Diagnostic and prognostic biomarker discovery strategies for autoimmune disorders. J Proteomics. 2010;73:1045-1060. [PMID: 19995622 DOI: 10.1016/j.jprot.2009.11.013]

Bibliometric and visualization analysis of the application of inorganic nanomaterials to autoimmune diseases

Objective: To conduct bibliometric analysis of the application of inorganic nanomaterials to autoimmune diseases to characterize current research trends and to visualize past and emerging trends in this field in the past 15 years. Methods: The evolution and thematic trends of the application of inorganic nanomaterials to autoimmune diseases from January 1, 1985, to March 15, 2024, were analyzed by bibliometric analysis of data retrieved and extracted from the Web of Science Core Collection (WoSCC) database. A total of 734 relevant reports in the literature were evaluated according to specific characteristics such as year of publication, journal, institution, country/region, references, and keywords. VOSviewer was used to build co-authorship analysis, co-occurrence analysis, co-citation analysis, and network visualization. Some important subtopics identified by bibliometric characterization are further discussed and reviewed. Result: From 2009 to 2024, annual publications worldwide increased from 11 to 95, an increase of 764%. ACS Nano published the most papers (14) with the most citations (1372). China (230 papers, 4922 citations) and the Chinese Academy of Sciences (36 papers, 718 citations) are the most productive and influential country and institution, respectively. The first 100 keywords were co-clustered to form four clusters: (1) the application of inorganic nanomaterials in drug delivery, (2) the application of inorganic nano-biosensing to autoimmune diseases, (3) the use of inorganic nanomaterials for imaging applied to autoimmune diseases, and (4) the application of inorganic nanomaterials in the treatment of autoimmune diseases. Combination therapy, microvesicles, photothermal therapy (PTT), targeting, diagnostics, transdermal, microneedling, silver nanoparticles, psoriasis, and inflammatory cytokines are the latest high-frequency keywords, marking the emerging frontier of inorganic nanomaterials in the field of autoimmune diseases. Sub-topics were further discussed to help researchers determine the scope of research topics and plan research directions. Conclusion: Over the past 39 years, the application of inorganic nanotechnology to the field of autoimmune diseases shows extensive cooperation between countries and institutions, showing a continuous increase in the number of reports in the literature, and has clinical translation prospects. Future research should further improve the safety of inorganic nanomaterials, clarify the mechanism of action of nanomaterials, establish a standardized nanomaterial preparation and performance evaluation system, and ultimately achieve the goal of early detection and precise treatment of autoimmune diseases.

Proteomic-Based Discovery of Predictive Biomarkers for Drug Therapy Response and Personalized Medicine in Chronic Immune Thrombocytopenia

Purpose

ITP is the most prevalent autoimmune blood disorder. The lack of predictive biomarkers for therapeutic response is a major challenge for physicians caring of chronic ITP patients. This study is aimed at identifying predictive biomarkers for drug therapy responses.

Methods

2D gel electrophoresis (2-DE) was performed to find differentially expressed proteins. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF MS) analysis was performed to identify protein spots. The Cytoscape software was employed to visualize and analyze the protein-protein interaction (PPI) network. Then, enzyme-linked immunosorbent assays (ELISA) were used to confirm the results of the proteins detected in the blood. The DAVID online software was used to explore the Gene Ontology and pathways involved in the disease.

Results

Three proteins, including APOA1, GC, and TF, were identified as hub-bottlenecks and confirmed by ELISA. Enrichment analysis results showed the importance of several biological processes and pathway, such as the PPAR signaling pathway, complement and coagulation cascades, platelet activation, vitamin digestion and absorption, fat digestion and absorption, cell adhesion molecule binding, and receptor binding. Conclusion and Clinical Relevance. Our results indicate that plasma proteins (APOA1, GC, and TF) can be suitable biomarkers for the prognosis of the response to drug therapy in ITP patients.

Proteomic Data Analysis for Differential Profiling of the Autoimmune Diseases SLE, RA, SS, and ANCA-Associated Vasculitis

