Antibodies reacting with JCPyV_VP2 _167-15mer as a novel serological marker for JC polyomavirus infection

JC Polyomavirus (JCPyV) is a human neurotropic polyomavirus that was found to be the causative agent of progressive multifocal leukoencephalopathy (PML), a fatal demyelinating disease [1‐4]. JCPyV can switch from its latent state to an activated state in immunocompromised subjects such as HIV-1 infected patients and in multiple sclerosis (MS) patients treated with natalizumab [5‐7]. The JC Polyomavirus capsid is composed of 72 pentamers of the major capsid protein VP1, with one of the minor coat proteins (VP2 or VP3) in the center of each pentamer Both minor proteins are essential for the viral life cycle [8, 9] and were shown to act as membrane proteins during infection and to form pores in host cell membranes [10].

Antibodies to JCPyV VP1 are widely prevalent in healthy subjects indicating that most individuals have been exposed to or are latently infected with the virus [11‐17]. Antigenic epitopes have been described for VP1, with most of these epitopes being shared between JCPyV and the other polyomaviruses BKPyV and SV40 [18]. Despite this epitope sharing, JCPyV specific serology assays using full length recombinant JCPyV VP1 as antigen were developed. Specificity was shown by inhibition experiments using VP1 from other known polyomaviruses [19‐21]. Serological results should however be interpreted with caution as serological cross-reaction with closely related, yet unidentified human polyomaviruses can never be excluded [22‐24]. Currently, the STRATIFY JCPyV ELISA using baculovirus-expressed VP1 virus-like-particles (VLP) as antigen, is the only Food and Drug Administration (FDA) approved assay for JCPyV [12, 25].

Little attention has been paid so far to JCPyV VP2 or VP3 as immunogenic proteins, although some examples have been described of the immunogenic nature of these minor capsid proteins in other polyomaviruses. A high prevalence of antibodies against VP2 has been described for WU Polyomavirus [26]. Furthermore, a linear epitope was identified in SV40 VP2/VP3 that showed immunoreactivity in serum from 21.9% of blood donors [27]. Also BKPyV VP2 and VP3 were identified as targets of cellular immunity [28]. Peptide microarray analysis using a comprehensive set of polyomavirus derived peptides demonstrated that several non-VP1 peptides were recognized by antibodies in human plasma and could potentially represent linear epitopes of these proteins [29].

In this work we have investigated, using a peptide microarray setup, whether linear epitopes could be identified in JCPyV VP2. A 15-mer peptide was identified that was thereafter used for the development of a peptide ELISA. The immunoreactivity of this peptide was further characterized and its relationship with other JCPyV markers was investigated.

A total of 82 15-mer peptides derived from JCPyV VP2 were incubated in a peptide microarray format with plasma samples from 49 healthy subjects (HS), resulting in 4018 data points. All individual data points were plotted per peptide and the mean value and standard deviation was calculated per peptide (Figure 1A). Upon plotting these descriptive statistics on an x-y plot, 4 peptides clearly had different responses compared to the other peptides, with high average response and high variation over the different subjects (Figure 1B). These peptides were JCPyV_VP2_116-15mer, JCPyV_VP2_167-15mer (variant with S₁₇₅ and variant with A₁₇₅) and JCPyV_VP2_286-15mer. Remarkably, two variants of the same peptide (JCPyV_VP2_167-15mer) both had similar results, suggesting that the variant position is not involved in the epitope recognition. Since JCPyV VP2 is highly homologous to BKPyV VP2 and SV40 VP2, sequence similarity was assessed between the identified JCPyV peptides and the corresponding peptides in BKPyV and SV40 (Figure 1C). For peptide JCPyV_VP2_167-15mer this analysis showed that the corresponding SV40 peptide overlaps largely with a peptide that was identified earlier as an epitope that is recognized by antibodies in serum samples from healthy donors carrying SV40 [27]. As there is also low sequence homology of this peptide with the corresponding BKPyV and SV40 peptides, we decided to further investigate this specific JCPyV peptide. In order to verify that human plasma samples contain IgG antibodies that react with this specific peptide, a peptide ELISA was set up using the synthetic peptides JCPyV_VP2_167-15mer and BKPyV_VP2_167-15mer. This ELISA was used to test for anti-peptide antibody responses in plasma from 50 HSs that had been diluted 200-fold (Figure 1D). This confirmed that plasma from healthy individuals indeed contains IgG antibodies reacting with this peptide, with an overall prevalence of 64% (32/50) for JCPyV_VP2_167-15mer and only 14% (7/50) for BKPyV_VP2_167-15mer.Molecular modelling was performed on a 36-mer, covering amino acids 154 to 189 of JCPyV VP2 (Figure 2). This modelling predicts that this peptide is characterized by a stable secondary structure consisting of 2 α helix domains flanking a smaller exposed amino acid stretch. This computational modelling indicates that the majority of JCPyV_VP2_167 is located in an exposed region of the VP2 protein and as such this physical configuration might favour its immunological reactivity, in line with the results observed in the peptide ELISA.

