Rheumatic diseases: Environment and genetics

Challenges and promise of targeting miRNA in rheumatic diseases: a computational approach to identify miRNA association with cell types, cytokines, and disease mechanisms

MicroRNAs (miRNAs) are small non-coding RNAs that alter the expression of target genes at the post-transcriptional level, influencing diverse outcomes in metabolism, cell differentiation, proliferation, cell survival, and cell death. Dysregulated miRNA expression is implicated in various rheumatic conditions, including ankylosing spondylitis (AS), gout, juvenile idiopathic arthritis (JIA), osteoarthritis (OA), psoriatic arthritis, rheumatoid arthritis (RA), Sjogren's syndrome, systemic lupus erythematosus (SLE) and systemic sclerosis. For this review, we used an open-source programming language- PowerShell, to scan the massive number of existing primary research publications on PubMed on miRNAs in these nine diseases to identify and count unique co-occurrences of individual miRNAs and the disease name. These counts were used to rank the top seven most relevant immuno-miRs based on their research volume in each rheumatic disease. Individual miRNAs were also screened for publication with the names of immune cells, cytokines, and pathological processes involved in rheumatic diseases. These occurrences were tabulated into matrices to identify hotspots for research relevance. Based on this information, we summarize the basic and clinical findings for the top three miRNAs - miR-146, miR-155, and miR-21 - whose relevance spans across multiple rheumatic diseases. Furthermore, we highlight some unique miRNAs for each disease and why some rheumatic conditions lack research in this emerging epigenetics field. With the overwhelming number of publications on miRNAs in rheumatic diseases, this review serves as a 'relevance finder' to guide researchers in selecting miRNAs based on the compiled existing knowledge of their involvement in disease pathogenesis. This approach applies to other disease contexts with the end goal of developing miRNA-based therapeutics.

Traditional and modern management strategies for rheumatoid arthritis

Rheumatoid arthritis (RA) is a serious disorder of the joints affecting 1 or 2% of the population aged between 20 and 50 years worldwide. RA is the foremost cause of disability in developing and Western populations. It is an autoimmune disease-causing inflammation and pain involving synovial joints. Pro-inflammatory markers, including cytokines, such as interleukin -1 (IL-1), IL-6, IL-7, IL-8, and tumor necrosis factor-α (TNF-α) are involved in RA. RA treatment involves TNF-α blockade, B cell therapy, IL-1 and IL-6 blockade, and angiogenesis inhibition. Synthetic drugs available for the treatment of RA include disease-modifying anti-rheumatic drugs (DMARD), such as cyclophosphamide, sulfasalazine, methotrexate, nonsteroidal anti-inflammatory drugs (NSAIDs), and intramuscular gold. These agents induce adverse hepatorenal effects, hypertension, and gastric ulcers. We found that patients diagnosed with chronic pain, as in RA, and those refractory to contemporary management are most likely to seek traditional medicine. Approximately 60-90% of patients with arthritis use traditional medicines. Therefore, the efficacy and safety of these traditional medicines need to be established. The treatment for RA entails a comprehensive multidisciplinary strategy to reduce pain and inflammation and to restore the activity of joints. The potential medicinal plants exhibiting anti-arthritic and anti-rheumatic pharmacological activity are reviewed here.

circFADS2 protects LPS-treated chondrocytes from apoptosis acting as an interceptor of miR-498/mTOR cross-talking

We aimed to investigate the regulation of circular RNAs in lipopolysaccharide (LPS)-treated chondrocytes isolated from SD rat. In this study, we analyzed how circFADS2 was regulated in LPS-treated chondrocytes and isolates from Rheumatoid arthritis (RA) patients and found that circFADS2 and mTOR were highly expressed whereas miR-498 expression was significantly reduced. We then silenced circFADS2 in LPS-treated chondrocytes; this resulted in a declined expression of type II collagen, but an increase in the expression of MMP-13, COX-2, and IL-6. Overall, silencing circFADS2 caused a significant reduction in the proliferative rate of LPS-treated chondrocytes, increased apoptotic levels, miR-498 upregulation, and mTOR downregulation. Dual-luciferase reporter assay indicated that circFADS2 directly targeted miR-498. In contrast, miR-498 down-regulation affected circFADS2 silencing, promoting extracellular matrix (ECM) degradation and apoptosis. The 3’ UTR of the mTOR gene is targeted by miR-498, and consequently, in cells transfected with miR-498, there was a significant reduction of mTOR expression at the protein and mRNA levels. Silencing mTOR had a similar effect to circFADS2 silencing on type II collagen, MMP-13, COX-2, and IL-6 expression, as well as cell proliferation and apoptosis. In conclusion, circFADS2 may affect LPS-induced chondrocytes properties by regulating the ECM catabolism, inflammation, and apoptosis in chondrocytes.

