains the standard method for research on many types of autoantibodies, due to its characteristics of diagnostic sensitivity and also to recent technological innovations which permit it a greater level of automation and standardization. The recent multiplex immunometric methods, with varying levels of automation, present characteristics of higher diagnostic accuracy, but are not yet widely diffused in autoimmunology laboratories due to the limited number of autoantibodies that are detectable, and due to the high cost of reagents and systems. Technological advancement in autoimmunology continues to evolve rapidly, and in the coming years new proteomic techniques will be able to radically change the approach to diagnostics and possibly also clinical treatment of autoimmune diseases. The scope of this review is to update the state of the art of technologies and methods for the measurement of autoantibodies, with special reference to innovations in indirect immunofluorescence and in multiple proteomic methods.

Molecular diagnostics of primary biliary cirrhosis

BACKGROUND

Primary biliary cirrhosis (PBC) is an autoimmune liver disease of unknown etiology characterized by the presence of antimitochondrial antibodies (AMA) in 90 - 95% of patients. AMA are directed against members of 2-oxo-acid dehydrogenase complex, including mainly the E2 subunit of pyruvate dehydrogenase, the E2 subunit of branched chain 2-oxo-acid dehydrogenase complex and the E2 subunit of the oxoglutarate dehydrogenase complex. Apart from AMA, PBC is characterized by the presence of PBC-specific antinuclear antibodies (ANA). The molecular targets of these PBC-specific ANA have been characterized as gp210, lamin B receptor, nucleoporin 62, sp100 and promyelocytic leukemia proteins.

OBJECTIVE

To discuss the molecular diagnostics of PBC in the context of AMA and PBC-specific ANA detection by the use of conventional and 'new' novel technologies.

METHODS

Critical analysis of all published data regarding PBC serology between 1985 and 2007 was performed in order to suggest a diagnostic algorithm for the serological diagnosis of PBC.

RESULTS/CONCLUSIONS

AMA are first detected by indirect immunofluorescence (IIF) on frozen sections of rat liver, kidney and stomach substrates. However, because IIF is time-consuming, labor-intensive and observer-dependent, molecular-based assays such as immunoblot and enzyme-linked immunosorbent assays have been developed with high sensitivity and specificity. Similarly, molecular-based assays have also been developed for the detection of PBC-specific ANA. The latter investigation seems to be of outmost importance because these autoantibodies can be used as a positive tool in the diagnosis of AMA-negative PBC while at the same time identifying a subgroup of PBC patients with more advanced disease. New test systems for the detection of PBC-specific antibodies based on the xMultiple Analyte Profiling Luminex methodology seems to be the future in molecular diagnostics of PBC as it was expected first to decrease the cost and second to speed up an accurate serological profile, although they may decrease further the proportion of AMA-negative PBC cases.

Isolation of human brain endothelial cells and characterization of lipid raft-associated proteins by mass spectroscopy

The blood-brain barrier (BBB) limits the movements of molecules, nutrients, and cells from the systemic blood circulation into the central nervous system (CNS), and vice versa, thus allowing an optimal microenvironment for CNS development and function. The brain endothelial cells (BECs) form the primary barrier between the blood and the CNS. In addition, pericytes, neurons, and astrocytes that make up the neurovascular unit support the BEC functions and are essential to maintain this restrictive permeability phenotype. To better understand the molecular mechanisms underlying BBB properties, we propose a method to study the proteome of detergent resistant microdomain, namely lipid rafts, from human primary cultures of BECs. This chapter describes a robust human BECs isolation protocol, standard tissue culture protocols, ECs purity assessment protocols, lipid raft microdomain isolation method, and a mass spectrometry analysis technique to characterize the protein content of membrane microdomains.

Diagnostic accuracy of immunoassays for the detection of antibodies to citrullinated proteins

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.

The diagnostic role of autoantibodies in the prediction of organ-specific autoimmune diseases

Due to their pathogenetic role, many serum autoantibodies can be detected a long time before the clinical onset and during the course of organ-specific autoimmune diseases. For these reasons, autoantibodies can be used as predictive markers of an ongoing disease (in healthy subjects) and of disease activity and severity (in ill patients). The new multiplex diagnostic technologies introduced recently in laboratory medicine allow the simultaneous detection of several different autoantibodies and can be used for screening purposes in open populations or high-risk groups. This review examines the various autoantibodies of demonstrated predictive role in organ-specific autoimmune diseases and it introduces the state-of-the-art in the detection of multiple autoantibodies with proteomic systems.