In order to better characterize the immunoreactivity of this JCPyV VP2 derived peptide, epitope mapping experiments were performed. For this investigation, a peptide ELISA was employed to test 3 plasma samples that were highly reactive towards JCPyV_VP2_167-15mer using different specifically designed synthetic peptides. On the one hand a series of 7-mers, 9-mers, 11-mers and 13-mers, overlapping with all but one residue was tested (Figure 3A). This test showed that a minimal peptide required to retain immunoreactivity consisted of the sequence LPALTSQEI. This observation was confirmed by the analysis of anti-peptide antibody responses in plasma from 50 HSs using the 9-mer, 11-mer, 13-mer and 15-mer that was found to retain immunoreactivity (Figure 3B). On the other hand each of the amino acids in JCPyV_VP2_167-15mer was replaced individually by alanine (alanine walking) (Figure 3C). Using this approach the contribution of each specific residue used to the immunoreactivity of the peptide is determined [30, 31]. The data obtained using these peptides in the peptide ELISA indicate that three residues in JCPyV_VP2_167-15mer are important for antibody recognition: P₁₇₄, L₁₇₆ and E₁₈₀. Replacement of any of these residues by alanine resulted in the complete elimination of immunoreactivity of the peptide. These data also confirmed the results of the previous experiment as all essential amino acid residues are located within the minimal peptide affirmed. Remark that the corresponding BKPyV peptide (IPSITSQEL) has an isoleucine residue at position 176 instead of leucine.

Since several mutations have been described in the VP2 region of JCPyV, it might be of interest to investigate whether some of these mutations are located in the JCPyV_VP2_167-15mer. A first mutation that is known, is the E₁₇₂ mutation [32]. However, this residue is not located in the minimal epitope and as such is unlikely to play a role in antibody recognition. A second mutation is the S₁₇₅ mutation which was already part of our initial investigation on the peptide array. Based on both the array data and the epitope mapping data, it is clear that this residue also does not play a role in antibody recognition. Taken together, we might conclude that the peptide ELISA using the JCPyV_VP2_167-15mer NLVRDDLPALTSQEI is capable of detecting antibodies against all JCPyV strains, independent of the strain specific sequence of this VP2 region.

The data presented above are demonstrative of the immunoreactivity of JCPyV_VP2_167-15mer and its minimal epitope LPALTSQEI. This does however not imply that the immune responses observed are elicited by exposure to or infection with JCPyV. Any protein containing the LPALTSQEI sequence or closely related sequence might in fact be the antigen responsible for the positive immune responses observed. The responses observed with JCPyV_VP2_167-15mer would then be non-specific responses. In order to investigate the possibility that a protein from another organism might be at the basis of the observed responses, a protein BLAST search was performed against the non-redundant protein database using JCPyV_VP2_171-11mer as query sequence [33] (Additional file 1: Table S1). Within the Viridae only SA12 VP2 and BKPyV VP2 were identified, respectively with 1 or 4 mismatches compared to the query sequence. Also in the human proteome no proteins were identified with less than 4 mismatches. Most proteins with less than 4 mismatches compared to JCPyV_VP2_171-11mer, however, were found in Bacteria and Animalia. Also one protein from protozoan origin and one protein from a grass species were identified. Of all identified sequences the corresponding 15-mer peptide was synthesized and used for assessment of their immunoreactivity in 3 plasma samples that were highly reactive towards JCPyV_VP2_167-15mer. Out of the 30 peptides tested, 9 showed some response in the peptide ELISA that were similar as JCPyV_VP2_167-15mer (Figure 4). The strongest signals were observed for isopropylmalate isomerase from Micrococcus luteus, anti-FecI sigma factor FecR from Spirosoma linguale DSM 74, hypothetical protein from Beggiatoa alba, putative perixosomal biogenesis factor from Ixodes scapularis and probable E3 ubiquitin-protein ligase ARI1-like from Brachypodium distachyon. Although it cannot be excluded, it is very unlikely that one of these proteins is responsible for the immune response observed in the peptide ELISA using JCPyV_VP2_167-15mer. First of all some of these organisms are either rare or occur only at specific locations. Secondly, the proteins identified are not expected to be strong antigens as they are known to be located intracellularly and as such are unlikely to be exposed to the host’s humoral immune system. All together, these data suggest that an immune response against JCPyV VP2 can be observed in HSs and that the amino acid stretch with sequence LPALTSQEI functions as an epitope on this protein.

