Rheumatoid Arthritis (RA) is a chronic, progressive, autoimmune inflammatory disease affecting various organs and tissues, predominantly the synovial membrane, leading to joint destruction [1
]. Anti-citrullinated protein antibodies (ACPA) are important markers of RA, recognized as being the most specific. Starting from 2010, along with rheumatoid factor (RF), ACPA are used as serological markers according to the classification criteria of the American College of Rheumatology (ACR) and the European League Against Rheumatism (EULAR) [2
]. Their sensitivity and specificity for the diagnosis of RA are 64.9% and 97.9%, respectively [3
]. They recognize post-translationally modified auto-antigens generated by the peptidylarginine deiminases (PADs) enzymes family, mostly type 4 (PAD4), which transform arginine to new amino acid citrulline in fibrinogen, α-enolase, vimentin, filaggrin, collagen type I and type II and other various proteins, resulting in the production of immunogenic neoepitopes [4
]. There are five isoforms of PADs. PAD4 is found in neutrophils, monocytes, eosinophils, spleen, secretory glands and is connected to myeloid differentiation. The antibodies detected in RA can also be directed against PAD4, but their diagnostic application has not yet been established [5
]. Following the ENSEMBL database the PADI4
gene is placed on chromosome 1 in location 17,308,195–17,364,004 on the forward strand with references to assembly GRCh38. The gene has 5 transcript variants. However only 2 of them have an open reading frame (ORF) and can form transcripts called PADI-201
. The first consists of 663 amino acids (aa) and molecular weight 74.1 kDa, the second one 127 aa and 13.1 kDa [8
The activity of PAD4 demands supraphysiologic calcium concentration, but the presence of anti-PAD4 auto-antibodies (anti-PAD4) may reduce the PADs calcium requirements to the physiological scope [9
]. The synthesis of anti-PAD4 may facilitate the production of citrullinated proteins and contribute to the formation of ACPA [11
]. The post-translational proteins modifications like homocitrullination or citrullination lead to the synthesis of anti-carbamylated protein antibodies (aCarP) or ACPA, respectively. This may play a crucial role in RA pathogenesis. The data indicate that the presence of aCarP and ACPA predates RA development by about 7 (4–10) and 6 years (3–10), respectively. RF can be detected 2 (1–5) years before the onset of the symptoms [1
]. In other studies, RF was found to be present on average 6 years before disease onset [13
]. The citrullination leads to the synthesis of ACPA to a significant extent [14
]. This means that citrullination is a very important process causing immunization in RA, and activity of PAD4 enzyme can play a significant role in the pathogenesis of the disease. The chronic presence of post-translationally modified proteins (as a consequence of the infections of Porphyromonas gingivalis
or Aggregatibacter actinomycetemcomitans
and the action of other environmental factors, e.g., cigarette smoking) leads to the production of ACPA.
DNA methylation plays a key role in the control of gene expression. The process concerns CpG islands in the promoter regions of about 75% of genes and leads to gene silencing when over-expressed [15
]. Epigenetic mechanisms are considered a way of transmitting information from the environment to the inside of a cell through increasing or decreasing gene expression. This process occurs mainly before transcription (DNA methylation, histone modifications), but some of the regulatory mechanisms may also influence the formation of the final gene product after the creation of mRNA (a huge variety of non-coding RNAs) [16
]. An increasing number of studies are performed to better understand the role DNA methylation in rheumatoid arthritis, from initial studies showing the hypo-methylation of the genome to advanced epigenome studies using modern technology, which can identify differentially methylated genes (DMGs) and discover new candidate genes involved in RA [16
]. No studies on methylation of the PADI4
gene promoter have been conducted so far.
The expression of the PADI4 gene may be the spiritus movens of all processes leading to the development of RA and include environmental and disease-modifying factors. As the role of ACPA is well documented, it is important to determine whether epigenetic mechanisms, especially DNA methylation, are involved in protein citrullination and indirectly ACPA synthesis. Therefore, the primary aim of our study is to check whether the promoter region of the PADI4 gene is susceptible to epigenetic regulation by methylation and whether the degree of methylation is connected to DAS28 activity in RA group and compare this to healthy individuals. If such regulation takes place, we assume the lower degree of PADI4 methylation in RA vs. HC and the trend of decreasing methylation along with increasing disease activity. The relationships between the concentrations of anti-PAD4, ACPA and the disease activity and PADI4 methylation will also be evaluated.
