Abstract: Rheumatoid arthritis (RA) is the most common inflammatory arthropathy. The majority of evidence, derived from genetics, tissue analyses, models, and clinical studies, points to an immune-mediated etiology associated with stromal tissue dysregulation that together propogate chronic inflammation and articular destruction. A pre-RA phase lasting months to years may be characterized by the presence of circulating autoantibodies, increasing concentration and range of inflammatory cytokines and chemokines, and altered metabolism. Clinical disease onset comprises synovitis and systemic comorbidities affecting the vasculature, metabolism, and bone. Targeted immune therapeutics and aggressive treatment strategies have substantially improved clinical outcomes and informed pathogenetic understanding, but no cure as yet exists. Herein we review recent data that support intriguing models of disease pathogenesis. They allude to the possibility of restoration of immunologic homeostasis and thus a state of tolerance associated with drug-free remission. This target represents a bold vision for the future of RA therapeutics. Rheumatoid arthritis (RA) is the most common inflammatory arthropathy. The majority of evidence, derived from genetics, tissue analyses, models, and clinical studies, points to an immune-mediated etiology associated with stromal tissue dysregulation that together propogate chronic inflammation and articular destruction. A pre-RA phase lasting months to years may be characterized by the presence of circulating autoantibodies, increasing concentration and range of inflammatory cytokines and chemokines, and altered metabolism. Clinical disease onset comprises synovitis and systemic comorbidities affecting the vasculature, metabolism, and bone. Targeted immune therapeutics and aggressive treatment strategies have substantially improved clinical outcomes and informed pathogenetic understanding, but no cure as yet exists. Herein we review recent data that support intriguing models of disease pathogenesis. They allude to the possibility of restoration of immunologic homeostasis and thus a state of tolerance associated with drug-free remission. This target represents a bold vision for the future of RA therapeutics. Immune dysregulation was first implicated in the pathogenesis of rheumatoid arthritis (RA) by the discovery of anti-immunoglobulin G (IgG) antibodies known as rheumatoid factors, initially by Erik Waaler and then more fully described by H.M. Rose in the 1940s. However, concepts of how immune responses contribute to disease have evolved dramatically over the last 50 years. Autoreactivity as a pivotal step dominates the conceptual landscape, although other mechanisms, both immunologic and tissue-derived, clearly contribute to disease pathogenesis. Thus, RA is characterized by evidence of disordered innate immunity, including immune complex-mediated complement activation, adaptive immune responses against “self”-antigens comprising predominantly post-translationally modified proteins, dysregulated cytokine networks, osteoclast and chondrocyte activation, and imprinting of resident stromal cells that in turn develop semi-autonomous features that support disease progression (Arend and Firestein, 2012Arend W.P. Firestein G.S. Pre-rheumatoid arthritis: predisposition and transition to clinical synovitis.Nat. Rev. Rheumatol. 2012; 8: 573-586Crossref PubMed Scopus (0) Google Scholar, Firestein, 2003Firestein G.S. Evolving concepts of rheumatoid arthritis.Nature. 2003; 423: 356-361Crossref PubMed Scopus (1954) Google Scholar). Based on substantial new data identifying the immunologic and metabolic events that precede onset of clinical disease, even by years (i.e., “pre-RA”), and the increasing impact of the application of the advanced molecular “omics” revolution to disease investigation, an integrated hypothesis for disease pathology is emerging (Catrina et al., 2016Catrina A.I. Joshua V. Klareskog L. Malmström V. Mechanisms involved in triggering rheumatoid arthritis.Immunol. Rev. 2016; 269: 162-174Crossref PubMed Scopus (29) Google Scholar, Tan and Smolen, 2016Tan E.M. Smolen J.S. Historical observations contributing insights on etiopathogenesis of rheumatoid