International Journal of Molecular Sciences Review Effects of Biological Therapies on Molecular Features of Rheumatoid Arthritis , Chary Lopez-Pedrera * y , Nuria Barbarroja y, Alejandra M. Patiño-Trives, Maria Luque-Tévar, Eduardo Collantes-Estevez , Alejandro Escudero-Contreras z and Carlos Pérez-Sánchez z Rheumatology Service, Reina Sofia Hospital, Maimonides Institute for Research in Biomedicine of Cordoba (IMIBIC), University of Cordoba, E-14004 Córdoba, Spain; [email protected] (N.B.); [email protected] (A.M.P.-T.); [email protected] (M.L.-T.); [email protected] (E.C.-E.); [email protected] (A.E.-C.); [email protected] (C.P.-S.) * Correspondence: [email protected] or [email protected]; Tel.: +34-957-213-795 These authors shared first authorship. y These authors shared last authorship. z Received: 31 October 2020; Accepted: 27 November 2020; Published: 28 November 2020 Abstract: Rheumatoid arthritis (RA) is an autoimmune and chronic inflammatory disease primarily affecting the joints, and closely related to specific autoantibodies that mostly target modified self-epitopes. Relevant findings in the field of RA pathogenesis have been described. In particular, new insights come from studies on synovial fibroblasts and cells belonging to the innate and adaptive immune system, which documented the aberrant production of inflammatory mediators, oxidative stress and NETosis, along with relevant alterations of the genome and on the regulatory epigenetic mechanisms. In recent years, the advances in the understanding of RA pathogenesis by identifying key cells and cytokines allowed the development of new targeted disease-modifying antirheumatic drugs (DMARDs). These drugs considerably improved treatment outcomes for the majority of patients. Moreover, numerous studies demonstrated that the pharmacological therapy with biologic DMARDs (bDMARDs) promotes, in parallel to their clinical efficacy, significant improvement in all these altered molecular mechanisms. Thus, continuous updating of the knowledge of molecular processes associated with the pathogenesis of RA, and on the specific effects of bDMARDs in the correction of their dysregulation, are essential in the early and correct approach to the treatment of this complex autoimmune disorder. The present review details basic mechanisms related to the physiopathology of RA, along with the core mechanisms of response to bDMARDs. Keywords: rheumatoid arthritis; autoimmunity; inflammation; oxidative stress; NETosis; genome; epigenetic and pos-transcriptional mechanisms; bDMARDs 1. Introduction Rheumatoid arthritis (RA) is a systemic inflammatory autoimmune disease identified by continuous joint inflammation promoting cartilage and bone damage, incapacity, and eventually systemic complications. The progression of the disease promotes loss of function, reduced quality of life and increased morbidity and mortality. In addition, RA can also affect organs outside the joints, mainly the lungs, skin, and cardiovascular system. The precise etiology of RA is still unknown, but genetic and environmental stimuli clearly participate. Dysregulated adaptive immunity can precede the clinical manifestations for many years, and it is likely that the repeated activation of innate immunity can contribute to a breakdown of tolerance. Int. J. Mol. Sci. 2020, 21, 9067; doi:10.3390/ijms21239067 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2020, 21, 9067 2 of 31 Regarding the mechanism of RA, it was shown that post-translational modifications in the mucosa Int. J. Mol. Sci. 2020, 21, 9067 2 of 30 (such as citrullination or carbamylation) generate new epitopes recognized by the adaptive immune system. ModifiedRegarding peptides the mechanism are then of presented RA, it was by APCshown (antigen-presenting that post-translational cells) modifications that in turn in activate the in lymphoidmucosa tissues (such the as adaptivecitrullination immune or carbamylation) response and generate promote new autoantibodies epitopes recognized formation. by the Fibroblast-like adaptive synovialimmune cells system. (FLS), Modified macrophages peptides and are APCs then presente can bed activated by APC (antigen-presenting in the synovium cells) to produce that in turn several inflammatoryactivate in factors.lymphoid Next, tissues the the autoimmuneadaptive immune response response caused and promote by the autoantibodies immune system formation. generates synovialFibroblast-like inflammation, synovial thus cells promoting (FLS)), macrophages cytokine secretion and APCs and can synovial be activated blood in vessel the synovium leakage. to Lastly, the autocrineproduce several and paracrine inflammatory effects factors. of cytokines Next, the au andtoimmune the continuous response