Recent advances in diagnostic technologies for autoimmune diseases

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.

Autoantibody profiling of Chinese patients with autoimmune hepatitis using immunoproteomic analysis

In the present study, immunoproteomic analysis was utilized to systemically characterize global autoantibody profiles in autoimmune hepatitis (AIH). Sera from 21 patients with AIH and 15 healthy controls were analyzed for the antibody reactivity against the protein antigens of HepG2, a human hepatoma cell line. The lysates of HepG2 cells were separated by two-dimensional electrophoresis and then immunoblotted with each serum sample. Matrix-assisted laser desorption/ionization mass spectrometry or/and nanoelectrospray ionization MS/MS were then used to identify antigens, among which a bifunctional enzyme in mitochondrial, fumarate hydratase (FH), was further analyzed by ELISA using recombinant FH as a coating antigen. A total of 18 immunoreactive spots were identified as 13 proteins, 8 of which have not been reported in AIH. Immune reactivity to FH was detected in 66.67% of patients with AIH, 19.35% of patients with primary biliary cirrhosis (PBC), 12.31% of patients with chronic hepatitis B (CHB), 6.35% of patients with chronic hepatitis C (CHC), 11.32% of patients with systemic lupus erythematosus (SLE), and 3.57% of normal individuals. The differences of prevalence between AIH patients and healthy controls as well as other diseases were of statistical significance (P<0.001). These data demonstrate the serological heterogeneity in AIH and suggest the diversity of the mechanisms underlying AIH. FH, recognized mainly in AIH rather than in viral hepatitis and other autoimmune diseases, may have utility in improved diagnosis of AIH.

Acid deprotection of covalently immobilized peptide probes on glass slides for peptide microarrays

Protein microarray technology has shown great advancements in the field of biomedical research and diagnosis, it allows to study and understand protein activities and protein - ligand interactions (e.g. detection of antigen-autoantibody interaction in autoimmune diseases. Autoantibodies are frequently targeted against antigens of the cell nucleus (double and single stranded DNA, histones, and nuclear antigens). The biological activities of proteins (e.g. enzymes, antibodies...) are controlled by peptides sequences of the active site. Consequently, we were interested in the investigation of peptide microarrays in order to further implement in situ peptide synthesis, in particular, deprotection reaction on glass supported peptides. In this work, a protected and biotinylated synthetic peptide was covalently immobilized onto amino functionalized glass surface by activation of its the C-terminus; this allows to orientate the peptide onto the surface. The peptide contains a fragment of the C-terminal end of the human histone H3 protein. The immobilized peptide was then deprotected by using concentrated trifluoroacetic acid solution. After the deprotection, surface stability and peptide grafting density were evaluated by indirect labelling of the immobilized peptide using Cy3 streptavidin conjugates. We also studied biological interaction of IgG polyclonal anti-histone H3 antibody with the immobilized peptide epitope to insure the efficiency of the acid deprotection. The specificity of the antibody interaction with the protected versus non protected peptides. This approach may be applied to in situ synthetic and prototected peptides, in order to elaborate a micro-immunoassay prototype for measurement of peptide-protein interactions on high density microarrays, and detection of antibodies in biological fluids such as serum.

Proteomic strategies in multiple sclerosis and its animal models

The early and precise diagnosis, the prognosis, and the clinical management of multiple sclerosis, remain a considerable challenge. In recent years, the development of novel and powerful proteomic techniques prompted the use of these approaches for the search of unique biomarkers in the cerebrospinal fluid of multiple sclerosis patients. A few studies have also utilized proteomics to delineate the profile of differentially expressed proteins in animal models of the human disease in order to gain global insights into affected pathways. The identification of differentially expressed proteins may be an initial step in the discovery of novel targets and mechanisms that play critical roles in the pathology of multiple sclerosis. Based on these findings, future investigations may elucidate the events leading to demyelination, axonal damage, and neurodegeneration, providing better insights into mechanisms governing the onset and progression of the disease. Although these proteomic studies provide valuable information, they are also faced with a number of challenges. The present review discusses some of the strengths and limitations of proteomic investigations as applied to multiple sclerosis.