arthritis and role of rheumatoid factor.J. Exp. Med. 2016; 213: 1937-1950Crossref PubMed Google Scholar). In this review, we will posit that RA starts with a high-risk genetic background that, in combination with epigenomic marks that contribute to heritability and disease chronicity and stochastic environmental exposures that create neo-epitopes, launches a cascade of events inducing synovitis and ultimately chronic destructive arthritis (Figure 1). Based on the diversity of clinical responses to highly targeted therapeutic agents, we propose that RA probably does not comprise a single entity. Rather, it is perhaps more appropriately considered a syndrome with a common clinical phenotype arising from diverse pathways operating variably, albeit often with overlap, in individual patients (Firestein, 2014Firestein G.S. The disease formerly known as rheumatoid arthritis.Arthritis Res. Ther. 2014; 16: 114Crossref PubMed Scopus (8) Google Scholar). Genetic factors clearly play a role in RA risk, severity, and progression. Monozygotic twins share RA on about 12%–15% of occasions compared to 1% for the general population and around 2%–5% for fraternal twins or other first-degree relatives. This relatively low concordance implicates many other factors, including those in the environment and the microbiome in pathogenesis. Note also that gene sequences are not the sole determinant of heritability, and epigenetic marks probably also contribute, especially for monozygotic twins (Kaminsky et al., 2009Kaminsky Z.A. Tang T. Wang S.C. Ptak C. Oh G.H. Wong A.H. Feldcamp L.A. Virtanen C. Halfvarson J. Tysk C. et al.DNA methylation profiles in monozygotic and dizygotic twins.Nat. Genet. 2009; 41: 240-245Crossref PubMed Scopus (420) Google Scholar). The most important genetic risk allele for RA resides in the class II major histocompatibility (MHC) locus, accounting for about 40% of the genetic influence. The odds ratio of developing RA in individuals with MHC class II HLA-DR4 alleles is about 5:1. This link between HLA-DR and RA was initially described in the 1970s with the observation that HLA-DR4 is present in 70% of RA patients, compared with about 30% of controls. A so-called shared “susceptibility epitope” (SE) was identified in amino acids 70 through 74 in the third hypervariable region of the DRβ chain. The sequence associated with disease is generally glutamine-leucine-arginine-alanine-alanine (QKRAA), which is present in some DR4 and DR14, in addition to DR1β chains. The SE with the closest links to RA include DRB∗0401, DRB∗0404, DRB∗0101, and DRB∗1402. More than 90% of patients with RA express at least one of these variants (Weyand et al., 1992Weyand C.M. Hicok K.C. Conn D.L. Goronzy J.J. The influence of HLA-DRB1 genes on disease severity in rheumatoid arthritis.Ann. Intern. Med. 1992; 117: 801-806Crossref PubMed Google Scholar). The SE is also associated with increased disease severity, such as extra-articular manifestations and progression of erosions. The SE region predominantly faces away from the antigen-binding groove that binds processed peptides for presentation to T cells, which has raised some questions about their precise contributory role (Firestein and Zvaifler, 2002Firestein G.S. Zvaifler N.J. How important are T cells in chronic rheumatoid synovitis?: II. T cell-independent mechanisms from beginning to end.Arthritis Rheum. 2002; 46: 298-308Crossref PubMed Scopus (0) Google Scholar). RA-specific peptides that bind to QKRAA-containing molecules have been difficult to identify (Kirschmann et al., 1995Kirschmann D.A. Duffin K.L. Smith C.E. Welply J.K. Howard S.C. Schwartz B.D. Woulfe S.L. Naturally processed peptides from rheumatoid arthritis associated and non-associated HLA-DR alleles.J. Immunol. 1995; 155: 5655-5662PubMed Google Scholar). This observation led to the notion that SE might also partially contribute by shaping the T cell repertoire in the thymus, altering intracellular HLA-DR trafficking and antigen loading, or serving as an autoantigen. More recently, linkage disequilibrium and informatics-based studies to understand the role of the SE identified additional amino acids located in the base of the antigen binding groove as a likely explanation for antigen selection, especially leucine or valine variants at amino acid 11 (Raychaudhuri et al., 2012Raychaudhuri S. Sandor C. Stahl E.A. Freudenberg J. Lee H.S. Jia X. Alfredsson L. Padyukov L. Klareskog L. Worthington J. et al.Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis.Nat. Genet. 2012; 44: 291-296Crossref PubMed Scopus (327) Google Scholar). Serine at amino acid 11 confers decreased risk for RA. The risk alleles, especially deep within the cleft, could directly increase risk via presentation of arthritogenic antigens, such as citrullinated proteins. For example, citrullinated vimentin peptides bind much more avidly to the RA HLA-DR than does native protein; in contrast, other MHCs do not exhibit this differential binding (Hill et al., 2003Hill J.A. Southwood S. Sette A. Jevnikar A.M. Bell D.A. Cairns E. Cutting edge: the conversion of arginine to citrulline allows for a high-affinity peptide interaction with the rheumatoid arthritis-associated HLA-DRB1∗0401 MHC class II molecule.J. Immunol. 2003; 171: 538-541Crossref PubMed Google Scholar, Law et al., 2012Law S.C. Street S. Yu C.H. Capini C. Ramnoruth S. Nel H.J. van Gorp E. Hyde C. Lau K. Pahau H. et al.T-cell autoreactivity to citrullinated autoantigenic peptides in rheumatoid arthritis patients carrying HLA-DRB1 shared epitope alleles.Arthritis Res. Ther. 2012; 14: R118Crossref PubMed Scopus (0) Google Scholar). Subsequent crystal studies have characterized in detail the nature of the citrullinated peptide binding to HLADRB1 (Scally et al., 2013Scally S.W. Petersen J. Law S.C. Dudek N.L. Nel H.J. Loh K.L. Wijeyewickrema L.C. Eckle S.B. van Heemst J. Pike R.N. et al.A molecular basis for the association of the HLA-DRB1 locus, citrullination, and rheumatoid arthritis.J. Exp. Med. 2013; 210: 2569-2582Crossref PubMed Scopus (0) Google Scholar). RA-associated alleles present citrullinated peptides efficiently to T cells, which, in turn, produce higher amounts of cytokines IL-17 and IFN-γ than to native peptide. Adaptive immune responses to citrullinated peptides are also characterized by the presence of “anti-citrullinated peptide antibodies” (ACPAs), observed in 80%–90% of RA patients. Together these data support the notion that HLA-DR risk for RA is based at least in part on the increased efficiency of antigen presentation for altered peptides rather than native proteins (van der Helm-van Mil et al., 2006van der Helm-van Mil A.H. Verpoort K.N. Breedveld F.C. Huizinga T.W. Toes R.E. de Vries R.R. The HLA-DRB1 shared epitope alleles are primarily a risk factor for anti-cyclic citrullinated peptide antibodies and are not an independent risk factor for development of rheumatoid arthritis.Arthritis Rheum. 2006; 54: 1117-1121Crossref PubMed Scopus (0) Google Scholar). Citrullination of peptides in the presence of environmental stress is ubiquitous in mammalian cells and is not a unique feature of RA. Instead, production of antibodies recognizing citrullinated peptides differentiates individuals at risk. The emergence of numerous other post-translationally modified protein targets, e.g., via carbamylation or acetylation, recognized by autoantibodies in RA is consistent with the notion of altered presentation of post-translationally modified peptides; other families of altered peptides could be implicated in discrete subsets of patients. Overall, genome-wide association studies (GWASs) and meta-genomic analyses have identified more than 100 single-nucleotide polymorphisms (SNPs) and genes associated with ACPA+ RA beyond the HLA. RA-associated SNPs tend to cluster around immune genes (Okada et al., 2014Okada Y. Wu D. Trynka G. Raj T. Terao C. Ikari K. Kochi Y. Ohmura K. Suzuki A. Yoshida S. et al.RACI consortiumGARNET consortiumGenetics of rheumatoid arthritis contributes to biology and drug discovery.Nature. 2014; 506: 376-381Crossref PubMed Scopus (514) Google Scholar). The genetic architecture of RA has recently been extensively reviewed (Kim et al., 2017Kim K. Bang S.Y. Lee H.S. Bae S.C. Update on the genetic architecture of rheumatoid arthritis.Nat. Rev. Rheumatol. 