Gene expression is subject to overlapping mechanisms of epigenetic regulation, such as methylation of gene promoters, and modifications of histone proteins (methylation, acetylation, phosphorylation, ubiquitination, etc.) Approximately 75% of the genes encoding proteins are regulated through the mechanism of methylation of their promoter regions which are rich in CpG islands [26
]. Genetic studies do not explain sufficiently the pathogenesis of RA. Viatte et al. suggest that interaction between genetic and environmental factors are a very promising and poorly understood new area of research [27
]. The literature contains no reports concerning the influence of PADI4
promoter region methylation on the development and course of RA. The results of our research indirectly prove that such an impact exists. The study did not evaluate the concentration or enzymatic activity of PAD4 but the effects of its presence—anti-PAD4 and ACPA. Our results hopefully open this area up for further studies.
The results and trends observed in our study seem to remain in line with the general rule of influence of methylation on gene expression. The reduced PADI4 methylation in RA patients results in increased expression of PAD enzyme (expression and activity not measured) and, consequently, increased protein citrullination and finally the excessive ACPA production. The results of our study suggest for the first time that the expression of the PADI4 gene is regulated by the methylation of its promoter region and has an impact on the course of RA. A lower degree of methylation of the PADI4 gene promoter is associated with the higher activity of RA. The effective treatment leads to a significant increase in methylation of this region, with the highest levels in patients in remission. However, the degree of methylation in effectively treated patients did not reach the level reported in HC. The study results may support the assumption that the higher methylation of CpG islands in the PADI4 promoter region implies a decrease in the synthesis of the PAD4 enzyme and consequently a reduction in the citrullination of various proteins. We also have found the lower concentration of anti-PAD4 and ACPA, along with a decrease in disease activity.
The subject of our study was not to assess the impact of individual drugs on the level of methylation of the PADI4
gen, but it is a very interesting issue that requires research. The literature is rich regarding the impact of various drugs for DNA methylation. Differentially methylated positions in DNA have recently been detected in MTX and etanercept treated patients between responders and non-responders. Further research is required to explain their role in RA [28
No single nucleotide polymorphism (SNP) of the PADI4
gene has been shown to be an important risk factor for RA in the European population [19
]. All recognized genetic risk alleles can explain up to 16% of overall disease probability [20
]. This indicates the huge importance of environmental factors and their impact on gene expression through epigenetic mechanisms, such as methylation of gene promoters [30
]. It has been demonstrated that cigarette smoking, which is one of the environmental factors, stimulates PADI4
gene expression [21
]. The latest research of Meng et al. confirms that gene and smoking-specific interaction may exist, especially in ACPA positive RA patients [31
]. The second environmental factor that is suspected to affect the development of RA is the chronic Porphyromonas gingivalis
infection. It is indicated as the responsible mechanism for the disturbance of citrullination caused by PAD bacterial activity and change in the expression of endogenous PAD [32
]. The suggested pathophysiological pathway of RA was shown in Figure 3
Our research indicates a modest or weak correlation between the low methylation of the PADI4 promoter region (responsible for high gene expression) and the high activity of the disease. As for RA pathogenesis, it can be concluded that the increased expression of PAD4 through various mechanisms (infection, smoking) results in protein citrullination. Consequently, pre-RA is induced, and then under favorable circumstances, symptomatic RA is developed.
A negative moderate or weak correlation between the methylation of the PADI4 gene promoter and anti-PAD4, ACPA and DAS28, which was found in our study, may indicate constant modulating effect of citrullination during the course and treatment of RA.