Recent advances in diagnostic technologies and their impact in autoimmune diseases

Conventional immunological methods for the detection of serum autoantibodies have been an essential tool for the diagnosis of autoimmune diseases for 40 years: in the last decade autoantibody tests have become accepted criteria for the diagnosis and classification of the main systemic and organ-specific autoimmune diseases. The high degree of purification reached by the autoantigens used in these methods has allowed high diagnostic sensitivity and specificity, especially in the case of some new autoantibodies of particular clinical significance, such as anti-nucleosome, anti-transglutaminase, anti-TSH receptor and anti-citrullinated protein autoantibodies. In the last 5 years the advent of proteomic technology, which allows the simultaneous measurement of a number of autoantibodies (multiplexing), has opened up new horizons in the diagnosis of autoimmune diseases. Multiplexing is particularly interesting for clinical laboratories, for organisational, logistical/managerial, physiopathological and research reasons. The emerging technologies are represented by systems based on planar or non-planar (suspension) arrays: the latter include methods which use addressable microbeads or nanobarcoded particles. Within a few years, the new methods will allow testing of individual autoantibody profiles, which will probably improve understanding of the physiopathology of autoimmunity, allow early diagnosis (due to the predictive value of autoantibodies), and drive the diffusion of antigen-specific therapies in autoimmune diseases.

The application of genomic and proteomic technologies in predictive, preventive and personalized medicine

The long asymptomatic period before the onset of chronic diseases offers good opportunities for disease prevention. Indeed, many chronic diseases may be preventable by avoiding those factors that trigger the disease process (primary prevention) or by use of therapy that modulates the disease process before the onset of clinical symptoms (secondary prevention). Accurate prediction is vital for disease prevention so that therapy can be given to those individuals who are most likely to develop the disease. The utility of predictive markers is dependent on three parameters, which must be carefully assessed: sensitivity, specificity and positive predictive value. Specificity is important if a biomarker is to be used to identify individuals either for counseling or for preventive therapy. However, a reciprocal relationship exists between sensitivity and specificity. Thus, successful biomarkers will be highly specific without sacrificing sensitivity. Unfortunately, biomarkers with ideal specificity and sensitivity are difficult to find for many diseases. One potential solution is to use the combinatorial power of a large number of biomarkers, each of which alone may not offer satisfactory specificity and sensitivity. Recent technological advances in genetics, genomics, proteomics, and bioinformatics offer a great opportunity for biomarker discovery. The newly identified biomarkers have the potential to bring increased accuracy in disease diagnosis and classification, as well as therapeutic monitoring. In this review, we will use type 1 diabetes (T1D) as an example, when appropriate, to discuss pertinent issues related to high throughput biomarker discovery.

Model of stimulation-responsive splicing and strategies in identification of immunogenic isoforms of tumor antigens and autoantigens

We recently proposed a novel model of stimulation-responsive splicing for the selection of autoantigens and self-tumor antigens. Our model theorizes that the significantly higher rates of alternative splicing of autoantigen and self-tumor antigen transcripts that occur in response to stimuli could induce extra-thymic expression of untolerized antigen epitopes for elicitation of autoimmune and anti-tumor responses. To facilitate the identification of immunogenic isoforms of antigens, we have developed strategies using improved SEREX in conjunction with database-mining and immunogenic isoform mapping. Identification of immunogenic isoforms of autoantigens and self-tumor antigens is very important for the development of novel therapeutics and diagnostic tools for autoimmune diseases and tumors, such as: (1) autoantigen isoform microarrays for disease diagnosis and prognosis; (2) autoantigen isoform-specific tolerizing vaccines and splicing-redirection therapies, as well as (3) immunogenic antigen isoform-specific immunotherapy for tumors.

Alternative splicing factor ASF/SF2 is down regulated in inflamed muscle

BACKGROUND

In our recent studies, alternative splicing has been shown to have a major role in inflammation and autoimmune muscle diseases.