Based on these data, we believe JCPyV_VP2_167-15mer truly acts as an epitope and therefore the peptide ELISA using JCPyV_VP2_167-15mer as antigen was employed to analyse the immune response against this peptide in a larger cohort of 204 HSs (Figure 5). As was already seen in the smaller cohort of 50 HSs, there was a large variation over the different subjects. Subjects were further categorized based on their JCPyV VP1 serology and JCPyV urinary viral load (Figure 5A). However, no difference (P > 0.05) between JCPyV VP1 seropositive and seronegative subjects could be observed. The same was observed when comparing subjects shedding virus in their urine and virus with a negative urinary viral load. Although we have shown before there is no cross-reactivity with BKPyV, we investigated the possibility that infection with BKPyV was interfering in the assay. Therefore, also BKPyV VP1 antibody levels were determined and subjects were categorized based on their JCPyV VP1 and BKPyV VP1 serology (Figure 5B). Again, no difference (P > 0.05) was observed between any of the groups. It is known urinary viral load and JCPyV VP1 antibody levels are correlated [34]. We have investigated whether this is also true for JCPyV_VP2_167 antibody levels (Figure 5C). In contrast to VP1 antibody levels, no correlation was found between urinary viral load and JCPyV_VP2_167 antibodies (P > 0.05). It was also apparent that JCPyV_VP2_167 antibody levels were not correlated with donor age (P > 0.05, Figure 5D). It will also be of interest for future studies to investigate whether JCPyV_VP2_167 antibody levels remain constant over time as is the case for VP1 antibody levels [35, 36].

The lack of correlation between JCPyV_VP2_167 and JCPyV VP1 antibody levels is an interesting, but surprising finding. It is however not the first time that JCPyV VP1 serology is debated for its use as the sole infection marker as several examples have been described where JCPyV DNA was detected in urine, plasma or specific blood cell populations of individuals who were seronegative for JCPyV VP1 [37‐40]. In recent work, also a lack of correlation was observed between the level of anti-JCPyV antibody and anti-JCPyV neutralizing activity as 28.6% of JCPyV VP1 Ab⁺ samples were not capable of neutralizing the in vitro infection of COS7 cells by JCPyV [41]. Further research would however be needed to investigate whether JCPyV_VP2_167 antibodies are capable of neutralizing JCPyV infection.

It might be debated whether JCPyV VP2 can be recognized by the immune system as it was proposed that VP2 is located at the inner side of the capsid [42]. Crystal structure analysis however showed that the N-terminal part of VP2, including the JCPyV_VP2_167-15mer region is not tightly folded and retains high flexibility, making it easier for VP2 to emerge from inside the virion [43, 44]. The fact that it was also shown that 52.3% of serum samples show immunoreactivity with WU Polyomavirus VP2 and 21.9% of blood donors react with SV40 VP2 derived peptides, strengthens the conclusion that JCPyV VP2 acts as an antigen recognized by the immune system upon JCPyV infection [26, 27]. We postulate that the peptide studied in this work, JCPyV_VP2_167-15mer, acts as one of the epitopes responsible for the antigenic properties of JCPyV VP2.

The work presented here shows that plasma from a large portion of HSs reacts specifically with a peptide derived from JCPyV VP2 capsid protein. Epitope mapping experiments demonstrated that the minimal epitope consisted of L₁₇₃PALTSQEI₁₈₁ with amino acids P₁₇₄, L₁₇₆ and E₁₈₀ essential for antibody recognition. Computational analysis was used to show that this epitope is located at an exposed domain of the VP2 capsid protein, readily accessible for immune recognition upon infection. Furthermore, this peptide is also located in a region homologous to an immunoreactive domain in SV40 VP2 [27]. BLAST analysis of this peptide and subsequent experimental analysis of the obtained peptides showed that a number of alternative proteins might exist that could have elicited the observed immune responses. However, based on the limited geographical distribution of some of the organisms encoding these proteins and the intracellular localization of most of these proteins, it is unlikely that this would be the case, indicating that the immune responses should have been induced by infection with or exposure to JCPyV. The fact that there appears to be no correlation with JCPyV VP1 antibody levels, nor urinary viral load, indicates that these specific antibodies might be considered as a novel marker for infection with JCPyV.