Biomarker identification and pathway analysis of rheumatoid arthritis based on metabolomics in combination with ingenuity pathway analysis

Abstract

Rheumatoid arthritis (RA) is a common autoimmune and inflammatory disease worldwide, but understanding its pathogenesis is still limited. In this study, plasma untargeted metabolomics of a discovery cohort and targeted analysis of a verification cohort were performed by gas chromatograph mass spectrometry (GC/MS). Univariate and multivariate statistical analysis were utilized to reveal differential metabolites, followed by the construction of biomarker panel through random forest (RF) algorithm.The pathways involved in RA were enriched by differential metabolites using Ingenuity Pathway Analysis (IPA) suite. Untargeted metabolomics revealed eighteen significantly altered metabolites in RA. Among these metabolites, a three-metabolite marker panel consisting of L-cysteine, citric acid and L-glutamine was constructed, using random forest algorithm that could predict RA with high accuracy, sensitivity and specificity based on a multivariate exploratory receiver operator characteristic (ROC) curve analysis. The panel was further validated by support vector machine (SVM) and partial least squares discriminant analysis (PLS-DA) algorithms, and also verified with targeted metabolomics using a verification cohort. Additionally, the dysregulated taurine biosynthesis pathway in RA was revealed by an integrated analysis of metabolomics and transcriptomics. Our findings in this study not only provided a mechanism underlying RA pathogenesis, but also offered alternative therapeutic targets for RA. K E Y W O R D Sbiomarker, metabolomics, rheumatoid arthritis, taurine biosynthesis, transcriptomics 1 INTRODUCTION Rheumatoid arthritis (RA) is a chronic autoimmune joint disease where persistent inflammation affects bone remodeling, leading to progressive bone destruction [1]. The prevalence of RA worldwide is between 0.5% and 1%, and RA often leads to disablement and subsequently reduced quality of life [2]. In RA, abnormal activation of the immune system elevates pro-inflammatory cytokines and chemokines levels, which can promote synovial angiogenesis and inflammation [3]. The synovium forms a hyperplastic pannus with infiltrated macrophage-like and fibroblast-like synoviocytes (FLS), which invades joints by secret-ing proteinases and inducing osteoclast differentiation [4-6]. In addition, RA is probably associated with various environmental triggers, and its symptoms can develop at different rates and in different joints from young age to old age [7]. Over the past decades, the treatment paradigms and therapeutic approaches have been rapidly enhanced, which transformed RA from a chronic and disabling condition requiring palliative measures to a potentially curable illness [8].Early disease diagnosis generally increases the chances for successful treatment, however, for RA patients at early stage the bone damage will not be detected by x-ray before months of diagnosis [9].Biomarkers, as an indicator of pathogenic processes, have been proved

A Review of Metabolomic Profiling in Rheumatoid Arthritis: Bringing New Insights in Disease Pathogenesis, Treatment and Comorbidities

“…Later, similar studies identified decreased levels of amino acids and glucose; increased levels of fatty acids and cholesterol, which were primarily associated with glycolytic pathway, fatty acid and amino acid metabolism; and other related pathways including TCA and urea cycles ( Table 2 ) [ 103 , 117 , 118 ]. In this sense, it was found that serum metabolites are differentially expressed in rheumatic diseases from healthy controls constituting a unique metabolic signature of each type of arthritis, which may be used as biomarkers for diagnosis and patient stratification [ 119 , 120 ]. Among the metabolites identified, homoserine, 4,8-dimethylnonanoyl carnitine, glyceraldehyde, lactic acid, dihydroxyfumaric acid and aspartic acid were possible candidates as biomarkers shared by four types of arthritis (rheumatoid arthritis, osteoarthritis, ankylosing arthritis and gout) compared with healthy controls [ 120 ] ( Table 2 ).…”

“…In addition to the potential of a metabolic fingerprint in RA, metabolites in plasma have been linked to disease status, since acylcarnitine metabolites increase in lower disease activity and glucuronate, and hypoxanthine increased in higher disease activity [ 95 ]. As blood samples are beginning to be a powerful tool for metabolome analysis in RA patients, a study also provided a candidate biomarker panel with three metabolites in plasma samples, which may be a more filtrate technique in a metabolic profile for complement with transcriptome analysis ( Table 2 ) [ 119 ].…”

Metabolic Profiling in Rheumatoid Arthritis, Psoriatic Arthritis, and Psoriasis: Elucidating Pathogenesis, Improving Diagnosis, and Monitoring Disease Activity

“…In particular, lower concentrations of glutamine were reported in plasma [ 28 ] and serum [ 26 , 29 , 30 ]. Glutamine is the most abundant free amino acid in human blood and acts as an immunomodulator since it affects T-cell-mediated immunity [ 29 ].…”

“…Moreover, responders to treatment with etanercept, a tumor necrosis factor inhibitor (TNFi), showed increased serum levels of BCAAs [ 39 ]. The taurine biosynthesis pathway was also found to be dysregulated in RA patients, and lower taurine levels were detected in patients with RA [ 28 ]. Additionally, taurine showed the potential to be employed as a biomarker for response to methotrexate (MTX) and TNFi therapy in RA serum samples, as elevated levels were found in MTX responders and decreased levels were found in TNFi responders [ 40 ].…”

Metabolomics in Autoimmune Diseases: Focus on Rheumatoid Arthritis, Systemic Lupus Erythematous, and Multiple Sclerosis

“…[47] Plasma GC-MS L-cysteine, citric acid, L-glutamine [48] In a clinical study on RA patients, amino acids such as isoleucine, valine, methionine, threonine, alanine, and histidine significantly decreased. Glucose and lactic acid also changed in the RA group, showing different trends in all studies.…”