Identification of naturally presented HLA-DR peptides (T cell epitopes). In a recent study (20), we identified HLA-DR–presented peptides in synovial tissue, SFMCs, and PBMCs from 5 patients with RA using LC-MS/MS, and the immunogenicity of the peptides was determined using patients’ samples in enzyme-linked immunospot (ELISpot) assays. The findings from 1 patient (referred to here as RA1) were of particular interest. She had classic, seropositive RA, with severe symmetrical polyarthritis, a positive test for ACPAs, and 2 copies of SE alleles (HLA-DRB1*0401 and *0101). In this patient, an immunogenic HLA-DR–presented peptide derived from a P. copri protein (Pc-p27) was identified from the patient’s PBMCs (25). We then showed that approximately 40% of patients with RA have T and/or B cell responses to Pc-p27 or to the whole P. copri organism (25).

In patient RA1, 2 immunogenic HLA-DR–presented human self-peptides derived from GNS and FLNA were also identified from her synovial tissue, and the same FLNA peptide was also found in her PBMCs (20). The HLA-DR–presented peptide derived from GNS was predicted to be promiscuous, binding to 24 of the 25 HLA-DR molecules modeled in the program TEPITOPE (26), and the FLNA-derived peptide was predicted to bind 9 of the 25 HLA-DR molecules. With both peptides, this included binding by HLA-DR molecules encoded by SE alleles *0101, *0401, *0404, and *0405. Neither the GNS protein, nor the FLNA protein, nor the P. copri protein had previously been noted to be antigens in RA.

T cell reactivity to GNS and FLNA peptides. To determine the immunogenicity of HLA-DR–presented peptides and their source proteins more broadly, we have developed a cohort of NORA patients seen prior to commencing therapy with disease-modifying antirheumatic drugs (DMARDs), which is a time when immune responses would be expected to be most robust. For comparison, we tested samples from patients with Lyme arthritis (LA) and from HC subjects. HLA-DR typing showed that 60% of the 40 RA patients had SE alleles, and 50% of the 10 LA patients and 42% of the 15 healthy subjects also had SE alleles. Nevertheless, since the patients and HCs had a range of different HLA-DR alleles, and since cell numbers are limited in human patients, our initial approach for determining T cell responses in multiple individuals consisted of pooling the original peptide with 3 additional peptides from the same protein that are predicted by the program TEPITOPE to be promiscuous HLA-DR binders (26). In addition, because of a limited number of cells, we did not include the testing of irrelevant control peptides in these experiments. However, we have previously shown that patients with RA do not have reactivity to peptides derived from endothelial cell growth factor (ECGF) or MMP-10 peptides (21, 23). These autoantigens in LA are irrelevant in RA.

When PBMCs from 40 patients with NORA were stimulated with the GNS peptides, we found that 14 of the 40 patients (35%) secreted levels of IFN-γ that were greater than 3 SD above the mean value for HCs (P = 0.006), as determined by an IFN-γ/IL-17 double-color ELISpot assay (Figure 1A). In comparison, PBMCs from patients with LA lacked reactivity to these peptides (P = 0.005). When FLNA peptides were used to stimulate PBMCs from the same set of patients and control subjects, 17 of the 40 patients with NORA (42%) had IFN-γ levels that were greater than 3 SD above the mean value for HCs (P = 0.001) and for patients with LA (P = 0.0005) (Figure 1B). In patients with RA, the predominant response to stimulation with both peptide sets was a Th1-type response with IFN-γ secretion, whereas PBMCs from only 3 RA patients secreted IL-17 (data not shown). Altogether, 21 of the 40 patients (52%) had T cell reactivity to GNS and/or FLNA peptides, and 10 (25%) had reactivity to both.

