Altered gut transcriptome in spondyloarthropathy

Differentially Methylated DNA Regions in Monozygotic Twin Pairs Discordant for Rheumatoid Arthritis: An Epigenome-Wide Study

Objectives

In an explorative epigenome-wide association study (EWAS) to search for gene independent, differentially methylated DNA positions and regions (DMRs) associated with rheumatoid arthritis (RA) by studying monozygotic (MZ) twin pairs discordant for RA.

Methods

Genomic DNA was isolated from whole blood samples from 28 MZ twin pairs discordant for RA. DNA methylation was measured using the HumanMethylation450 BeadChips. Smoking, anti-cyclic citrullinated peptide antibodies, and immunosuppressive treatment were included as covariates. Pathway analysis was performed using GREAT.

Results

Smoking was significantly associated with hypomethylation of a DMR overlapping the promoter region of the RNF5 and the AGPAT1, which are implicated in inflammation and autoimmunity, whereas DMARD treatment induced hypermethylation of the same region. Additionally, the promotor region of both S100A6 and EFCAB4B were hypomethylated, and both genes have previously been associated with RA. We replicated several candidate genes identified in a previous EWAS in treatment-naïve RA singletons. Gene-set analysis indicated the involvement of immunologic signatures and cancer-related pathways in RA.

Conclusion

We identified several differentially methylated regions associated with RA, which may represent environmental effects or consequences of the disease and plausible biological pathways pertinent to the pathogenesis of RA.

The Effect of Cigarette Smoke Exposure on the Development of Inflammation in Lungs, Gut and Joints of TNFΔARE Mice

The inflammatory cytokine TNF-α is a central mediator in many immune-mediated diseases, such as Crohn’s disease (CD), spondyloarthritis (SpA) and chronic obstructive pulmonary disease (COPD). Epidemiologic studies have shown that cigarette smoking (CS) is a prominent common risk factor in these TNF-dependent diseases. We exposed TNF^ΔARE mice; in which a systemic TNF-α overexpression leads to the development of inflammation; to 2 or 4 weeks of air or CS. We investigated the effect of deregulated TNF expression on CS-induced pulmonary inflammation and the effect of CS exposure on the initiation and progression of gut and joint inflammation. Upon 2 weeks of CS exposure, inflammation in lungs of TNF^ΔARE mice was significantly aggravated. However, upon 4 weeks of CS-exposure, this aggravation was no longer observed. TNF^ΔARE mice have no increases in CD4+ and CD8+ T cells and a diminished neutrophil response in the lungs after 4 weeks of CS exposure. In the gut and joints of TNF^ΔARE mice, 2 or 4 weeks of CS exposure did not modulate the development of inflammation. In conclusion, CS exposure does not modulate gut and joint inflammation in TNF^ΔARE mice. The lung responses towards CS in TNF^ΔARE mice however depend on the duration of CS exposure.

Monitoring host responses to the gut microbiota

The gastrointestinal (GI) ecosystem is increasingly understood to be a fundamental component of health, and has been identified as a new focal point for diagnosing, correcting and preventing countless disorders. Shotgun DNA sequencing has emerged as the dominant technology for determining the genetic and microbial composition of the gut microbiota. This technology has linked microbiota dysbioses to numerous GI diseases including inflammatory bowel disease, obesity and allergy, and to non-GI diseases like autism and depression. The importance of establishing causality in the deterioration of the host-microbiota relationship is well appreciated; however, discovery of candidate molecules and pathways that underlie mechanisms remains a major challenge. Targeted approaches, transcriptional assays, cytokine panels and imaging analyses, applied to animals, have yielded important insight into host responses to the microbiota. However, non-invasive, hypothesis-independent means of measuring host responses in humans are necessary to keep pace with similarly unbiased sequencing efforts that monitor microbes. Mass spectrometry-based proteomics has served this purpose in many other fields, but stool proteins exist in such diversity and dynamic range as to overwhelm conventional proteomics technologies. Focused analysis of host protein secretion into the gut lumen and monitoring proteome-level dynamics in stool provides a tractable route toward non-invasively evaluating dietary, microbial, surgical or pharmacological intervention efficacies. This review is intended to guide GI biologists and clinicians through the methods currently used to elucidate host responses in the gut, with a specific focus on mass spectrometry-based shotgun proteomics applied to the study of host protein dynamics within the GI ecosystem.