2017; 13: 13-24Crossref PubMed Google Scholar). In brief, individual SNPs usually provide modest contribution to risk with odds ratios typically in the 1.05- to 1.2-fold range, though this need not infer low functional impact. Combinations of these genes can potentially interact to increase risk. For example, a relatively rare combination of HLA-DR, PTPN22, and TRAF1-C5 SNPs increases risk more than 40-fold. While there are undoubtedly additional combinations or rare variants with high penetrance, the contribution of newly identified genes to overall risk is growing increasingly small. Notably, meta-analyses of patients with ACPA− RA show some differences from ACPA+ disease, consistent with the idea that “seronegative RA” should be considered a distinct clinical pathologic entity. Intriguing individual non-MHC linkages are associated with peptidyl arginase deiminase (PADI) and PTPN22. PADI gene products are enzymes that convert arginine to citrulline, creating new potential antigens that bind to RA-associated MHC proteins. An extended PADI4 haplotype prolongs its mRNA stability and could, therefore, increase peptide citrullination (Suzuki et al., 2003Suzuki A. Yamada R. Chang X. Tokuhiro S. Sawada T. Suzuki M. Nagasaki M. Nakayama-Hamada M. Kawaida R. Ono M. et al.Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis.Nat. Genet. 2003; 34: 395-402Crossref PubMed Scopus (746) Google Scholar). Up to a 2-fold increase in risk of RA was observed with PADI4 SNPs in Asian and North American cohorts. The PTPN22 allele with an amino acid substitution (R620W) doubles the risk of developing ACPA+ but not ACPA− RA. This SNP is also associated with many other immune-mediated diseases, including systemic lupus erythematosus (SLE) and type 1 diabetes (Rawlings et al., 2015Rawlings D.J. Dai X. Buckner J.H. The role of PTPN22 risk variant in the development of autoimmunity: finding common ground between mouse and human.J. Immunol. 2015; 194: 2977-2984Crossref PubMed Scopus (16) Google Scholar). The R620W allele is a gain-of-function change mutation in the PTPN22 protein, a phosphatase that regulates (among other signal proteins) Lck and ZAP70. Thus, modified T cell receptor signaling could alter either the T cell repertoire in the thymus or immune responses, or tolerance in the periphery. The R620W allele, however, also positively regulates TLR-induced type 1 IFN expression in myeloid cells via reduced efficiency of PTPN22W-mediated TRAF3 ubiquitination and thus could amplify innate cytokine expression to promote disease (Wang et al., 2013Wang Y. Shaked I. Stanford S.M. Zhou W. Curtsinger J.M. Mikulski Z. Shaheen Z.R. Cheng G. Sawatzke K. Campbell A.M. et al.The autoimmunity-associated gene PTPN22 potentiates toll-like receptor-driven, type 1 interferon-dependent immunity.Immunity. 2013; 39: 111-122Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar). A number of genes involved with adaptive immunity have RA-associated SNPs in a various populations (Yamamoto et al., 2015Yamamoto K. Okada Y. Suzuki A. Kochi Y. Genetics of rheumatoid arthritis in Asia--present and future.Nat. Rev. Rheumatol. 2015; 11: 375-379Crossref PubMed Scopus (8) Google Scholar). In addition to PTPN22, the co-stimulation receptors CTLA and CD28 have emerged from GWASs. Other genes associated with B cell function and/or antigen presentation such as BTLA (B and T lymphocyte attenuator), Fc receptors, and CD40 have been identified. Signal transduction genes and pathways that regulate immune function such as TRAF1-C5 and STAT4, cell migration (ELMO1), and fetal development (LBH) are also identified. Finally, multiple gene polymorphisms have been identified in cytokine or cytokine receptor coding loci, including TNF. This is especially relevant in light of the pivotal role of cytokines in synovitis described below and the consequent efficacy of targeted anti-cytokine, and cytokine receptor signal pathway therapeutics. In some cases, the causative mutations can alter expression or function. For instance, RA-associated TNF promoter polymorphisms at positions −238 and −308 can potentially modulate TNF gene expression (Fonseca et al., 2007Fonseca J.E. Cavaleiro J. Teles J. Sousa E. Andreozzi V.L. Antunes M. Amaral-Turkman M.A. Canhão H. Mourão A.F. Lopes J. et al.Contribution for new genetic markers of rheumatoid arthritis activity and severity: sequencing of the tumor necrosis factor-alpha gene promoter.Arthritis Res. Ther. 2007; 9: R37Crossref PubMed Scopus (0) Google Scholar). An IL-6 receptor polymorphism that is functionally implicated in the intensity of IL-6 signaling is also associated with RA (Ferreira et al., 2013Ferreira R.C. Freitag D.F. Cutler A.J. Howson J.M. Rainbow D.B. Smyth D.J. Kaptoge S. Clarke P. Boreham C. Coulson R.M. et al.Functional IL6R 358Ala allele impairs classical IL-6 receptor signaling and influences risk of diverse inflammatory diseases.PLoS Genet. 