Figure 1 T cell reactivity to GNS and FLNA peptides in RA patients and comparison group subjects. In initial experiments, (A) PBMCs from patients with RA or LA or from HC subjects were stimulated with a pool of 4 peptides, including the single GNS HLA-DR–presented peptide isolated from the synovial tissue of patient RA1, and 3 predicted promiscuous HLA-DR–binding peptides from GNS (1 μM each). (B) PBMCs from patients and HCs were incubated with a pool of 4 peptides, including the single FLNA HLA-DR–presented peptide identified from the synovial tissue and PBMCs from patient RA1, and 3 predicted promiscuous HLA-DR–binding peptides from FLNA (1 μM each). In each assay, a positive control (phytohemagglutinin) and a negative control (no peptide) were included. The amount of IFN-γ secretion, as determined by an ELISpot assay, is shown. A positive response was defined as greater than 3 SD above the mean value for HCs (area above the shaded region). The values for patient RA1 are indicated with a star. Horizontal lines represent the mean values for each group. P values were determined by unpaired, 2-tailed t test with Welch’s correction. SFU, spot-forming units per million PBMCs.

B cell reactivity to GNS and FLNA proteins. Since the role of CD4+ T cells would likely be to help B cells produce autoantibodies against GNS or FLNA, we examined IgG levels for these proteins in serum samples from patients with RA and control group subjects. Since sera (but not PBMCs) were also available from patients with chronic RA (CRA), testing was done in 48 NORA patients and 53 CRA patients. Because the results were similar in both groups, they are presented together here.

Of the 101 patients with RA, 32 (32%) had IgG antibody responses against GNS that were greater than 3 SD above those in HCs (P < 0.0001) (Figure 2A). In contrast, none of the 106 patients with other diseases, including those with LA, spondyloarthropathy (SpA), or connective tissue diseases (CTD), and none of the 50 HC subjects had positive IgG antibody responses against the protein (in each instance, P < 0.0001). Similarly, 27 of the 101 (27%) patients with RA had levels of IgG antibodies against FLNA that were greater than 3 SD above those in HCs (P < 0.0001), whereas only 2 patients with CTD had borderline positive IgG antibody responses against FLNA, and none of the other control subjects had positive responses (Figure 2B). Altogether, 48 (48%) of the 101 RA patients had IgG autoantibodies against GNS and/or FLNA, and 10 (10%) had IgG reactivity against both proteins.

Figure 2 IgG and IgA responses to GNS and FLNA in RA patients and comparison group subjects. Serum samples from 259 patients with RA, patients with other forms of chronic inflammatory arthritis, and HCs were tested by ELISA for autoantibodies. (A and C) Plates were coated with the GNS protein and incubated with serum from patients or HCs. All serum samples were tested in duplicate for anti-GNS IgG (A) or IgA (C) antibody responses. (B and D) Plates were coated with the FLNA protein and incubated with serum from patients or control subjects. All serum samples were tested in duplicate for anti-FLNA IgG (B) or IgA (D) antibody responses. For all analyses, positivity was defined as greater than 3 SD above the mean value for HCs (area above the shaded region). Symbols represent values in individual patients, and horizontal lines show the mean values. Values for patient RA1 are indicated with a star. Only significant P values, determined by unpaired, 2-tailed t test with Welch’s correction, are shown.

Because autoimmune processes in RA may be triggered at mucosal sites, we also tested the levels of IgA antibodies against GNS and FLNA in serum samples from patients and control subjects. Of the 101 patients with RA, 16 (16%) had elevated IgA antibody responses against GNS that were greater than 3 SD above those in HCs (P < 0.0001) (Figure 2C). In contrast, of the 106 patients with other rheumatic diseases and the 50 HC subjects, only 1 patient with SpA had borderline positive IgA antibodies. Similarly, 15 (15%) of the 101 RA patients had FLNA IgA responses that were greater than 3 SD above those in HCs (P = 0.0002), whereas only 1 HC subject and 2 patients with LA had low-level positive responses (Figure 2D). Altogether, 21 (21%) of the 101 RA patients had IgA antibody responses against GNS and/or FLNA, and 10 (10%) had IgA antibody responses against both proteins.