AIM

To examine the novel hypothesis that the expression of an essential alternative splicing factor, alternative splicing factor 2 (ASF/SF2), is modulated in muscle inflammation.

METHODS

ASF/SF2 expression in muscle biopsy samples from eight patients with inflammatory myopathy and six non-myositic controls was determined by using western blot with anti-ASF/SF2 antibodies. To further elucidate the mechanism of reduced ASF/SF2 expression in inflamed muscle, differentiated C2C12 myotubes were stimulated with proinflammatory cytokine tumour necrosis factor alpha (TNFalpha), followed by western blot analysis of ASF/SF2 expression.

RESULTS

ASF/SF2 expression in the muscle biopsy samples from patients with inflammatory myopathy was found to be lower (mean of relative densitometric units 41.1 (2SD 20.7)) than that of the non-myositic controls (mean of relative densitometric units 76.7 (39.6); p<0.05). In addition to this, ASF/SF2 expression was seen to be significantly down regulated (sevenfold) in C2C12 myotubes compared with expression variations in the beta-actin control (0.62-fold; mean 1.22 (0.40); p<0.05).

CONCLUSION

Collectively, it is shown, for the first time, that alternative splicing factor ASF/SF2 is down regulated in autoimmune inflammatory myositis-potentially via a TNFalpha-mediated pathway. The development of (1) novel autoantigen isoform microarrays for disease diagnosis and prognosis; (2) novel autoantigen-tolerising treatments for autoimmune diseases; and (3) novel splicing-redirection treatments can be facilitated by the ongoing study of alternative splicing of autoantigen transcripts.

Multiplexed protein array platforms for analysis of autoimmune diseases

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.

Present and future of the autoimmunity laboratory

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.

Identification of autoantibody clusters that best predict lupus disease activity using glomerular proteome arrays

Nephrophilic autoantibodies dominate the seroprofile in lupus, but their fine specificities remain ill defined. We constructed a multiplexed proteome microarray bearing about 30 antigens known to be expressed in the glomerular milieu and used it to study serum autoantibodies in lupus. Compared with normal serum, serum from B6.Sle1.lpr lupus mice (C57BL/6 mice homozygous for the NZM2410/NZW allele of Sle1 as well as the FAS defect) exhibited high levels of IgG and IgM antiglomerular as well as anti-double-stranded DNA/chromatin Abs and variable levels of Abs to alpha-actinin, aggrecan, collagen, entactin, fibrinogen, hemocyanin, heparan sulphate, laminin, myosin, proteoglycans, and histones. The use of these glomerular proteome arrays also revealed 5 distinct clusters of IgG autoreactivity in the sera of lupus patients. Whereas 2 of these IgG reactivity clusters (DNA/chromatin/glomeruli and laminin/myosin/Matrigel/vimentin/heparan sulphate) showed association with disease activity, the other 3 reactivity clusters (histones, vitronectin/collagen/chondroitin sulphate, and entactin/fibrinogen/hyaluronic acid) did not. Human lupus sera also displayed 2 distinct IgM autoantibody clusters, one reactive to DNA and the other apparently polyreactive. Interestingly, the presence of IgM polyreactivity in patient sera was associated with reduced disease severity. Hence, the glomerular proteome array promises to be a powerful analytical tool for uncovering novel autoantibody disease associations and for distinguishing patients at high risk for end-organ disease.

Proteomics in rheumatology: a new direction for old diseases

OBJECTIVES

Completion of the human genome project has stimulated scientists to begin looking for the next step in unraveling normal and abnormal functions within biological systems. Consequently, there is new focus on the role of proteins in these processes. Proteomics is a rapidly growing field that may provide a valuable approach to evaluate the field of rheumatology. The objectives of this article is to provide an overview of biophysical techniques, as "re-invented" research tools, as applied to the investigation of rheumatoid arthritis and osteoarthritis.

METHODS

MEDLINE search of articles in English-language journals from 1966 to 2004. The index words "Rheumatoid/osteoarthritis/connective tissue disorders" and the following co-indexing terms were used: "mass spec," "NMR," "SPR" and "Proteomics." Papers identified were reviewed, abstracted, and summarized. The authors' own work in the field is also presented.