2013; 9: e1003444Crossref PubMed Scopus (65) Google Scholar). Thus, the genetic clues to RA pathogenesis implicate inflammation and adaptive and innate immunity at the core of pathogenesis. RA is properly considered an immune-mediated disease with a strong genetic influence. However, its origins may involve the interface between external influences and the immune system, manifest especially at mucosal surfaces. Three sites have been associated particularly with RA, namely (1) the lungs, (2) the oral mucosa, and (3) the gastrointestinal tract. Whereas precise mechanisms that enhance risk are not fully understood for each, it is likely that local tissue stress leads to post-translational modification of peptides with subsequent antibody formation serving as a common mechanism. Epidemiologic/genetic studies, particularly those arising from impressive Swedish registries, have highlighted the role of cigarette smoking as a prominent environmental risk factor for RA, pointing to a role for pulmonary mucosal biology in disease etiology. The amount and duration of smoking are important, with the highest risk observed with greater than 20 pack-years of exposure. Risk declines slowly back to normal within 10 years of smoking cessation (Källberg et al., 2011Källberg H. Ding B. Padyukov L. Bengtsson C. Rönnelid J. Klareskog L. Alfredsson L. EIRA Study GroupSmoking is a major preventable risk factor for rheumatoid arthritis: estimations of risks after various exposures to cigarette smoke.Ann. Rheum. Dis. 2011; 70: 508-511Crossref PubMed Scopus (151) Google Scholar), suggesting that effects are not solely toxin dependent but may also arise by altering immunologic function. Notably, other pulmonary exposures can replace smoking in increasing risk, e.g., silica or textile dust. Nevertheless, mechanisms underlying the relationship with smoking are uncertain (Catrina et al., 2014Catrina A.I. Ytterberg A.J. Reynisdottir G. Malmström V. Klareskog L. Lungs, joints and immunity against citrullinated proteins in rheumatoid arthritis.Nat. Rev. Rheumatol. 2014; 10: 645-653Crossref PubMed Scopus (41) Google Scholar). Exposure to inhaled toxic chemicals in cigarette smoke can potentially increase PADI expression in the airway and increase protein citrullination (Vassallo et al., 2014Vassallo R. Luckey D. Behrens M. Madden B. Luthra H. David C. Taneja V. Cellular and humoral immunity in arthritis are profoundly influenced by the interaction between cigarette smoke effects and host HLA-DR and DQ genes.Clin. Immunol. 2014; 152: 25-35Crossref PubMed Scopus (14) Google Scholar). Smoking-related risk interacts in a synergistic manner with MHC risk alleles. The QKRAA-containing HLA chains alone modestly increase the likelihood of developing RA 4- to 6-fold, but this risk increases up to 20- to 40-fold when combined with smoking (Lundström et al., 2009Lundström E. Källberg H. Alfredsson L. Klareskog L. Padyukov L. Gene-environment interaction between the DRB1 shared epitope and smoking in the risk of anti-citrullinated protein antibody-positive rheumatoid arthritis: all alleles are important.Arthritis Rheum. 