When IgG and IgA responses were considered together, 48 of the 101 patients with RA (48%) had IgG antibody responses against GNS and/or FLNA; 21 (21%) had IgA responses against 1 or both of the proteins; and 56 (55%) had IgG and/or IgA responses against the proteins. Of the 14 patients who had T cell responses to GNS peptides, 11 (79%) had IgG and/or IgA antibody responses against the GNS protein. Among the 17 patients who had T cell reactivity to the FLNA peptides, 6 (35%) had IgG and/or IgA antibody responses against the FLNA protein. Thus, T and B cell concordance was greater with GNS than with FLNA.

Correlation of antibody responses against P. copri, GNS, and FLNA. Using these same serum samples (25), we have previously tested IgG and IgA antibody responses against 2 RA-associated bacteria, P. copri, a gut microbe, and Porphyromonas gingivalis, a periodontal pathogen (27). Antibody responses against P. copri were found in 32% of RA patients, but were absent in patients with other CTDs, SpA, or LA, as well as in healthy subjects (25). Therefore, using these data, we correlated IgG and IgA antibody responses against these 2 organisms with the GNS and FLNA antibody responses determined here.

In patients with RA, the levels of anti-GNS IgG and IgA antibodies strongly correlated with P. copri antibody responses (P = 0.002 and P < 0.0001, respectively), and we found a similar correlation between anti-FLNA IgG and IgA antibody responses and P. copri antibodies (P < 0.0001 and P < 0.0001) (Figure 3A). In contrast, anti-GNS and anti-FLNA IgG or IgA levels did not correlate with P. gingivalis antibody responses (Figure 3B). Additionally, we observed no correlations among these parameters in healthy subjects. Thus, in RA patients, the higher the IgG or IgA antibody responses against P. copri, the greater the autoantibody responses against these autoantigens.

Figure 3 Autoantibody correlations with P. copri and P. gingivalis antibodies. Correlations between anti-GNS or anti-FLNA antibodies (IgG or IgA) and antibodies against P. copri (A) or P. gingivalis (B) in 101 RA patients. The r and P values for the corresponding statistical comparisons were determined by Spearman’s correlation test.

Testing of citrullinated GNS and FLNA proteins. Because citrullinated autoantigens are thought to play a central role in RA, particularly in patients with SE alleles, we investigated whether autoantibody responses against GNS or FLNA were greater when these proteins were citrullinated. For this purpose, the native proteins were citrullinated in vitro using recombinant human (rh) peptidylarginine deiminase 4 (PAD4) enzyme. Using samples from 46 RA patients in whom a sufficient amount of serum still remained, IgG antibody responses were higher against citrullinated GNS compared with responses against the uncitrullinated protein (P = 0.005), whereas the responses were negative against both forms of the protein in 15 HC subjects (Figure 4A). Moreover, the magnitude of anti–citrullinated GNS antibody responses correlated with ACPA levels in these patients (P = 0.03) (Figure 4B). In contrast, IgG antibody responses against citrullinated and uncitrullinated FLNA were not significantly different in the 46 patients (Figure 4C), and the levels of anti–citrullinated FLNA antibodies did not correlate with ACPA levels (Figure 4D). These results suggest that the GNS protein, but not the FLNA protein, may be citrullinated in vivo in patients with RA.

Figure 4 Autoantibody responses to citrullinated GNS and FLNA, and correlations with ACPAs. Serum samples from 46 patients with RA and 15 healthy individuals were tested for IgG antibody responses against citrullinated versus uncitrullinated GNS or FLNA. Plates were coated with GNS (A) or FLNA (C), with or without citrullination, incubated with serum from patients or HC subjects, and tested in duplicate. Symbols represent values for individual patients, and horizontal lines indicate the mean values. In A and C, only significant P values, calculated by an unpaired, 2-tailed t test with Welch’s correction, are shown. (B) Correlation between IgG antibody responses against citrullinated GNS or citrullinated FLNA (D) and ACPA levels in the 46 patients with RA. The r and P values shown in B and D were determined by Spearman’s correlations. citGNS, citrullinated GNS; citFLNA, citrullinated FLNA.