Early and correct diagnosis of inflammatory rheumatic diseases (IRD) poses a clinical challenge due to the multifaceted nature of symptoms, which also may change over time. The aim of this study was to perform protein expression profiling of four systemic IRDs, systemic lupus erythematosus (SLE), ANCA-associated systemic vasculitis (SV), rheumatoid arthritis (RA), and Sjögren’s syndrome (SS), and healthy controls to identify candidate biomarker signatures for differential classification. A total of 316 serum samples collected from patients with SLE, RA, SS, or SV and from healthy controls were analyzed using 394-plex recombinant antibody microarrays. Differential protein expression profiling was examined using Wilcoxon signed rank test, and condensed biomarker panels were identified using advanced bioinformatics and state-of-the art classification algorithms to pinpoint signatures reflecting each disease (raw data set available at https://figshare.com/s/3bd3848a28ef6e7ae9a9.). In this study, we were able to classify the included individual IRDs with high accuracy, as demonstrated by the ROC area under the curve (ROC AUC) values ranging between 0.96 and 0.80. In addition, the groups of IRDs could be separated from healthy controls at an ROC AUC value of 0.94. Disease-specific candidate biomarker signatures and general autoimmune signature were identified, including several deregulated analytes. This study supports the rationale of using multiplexed affinity-based technologies to reflect the biological complexity of autoimmune diseases. A multiplexed approach for decoding multifactorial complex diseases, such as autoimmune diseases, will play a significant role for future diagnostic purposes, essential to prevent severe organ- and tissue-related damage.

Integrative Analysis of lncRNAs in Th17 Cell Lineage to Discover New Potential Biomarkers and Therapeutic Targets in Autoimmune Diseases

Th17 cells play a critical role in the pathogenesis of autoimmune diseases, including multiple sclerosis, rheumatoid arthritis, systemic lupus erythematosus, Sjogren's syndrome, and inflammatory bowel disease. Despite the extensive investigation into this T cell lineage, little is understood regarding the role of Th17 lineage-specific lncRNAs (long non-coding RNAs) > 200 nt. lncRNAs may influence disease through a variety of mechanisms; their expression could be regulated by SNPs. lncRNAs can also affect the expression of neighboring genes or complementary miRNAs, and their expression may have lineage-specific patterns. In the system biology study presented here, the effective lncRNAs from different criteria were predicted for each autoimmune disease, and we then evaluated their expression levels in 50 MS patients compared to 25 controls using qRT-PCR. We identified changes in the expression levels of AL450992.2, AC009948.5, and RP11-98D18.3 as potential peripheral blood mononuclear cell (PBMC) biomarkers for MS among our studied lncRNAs in which co-expression analysis of AL450992.2 had the most AUCs, and the relationship to RORC was also assessed. We propose that the recurrently deregulated lncRNAs identified in this report could provide a valuable resource for studies aimed at delineating the relationship between functional lncRNAs and autoimmune disorders.

Defining the proteomic landscape of rheumatoid arthritis: progress and prospective clinical applications

INTRODUCTION

The heterogeneity of Rheumatoid Arthritis (RA) and the absence of clinical tests accurate enough to identify the early stages of this disease have hampered its management. Therefore, proteomics research is increasingly focused on the discovery of novel biological markers, which would not only be able make an early diagnosis, but also to gain insight into the different pathological mechanisms underlying the heterogeneity of RA and also to stratify patients, which is critical to enabling effective treatments. Areas covered: The proteomic approaches that have been utilised to provide knowledge about RA pathogenesis, and to identify biomarkers for RA diagnosis, prognosis, disease monitoring and prediction of response to therapy, are summarized. Expert commentary: Although each proteomic study is unique in its design, all of them have contributed to the understanding of RA pathogenesis and the discovery of promising biomarkers for patient stratification, which would improve clinical care of RA patients. Still, efforts need to be made to validate these findings and translate them into clinical practice.

Design of Chemical Conjugate for Targeted Therapy of Multiple Sclerosis Based of Constant Fragment of Human Antibody Heavy Chain and Peptoid Analog of Autoantigen MOG35-55

Elimination of B cells producing autoantibodies to neuroantigens is considered as beneficial in the treatment of multiple sclerosis. Myelin oligodendrocyte glycoprotein (MOG) is a significant autoantigen in multiple sclerosis. It was shown that MOG-like peptoid AMogP3 can bind autoantibodies produced by pathological lymphocytes. We propose a structure of an innovative drug for targeted elimination of the pool of autoreactive B cells responsible for multiple sclerosis pathogenesis; this compound is a complex of peptoid AMogP3 with Fc fragment of human immunoglobulin. The obtained Fc-PEG-AMogP3 conjugate effectively interact with autoreactive antibodies, which attests to their high therapeutic potential.