Applications of systems approaches in the study of rheumatic diseases

The complex interaction of molecules within a biological system constitutes a functional module. These modules are then acted upon by both internal and external factors, such as genetic and environmental stresses, which under certain conditions can manifest as complex disease phenotypes. Recent advances in high-throughput biological analyses, in combination with improved computational methods for data enrichment, functional annotation, and network visualization, have enabled a much deeper understanding of the mechanisms underlying important biological processes by identifying functional modules that are temporally and spatially perturbed in the context of disease development. Systems biology approaches such as these have produced compelling observations that would be impossible to replicate using classical methodologies, with greater insights expected as both the technology and methods improve in the coming years. Here, we examine the use of systems biology and network analysis in the study of a wide range of rheumatic diseases to better understand the underlying molecular and clinical features.

Whole blood transcriptional profiling in ankylosing spondylitis identifies novel candidate genes that might contribute to the inflammatory and tissue-destructive disease aspects

INTRODUCTION

A number of genetic-association studies have identified genes contributing to ankylosing spondylitis (AS) susceptibility but such approaches provide little information as to the gene activity changes occurring during the disease process. Transcriptional profiling generates a 'snapshot' of the sampled cells' activity and thus can provide insights into the molecular processes driving the disease process. We undertook a whole-genome microarray approach to identify candidate genes associated with AS and validated these gene-expression changes in a larger sample cohort.

METHODS

A total of 18 active AS patients, classified according to the New York criteria, and 18 gender- and age-matched controls were profiled using Illumina HT-12 whole-genome expression BeadChips which carry cDNAs for 48,000 genes and transcripts. Class comparison analysis identified a number of differentially expressed candidate genes. These candidate genes were then validated in a larger cohort using qPCR-based TaqMan low density arrays (TLDAs).

RESULTS

A total of 239 probes corresponding to 221 genes were identified as being significantly different between patients and controls with a P-value <0.0005 (80% confidence level of false discovery rate). Forty-seven genes were then selected for validation studies, using the TLDAs. Thirteen of these genes were validated in the second patient cohort with 12 downregulated 1.3- to 2-fold and only 1 upregulated (1.6-fold). Among a number of identified genes with well-documented inflammatory roles we also validated genes that might be of great interest to the understanding of AS progression such as SPOCK2 (osteonectin) and EP300, which modulate cartilage and bone metabolism.

CONCLUSIONS

We have validated a gene expression signature for AS from whole blood and identified strong candidate genes that may play roles in both the inflammatory and joint destruction aspects of the disease.

Gene expression profiling in peripheral blood cells of patients with rheumatoid arthritis in response to anti-TNF-alpha treatments

The efficacy of anti-TNF-α therapies highlights the role of TNF-α in the pathogenesis of rheumatoid arthritis (RA). However, the mechanism of action of these agents is poorly understood at the molecular level. The aim of this study was to characterize the effects of anti-TNF-α treatment on the global gene expression profile in peripheral blood mononuclear cells (PBMCs) of responder RA patients. Changes in gene expression were determined using oligonucleotide microarrays (25,341 genes) in PBMCs obtained before and after 12 wk of treatment with either etanercept or adalimumab from responder RA patients. Two hundred fifty-one genes displayed significant changes (false discovery rate < 0.1%) in expression level (178 upregulations with mean fold change = 1.5 and 73 downregulations with mean fold change = -1.50) after 12 wk of treatment. Importantly, the expression of several genes, including those coding for the calcium binding proteins S100A12 and A8, CD14 antigen, Selectin P, or ribosomal protein L39, reported to be upregulated in RA patients, were found to be decreased after anti-TNF-α treatment. Globally, inflammation, immune response, apoptosis, protein synthesis, and mitochondrial oxido-reduction were the most affected pathways in response to anti-TNF-α treatment. The obtained gene expression signature in PBMCs provides new information to better understand the mechanisms of action of anti-TNF-α treatment in RA patients.

Interactions between gut inflammation and arthritis/spondylitis

PURPOSE OF REVIEW

The spectrum of spondyloarthritis is characterized by the intriguing co-occurrence of gut and joint inflammation, although no obvious anatomical link exists.

RECENT FINDINGS

Data from animal models identify stromal cells as important players in pathogenesis, although signalling through TNFRI appeared to be sufficient for development of combined gut and joint inflammation. Interleukin-23 receptor was identified as a susceptibility locus for ankylosing spondylitis.

SUMMARY

Human genome studies combined with animal model research provide us with new evidence in the fascinating field of the gut-joint axis. However, how these newly identified genetic associations can influence the immunological environment remains to be elucidated.

