In the present work, we demonstrated the presence of PTMs related to ubiquitin tag (total ubiquitin and ISG15), in NETs from SLE patients, and their impact in the reactivation, proliferation and polarization of CD4+ cells of SLE patients and controls. Furthermore, to our knowledge this is the first report on the differential patterns of water molecules and conformational changes in residues near the catalytic site of MPO conjugated to ubiquitin. Interestingly, our data also suggest NETs as a source of ISG15 in SLE, shows that H2B interact with this PTM and a potential role in regulating IFNγ secretion by T lymphocytes in SLE.
The trend towards increased proliferative responses of CD4+ T lymphocytes from patients with SLE, as well as the polarization towards Th1 and Th17 subpopulations producing IFNγ or IL17A in the presence of components of NETs such as recombinant MPO and ubiquitylated MPO is consistent with a previous study in which CD4+ and CD8+ T lymphocytes from controls stimulated with supernatants of NETs induced in vitro, had higher levels of CD25, CD69, phosphorylation of ZAP70, secretion of IFNγ and IL17A; however, there was no increase in the percentage of proliferation with ethinyl deoxyuridine (EdU) (40). The difference described between patients and controls in CD25 or Ki67% could be related to a differential threshold for activation and proliferation signals, which could be reached by some of the NET components and therefore able to induce the production of effector cytokines such as IFNγ and IL17A, but insufficient to fully activate T cell proliferation. In agreement to this, other studies have described proliferation of PBMCs from patients with vasculitis associated with anti-neutrophil cytoplasm antibody (ANCA) by increasing MPO concentrations to 10μg/mL (7, 41), which corroborates the requirement for a high concentration of MPO for the regulation of proliferation in T lymphocytes. Furthermore, the ability to produce IFNγ by PBMCs from patients with ANCA vasculitis at the dose we used for the activation of dendritic cells (5μg/mL), had been previously described by ELISA and this production was not carried out when using lower doses (0.5μg / mL) (8). This is the first study addressing the biological effect of the ubiquitin tag in MPO in the context of systemic autoimmunity. Interestingly, the proliferative response of CD4+ lymphocytes depends on the ubiquitin tag as well as the disease state (ie healthy controls vs SLE). It has been described that the type of response that is mounted (proinflammatory vs anti-inflammatory) is mainly related to the context in which the antigenic determinant (immunogen or tolerogen) is seen, highlighting the microenvironment, the PTMs and the disease state as key elements for the functional effect of every antigen (42). In patients with anti-MPO glomerulonephritis, MPO-specific CD4+ T cells mediate organ damage, recognizing MPO released by NETosis as an autoantigen, conducting delayed-type hypersensitivity promoting IFN-γ and IL17A production (43). Accordingly, we have shown that SLE patients have high titers of anti-MPO antibodies, and higher titers of anti-UbMPO (11). However, in other scenario were endogenous MPO is not an autoantigen (like collagen-induced arthritis, pristine-induced lupus nephritis or healthy donors) MPO attenuates or even suppresses T cells responses, including decreased proliferation of human T cells in vitro (44), lower DC activation and migration, showing an increased proliferation, activation and proinflammatory cytokine production in MPO−/− mice (6). These differentiation of responses may depend of unusual mechanisms driven by MPO (45), making clear that the context in which the immune response is mounted, matters.
It is feasible that the relationship of ubiquitin with a lower activation and proliferation of CD4+ T cells in controls is due to its ability to mask potentially dangerous antigens for the system (such as MPO in NETs) (46). Nonetheless, this relationship is in turn unbalanced in the context of SLE where both MPO with and without ubiquitin was able to induce polarization of CD4+ T cells towards a Th1 and Th17 effector phenotype. This is in agreement with previous data from our research group suggesting that lupus patients have a ubiquitin deficiency state involving diverse cellular subsets and processes, in which they express lower amounts of E3 ligases (key enzymes for ubiquitylation) in T cells (47, 48) as well as diminished polyubiquitin K63 chains in NETs (11), both with functional impact, such as resistance to anergy and altered macrophage responses, respectively. Accordingly, in healthy controls, the presence of ubiquitin tag involves a suppressive mechanism when it is bound to a molecule with a dual role in inflammatory signaling, such as MPO, which might be diminished in the context of systemic autoimmune diseases, such as SLE, explaining the shift towards Th1 and Th17 in CD4+ cells in patients and the tolerogenic role in controls, diminishing the activation and proliferative responses.
The molecular dynamics simulations allowed to describe the closeness of arginine 239 (R239) when ubiquitin was bound to K505 or K488 residues, compared to native MPO. R239 is an important residue of the polypeptide chain lying near the distal face of the HEME group (49) and has been involved in the catalytic mechanism of MPO (50). There is evidence using molecular docking that the LGM2605 peptide, by its hydroxyl group, inhibits the enzymatic activity of MPO by blocking R239. The authors propose that while this position may not directly displace H2O2 binding, blocking the substrate channel may slow H2O2 access to HEME (51). Our results using contact map analysis allowed us to find that R239 decreased its distance from the HEME group when ubiquitin was conjugated to K505 or K488 compared to native MPO.
