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Large-scale mapping of the Ebola NP and GP proteins reveals multiple immunoprevalent and conserved CD4 T-cell epitopes

Cellular & Molecular Immunology volume 18, pages 1323–1325 (2021)Cite this article

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Humankind faces regular outbreaks from emerging viruses, such as Ebola and the current SARS-CoV-2, or from viruses circulating at low levels in the wild animal reservoir. Owing to the suddenness of virus expansion, the lack of knowledge of immune determinants and correlates of protection severely limit the ability to address the outbreaks. Identified in 1976, Ebola virus is part of the Filoviridae family and causes severe hemorrhagic fever with a mortality rate between 50% and 90%. From 2013 to 2020, more than 30,000 infections and 15,000 deaths have been reported worldwide. High antibody titers against Ebola virus GP are found in patients recovering from Ebola virus infection and correlate with protection in vaccination models.1 Both CD8 and CD4 T-cell responses also seem to participate in the control of Ebola virus infection in animals, and CD4 T cells are necessary to induce resistance to Ebola virus challenge.2 In addition to GP, NP induces strong T-cell responses in animal models that protect against Ebola virus infection, and in convalescent Ebola patients, most of the T-cell responses mounted against Ebola virus were found to target NP.3 However, very few T-cell epitopes specific for both the Ebola GP and NP proteins have yet been identified in humans.4,5 Only one study reported CD4 T-cell epitopes restricted to HLA-DR3.6 We therefore established a large-scale approach to identify CD4 T-cell epitopes using donors not exposed to infection to anticipate the sudden rise of emerging viruses and applied this approach to the Ebola GP and NP proteins.

Ten NP and eight GP peptides generated specific T-cell lines in at least 50% of the tested donors. Interestingly, only a combination of four peptides (three from NP and one from GP) suffices to induce a T-cell response in all donors (Fig. S2) but corresponds to only 15% of the total response. Alternatively, a combination of 18 peptides accounted for more than 50% of the total response (Fig. S2). We therefore extended the characterization of the T cells raised against these peptides. Using HLA-specific antibodies, we found that most of the 18 T-cell epitopes are restricted to HLA-DR molecules, as predicted in silico (Fig. 1c–e). Eight peptides were restricted at least partly to HLA-DP molecules, which shared HLA-DR common anchor residues, with the peptide NP80-99 being restricted to HLA-DP only. We also assessed the T-cell cross-reactivity for the other Ebola strains (Fig. 1c–e). The initial peptide sequences were from the Ebola Zaire strain, as this strain is the first one reported and is among the most virulent strains. Two other Ebola strains lethal to humans have been identified (Sudan and Bundibugyo), with the Reston strain being nonlethal in humans, and there is only one nonfatal case reported (1994) with the Tai Forest strain (not considered here). The specificity of T-cell lines raised against Zaire epitopes was evaluated with corresponding Sudan, Reston, and Bundibugyo peptides by IFN-γ ELISpot (Fig. 1c–e). Examples of partial and full cross-reactivity are shown in Fig. 1c and Fig. 1d, respectively. In addition to three NP peptides, which were completely conserved across the Ebola strains, one NP peptide was completely conserved between the Sudan and Reston strains and presented 86% cross-reactivity with Bundibugyo. Three NP peptides and two GP peptides exhibited a cross-reactivity greater than 66% to Sudan-derived peptides, which is the second most virulent Ebola strain. Another peptide cross-reacted with the other strains, while 2 peptides cross-reacted with Bundibugyo only. Variants of three GP epitopes were not tested because they were too divergent from their Zaire strain counterparts. We also investigated whether the identified T-cell epitopes were immunodominant and hence were naturally processed from the whole Ebola proteins and presented to T cells. Peptide-specific T-cell lines were tested for their capacity to be activated by dendritic cells loaded with either the recombinant NP or GP Ebola protein (Fig. 1c–e). Aside from those recognizing the peptide NP390-409, all the peptide-specific T-cell lines were stimulated by either the recombinant NP or GP protein. TCR V-Beta repertoire analysis of 23 T-cell lines specific for 3 NP peptides (NP27-46, NP80-99 and NP147-166) and 8 T-cell lines specific for 3 GP peptides (GP31-50, GP60-79 and GP123-142) from 3 different donors was conducted, showing that the T-cell response was shaped mainly by the individual repertoire of the donor (Table S2).

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Acknowledgements

The research leading to these results was supported by the Innovative Medicines Initiative Joint Undertaking PEVIA project under grant agreement #116088, the resources of which comprise financial contributions from the European Union. The authors thank Tiphanie Pruvost and Evelyne Correia from SIMoS for helpful discussions and technical advice.

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Authors and Affiliations

  1. Département Médicament et Technologie pour la Santé, SIMoS, Université Paris-Saclay, CEA-Saclay, 91191, Gif surYvette, France

    Yann Gallais, Raphaël Sierocki, Gautier Lhomme, Coline Sivelle & Bernard Maillère

  2. Excellgene, Monthey, Switzerland

    Divor Kiseljak & Florian Wurm

  3. Wiratech Europe, Genopole, 91000, Evry, France

    Sami Djoulah

  4. Vaxeal holding SA, Vevey, Switzerland

    Ahmed Bouzidi & Jérôme Kerzerho

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  1. Yann Gallais
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Contributions

Y.G., B.M., A.B, J.K., S.D., and F.W. designed the experiments; Y.G., R.S., G.L., C.S, and D.K. performed the experiments; Y.G., G.L., and B.M. analyzed the data; and Y.G. and B.M. wrote the paper.

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Correspondence to Bernard Maillère.

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Y.G. and B.M. are inventors of a pending patent.

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Gallais, Y., Sierocki, R., Lhomme, G. et al. Large-scale mapping of the Ebola NP and GP proteins reveals multiple immunoprevalent and conserved CD4 T-cell epitopes. Cell Mol Immunol 18, 1323–1325 (2021). https://doi.org/10.1038/s41423-020-0455-2

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