Research Article

Modulation of MHC-E transport by viral decoy ligands is required for RhCMV/SIV vaccine efficacy

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Science  30 Apr 2021:
Vol. 372, Issue 6541, eabe9233
DOI: 10.1126/science.abe9233

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Viral peptide is key to T cell priming

Simian immunodeficiency virus (SIV) vaccines containing a strain 68-1 rhesus cytomegalovirus (RhCMV) vector elicit strong CD8+ T cell responses that can control and clear SIV infections. The SIV peptides targeted by these T cells are presented on major histocompatibility complex (MHC) II and the nonclassical MHC-Ib molecule MHC-E rather than the more typical MHC-Ia. Verweij et al. show that the 68-1 RhCMV–encoded peptide VL9 drives intracellular transport of MHC-E and recognition of RhCMV-infected targets by MHC-E–restricted CD8+ T cells. Rhesus macaques vaccinated with a mutant 68-1 RhCMV lacking VL9 showed no priming of MHC-E–restricted CD8+ T cells and no protection against SIV. This work strongly suggests that future effective CMV-based HIV vaccines in humans will also require MHC-E–restricted CD8+ T cell priming.

Science, this issue p. eabe9233

Structured Abstract


Strain 68-1 rhesus cytomegalovirus (RhCMV) vaccine vectors expressing simian immunodeficiency virus (SIV) antigens elicit immune responses that stringently control and ultimately clear highly pathogenic SIV challenge in more than half of rhesus monkeys (RMs). The high frequency of effector-differentiated CD8+ T cells elicited by this vaccine contribute to this efficacy, mediating SIV replication arrest before the establishment of long-lived SIV reservoirs. However, we unexpectedly found that SIV peptides targeted by these CD8+ T cells are presented by major histocompatibility complex-E (MHC-E) or MHC-II instead of MHC-Ia. This raised the question of how these unconventional T cell responses arise and whether they are necessary for vaccine efficacy.


MHC-E binds the conserved VL9 peptide embedded in the leader sequence of MHC-Ia proteins. This MHC-E–VL9 complex predominantly engages inhibitory receptors on natural killer (NK) cells, thus serving as a protective “self” signal for healthy cells. To evade NK cells, both rhesus and human CMVs encode viral glycoproteins (Rh67 and UL40, respectively) that contain a VL9 sequence providing the MHC-E/VL9 complex to NK cells when cellular VL9 is not available because of viral MHC-Ia downregulation. We hypothesized that viral-encoded VL9 also controls the ability of 68-1 RhCMV to elicit MHC-E–restricted CD8+ T cells. This allowed us to examine the role of these cells in RhCMV/SIV vaccine efficacy.


We show that Rh67-embedded VL9 is required for intracellular transport of MHC-E in RhCMV-infected fibroblasts and for their recognition by MHC-E–targeting CD8+ T cells. Rh67 deletion did not substantially affect the character of RhCMV/SIV–elicited T cell responses, but such deletion, or VL9 mutation within Rh67, completely abrogated MHC-E–restricted CD8+ T cell priming, leaving vaccine-elicited T cell responses entirely MHC-II restricted. In contrast to RMs vaccinated with the parent 68-1 RhCMV/SIV vaccine, post-SIV challenge replication arrest was not observed among RMs vaccinated with the Rh67-deleted vaccine. Thus, 68-1 RhCMV/SIV vaccine efficacy requires Rh67-induced, MHC-E–restricted CD8+ T cell priming, implicating this response in the mechanism of protection.


RhCMV appears to elicit MHC-E–restricted T cells as a consequence of viral NK cell evasion. However, as separately reported, these responses are only manifest in 68-1 RhCMV because of a genetic rearrangement that abrogates the function of eight independent viral inhibitors of these responses. Thus, RhCMV has evolved to evade both NK cells and the MHC-E–restricted CD8+ T cells ­that result from this evasion. By contrast, SIV neither elicits nor seems to evade these responses. Our results strongly suggest that CD8+ T cells targeting MHC-E–presented HIV peptides will be necessary for an effective CMV-based HIV vaccine Fortunately, both the positive and negative RhCMV regulators of MHC-E–restricted responses are conserved in human CMV, suggesting that human CMV and/or HIV vaccines might also be programmed to elicit this unusual type of protective immunity.

68-1 RhCMV/SIV vectors encode an MHC-E peptide ligand that enables antigen presentation by MHC-E and the induction of the MHC-E–restricted CD8+ T cells required for protection against SIV challenge.

Fibroblasts infected in vitro with 68-1 RhCMV can stimulate MHC-E–restricted CD8+ T cells only if the MHC-E VL9 peptide ligand (in red) embedded within the Rh67 gene is expressed. This peptide is loaded onto MHC-E in the endoplasmic reticulum, thus enabling the intracellular transport of MHC-E to the cell surface. MHC-E is rapidly internalized from the cell surface and is followed by a (still hypothetical) exchange of VL9 with virus-derived antigenic peptides (in green). The T cell response elicited by 68-1 RhCMV vectors lacking viral VL9 is entirely MHC-II restricted and fails to protect against SIV. Thus, MHC-E–restricted CD8+ T cells are essential for 68-1 RhCMV/SIV vaccine–mediated SIV replication arrest.


Strain 68-1 rhesus cytomegalovirus (RhCMV) vectors expressing simian immunodeficiency virus (SIV) antigens elicit CD8+ T cells recognizing epitopes presented by major histocompatibility complex II (MHC-II) and MHC-E but not MHC-Ia. These immune responses mediate replication arrest of SIV in 50 to 60% of monkeys. We show that the peptide VMAPRTLLL (VL9) embedded within the RhCMV protein Rh67 promotes intracellular MHC-E transport and recognition of RhCMV-infected fibroblasts by MHC-E–restricted CD8+ T cells. Deletion or mutation of viral VL9 abrogated MHC-E–restricted CD8+ T cell priming, resulting in CD8+ T cell responses exclusively targeting MHC-II–restricted epitopes. These responses were comparable in magnitude and differentiation to responses elicited by 68-1 vectors but did not protect against SIV. Thus, Rh67-enabled direct priming of MHC-E–restricted T cells is crucial for RhCMV/SIV vaccine efficacy.

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