A bioinformatics approach for identifying the probable cause of the cross-interaction of antibodies to the antigenic protein HPV16 L1 with the HPV6 L1 protein

This paper describes an attempt to analyze, with the aid of bioinformatics resources (programs and databases), the probable cause of the cross-interaction of antibodies against HPV16 L1 with antigenic protein HPV6 L1, which has been revealed in the investigation of the candidate vaccine obtained on the base of a plant expression system (tomato plants). In our opinion, the most likely reason for the cross-interaction of antibodies with antigens of different pathogenic HPV types is the similarity of their antigenic determinants. In this work, the amino acid sequences of HPV16 L1 and HPV6 L1 used for the development of a binary vaccine against cervical cancer and anogenital papillomatosis have been analyzed. For the analysis of antigenic determinants, the programs BepiPred-2.0: Sequential B-Cell Epitope Predictor, DiscoTope 2.0 Server and SYFPEITHI have been used. As a result of the analysis of probable B-cell linear determinants (epitopes), it has been found that in both types of HPV the proteins have approximately the same location and size of linear antigenic determinants; the difference is observed only in the form of small shifts in the size of several amino acid residues. However, there are some differences in the amino acid composition of epitopes; therefore, the possibility for cross-interaction of the antibodies with the antigens due to the similarity of linear antigenic determinants for B-cells is very small. The analysis of potential threedimensional epitopes for B-cells has shown that due to little difference between them the HPV16 L1 and HPV6 L1 proteins have no prerequisites for cross-interaction of the antibodies with the antigens belonging to the two different pathogenic HPV types. The analysis of probable linear epitopes for T-cells has revealed a common antigenic determinant in the two protein sequences. According to the rank made with the SYFPEITHI program, the amino acid sequence AQL(I)FNKPYWL is the second most likely antigenic determinant for T-cells. Meanwhile, the amino acid sequences of this determinant in HPV16 L1 and HPV6 L1 are virtually identical. There is a difference in only one position, but it is not critical due to the similarity of the physicochemical properties of amino acids, for which there is a replacement in the amino acid sequence of antigenic determinants. Consequently, some moderate cross-interaction of the antibodies to HPV16 L1 with the antigens of HPV6 L1 may be expected.

1. Brown D.R., Kjaer S.K., Sigurdsson K., Iversen O.E., Hernandes-Avila M., Wheeler C.M., Perez G., Koutsky L.A., Tay E.H., Garcia P., Ault K.A., Garland S.M., Leodolter S., Olsson S.E., Tang G.W., Ferris D.G., Paavonen J., Steben M., Bosch F.X., Dillner J., Joura E.A., Kurman R.J., Majewski S., Muñoz N., Myers E.R., Villa L.L., Taddeo F.J., Roberts C., Tadesse A., Bryan J., Lupinacci L.C., Giacoletti K.E., Sings H.L., James M., Hesley T.M., Barr E. The impact of quadrivalent human papillomavirus (HPV; types 6, 11, 16, and 18) L1 virus-like particle vaccine on infection and disease due to oncogenic nonvaccine HPV types in generally HPV-naive women aged 16–26 years. J. Infect. Dis. 2009;199(7):926-935. DOI 10.1086/597307.

2. Jespersen M.C., Peters B., Nielsen M., Marcatili P. BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res. 2017;45(W1):W24-W29. DOI 10.1093/nar/gkx346.

3. Kemp T.J., Hildesheim A., Safaeian M., Dauner J.G., Pan Y., Porras C., Schiller J.T., Lowy D.R., Herrero R., Pinto L.A. HPV16/18 L1 VLP vaccine induces cross-neutralizing antibodies that may mediate crossprotection. Vaccine. 2011;29(11):2011-2014. DOI 10.1016/j.vaccine.2011.01.001.

4. Kringelum J.V., Lundegaard C., Lund O., Nielsen M. Reliable B cell epitope predictions: impacts of method development and improved benchmarking. PLoS Comput. Biol. 2012;8(12):e1002829. DOI 10.1371/journal.pcbi.1002829.

5. Li Z., Song S., He M., Wang D., Shi J., Liu X., Li Y., Chi X., Wei S., Yang Y., Wang Z., Li J., Qian H., Yu H., Zheng Q., Yan X., Zhao Q., Zhang J., Gu Y., Li S., Xia N. Rational design of a triple-type human papillomavirus vaccine by compromising viral-type specificity. Nat. Commun. 2018;9(1):5360. DOI 10.1038/s41467-018-07199-6.

6. McClements W.L., Wang X.M., Ling J.C., Skulsky D.M., Christensen N.D., Jansen K.U., Ludmerer S.W. A novel human papillomavirus type 6 neutralizing domain comprising two discrete regions of the major capsid protein L1. Virology. 2001;289(2):262-268. DOI 10.1006/viro.2001.1146.

7. McLaughlin-Drubin M.E., Münger K. Oncogenic activities of human papillomaviruses. Virus Res. 2009;143(2):195-208. DOI 10.1016/j.virusres.2009.06.008.

8. Nakagawa M., Greenfield W., Moerman-Herzog A., Coleman H.M. Cross-reactivity, epitope spreading, and de novo immune stimulation are possible mechanisms of cross-protection of nonvaccine human papillomavirus (HPV) types in recipients of HPV therapeutic vaccines. Clin. Vaccine Immunol. 2015;22(7):679-687. DOI 10.1128/CVI.00149-15.

9. Namvar A., Bolhassani A., Javadi G., Noormohammadi Z. In silico/ in vivo analysis of high-risk papillomavirus L1 and L2 conserved sequences for development of cross-subtype prophylactic vaccine. Sci. Rep. 2019;9(1):15225. DOI 10.1038/s41598-019-51679-8.

10. Rammensee H.G., Bachmann J., Emmerich N.P.N., Bacho O.A., Stevanovic S. SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics. 1999;50:213-219. DOI 10.1007/s002510050595.

11. Rekoslavskaya N.I., Salyaev R.K., Stolbikov A.S. The synthesis of main capsid protein of anogenital type HPV6 L1 in plant expression system on the basis of tomato fruits. Doklady Biochemistry and Biophysics. 2021;498(1):193-198. DOI 10.1134/S160767292103008X.

12. Salyaev R.K., Rekoslavskaya N.I., Stolbikov A.S. Cross-reactivity of antigens and antibodies belonging to different pathogenic types of human papillomaviruses. Doklady Biochemistry and Biophysics. 2017;477(1):372-376. DOI 10.1134/S1607672917060084.

13. Scherpenisse M., Schepp R.M., Mollers M., Meijer C.J.L.M., Berbers G.A.M. Characteristics of HPV-specific antibody responses induced by infection and vaccination: cross-reactivity, neutralizing activity, avidity and IgG subclasses. PLoS One. 2013;8(9):e74797. DOI 10.1371/journal.pone.0074797.

14. Stolbikov A.S., Salyaev R.K., Rekoslavskaya N.I. Bioinformatics analysis of putative causes for сross-reactive antibodies interacting with antigens derived from various pathogenic human papillomaviruses. Infektsiya i Immunitet = Infection and Immunity. 2020;10(4):695- 706. DOI 10.15789/2220-7619-TBA-1263. (in Russian)