adaptivecaused by the immune immune response system can generates synovial inflammation, thus promoting cytokine secretion and synovial blood vessel make the disease permanent and eventually lead to cartilage and bone destruction [1]. leakage. Lastly, the autocrine and paracrine effects of cytokines and the continuous adaptive immune In addition, oral infections with specific microorganisms such as Porphyromonas gingivalis have response can make the disease permanent and eventually lead to cartilage and bone destruction [1]. been associatedIn addition, with theoral RA infections development. with specific The pathogenic microorganisms mechanisms such as involvedPorphyromonas in the relationshipgingivalis of periodontalhave been disease associa andted RA with comprise the RA the development. increased production The pathogenic of T helpermechanisms 17 by theinvolved microorganisms, in the the burdenrelationship of citrullination, of periodonta thel disease generation and RA of comprise self-antigens the increased that may production cross-react of withT helper host 17 protein by the and convertmicroorganisms, to autoantigens the burden and the of possibilitycitrullination, of the the gene bacterialration of translocation self-antigens that to the may joints cross-react increasing with the inflammatoryhost protein burden and convert leading to autoantigens to the osteoclastic and the activation, possibility of among the bacterial others. translocation All these mechanisms to the joints can triggerincreasing the onset the of inflammatory RA and the perpetuationburden leading of to the the inflammation,osteoclastic activation, worsening among the others. progression All these of the diseasemechanisms (reviewed can in Rooneytrigger the C.M. onset et of al., RA 2020) and [2the]. perpetuation of the inflammation, worsening the progression of the disease (reviewed in Rooney C.M. et al., 2020) [2]. RA is a dissimilar disease, involving multiple clinical manifestations and pathogenic mechanisms among individuals with the same diagnosis and/or throughout different disease stages. Indeed, although autoantibodies are an important feature of RA, several RA patients are negative for these autoantibodies. These traits further support the complexity of the disease and the involvement of numerous factors in the trigger and the evolution of RA (Figure1). Figure 1. Cellular and molecular mechanisms involved in the pathogenesis of RA. The onset and progression of RA is orchestrated by several cellular and molecular pathologic mechanisms that participate in an integrated and coordinated way. The interaction between multiple genetic and environmental factors increase the risk of RA development. Autoimmune factors such as autoantigens and autoantibodies along with inflammatory mediators released by activated immune cells -including several cytokines and chemokines- are well recognized molecular features that influence the clinical manifestations of RA, characterized by tender and swollen joints and other related comorbidities. In recent years, novel mechanisms have been further associated with the pathogenesis of RA, including oxidative stress and NETosis and the interplay among gene expression and epigenetic and post-transcriptional mechanisms such as methylation and microRNAs. ACPAS, Anti-citrullinated peptide antibodies; RF, Rheumatoid Factor. Int. J. Mol. Sci. 2020, 21, 9067 3 of 31 Thus, it was widely demonstrated that along with synovium and immune cells, cytokines play key roles in the pathophysiology of the disease, through their involvement in cell growth, proliferation, differentiation, tissue repair and regulation of the immune response, being responsible for inflammation and joint destruction, and even for the systemic involvement in this autoimmune disorder [3]. RA is also related to oxidative stress. In RA patients, reactive oxygen species (ROS) produced by joints and circulating neutrophils, monocytes and macrophages can damage various cell constituents, including carbohydrates, proteins, lipids, and DNA. Accordingly, ROS may induce death of chondrocytes and promote a higher inflammatory damage both at articular and systemic levels. Moreover, a robust positive correlation between free radicals (generated both in synovial fluid and peripheral blood) and DAS28 score was proven, underscoring that ROS can be considered a predictive marker for the inflammatory status in patients with RA [4]. Accelerated NETosis (the process wherein neutrophils release highly decondensed chromatin and granular contents to the extracellular space, called neutrophil extracellular traps -NETs-) was also related to the pathogenesis of RA patients, through the externalization of immunostimulatory molecules and citrullinated autoantigens