Tuning antiviral CD8 T-cell response via proline-altered peptide ligand vaccination

Adil Doganay Duru; Renhua Sun; Eva B. Allerbring; Jesseka Chadderton; Nadir Kadri; Xiao Han; Hannes Uchtenhagen; Chaithanya Madhurantakam; Sara Pellegrino; Tatyana Sandalova; Per-Åke Nygren; Stephen J. Turner; Adnane Achour

Y4F is restored following vaccination with a proline-altered peptide ligand (APL). The APL 9 increases MHC/peptide (pMHC) complex stability, rigidifies the peptide and facilitates T cell 10 receptor (TCR) recognition through reduced entropy costs. Structural analyses of pMHC 11 complexes before and after TCR binding, combined with biophysical analyses, revealed that 12 although the TCR binds similarly to all complexes, the p3P modification alters the conformations 13 of a very limited amount of specific MHC and peptide residues, facilitating efficient TCR 14 recognition. This approach can be easily introduced in peptides restricted to other MHC alleles, 15 and can be combined with currently available and future vaccination protocols in order to prevent 16 viral immune escape. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/862144 doi: bioRxiv preprint 3 understanding of the molecular mechanisms underlying this reestablished recognition. We 24 believe that this approach can be implemented to currently available or novel vaccination 25 approaches to efficiently restore T cell recognition of virus escape variants to control disease 26 progression. pMHC stability and immunogenicity has been to optimize interactions between peptide anchor 62 residues and MHC binding pockets [17] [18] [19] . However, escape variants that target TCR recognition 63 often exhibit optimal MHC anchor residues, reducing possibilities for such modifications. 64 . CC-BY 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. Next, P14 TCR down-regulation was assessed upon exposure to gp33, V3P, Y4F or PF-loaded H-120 2D b+ RMA cells (Fig. 1C) . While H-2D b /gp33 induced significant TCR down-regulation, none 121 was detected with Y4F, even at high peptide concentrations. Exposure of P14 T cells to V3P 122 equaled or increased TCR internalization compared to gp33. Importantly, exposure to PF 123 significantly increased P14 TCR down-regulation compared to Y4F (Fig. 1C) . The crystal 124 structures of H-2D b /V3P and H-2D b /PF were determined to 2.5 and 2.6 Ã… resolution, respectively 125 . CC-BY 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/862144 doi: bioRxiv preprint 8 (Table S1) , and compared with H-2D b /gp33 [3] and H-2D b /Y4F [2] (Fig. 1D, Fig. S2, Fig. S9 ). 126 The overall structures of all pMHCs are nearly identical, and the amount of hydrogen bond and 127 van der Waals interactions formed between H-2D b and each p3P-APL was equivalent to each wild-128 type epitope counterpart. The backbone of the p3P-APL corresponds exactly to the wild-type 129 peptides, indicating strict molecular mimicry (Fig. 1D) The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/862144 doi: bioRxiv preprint 10 and TNF towards gp33. This is well in line with previous studies in which the Y4F-specific T cell 174 clone YF.F3 killed efficiently targets presenting gp33 but did not produce IFNg [32] . Similar 175 results were obtained using bronchoalveolar lavage (BAL)-derived T cells (Fig. S4 ). In conclusion, The p3P modification facilitates TCR recognition 209 The three ternary TCR/MHC/peptide structures were compared with each corresponding