Association of microRNAs genes polymorphisms with arthritis: a systematic review and meta-analysis

Objective: To investigate whether microRNAs genes’ polymorphisms are associated with arthritis. Methods: The PubMed, Cochrane Library et al. were systematically searched to identify case–control studies, systematic reviews and meta-analyses. A meta-analysis was performed to calculate odds ratios (ORs), and confidence intervals (CIs) at 95% using fixed-effect model or random-effects model. Results: Twenty-two case–control studies involving 10489 participants fulfilled the inclusion criteria. MiR-146a rs2910164 (G/C) was not significantly associated with the risk of rheumatoid arthritis (RA) in any model. Significant associations were found between miR-146a rs2910164 (G/C) and the risk of psoriatic arthritis (PsA) in the heterozygous model and the dominant model. The heterozygous model showed a significant association between the miR-146a rs2910164 (G/C) polymorphism and ankylosing spondylitis (AS). And there was no significant association of miR-146a rs2910164 (G/C) with risk of juvenile rheumatoid arthritis (JRA) at any model. Additionally, there was a significant association of miR-499 rs3746444 (T/C) with risk of RA at two genetic models, and with a moderate heterogeneity. When subgroup analysis by ethnicity, significant associations were almost found between miR-499 rs3746444 (T/C) and the risk of RA in any model in Caucasian populations, and there is no heterogeneity. Conclusions: The association of miR-146a rs2910164 (G/C) with RA was not found. And there was a significant association between miR-146a rs2910164(G/C) and PsA or AS. MiR-499 rs3746444 (T/C) was associated with RA in Caucasian populations. These findings did not support the genetic association between miR-146a rs2910164 (G/C) and JRA susceptibility, as well as the association of miR-196a-2 rs11614913 (C/T), miR-146a rs2431697, miR-146a rs57095329, miR-149 rs22928323 with arthritis.

The recurrence risk of genetic complex diseases

Complex inherited diseases affected by an interaction between collective effects of the genotype at one or multiple loci either to increase or to lower susceptibility to disease, combined with a variety of environmental exposures that may trigger, accelerate, exacerbate, or protect against the disease process. The new aspects of genetic techniques have been opened for diagnosis and analysis of inherited disorders. While appropriate Mendelian laws is applied to estimate the recurrence risk of single gene diseases, using empirical recurrence risks are the most important and available method to evaluate pedigree of complex (multifactorial), chromosomal, and unknown etiology disorders. Although, generally, empirical recurrent risks are not accurate, either because of the difference of gene frequencies and environmental factors among populations or heterogeneity of disease; using results of plenty family population studies, computerized estimating programs, genotyping technologies, and Genome-wide association studies (GWASs) of single nucleotide polymorphisms (SNPs), can make it possible nowadays to estimate these risks. The specific family situation and importance recurrence risks of some common complex genetic diseases will be presented in this review and some important multifactorial disorders’ recurrence risks will be summarized to help genetic counselors for supporting families and representing better view of genetic disorders.

TMEM187-IRAK1 Polymorphisms Associated with Rheumatoid Arthritis Susceptibility in Tunisian and French Female Populations: Influence of Geographic Origin

Polymorphisms have been identified in the Xq28 locus as risk loci for rheumatoid arthritis (RA). Here, we investigated the association between three polymorphisms in the Xq28 region containing TMEM187 and IRAK1 (rs13397, rs1059703, and rs1059702) in two unstudied populations: Tunisian and French. The rs13397 G and rs1059703 T major alleles were significantly increased in RA patients (n = 408) compared with age-matched controls (n = 471) in both Tunisian and French women. These results were confirmed by a meta-analysis replication study including two independent Greek and Korean cohorts. The rs1059702 C major allele was significantly associated with RA, only with French women. In the French population, the GTC haplotype displayed a protective effect against RA, while the ATC, GCC, and GTT haplotypes conferred significant risk for RA. No association for these haplotypes was found in the Tunisian population. Our results replicated for the first time the association of the three Xq28 polymorphisms with RA risk in Tunisian and French populations and suggested that RA susceptibility is associated with TMEM187-IRAK1 polymorphisms in women. Our data further support the involvement of X chromosome in RA susceptibility and evidence ethnicities differences that might be explained by differences in the frequencies of SE HLA-DRB1 alleles between both populations.