One of the most relevant changes in the structural dynamics of the MPO was the differential hydration of the active site mediated by the ubiquitinated lysine residue. Water molecules are relevant to receptor-ligand recognition because they modify the geometry of the active site and contribute to binding affinity. Our results propose that when ubiquitin conjugates to K129 or K488, the number of water molecules close to the HEME group increases, and the opposite occurs when ubiquitin binds to K505.
Together, the closeness of R239 and the increased amount of internal water molecules in the active site; implies a higher probability of entry to the active site by the reaction substrates (Cl- and H2O2), and therefore may increase the production of reactive intermediates such as taurine chloramine, implying amplified peroxidase activity. Taurine chloramine is an inhibitory mechanism of activation and proliferation that diminish the release of IL12 and TNFα from DC and subsequently IL2 and IL10 from T cells in vitro (52).
Furthermore, the evolution of structures is consistent with functional specificity, and ubiquitin-like proteins are an obvious example of the pleiotropism inherent in their function, as is the case with the 15 kDa IFN-related gene. ISG15 is another PTM that has a great diversity of functions depending on its location. Recently it has been identified the lymphocyte function-associated antigen 1 (LFA-1) or CD11a/β1 integrin as the putative receptor of ISG15 in NK cells inducing the activation of Src kinases and IFNγ and IL10 synthesis (52). However, currently, the release mechanism is unknown, secretory granules of neutrophils, lysosomes, exosomes, apoptotic bodies and microvesicles released from infected macrophages have been suggested as probable mechanisms (53). Based on our results, we can propose a new non-canonical secretion mechanism of ISG15 by NETosis in patients with SLE. To our knowledge, this is the first report of extracellular ISG15 as a component of NETs only in SLE patients, highlighting its role in this disease. It is feasible to propose NETosis as one of the non-canonical secretion mechanisms of extracellular ISG15, since the increased levels of type I IFN, and the molecular transcriptional signature of SLE are suggested to be key pathogenic players in the disease. (14) (54).
In cells that respond to interferon, free extracellular ISG15 has a "cytokine-like" activity with evidence supporting its ability to induce the production of IFNγ (55, 56). Additionally, controversy exists about the pathogenic role of ISG15, since the overexpression of ISG15 in NETs of SLE patients could be both a consequence of the overstimulation by the IFNα/β signature, and a signal from NETs involved in the production of IFNγ by lymphocyte subpopulations (13, 57). Our data show that indeed NETs from SLE patients are capable of inducing IFNγ production in CD4+ T lymphocytes as has been previously shown by Tillack KB, et al (40).
Finally, we show that the protein cargo of NETs from SLE patients contain ISG15 and able to induce IFNγ production, which agrees with previous data by Iglesias-Guimarais, et al (58) which show that in addition to CD4+ lymphocytes, IFNγ production was also reported by other subpopulations such as CD8+ and NK cells, both known targets of action of extracellular ISG15 (58), which is also produced by lupus plasma cells (57). Therefore, it can be argued that NETs promote the activation of these cells with the subsequent production of IFNγ in response (among other stimuli) to free ISG15. (59, 60) Thus, we propose ISG15 in NETs as a new component in the physiopathogenic scheme of autoimmune diseases such as SLE, with an effector correlate that includes the induction of Th1 lymphocytes with a proinflammatory potential (Figure 5. Proposed hypothetic model). There is evidence that the deficiency of ISG15, through the ISGylation of USP18, can degrade this potent inhibitor of IFNα/β-mediated signaling and promote its accumulation (12), therefore ISG15 has even been proposed as a down regulator of type 1 IFN (59), and may have a different functional profile depending on its interactions to another extracellular proteins or its release, as shown in the present study and previous reports in which the administration of free ISG15 as an adjuvant, helps to enhance the production of IFNγ and an increase in the cytolytic activity of CD8+ T cells against papillomavirus (61).
More than 30% of the ISG15 targets were described by mass spectrometry as nuclear proteins (13). These data suggest histones (nuclear proteins that are part of NETs) as potential targets for this PTM (62, 63). The ubiquitin label in H2B (K123) has been found to affect chromatin dynamics and RNA polymerase passage to facilitate a robust transcription system (64), (65). So far, this has been the closest evidence that ubiquitin or some other ubiquitin-like protein is related to histone interaction, specifically H2B. This contact might induce changes in structure and function as previously reported with other PTMs in chromatin, and a source of autoantigens in autoimmune pathologies (63). However, it had been described that intracellular ISGylation inhibits the secretion of ISG15, so it seems that that they have separated pathways, one inhibiting the other. Novel de-ISGylases can reverse intracellular ISGylation improving the extracellular ISG15 secretion (66). Consequently, is more plausible that ISG15 coming from lupus NETs is in a free, extracellularly, cytokine-like form accounting, at least in part, for durable pro-inflammatory responses. Subsequent studies will be needed to demonstrate this issue.
Our study has many limitations. First, it is a transversal study with no tracing of patient’s characteristics. Also, we used effector CD4+ in the cocultures with DC, instead of naïve CD4+, resulting in a reactivation profile of ex vivo Th1 or Th17 instead of in vitro Th0 polarization. Nevertheless, it is the first study to address the in vitro, in silico and ex vivo role of ubiquitin and NETosis-released-ISG15, their impact on cellular responses from SLE patients as well as the improvement in our knowledge of the pathophysiology of lupus and autoimmunity.