Utility of GNS and FLNA autoantibody evaluation in the diagnosis of RA. In our patient cohort, 70 (69%) of the 101 NORA and CRA patients were seropositive for ACPAs and/or RF, which are standard, commercially available autoantibody determinations for support of the diagnosis of RA. Among the 31 patients who did not have a positive test for ACPAs and/or RF, 13 had a positive test for IgG and/or IgA GNS autoantibodies and 9 had a positive test for IgG and/or IgA FLNA autoantibodies. Taken together, 17 of the 31 seronegative patients (55%) had such autoantibodies, 15 of whom could be identified with the IgG test alone. Overall, when autoantibody responses against GNS and FLNA were combined with standard autoantibody determinations, 87 (86%) of the 101 patients with RA had a positive test result for support of the diagnosis, and only 14 (14%) lacked a specific marker for RA.

GNS and FLNA protein levels in serum and joints. For a self-protein to become the target of autoimmune responses in RA patients’ inflamed joints, one would predict that the protein would be present at high concentrations there. For this purpose, we measured GNS and FLNA protein concentrations in serum samples from the 101 patients with RA and in synovial fluid (SF) from 17 patients for whom such samples were available. The levels of GNS were higher in the serum of RA patients than were GNS levels in the control groups (P ≤ 0.002) (Figure 5A), and in RA patients, the levels of this protein tended to be higher in SF than in serum. Similarly, FLNA protein levels were significantly higher in the serum of RA patients than in HCs (P < 0.0001), but in RA patients, FLNA protein levels in SF and serum were similar (Figure 5B).

Figure 5 GNS and FLNA protein levels in RA patients and comparison group subjects. GNS and FLNA protein concentrations were measured in serum and SF samples from patients with RA, serum samples from patients with CTD, SpA, or LA, and serum samples from HCs. (A) GNS protein concentrations and (B) FLNA protein concentrations are shown, as measured by ELISA assay. For both analyses, positivity was defined as greater than 3 SD above the mean value for HC subjects (area above the shaded region). Symbols represent values for individual patients, and horizontal lines indicate the mean values. The values for patient RA1 are indicated with a star. Only significant P values, determined by unpaired, 2-tailed t test with Welch’s correction, are shown. SLE, systemic lupus erythematosus.

To gain further insight into the protein abundance and distribution, synovial tissues from 10 patients, 4 with RA and 3 each with LA or osteoarthritis (OA), were stained for expression of GNS and FLNA, using immunohistologic methods. GNS showed a fine, reticular pattern in and around endothelial cells in 3 of the 4 patients with RA, but not in those with LA or OA (Figure 6). We observed that FLNA was intensely expressed in the tunica muscularis around blood vessels and in large or elongated cells, presumably synoviocytes, and it was also faintly expressed in the extracellular matrix. We detected FLNA expression in all RA patients, lesser staining in 2 of the LA patients, but no staining in the OA patients (Figure 6). Thus, in RA, these 2 proteins were present in inflamed synovial tissue, particularly around blood vessels, where they could become targets of autoimmune responses.

Figure 6 Immunohistochemical staining of synovial tissue for GNS and FLNA. Representative synovial tissue images from 1 patient with RA, 1 with LA, and 1 with OA are shown for expression of GNS or FLNA protein. Brown color indicates specific staining of GNS or FLNA self-proteins, and purple indicates hematoxylin staining. Images were taken at ×20 magnification, and ×40 magnification was used for the RA patient to highlight the staining around blood vessels.

Sequence homology between T cell epitopes of microbial and self-peptides. In an effort to determine whether T cell epitope mimicry may play a role in linking Prevotella reactivity with GNS and FLNA autoimmune responses, the sequence of each of the 2 self-peptides isolated from patient RA1 was used first to search for regions of similarity with any microbial protein using the microbial protein database in BLASTP (Basic Local Alignment Search Tool, protein) (https://blast.ncbi.nlm.nih.gov/Blast.cgi). For both self-peptides, Prevotella spp. peptides were among the top sequences producing significant alignment, specifically in areas predicted to be in the HLA-DR–binding groove. Therefore, we refined the search for sequence similarity by screening only microbial sequences from Prevotellaceae (NCBI Entrez Genome taxid:171552). To evaluate sequence homology, self- and microbial peptides were aligned using the program Clustal Omega (28).