2009; 60: 1597-1603Crossref PubMed Scopus (87) Google Scholar). Thus in individuals carrying risk HLA alleles, such peptides could be more efficiently presented and ACPAs generated via subsequent T-B cell help. Alternatively, “innate” B cell subsets could initiate responses to modified self-peptides, and thereafter present peptide to T cells. In this model, production of “autoantibodies” could result from “auto-reactive” T cell clones that are available to respond to modified peptides because they were not deleted during development since the altered proteins/peptides were not present in the thymus (Linn-Rasker et al., 2006Linn-Rasker S.P. van der Helm-van Mil A.H. van Gaalen F.A. Kloppenburg M. de Vries R.R. le Cessie S. Breedveld F.C. Toes R.E. Huizinga T.W. Smoking is a risk factor for anti-CCP antibodies only in rheumatoid arthritis patients who carry HLA-DRB1 shared epitope alleles.Ann. Rheum. Dis. 2006; 65: 366-371Crossref PubMed Scopus (0) Google Scholar). A corollary to this would be that a major immunologic regulatory deficit in RA patients is a failure to regulate T cell recognition of post-translationally modified self-proteins across a range of specificities—as observed above, this is compatible with the expression of a relatively broad autoantibody spectrum in clinical disease. Broncho-alveolar immunohistology shows high levels of citrullinated proteins in pulmonary macrophages and smoking increases such citrullinated proteins in broncho-alveolar lavage fluid (Makrygiannakis et al., 2008Makrygiannakis D. Hermansson M. Ulfgren A.K. Nicholas A.P. Zendman A.J. Eklund A. Grunewald J. Skold C.M. Klareskog L. Catrina A.I. Smoking increases peptidylarginine deiminase 2 enzyme expression in human lungs and increases citrullination in BAL cells.Ann. Rheum. Dis. 2008; 67: 1488-1492Crossref PubMed Scopus (228) Google Scholar). However, citrullinated proteins can also be present in the context of other diseases or even in clinically normal lungs (Catrina et al., 2014Catrina A.I. Ytterberg A.J. Reynisdottir G. Malmström V. Klareskog L. Lungs, joints and immunity against citrullinated proteins in rheumatoid arthritis.Nat. Rev. Rheumatol. 2014; 10: 645-653Crossref PubMed Scopus (41) Google Scholar). Thus, risk from smoking might be more complex than via PADI induction and may include promotion of epigenetic alterations, notably DNA methylation with inflammatory potential (Tsaprouni et al., 2014Tsaprouni L.G. Yang T.P. Bell J. Dick K.J. Kanoni S. Nisbet J. Viñuela A. Grundberg E. Nelson C.P. Meduri E. et al.Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation.Epigenetics. 2014; 9: 1382-1396Crossref PubMed Google Scholar). Perhaps the location of citrullination and the stochastic combination of altered peptides, innate leukocyte subsets, and mucosal inflammation conspire a permissive microenvironment for the creation of ACPAs. High-resolution CT studies demonstrate associations between ACPA formation and bronchial thickening in the pre-RA stages and support the idea that inflammatory responses are required (Reynisdottir et al., 2014Reynisdottir G. Karimi R. Joshua V. Olsen H. Hensvold A.H. Harju A. Engström M. Grunewald J. Nyren S. Eklund A. et al.Structural changes and antibody enrichment in the lungs are early features of anti-citrullinated protein antibody-positive rheumatoid arthritis.Arthritis Rheumatol. 2014; 66: 31-39Crossref PubMed Scopus (67) Google Scholar). More recent studies have shown signs of local inflammation in bronchial tissues of untreated RA patients (Reynisdottir et al., 2016Reynisdottir G. Olsen H. Joshua V. Engström M. Forsslund H. Karimi R. Sköld C.M. Nyren S. Eklund A. Grunewald J. Catrina A.I. Signs of immune activation and local inflammation are present in the bronchial tissue of patients with untreated early rheumatoid arthritis.Ann. Rheum. Dis. 2016; 75: 1722-1727Crossref PubMed Scopus (14) Google Scholar). Using B cell barcoding techniques, the frequency of circulating IgA plasmablasts was found to be elevated in at-risk subjects without RA who are ACPA positive, providing further evidence for a mucosal origin for at least a proportion of the autoimmunity detected in RA (Kinslow et al., 2016Kinslow J.D. Blum L.K. Deane K.D. Demoruelle M.K. Okamoto Y. Parish M.C. Kongpachith S. Lahey L.J. Norris J.M. Robinson W.H. Holers V.M. Elevated IgA plasmablast levels in subjects at risk of developing rheumatoid arthritis.Arthritis Rheumatol. 