RESULTS

As we move into the postgenomics era, new and exciting tools are being developed to study protein expression and protein interactions and identify new biomarkers for disease diagnosis and prognosis. Proteomics is an emerging field with widespread potential applications to rheumatic disease.

CONCLUSIONS

In this review the biophysical techniques of nuclear magnetic resonance, mass spectroscopy, and surface plasmon resonance as proteomic tools in the study of rheumatoid and osteoarthritis were reviewed. What is emerging is the identification of new biomarkers with clinical and therapeutic relevance.

Profiling humoral autoimmune repertoire of dilated cardiomyopathy (DCM) patients and development of a disease-associated protein chip

Dilated cardiomyopathy (DCM) is a myocardial disease characterized by progressive depression of myocardial contractile function and ventricular dilatation. Thirty percent of DCM patients belong to the inherited genetic form; the rest may be idiopathic, viral, autoimmune, or immune-mediated associated with a viral infection. Disturbances in humoral and cellular immunity have been described in cases of myocarditis and DCM. A number of autoantibodies against cardiac cell proteins have been identified in DCM. In this study, we have profiled the autoantibody repertoire of plasma from DCM patients against a human protein array consisting of 37,200 redundant, recombinant human proteins and performed qualitative and quantitative validation of these putative autoantigens on protein microarrays to identify novel putative DCM specific autoantigens. In addition to analyzing the whole IgG autoantibody repertoire, we have also analyzed the IgG3 antibody repertoire in the plasma samples to study the characteristics of IgG3 subclass antibodies. By combining screening of a protein expression library with protein microarray technology, we have detected 26 proteins identified by the IgG antibody repertoire and 6 proteins bound by the IgG3 subclass. Several of these autoantibodies found in plasma of DCM patients, such as the autoantibody against the Kv channel-interacting protein, are associated with heart failure.

Light-directed maskless synthesis of peptide arrays using photolabile amino acid monomers

Novel photolabile amino acid monomers for photolithographic solid-phase peptide synthesis has been developed and a method for the maskless synthesis of individually addressable peptide microarrays using new building blocks has been described; these peptide microarrays are suitable for repetitive epitope-binding assays.

Multiplexed testing in the autoimmunity laboratory

A 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.

A suppressive oligodeoxynucleotide enhances the efficacy of myelin cocktail/IL-4-tolerizing DNA vaccination and treats autoimmune disease

Targeting pathogenic T cells with Ag-specific tolerizing DNA vaccines encoding autoantigens is a powerful and feasible therapeutic strategy for Th1-mediated autoimmune diseases. However, plasmid DNA contains abundant unmethylated CpG motifs, which induce a strong Th1 immune response. We describe here a novel approach to counteract this undesired side effect of plasmid DNA used for vaccination in Th1-mediated autoimmune diseases. In chronic relapsing experimental autoimmune encephalomyelitis (EAE), combining a myelin cocktail plus IL-4-tolerizing DNA vaccine with a suppressive GpG oligodeoxynucleotide (GpG-ODN) induced a shift of the autoreactive T cell response toward a protective Th2 cytokine pattern. Myelin microarrays demonstrate that tolerizing DNA vaccination plus GpG-ODN further decreased anti-myelin autoantibody epitope spreading and shifted the autoreactive B cell response to a protective IgG1 isotype. Moreover, the addition of GpG-ODN to tolerizing DNA vaccination therapy effectively reduced overall mean disease severity in both the chronic relapsing EAE and chronic progressive EAE mouse models. In conclusion, suppressive GpG-ODN effectively counteracted the undesired CpG-induced inflammatory effect of a tolerizing DNA vaccine in a Th1-mediated autoimmune disease by skewing both the autoaggressive T cell and B cell responses toward a protective Th2 phenotype. These results demonstrate that suppressive GpG-ODN is a simple and highly effective novel therapeutic adjuvant that will boost the efficacy of Ag-specific tolerizing DNA vaccines used for treating Th1-mediated autoimmune diseases.