The peptide derived from GNS had 67% sequence homology with a peptide from the Prevotella arylsulfatase protein (WP_062433009) (Figure 7A), which was predicted by CELLO software to have a periplasmic location (29). Importantly, the major area of homology for this microbial peptide was restricted to amino acids predicted to be in the HLA-DR–binding groove (Figure 7A). For the Prevotella peptide, 5 of the 9 amino acids were identical to one of the predicted binding registers (P1 = the first F) in the GNS peptide. Moreover, the peptides shared amino acid identity at the P1, P4, and P6 sites, which are critical for peptide binding, as well as in the flanking regions at each end of the peptide, which also influence peptide binding (Figure 7A). The FLNA peptide had 80% identity with a peptide derived from an uncharacterized Prevotella protein (WP_028897633) (Figure 7A), which was predicted to have an extracellular location (a secreted protein). Moreover, the major area of homology was again found in the HLA-DR–binding groove, where 7 of the 9 amino acids were identical in the Prevotella and FLNA peptides, and the remaining 2 amino acids had conserved properties (Figure 7A).

Figure 7 Sequence homology between self- and microbial peptides. (A) Sequence alignment of the self- and corresponding microbial peptides is shown (Clustal Omega), and the predicted binding frames of the self-peptides are given for the HLA-DRB1*0101 and *0401 molecules. Red residues indicate the P1 position (TEPITOPE predicted 3 binding registers for GNS [both HLA-DRB1*0101 and *0401], 2 for FLNA [HLA-DRB1*0401], and 1 for FLNA [HLA-DR*0101]), and blue residues indicate positions P2 through P9. The line through the amino acid residues indicates that the peptide-binding register contains an amino acid with an R-group that may not interact favorably with one of the MHC-binding pockets. (B) PBMCs from 24 RA patients and 10 HCs were incubated with 1 of the 2 self-peptides (GNS or FLNA) or each of the 2 corresponding microbial peptides (1 μM each). In each assay, a positive control (phytohemagglutinin) and a negative control (no peptide) were included. The amount of IFN-γ secretion is shown, as determined by ELISpot assay. A positive response was defined as greater than 3 SD above the mean value for the HCs (area above the shaded region). Horizontal lines represent the mean values for each group. *P < 0.05 and **P < 0.005, by unpaired, 2-tailed t test with Welch’s correction. (C) Correlations between the T cell reactivity to the GNS peptide and the 2 corresponding microbial peptides, 1 derived from the Prevotella arylsulfatase protein and the other from the Parabacteroides GNS protein. (D) Correlations between the T cell reactivity to the FLNA peptide and the 2 corresponding microbial peptides derived from 2 hypothetical proteins, 1 from the Prevotella sp. and the other from the Butyricimonas sp. P and r values shown in C and D were calculated using Spearman’s correlation test.

For comparison, we analyzed the GNS and FLNA sequences for homology with P. gingivalis, a periodontal pathogen of interest in RA, using Porphyromonadaceae (taxid:171551) as the reference database in the BLASTP search. However, we found no homology between P. gingivalis and GNS or FLNA sequences. P. gingivalis also stimulates antibody responses in the subgroup of RA patients who have periodontal disease (27, 30), but there is little overlap between RA patients with P. gingivalis antibodies and those with P. copri antibodies (25).