Different end-points to assess effects in systemic lupus erythematosus patients exposed to pesticide mixtures

Systemic Lupus Erythematosus (SLE) is an autoimmune disease with high female predominance in reproductive years. It is characterized by a pronounced inflammation and production of a variety of autoantibodies. SLE pathogenesis is influenced by genes, hormones and environmental agents. The aim of this study was assess the possible effect of environmental pesticide mixtures in SLE patients. Oxidative DNA damage was measured using the comet assay modified by enzyme Endo III for detection of oxidized bases (Endo Sites), and oxidative stress by the measurement of the activity of catalase (CAT), superoxide dismutase (SOD) and lipid peroxidation (TBARS). Eighty-nine patients with diagnosis of SLE were included, 46% of them came from areas highly sprayed with pesticides and were compared with patients from urban areas with the same clinical and socio-demographic characteristics (p≥0.155). In order to identify factors that could predict DNA damage and oxidative stress, a binary logistic regression model with independent variables was developed: place of residence (p=0.007) have 75% of positive predictive value while smoking habit (p=0.186) have a 56% negative predictive value. The Odd Ratio (OR) obtained indicate that lupus patients living in rural areas presented 3.52 times more oxidative DNA damage compared to those living in the city. The prospects of applying biomarkers to assess exposure and biological effects, such as DNA damage and oxidative stress in autoimmune diseases, allow improving the characterization of individual risk.

Knowledge-based analysis of genetic associations of rheumatoid arthritis to inform studies searching for pleiotropic genes: a literature review and network analysis

Introduction

Pleiotropy describes the genetic effect of a single gene on multiple phenotypic traits. Gene variants directly affect the normal processes of a series of physiological and biochemical reactions, and therefore cause a variety of diseases traits to be changed accordingly. Moreover, a shared genetic susceptibility mechanism may exist between different diseases. Therefore, shared genes, with pleiotropic effects, are important to understand the sharing pathogenesis and hence the mechanisms underlying comorbidity.

Methods

In this study, we proposed combining genome-wide association studies (GWAS) and public knowledge databases to search for potential pleiotropic genes associated with rheumatoid arthritis (RA) and eight other related diseases. Here, a GWAS-based network analysis is used to recognize risk genes significantly associated with RA. These RA risk genes are re-extracted as potential pleiotropic genes if they have been proved to be susceptible genes for at least one of eight other diseases in the OMIM or PubMed databases.

Results

In total, we extracted 116 potential functional pleiotropic genes for RA and eight other diseases, including five hub pleiotropic genes, BTNL2, HLA-DRA, NOTCH4, TNXB, and C6orf10, where BTNL2, NOTCH4, and C6orf10 are novel pleiotropic genes identified by our analysis.

Conclusions

This study demonstrates that pleiotropy is a common property of genes associated with disease traits. Our results ascertained the shared genetic risk profiles that predisposed individuals to RA and other diseases, which could have implications for identification of molecular targets for drug development, and classification of diseases.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0715-1) contains supplementary material, which is available to authorized users.

Targeting CD226/DNAX accessory molecule-1 (DNAM-1) in collagen-induced arthritis mouse models

Background

Genetic studies have pointed out that CD226 variants, encoding DNAM-1, could be associated with susceptibility to rheumatoid arthritis. Therefore, we aimed to determine the influence of DNAM-1 on the development of arthritis using the collagen-induced arthritis (CIA) mouse model.

Methods

CIA was induced in mice on a DBA/1 background, treated in parallel with a DNAM-1 neutralizing monoclonal antibody, a control IgG and PBS, respectively. CIA was also induced in mice deficient for DNAM-1(dnam1−/−) and control dnam-1+/+ mice on a C57/BL6 background. Mice were monitored for clinical and ultrasound signs of arthritis. Histological analysis was performed to search for inflammatory infiltrates and erosions. The Mann–Whitney U test for non-related samples was used for statistical analysis.