Immobilisation of oligo-peptidic probes for microarray implementation: Characterisation by FTIR, Atomic Force Microscopy and 2D fluorescence

Proteomic microarrays show a wide range of applications for the investigation of DNA-protein, enzyme-substrate as well as protein-protein interactions. Among many challenges to build a viable "protein microarray", the surface chemistry that will allow to immobilised various proteins to retain their biological activity is of paramount importance. Here we report a chemical functionalisation method allowing immobilisation of oligo-peptides onto silica surface (porous silica, glass, thermal silicon dioxide). Substrates were first derivatised with a monofunctional silane allowing the elaboration of dense and uniform monolayers in highly reproducible way. Prior to the oligo-peptides grafting, this organic layer was functionalised with an amino-polyethyleneglycol. The coupling step of oligo-peptides onto functionalised supports is achieved through activation of the C-terminal function of the oligo-peptides. Chemical surface modifications were followed by FTIR spectroscopy, AFM measurements and fluorescence scanning microscopy. A systematic study of the oligo-peptide grafting conditions (time, concentration, solvent) was carried out to optimise this step. The oligo-peptides grafting strategy implemented in this work ensure a covalent and oriented grafting of the oligo-peptides. This orientation is ensured through the use of fully protected peptide except the terminal primary amine. The immobilized peptides will be then deprotected before biological recognition. This strategy is crucial to retain the biological activity of thousands of oligo-probes assessed on a microarray.

Proteomic: New advances in the diagnosis of rheumatoid arthritis

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.

An array of possibilities for the study of autoimmunity

Since the completion of the sequencing of the human genome, scientific focus has shifted from studying genes to analysing the much larger number of proteins encoded by them. Several proteins can be generated from a single gene depending on how the genetic information is read (transcribed) and how the resultant protein is modified following translation (post-translational modification). Genomic and proteomic technologies are already providing useful information about autoimmune disease, and they are likely to lead to important discoveries within the next decade.

Chronically inflamed synovium from spondyloarthropathy and rheumatoid arthritis investigated by protein expression profiling followed by tandem mass spectrometry

We investigated the cytosolic proteome of inflamed synovial tissue by hierarchical clustering analysis and validated the feasibility of this proteome analysis by identifying proteins that were differentially expressed between rheumatoid arthritis (RA), spondyloarthropathy (SpA), and osteoarthritis (OA). Synovial biopsy samples were obtained from 18 patients undergoing needle arthroscopy for knee synovitis associated with RA (n = 6) and SpA (n = 6), and for joint effusion of the knee associated with OA (n = 6). Cytosolic proteins were extracted from the tissue and subjected to two-dimensional gel electrophoresis. Protein expression patterns were statistically analyzed and used for hierarchical cluster analysis. Proteins of interest were independently identified by matrix-assisted laser desorption/ionization- and electrospray ionization-mass spectrometry. Hierarchical cluster analysis of the complete match set, containing 640 spots, remarkably segregated SpA from RA and OA. Next, we used a subset of spots that was statistically, differentially expressed (P < 0.01), between RA and SpA, SpA and OA, or RA and OA, in both Student's t-test and Mann-Whitney U-test. The dendrograms revealed distinct clustering of RA versus SpA and RA versus OA. Spots that were differentially expressed between the groups were identified by tandem mass spectrometry. Fructose bisphosphate aldolase A and alpha-enolase showed higher expression levels in SpA than in OA (P < 0.01). Calgranulin A myeloid related protein-8 (MRP-8) was markedly up-regulated in RA and SpA patients in comparison to OA patients where this spot was below detection limit. The analysis of the cytosolic proteome of synovial tissue is a useful approach to identify disease-associated proteins in chronic inflammatory arthritis.

Protein arrays for studying blood cells and their secreted products

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.

Technical and clinical evaluation of anti-ribosomal P protein immunoassays

Autoantibodies to the three ribosomal phospho (-P) proteins P0, P1, P2, referred to as Rib-P, are specifically found in 10-40% of patients with systemic lupus erythematosus. The variations in the observed frequency of these autoantibodies is related to a number of factors such as the test system used to detect the antibodies. Several immunoassays that were designed for research and diagnostic laboratory use have been developed. The autoantigens employed in these tests include native proteins, recombinant polypeptides, and synthetic peptides. In this study, we compared the technical and clinical accuracy of anti-Rib-P antibody assays from different commercial suppliers including ELISA systems and a novel addressable laser bead assay (from Euroimmun, MBL, Pharmacia Diagnostics, INOVA). Although the assays from all suppliers used in this study performed well in the technical part of the study, relatively poor correlations and significant differences in the clinical accuracy were found. Based on the results, we conclude that the detection of anti-Rib-P antibodies strongly depends on both the nature of the antigen and the detection system. We recommend that anti-Rib-P assays should be standardized on an international level. The Varelisa Rib-P profile and the addressable laser bead Rib-P assays represent promising tools and platforms for the detection of anti-Rib-P antibodies in the future.