Instead, among the Porphyromonadaceae, the GNS epitope had partial sequence similarity with a peptide from the periplasmic protein N-acetylgalactosamine-6-sulfatase of the Parabacteroides sp. (WP_046148720) (Figure 7A). Thus, as with the homology between the GNS peptide and the peptide from the Prevotella arylsulfatase protein, the Parabacteroides protein was also a sulfatase. These enzymes are key in the adaptation and persistence of human commensal bacteria in the gut (31, 32). Moreover, the Parabacteroides peptide had 4 amino acids identical to the GNS peptide and 1 amino acid with conserved properties. These included amino acids with shared identity in the P1 through P4 and P6 sites. A similar evaluation of the FLNA peptide showed sequence homology with a predicted cytoplasmic uncharacterized protein of the Butyricimonas sp. (WP_065219401.1), another gut commensal. The Butyricimonas peptide shared identity with 6 of 9 amino acids in one of the predicted HLA-DR registers (P1 = F) of the FLNA peptide, and two of the three remaining amino acids had conserved properties (Figure 7A). Prevotella, Parabacteroides, and Butyricimonas are each members of the Bacteroidetes phylum, one of the two major phyla of gut commensal organisms.

T cell responses to homologous microbial and self-peptides. To address whether patients had reactivity to these self-epitopes and the corresponding microbial epitopes, we performed ELISpot assays with each of these peptides using PBMCs from the 24 patients with NORA in whom sufficient numbers of cells remained and from 10 HCs. When cells were stimulated with the GNS peptide or each of the 2 corresponding microbial peptides (1 derived from Prevotella and the other from Parabacteroides), we found Th1 cell reactivity to all 3 peptides. Of the 24 RA patients, 8 (33%) had T cell reactivity to the GNS peptide, 9 (38%) showed responses to the Prevotella peptide, and 6 (25%) had reactivity to the Parabacteroides peptide, all of which were responses that were 3 SD or more above the mean values for HCs (Figure 7B). Of the 8 patients who had reactivity to the GNS peptide, 7 also had responses to the microbial peptides. When PBMCs were incubated with the FLNA peptide, 9 of the 24 patients with RA (38%) had T cell responses, 10 (42%) showed reactivity to the corresponding Prevotella peptide, and 7 (29%) had responses to the Butyricimonas peptide (Figure 7B). Furthermore, all 9 patients with reactivity to the FLNA peptide also had responses to the microbial peptides. Thus, except for 1 patient, the same patients who had reactivity to the GNS and/or FLNA peptides also had responses to the corresponding microbial peptides. Additionally, among the microbial peptides, we observed a trend toward a higher percentage of patients who had reactivity to the Prevotella peptides than to the other gut commensals.

Moreover, when the magnitude of the T cell responses to each self-peptide was correlated with that of the corresponding microbial peptides, the responses to the GNS or FLNA peptide strongly correlated with reactivity to each of the 2 microbial peptides (in each instance, P < 0.0001) (Figure 7, C and D). Therefore, the stronger the response to the microbial peptides, the greater the response to the self-peptide. In contrast, PBMCs from 10 HC subjects did not show a correlation with any of the self- or microbial peptides (Figure 7, C and D).

Of the 24 RA patients tested with the single peptides of GNS and FLNA (Figure 7), 17 were initially analyzed for T cell reactivity to pools of 4 peptides derived from these proteins (Figure 1). Only 4 of the 17 patients responded to the pool of peptides and not to the single peptide, suggesting that the majority of patients had reactivity to the single peptide epitope. Only 2 of the 17 patients responded to the single peptides, but failed to respond to the peptide pools.

Using an in silico prediction method (Immune Epitope Database [IEDB] Analysis Resource tool; http://tools.immuneepitope.org/mhcii/), the GNS peptide and the corresponding microbial peptides were predicted to bind HLA-DR molecules encoded by SE alleles with significantly higher affinity than non-SE alleles (Figure 8A). In addition, there was a trend toward greater affinity of SE binding of the FLNA peptide and the corresponding microbial peptides (Figure 8B). Of the 24 patients with RA, 15 (62%) had SE alleles. Consistent with the IEDB binding predictions, 9 of 11 patients (82%) with self- and microbial T cell reactivity had SE alleles compared with 5 of 13 patients (38%) without T cell responses to these antigens (P = 0.05). Thus, patients who had reactivity to the self-peptides often responded to the corresponding microbial peptides; the magnitude of the self-responses showed a significant correlation with the microbial responses, and these were more frequent in patients with SE alleles.