Regardless of the drug used, effective therapy yields a statistically significant increase in methylation of the PADI4
gene promoter. Because patients from the RA group were treated with various drugs, we can conclude that medicines, regardless of their main mechanism of action, may have an influence on PADI4
methylation or that the efficacy of treatment may even depend on the final hyper-methylation of this DNA region. The evaluation of DNA methylation seems to be an important source of information useful for the diagnosis, evaluation and treatment of RA. Plant et al. found 5 specific regions that, if hyper-methylated, indicate etanercept non-responder patients [28
The sensitivity and specificity of anti-PAD4 in the European population of RA patients were estimated at 42% and 92%, respectively. A relationship was also found between the presence of these antibodies and the intensity of radiological changes [9
]. The prevalence of anti-PAD4 in RA was estimated at 35–45% [34
]. Our study population of 125 RA patients showed 53.6% of anti-PAD4 positivity for the whole RA group and 7.14% in HC group. The test used in our cohort simultaneously detected IgM, IgA and IgG isotypes of anti-PAD4 antibodies. This may explain the more frequent occurrence of these antibodies in our study. We have observed the decreasing concentration of these antibodies with the lowering disease activity and the smallest concentration in HC (below the cut-off point). The significance of anti-PAD4 in RA is still discussed. Laura Martinez-Prat et al. have analyzed anti-PAD4 in a large cohort of 1473 RA patients and found its discriminative value between RA and HC especially in early RA [36
]. Guderud et al. recently showed different results and conclusions that anti-PAD4 is a bystander autoantibody [37
]. Taking into account the small number of publication, the usefulness of these antibodies under certain conditions may still be a matter for further evaluation and discussion especially as a prognostic or predictive marker [38
Our observations regarding the methylation of the PADI4
promoter prompt us to propose paying more attention to the period when the changes leading to the development of RA start, i.e., before the appearance of inflammatory symptoms. The term pre-RA is now used retrospectively in people who have developed RA; it refers to various stages before the development of any symptoms until the period of unclassified arthritis [39
]. Redefinition of pre-RA should be considered in such a way as to stop using the term retrospectively and to use it to make a current diagnosis in specific individuals. This may apply to people who, based on the presence of measurable genetic, serological, epigenetic and other factors are at high risk of developing RA in the future. This creates a need to narrow the current definition of pre-RA only to individuals who have not yet shown any symptoms of inflammation. In the future, this diagnosis may be the basis for the treatment of such patients in the conviction that the symptoms will occur over time. The treatment of such patients will not include anti-inflammatory agents but will be based on affecting epigenetic pathways, for example, by increasing methylation of the PADI4
promoter in the targeted manner and reducing the synthesis of citrullinated proteins. This may interrupt the pathophysiological pathway and lead to a reduction in ACPA and RF levels and prevent the development of inflammation or prolong the pre-RA phase.
The most important dependencies of the RA pathogenesis model are gathered in Figure 4
. In this model, we postulate that the hypo-methylation of the PADI4
gene described in our study leads to its excessive expression and increased PAD4 enzyme activity (requires confirmation in further research) and, as a consequence, enhances protein citrullination and breaks immune tolerance leading to synthesis of ACPA. The presented hypothesis may explain the role of hypo-methylation of the PADI4
gene. However, many questions remain. For example, how environmental factors lead to a decrease in genes methylation.
We realize that the number of 125 patients, especially after dividing according to DAS28 activity score, resulted in difficulties in achieving statistical significance in various comparisons. It is worth indicating the differences in PADI4 methylation between RA moderate and remission groups (p-value = 0.054) and RA low and HC (p-value = 0.07). For anti-PAD4 RA remission and HC, we have found a difference with p = 0.07. The weak point of our study is that DNA was extracted from the whole blood and not the specific cell line. We did not have the possibility to measure the PADI4 gene expression, because only frozen whole blood samples were available, and the lack of mRNA expression indicates that our research needs to be supplemented by future studies. Blood samples for testing were obtained in the same way. Patients with infections or severe comorbidities were excluded from the study. However, it should be emphasized that the current study design hinders the elimination of the effect of cellular heterogeneity between studied patients and groups. PADI4 promoter methylation status might be in unknown degree affected by the diversity of the PADI4 gene expressing cells. In current literature, there are no studies on methylation of the PADI4 gene. This is the first research concerning PADI4 promoter methylation in RA and further investigation is required. The results in specific cell types might be even more distinct and may bring interesting conclusions; similarly, a study concerning histone proteins alterations or interactions between PADI4 gene and targeted micro-RNAs is needed to better understand the role of PADI4 gene in RA pathogenesis. It is interesting that in the epigenome studies in the analyzed literature we did not find information indicating the detection of the DMGs in the PADI4 gene region on chromosome 1.