High affinity binding of conformationally constrained synthetic oligomers to an antigen-specific antibody: Discovery of a diagnostically useful synthetic ligand for murine Type 1 diabetes autoantibodies

'Antigen surrogates' are synthetic, non-natural molecules that recognize the antigen-binding sites of antibodies. These molecules are of interest as replacements for native antigens as antibody 'capture agents' in ELISA-like assays of potential diagnostic utility, for example when the antibody is indicative of a disease state. Antigen surrogates for disease-related antibodies can be mined from one-bead one-compound (OBOC) libraries by first denuding the library of ligands for antibodies present in the serum of control patients or animals, followed by screening the remainder of the library against serum from individuals with a particular disease of interest. Most of the work in this area has been done with peptoids (oligomers of N-alkylated glycine), which provide antibody ligands with only modest affinity and selectivity. Here, we explore the hypothesis that this is due to the 'floppiness' of the peptoid backbone by creating libraries of peptoid-like molecules that have conformation-restricting structural elements inserted into their backbones. Indeed, we show here that these libraries can provide high affinity and selectivity antigen surrogates and that this much-improved binding is completely dependent on conformational restriction of the oligomer chain.

Multiplex planar microarrays for disease prognosis, diagnosis and theranosis

Advanced diagnostic methods and algorithms for immune disorders provide qualitative and quantitative multiplex measurement for pre-clinical prognostic and clinical diagnostic biomarkers specific for diseases. Choice of therapy is confirmed by modulating diagnostic efficacy of companion, theranotic drug concentrations. Assay methods identify, monitor and manage autoimmune diseases, or risk thereof, in subjects who have, or who are related to individuals with autoimmune disease. These same diagnostic protocols also integrate qualitative and quantitative assay test protocol designs for responder patient assessment, risk analysis and management of disease when integrating multiplex planar microarray diagnostic tests, patient theranostic companion diagnostic methods and test panels for simultaneous assessment and management of dysimmune and inflammatory disorders, autoimmunity, allergy and cancer. Proprietary assay methods are provided to identify, monitor and manage dysimmune conditions, or risk thereof, in subjects with pathological alterations in the immune system, or who are related to individuals with these conditions. The protocols can be used for confirmatory testing of subjects who exhibit symptoms of dysimmunity, as well as subjects who are apparently healthy and do not exhibit symptoms of altered immune function. The protocols also provide for methods of determining whether a subject has, is at risk for, or is a candidate for disease therapy, guided by companion diagnosis and immunosuppressive therapy, as well as therapeutic drug monitoring and theranostic testing of disease biomarkers in response to immuno-absorption therapy. The multiplex test panels provide the components that are integral for performing the methods to recognized clinical standards.

Roadblocks for integration of novel biomarker concepts into clinical routine: the peptoid approach

In the field of Alzheimer’s disease, the development of novel biomarker assays is critically needed to improve the early diagnosis of the disease, to estimate the risk of developing the disease, to predict the rate of cognitive decline, and to monitor the response or effectiveness of a therapy. The molecular mechanisms of the disease are becoming more evident. This basic knowledge has yet to be translated into novel biomarker tools with a clinical value for general use by the community. There is therefore high interest in evaluating new technological approaches beside the classical immunoassay approach. The present paper discusses the hypothesis that there might be an adaptive immune response, unique to Alzheimer’s disease, which can be visualized by the presence in body fluids of antibodies against specific analytes. Current technologies to identify such antibodies are reviewed. In addition, the major challenges to transfer discovery results of the novel antibody-based biomarker assays to a clinically relevant test will be discussed.

Discovery of biomarkers for systemic lupus erythematosus using a library of synthetic autoantigen surrogates

Antibodies to a wide range of self-antigens, including those directed against nucleic acids or nucleic acid-binding proteins are the essential biomarkers for diseases such as systemic lupus erythematosus (SLE). Highly complex libraries of nonamers consisting of N-substituted glycines (peptoids) were screened for compounds that bound IgG from patients with SLE and earlier, incomplete autoimmune syndromes. Peptoids were identified that could identify subjects with SLE and related syndromes with a high sensitivity (70%) and specificity (97.5%). Immobilized peptoids were used to isolate IgG from both healthy subjects and SLE patients that reacted with known RNA-binding proteins. In the case of SLE patients, the peptoid-purified IgG reacted with several autoantigens, suggesting that the peptoids are capable of interacting with multiple, structurally similar molecules. These results show that the measurement of IgG binding to peptoids can identify subjects with high levels of pathogenic autoantibodies.