Joint involvement in inflammatory bowel disease: managing inflammation outside the digestive system

Joint inflammation is present in approximately 30% of patients with inflammatory bowel disease. Peripheral arthritis can frequently be controlled by an optimal treatment of the gut inflammation in association with short-term use of NSAIDs. Recurrent inflammation requires the use of sulfasalazine. More therapy-resistant forms and axial arthropathy can be treated with anti-TNF drugs, predominantly infliximab and adalimumab. An intensified multidisciplinary approach in research and in the clinic may help to unravel the question of why common etiopathogenic mechanisms ultimately lead to different disease phenotypes. Animal models may help to identify the most promising therapeutic strategies including in the near future modulation of adhesion molecules, costimulatory molecules and the Th17 pathway.

Indications and challenges of probiotics, prebiotics, and synbiotics in the management of arthralgias and spondyloarthropathies in inflammatory bowel disease

Arthralgia and spondyloarthropathy of the peripheral and the axial joints are common in patients with inflammatory bowel diseases. Evidence for this association has been provided by clinical, epidemiologic, and immunologic studies confirming the presence of shared inflammatory pathways in gut and joint. Bacterial gut infections such as Salmonella typhimurium, Yersinia enterocolitica, Shigella, Campylobacter jejuni may induce reactive peripheral arthritis and 20% of these patients may develop chronic spondyloarthropathy. It is not certain that arthralgias in inflammatory bowel diseases are more frequent than in the general population but clinical articular manifestations compatible with spondyloarthropathy are present in 10% to 40% of patients with inflammatory bowel diseases. These enteropathic peripheral arthropathies without axial involvement are subdivided into a pauciarticular of large joints and a bilateral symmetrical polyarthropathy. The rationale and the challenges of using prebiotics, probiotics, and synbiotics in the management of patients with inflammatory bowel diseases with arthralgias and spondyloarthropathy are briefly reviewed. The rationale is based on the modulation of the ubiquitous intestinal flora by bacteria and their products that have been proven to be safe. The challenge is to find the "window of opportunity" to treat the evolutionary stage of joint inflammation. It seems to us that the major aim is not to treat patients who have a self-limited inflammatory joint disorder, but those patients with persistent arthralgias in an early phase of the disease. Seronegative and seropositive patients with early arthritis, before damage may occur, could be managed by this approach to improve the quality of life and to positively influence the natural course of the disease.

Joint expedition: linking gut inflammation to arthritis

The tight connection between intestinal inflammation and arthritis in spondyloarthritis (SpA) has been studied extensively. Subclinical gut inflammation, which can be considered as a model for early Crohn's disease, was shown to be strongly associated with joint inflammation. Several early mucosal abnormalities were uncovered even in the absence of histological signs of inflammation, providing clues into the pathogenesis of SpA. Nevertheless, many questions remain unanswered. In this review, we highlight recent progress on this intimate relationship between gut and joint inflammation. Emerging evidence exists favoring a role for genes beyond human leukocyte antigen B27 in the genetic predisposition of SpA and intestinal inflammation. Furthermore, the role of these predisposing genes in modulating host-pathogen interaction at mucosal surfaces and the subsequent link between gut and joint inflammation are of utmost importance in understanding the pathogenesis of SpA.

The inflammatory status of old age can be nurtured from the intestinal environment

PURPOSE OF REVIEW

Recent studies suggest an association between inflammation status and the presence of chronic disease in the elderly. The review examines publications that address the low level of chronic inflammation and emphasizes how an altered host-microbiota interaction at the gut level could contribute to maintaining a low systemic inflammatory status in the elderly.

RECENT FINDINGS

The first population cross-sectional studies with relevant numbers of healthy elderlies show age-related global changes in gut microbiota with a consistent increase in nonpathogenic Gram-negative mainly Enterobacteria and country-specific changes in bifidobacteria. Noninvasive methods have permitted us to detect subclinical intestinal inflammation in the elderly population. Furthermore, few studies report on immune and/or inflammatory response; however, prebiotics, probiotics or synbiotics might improve the inflammatory condition of the elderly.

SUMMARY

A better understanding of the mechanisms of host-gut microbiota cross-talk would significantly help in the design of novel nutritional strategies targeting immune reactivity at the mucosal level.

The intimate relationship between gut and joint in spondyloarthropathies

PURPOSE OF REVIEW

The aim of this article is to highlight recent progress in the combined joint and gut disease in spondyloarthropathies.

RECENT FINDINGS

A set of genes has been identified that are differentially expressed in the colon of spondyloarthropathy and Crohn's disease patients. Reduction of human leukocyte antigen B27 (HLA B27) misfolding by additional beta2-microglobulin in HLA B27 transgenic rats unexpectedly increased disease severity, with more similarities to spondyloarthropathies. By contrast, colitis disappeared.

SUMMARY

Human genomic studies combined with animal model research provide new clues concerning the common pathogenesis of spondyloarthropathy and Crohn's disease, further substantiating the unique relationship between gut and joint inflammation.