2016; 68: 2372-2383Crossref PubMed Scopus (10) Google Scholar). The relationship between the microbiome and RA has been suspected for many years and supported by pre-clinical studies. For example, arthritis susceptibility and severity in a variety of rodent strains is decreased when maintained germ-free or in environments with a restricted bacterial flora (Liu et al., 2016Liu X. Zeng B. Zhang J. Li W. Mou F. Wang H. Zou Q. Zhong B. Wu L. Wei H. Fang Y. Role of the gut microbiome in modulating arthritis progression in mice.Sci. Rep. 2016; 6: 30594Crossref PubMed Google Scholar). These data suggest that bacteria provide complex adjuvant functions that enhance autoimmunity, either directly (e.g., bacterial cell walls or lipopolysaccharides) or by critically altering the immunoregulatory mucosal environment. The latter could support particularly the generation of type 17 responses implicated in several animal models of RA (Miossec and Kolls, 2012Miossec P. Kolls J.K. Targeting IL-17 and TH17 cells in chronic inflammation.Nat. Rev. Drug Discov. 2012; 11: 763-776Crossref PubMed Scopus (433) Google Scholar). In humans, inflammation of the oral mucosa, particularly periodontitis, is associated with increased susceptibility to RA. The most common bacteria implicated in periodontitis is P. gingivalis, since it can express PADI. P. gingivalis could potentially citrullinate peptides in the oral mucosa that, in the context of inflammation, could promote ACPA generation (Wegner et al., 2010Wegner N. Wait R. Sroka A. Eick S. Nguyen K.A. Lundberg K. Kinloch A. Culshaw S. Potempa J. Venables P.J. Peptidylarginine deiminase from Porphyromonas gingivalis citrullinates human fibrinogen and α-enolase: implications for autoimmunity in rheumatoid arthritis.Arthritis Rheum. 2010; 62: 2662-2672Crossref PubMed Scopus (0) Google Scholar). While this concept is attractive, a clear association between P. gingivalis compared other bacteria is not consistently observed in unbiased microbiome studies. More recent data suggest that P. gingivalis or other bacteria could act, instead, by ligating Toll-like receptor 2 (TLR2) (de Aquino et al., 2014de Aquino S.G. Abdollahi-Roodsaz S. Koenders M.I. van de Loo F.A. Pruijn G.J. Marijnissen R.J. Walgreen B. Helsen M.M. van den Bersselaar L.A. de Molon R.S. et al.Periodontal pathogens directly promote autoimmune experimental arthritis by inducing a TLR2- and IL-1-driven Th17 response.J. Immunol. 2014; 192: 4103-4111Crossref PubMed Scopus (46) Google Scholar). This process could increase IL-1 production and stimulate local Th17 cell differentiation. An intriguing recent study identified that A. actinomycetemcomitans initiates hypercitrullination through the effect of a toxin, leukotoxin A (LtxA), mediated on neutrophils and was detected in RA patients’ oral microbiome wherein it could act as a bacterial trigger to disease (Konig et al., 2016aKonig M.F. Abusleme L. Reinholdt J. Palmer R.J. Teles R.P. Sampson K. Rosen A. Nigrovic P.A. Sokolove J. Giles J.T. et al.Aggregatibacter actinomycetemcomitans-induced hypercitrullination links periodontal infection to autoimmunity in rheumatoid arthritis.Sci. Transl. Med. 2016; 8: 369ra176Crossref PubMed Scopus (32) Google Scholar). In the colon, Prevotella copri species were enriched in an unbiased analysis of the gastrointestinal microbiome in early RA patients. Bacteroides species were decreased in the same patients (Scher et al., 2013Scher J.U. Sczesnak A. Longman R.S. Segata N. Ubeda C. Bielski C. Rostron T. Cerundolo V. Pamer E.G. Abramson S.B. et al.Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis.eLife. 2013; 2: e01202Crossref PubMed Google Scholar). While not fully understood, the over-representation of Prevotella was not observed in chronic RA or in other forms of arthritis. Subsequent studies in the Chinese population have extended these observations to include novel microbial species and demonstrated common expression in oral and GI mucosal sites in individuals that, remarkably, was correlated with ACPA levels and CRP. Moreover, further alterations in the microbiome occurred upon therapeutic immune modification (Zhang et al., 2015Zhang X. Zhang D. Jia H. Feng Q. Wang D. Liang D. Wu X. Li J. Tang L. Li Y. et al.The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment.Nat. Med. 2015; 21: 895-905Crossref PubMed Scopus (165) Google Scholar). Epigenetic modifications decorate genomic DNA and contribute to regulation of gene expression. The role of these marks had been widely viewed as key determinants of orderly gene expression during development as well as line