Results

There was a non-significant trend for a less arthritic phenotype in mice receiving anti-DNAM-1 mAb at both clinical, ultrasound and histological assessments. But, we did not observe any difference between dnam1+/+ and dnam1−/− mice for incidence nor severity of clinical arthritis. Histological analysis revealed inflammatory scores similar in both groups, without evidence of erosion. Collagen antibodies levels were similar in all mice, confirming immunization with collagen.

Conclusion

Despite some clues suggesting a role of DNAM-1 in arthritis, these complementary approaches demonstrate no contribution of CD226/DNAM-1 in the arthritic phenotype. These results contrast with previous studies showing a role in vivo of DNAM-1 in some autoimmune disorders.

Electronic supplementary material

The online version of this article (doi:10.1186/s12950-015-0056-5) contains supplementary material, which is available to authorized users.

Evidence of ERBB3 gene association with rheumatoid arthritis predisposition

AIM

ERBB3 (v-erb-b2 erythroblastic leukemia viral oncogene homolog 3) gene was reported to be related with susceptibility to several autoimmune diseases. Taking this into account, we searched, for the first time, the ERBB3 gene association with rheumatoid arthritis liability.

METHODS

One hundred and eighty-six RA patients and 147 controls were enrolled in the study. Polymerase chain reaction - restriction fragment length polymorphism assay was conducted in rs2271189 and rs2292239 genotyping.

RESULTS

A statistically significant difference was observed in rs2271189 allele distribution between RA patients and controls (P = 0.029, odds ratio: 1.460, 95% confidence interval: 1.040-2.050).

CONCLUSION

As far as we know, this is the first study which correlates ERBB3 gene with RA susceptibility, adding to a previous report of chromosome 12q13 association with RA liability. Furthermore, we confirmed that polymorphism rs2271189 can predict better ERBB3 gene association with disorders than the previously reported ERBB3 variants. More studies in other ethnic groups of patients are needed so as to reveal the extent of the herein observed genetic association.

The association between TNFα gene polymorphisms and susceptibility to rheumatoid arthritis in an ethnic Kashmiri population: relationship with disease activity and severity markers

AIM

The aim of our study was to determine the genetic associations between polymorphisms of the TNFα gene (-308G/A and -238G/A) with disease susceptibility and severity in patients with rheumatoid arthritis (RA) in an ethnic Kashmiri population.

METHODS

Allele and genotype frequencies of TNFα-308G/A and TNFα-238G/A polymorphisms were compared between 150 RA patients and 200 healthy controls by using polymerase chain reaction - restriction fragment length polymorphism method. Demographic, clinical and serological data were prospectively evaluated. Disease activity score (DAS28) was also assessed.

RESULTS

We did not find any significant association between TNFα-308G/A and TNFα-238G/A polymorphism and RA risk (P > 0.05), but TNFα-308GG genotype was associated significantly with rheumatoid factor seropositivity (P < 0.01) and TNFα-238GA genotype was associated with swollen joint count < 5 (P = 0.04) as well as with less severe disease activity as measured by DAS28 score (P = 0.02).

CONCLUSION

Our findings suggest the possible roles of TNFα-308GG and TNFα-238GA as important determinants for the development of certain manifestations and disease severity in RA in ethnic Kashmiri population.

Cigarette smoking is not a risk factor for systemic sclerosis

OBJECTIVE

To investigate the association of cigarette smoking with susceptibility to systemic sclerosis (SSc) in a large, well-defined patient population.

METHODS

We conducted a review of 1,379 patients with SSc enrolled in the Scleroderma Family Registry and DNA Repository and/or the Genetics versus Environment in Scleroderma Outcome Study cohort. Smoking history was obtained from chart review or via telephone interview. Patients with SSc were subsequently categorized as never smokers or ever smokers. Patients with SSc for whom smoking data were available were matched 2:1 by age, sex, ethnicity, and state of residence to control subjects, using the Behavioral Risk Factor Surveillance System.