Multiplexed assays for identification of biomarkers and surrogate markers in systemic lupus erythematosus

Validated biomarkers and surrogate markers are badly needed for monitoring patients with systemic lupus erythematosus (SLE), both for routine clinical care and for clinical trials research. SLE is difficult to study in clinical trials, in part because the disease is so heterogeneous. Very few useful markers have been identified, and even those that historically have been thought to be valid have been recently questioned. This report will focus on the use of emerging multiplexed assay formats that enable analysis of hundreds or even thousands of analytes simultaneously. Their potential and pitfalls for monitoring patients with SLE, particularly those enrolled in clinical trials testing novel therapeutics, will be discussed.

Microarray profiling of antiviral antibodies for the development of diagnostics, vaccines, and therapeutics

Multiplex analysis of antiviral antibody (Ab) responses provides a potentially powerful strategy for viral diagnosis, prognostication, and development of vaccines and prophylactic Abs. In the coming years, advancements in proteomic technologies will provide even more robust methods to characterize antiviral Ab responses. Biomedical researchers will be faced with the exciting challenge of identifying antiviral Ab specificities that correlate with improved outcomes and efficacious interventions, and translating the findings into more effective diagnostics, prophylactics, and therapeutics.

Autoantigens of the nuclear pore complex

The nuclear envelope (NE) is one of many intracellular targets of the autoimmune response in patients with autoimmune liver disease, systemic lupus erythematosus, and related conditions. In eukaryotic organisms the NE consists of five interconnected regions: an outer nuclear membrane (ONM) that is continuous with the endoplasmic reticulum, an intermembrane or perinuclear space, an inner nuclear membrane (INM) with a unique set of integral membrane proteins, the underlying nuclear lamina, and the pore domains that are regions where the ONM and INM come together. The pore domains are sites of regulated continuity between the cytoplasm and nucleus that are occupied by supramolecular structures, termed nuclear pore complexes (NPCs). Human autoantibodies identified to date bind to specific components in three of the five NE compartments. Autoantigen targets include the lamins A, B, and C of the nuclear lamina, gp210, p62 complex proteins, Nup153, and Tpr within the NPC, and LBR, MAN1, LAP1, and LAP2 that are integral proteins of the INM. Autoantibodies to these NE targets have been shown to be correlated with various autoimmune diseases such as primary biliary cirrhosis, other autoimmune liver diseases and systemic rheumatic diseases. Now that the proteome of the NE is more clearly defined, other autoantibodies to components in this cell compartment are likely to be defined.

A novel mechanism of alternative promoter and splicing regulates the epitope generation of tumor antigen CML66-L

This report describes the difference in the epitope generation of two isoforms of self-tumor Ag CML66 and the regulation mechanism. We identified a new CML66 short isoform, termed CML66-S. The previously identified long CML66 is referred to as CML66-L. CML66-S shares the C terminus with CML66-L but has its unique N terminus. CML66-S is predominantly expressed in testis, but is also expressed in very low levels in tumor cells, whereas CML66-L is expressed in tumor cells and testis. Differential expression of CML66-L and CML66-S in tumor cells resulted from regulation at transcription, although alternative splicing also participated in the generation of the isoforms. In addition, Ab titers to a CML66-L peptide were significantly higher than that to CML66-S peptide in the sera from patients with tumors. Finally, the Abs to full-length CML66-L in the sera from patients with tumors were correlated with the Abs in the sera from these patients to CML66-L-38, which is a fusion protein with a CML66-L-specific N terminus. This suggests that the CML66-L isoform is mainly responsible for the epitope generation. Our studies have identified the alternative promoter in combination with alternative splicing as a novel mechanism for regulation of the epitope generation of a self-tumor Ag.