Autoantibody profiling in multiple sclerosis using arrays of human protein fragments

Profiling the autoantibody repertoire with large antigen collections is emerging as a powerful tool for the identification of biomarkers for autoimmune diseases. Here, a systematic and undirected approach was taken to screen for profiles of IgG in human plasma from 90 individuals with multiple sclerosis related diagnoses. Reactivity pattern of 11,520 protein fragments (representing ∼38% of all human protein encoding genes) were generated on planar protein microarrays built within the Human Protein Atlas. For more than 2,000 antigens IgG reactivity was observed, among which 64% were found only in single individuals. We used reactivity distributions among multiple sclerosis subgroups to select 384 antigens, which were then re-evaluated on planar microarrays, corroborated with suspension bead arrays in a larger cohort (n = 376) and confirmed for specificity in inhibition assays. Among the heterogeneous pattern within and across multiple sclerosis subtypes, differences in recognition frequencies were found for 51 antigens, which were enriched for proteins of transcriptional regulation. In conclusion, using protein fragments and complementary high-throughput protein array platforms facilitated an alternative route to discovery and verification of potentially disease-associated autoimmunity signatures, that are now proposed as additional antigens for large-scale validation studies across multiple sclerosis biobanks.

Proteomics-based identification of haptoglobin as a favourable serum biomarker for predicting long-term response to splenectomy in patients with primary immune thrombocytopenia

BACKGROUND

Splenectomy is the most effective treatment for patients with primary immune thrombocytopenia (ITP) who fail to respond to steroid therapy. Thus far, there is no effective means to predict the long-term haematological response of the procedure. The purpose of this study was to identify serum biomarkers as predictors of long-term response based on a proteomics approach.

METHODS

The serum samples of ITP patients were collected before splenectomy and seven days after surgery. After depletion of the abundant serum proteins, pooled preoperative serum samples from four responders to splenectomy, four nonresponders and four healthy controls were subjected to two-dimensional gel electrophoresis (2-DE). Nine protein spots with at least a five-fold alteration in expression between responders and nonresponders were all identified as haptoglobin (Hp) by matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometer (MS) analysis. The validation of serum Hp expression was performed using enzyme-linked immunosorbent assays (ELISA) in thirty-seven responders, thirteen nonresponders and twenty-one healthy controls.

RESULTS

The preoperative serum levels of Hp in the nonresponders (925.9 ± 293.5 μg/ml) were significantly lower than those in the responders (1417.4 ± 315.0 μg/ml, p <0.001) and the healthy controls (1409.1 ± 354.2 μg/ml, p <0.001), while there was no significant difference between the latter two groups. The postoperative serum levels of Hp in responders and nonresponders were (1414.1 ± 225.0 μg/ml) and (952.9 ± 202.4 μg/ml), respectively. There were no significant differences between the serum Hp levels before and after surgery in both responders and nonresponders (p>0.05). The preoperative serum levels of Hp did not significantly correlate with preoperative platelet count of the same blood samples (r = 0.244, p = 0.087), while it positively correlated with postoperative peak platelet count (r = 0.622, p < 0.001). The optimal cutoff value of preoperative serum Hp levels (1173.80 μg/ml) derived from the receiver operating characteristic (ROC) curve led to 78.4% sensitivity and 84.6% specificity.

CONCLUSIONS

These results suggest that serum Hp levels may serve as a favourable predictor for the long-term response to splenectomy in ITP and may help to understand the pathophysiological differences between responders and nonresponders.

Musculoskeletal Findings in Behcet's Disease

Behcet's disease is a multisystem disease characterized by recurrent oral and genital ulcers, relapsing uveitis, mucocutaneous, articular, gastrointestinal, neurologic, and vascular manifestations. Rheumatologic manifestations may also occur in Behcet's disease, and arthritis and arthralgia are the most common musculoskeletal findings followed by enthesopathy, avascular necrosis, myalgia, and myositis. Although the main pathology of Behcet's disease has been known to be the underlying vasculitis, the etiology and exact pathogenesis of the disease are still unclear. Musculoskeletal findings of Behcet's disease, the relationship between Behcet's disease and spondyloarthropathy disease complex, and the status of bone metabolism in patients with Behcet's disease were discussed in this paper.

Identification of candidate IgG biomarkers for Alzheimer's disease via combinatorial library screening

The adaptive immune system is thought to be a rich source of protein biomarkers, but diagnostically useful antibodies remain unknown for a large number of diseases. This is, in part, because the antigens that trigger an immune response in many diseases remain unknown. We present here a general and unbiased approach to the identification of diagnostically useful antibodies that avoids the requirement for antigen identification. This method involves the comparative screening of combinatorial libraries of unnatural, synthetic molecules against serum samples obtained from cases and controls. Molecules that retain far more IgG antibodies from the case samples than the controls are identified and subsequently tested as capture agents for diagnostically useful antibodies. The utility of this method is demonstrated using a mouse model for multiple sclerosis and via the identification of two candidate IgG biomarkers for Alzheimer's disease.