RESULTS

The majority of patients were white (74.2%), with Hispanics and blacks representing 11.3% and 9.7%, respectively. Most patients had limited cutaneous involvement (54%). For our comparative analyses, 621 patients were matched with control subjects. There was no significant difference in age, sex, ethnicity, and SSc subtype between matched versus unmatched patients. The majority of patients had never smoked (57%), while 43% of patients were classified as ever smokers. The patients with SSc did not differ from control subjects in terms of their smoking behavior (odds ratio [OR] 1.020, 95% confidence interval [95% CI] 0.839-1.240, P=0.842). Anti-topoisomerase I antibody-positive patients were more likely to be never smokers (OR 0.648, 95% CI 0.421-0.998, P=0.049), whereas no such association was observed with anticentromere and anti-RNA polymerase III antibodies.

CONCLUSION

Unlike its role in rheumatoid arthritis, smoking does not confer a risk for development of SSc, although it may impact disease severity.

Altered sequence of the ETS1 transcription factor may predispose to rheumatoid arthritis susceptibility

OBJECTIVE

ETS1 belongs to the ETS family of transcription factors that regulate the expression of various immune-related genes. The aim of this study was to identify whether the ETS1 single nucleotide polymorphism (SNP) rs11221332, described in Caucasian subjects, plays a role in rheumatoid arthritis (RA) susceptibility.

METHODS

We genotyped this polymorphism in 136 unrelated patients with RA and 147 healthy individuals with no history of autoimmune disease. Genotyping was performed with a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay and the data were analysed using SPSS statistical software.

RESULTS

A statistically significant difference was observed in the distribution of the rs11221332 genotypes between RA patients and controls (p = 0.041). Comparing the distribution of rs11221332 alleles between the groups studied, a greater difference was found [odds ratio (OR) 1.504, 95% confidence interval (CI) 1.036-2.183; p = 0.039].

CONCLUSIONS

The present study revealed, for first time, the positive association of a polymorphism in the sequence of the ETS1 transcription factor with RA susceptibility. Further studies in other ethnic groups of patients are needed to confirm the results of the present genetic association study related to ETS1, a widely used transcription factor in the regulation of the expression of various genes.

Epigenetic mechanisms in systemic lupus erythematosus and other autoimmune diseases

The pathogenic origin of autoimmune diseases can be traced to both genetic susceptibility and epigenetic modifications arising from exposure to the environment. Epigenetic modifications influence gene expression and alter cellular functions without modifying the genomic sequence. CpG-DNA methylation, histone tail modifications and microRNAs (miRNAs) are the main epigenetic mechanisms of gene regulation. Understanding the molecular mechanisms that are involved in the pathophysiology of autoimmune diseases is essential for the introduction of effective, target-directed and tolerated therapies. In this review, we summarize recent findings that signify the importance of epigenetic modifications in autoimmune disorders while focusing on systemic lupus erythematosus. We also discuss future directions in basic research, autoimmune diagnostics and applied therapy.

Updating the genetics of systemic sclerosis

PURPOSE OF REVIEW

Systemic sclerosis (SSc) is a connective tissue disease characterized by early generalized microangiopathy, immune system disturbances and massive deposits of collagen and other matrix substances in the connective tissue. Although rare, SSc presents a major medical challenge, being recognized as the most severe connective tissue disorder in terms of its prognosis. Molecular biology has provided unparalleled insight into the susceptibility genes conferring a predisposition to this disease and has improved our understanding of its complex immune pathogenesis. In this review, we focus on recent large candidate gene studies that have included replication and very recent genome-wide approaches.

RECENT FINDINGS

Attention has recently focused on both known and new susceptibility genes. Large studies have revealed various striking associations within the immune system, but associations with vascular or fibrotic factors were found to be weaker or were not replicated. The major histocompatibility complex genes are the predominant genetic region of importance for many autoimmune disorders, including SSc. Candidate gene studies and genome-wide studies have also provided evidence that various autoimmune genes implicated in innate immunity, T-cell differentiation and immune signaling play a critical role in this disease.

SUMMARY

The use of powerful molecular tools has shed light on the nature of the susceptibility genes for SSc and the pathophysiology of this disease. Postgenomic studies are now required to clarify the role of these genes. Improvements in diagnostic and prognostic tools are anticipated in the near future, together with the development of more specific immune therapy.