The oral component of Sjögren's syndrome: pass the scalpel and check the water

The labial salivary gland biopsy is a diagnostic test for the oral component of Sjögren's syndrome (SS) that has been the subject of controversy and re-examination for many years. Despite multiple recent challenges to the significance of this test, when correctly done, it remains one of the most informative, specific, and technically simple tests available for the oral component of SS. Because of compromised salivary gland function, patients with SS are at risk for dental caries. Within the past decade, a paradigm shift has occurred within the field of caries research. The caries process was previously thought irreversible once initiated. Research has shown that the "early" carious lesion can be remineralized. Thus, the "early" carious lesion may be prevented and even repaired. The process of remineralization requires appropriate conditions to occur, and one of those conditions is pH. Because water is often the preferred wetting agent/beverage for patients with SS, the data show that, with regard to pH, not all waters are created equal.

Autoantibodies to protein transport and messenger RNA processing pathways: endosomes, lysosomes, Golgi complex, proteasomes, assemblyosomes, exosomes, and GW bodies

Over 50 years ago the lupus erythematosus (LE) cell phenomenon was described and this was quickly followed by the introduction of the LE cell test and indirect immunofluorescence (IIF) to detect antinuclear antibodies (ANA) in clinical laboratories. Recently, attention has turned to the identification of the autoantigens that bind to cytoplasmic organelles such as the Golgi complex, endosomes and other "cytoplasmic somes". Three endosome autoantigens include early endosome antigen 1 (EEA1, 160 kDa), cytoplasmic linker protein-170 (CLIP-170, 170 kDa), and lysobisphosphatidic acid (LBPA). Antibodies to EEA1 were seen in a variety of conditions but approximately 40% of the patients had a neurological disease. Despite the prominence of lysosomes in cells and tissues, reports of autoantibodies are limited to the lysosomal antigen h-LAMP-2 and the cytoplasmic antineutrophil antibodies (cANCA). Autoantigens in the Golgi complex include giantin/macrogolgin, golgin-245, golgin 160, golgin-97, golgin 95/gm130, and golgin-67. More recently, there has been an interest in autoantibodies that bind components of the "SMN complex" or the "assemblyosome". Arginine/glycine (RG)-rich domains in components of the SMN complex interact with Sm, like-Sm (LSm), fibrillarin, RNA helicase A (Gu), and coilin proteins, all of which are antigen targets in a variety of diseases. More recently, components of a novel cytoplasmic structure named GW bodies (GWBs) have been identified as targets of human autoantibodies. Components of GWBs include GW182, a unique mRNA-binding protein, like Sm proteins (LSms), and decapping (hDcp1) and exonuclease (Xrn) enzymes. Current evidence suggests that GWBs are involved in the cytoplasmic processing of mRNAs. Autoantibodies to the "cytoplasmic somes" are relatively uncommon and serological tests to detect most of them are not widely available.

Transcriptional analysis of targets in multiple sclerosis

Large-scale analyses of messenger RNA transcripts and autoantibody responses, taken from the actual sites of disease, provide us with an unprecedented view of the complexity of autoimmunity. Despite an appreciation of the large number of pathways and pathological processes that are involved in these diseases, a few practical targets and several new strategies have emerged from these studies. This review focuses on multiple sclerosis and on the approaches that are being used to identify new targets that might be manipulated to control this disease.

Advances in B-cell epitope analysis of autoantigens in connective tissue diseases

The characterization of autoantibody specificities in rheumatic diseases is important in both diagnostic and basic research areas. Identification of the epitopes recognized by autoantibodies and their clinical and biological significance is not a trivial task. Epitopes may range in complexity from simple linear sequences of amino acids to complex quaternary structures. In addition to this structural complexity the frequency with which an autoantigen and its epitopes are recognized in a patient population may be useful in diagnosis, defining disease subgroups, and may offer information on disease prognosis. In this review recent advances in the epitope mapping of autoantigens in connective tissue diseases are discussed, with particular emphasis placed on the methodologies used to identify epitopes and the classification of the structural features of epitopes. To illustrate the identification of epitope structure, clinically relevant autoantigens, including CENP-A, PM/Scl-100, fibrillarin, filaggrin, Ro-52, and dsDNA, are discussed as examples of each type of epitope.