1Wisconsin Regional Primate Research Center, 1220 Capitol Court, Madison, WI USA 53715 2Massachusetts General Hospital, Bldg. 149, 13th Street,Charlestown, MA USA 02113
Simian immunodeficiency virus (SIV) infected rhesus macaques are currently the most widely used animal model for evaluating different vaccine modalities. Most candidate vaccines now seek to engender cytotoxic T-lymphocyte (CTL) responses, either singly or in concert with other immune responses, as CTL are clearly important in the naturally occurring immune responses to HIV and SIV [1-4]. The lack of well-characterized CTL epitopes in SIV remains a serious bottleneck in vaccine research. Most vaccines evaluate the quality of the CTL response by determining the frequency of CTL directed against a single epitope, the Mamu-A*01 restricted Gag181-189CM9 epitope. The focus on this epitope is understandable in light of the facts that Mamu-A*01 positive animals are common in captive bred macaque populations [5] and that Gag181-189CM9 is conserved in several commonly used SIV challenge strains, including SIVmac239, SIVmac251, and SHIV89.6P. However, the intense selection of these animals for inclusion in vaccine studies has created an acute shortage of Mamu-A*01-positive animals [6]. Therefore, it remains important to identify and characterize SIV-specific CTL responses restricted by other common rhesus MHC class I alleles to expand the number of animals accessible to vaccine research.
Fortunately, Mamu-A*01 is not the only common MHC class I allele in captive bred macaques. Sequence-based genotyping of macaques has identified four additional alleles (Mamu-A*02, -A*08, -B*01, and -B*17) that are present in >10% of macaques (unpublished data). The peptide binding motif for Mamu-B*17 has already been determined, and this information is currently being used to identify putative CTL epitopes in commonly used SIV strains [7]. This work has been facilitated by the development of techniques such as intracellular cytokine staining (ICS) [8-10] and IFN-gamma EliSpot that allow rapid ex vivo detection of responding CTL without time-consuming in vitro restimulations. Within the next few years, rhesus with other common MHC alleles will likely supercede Mamu-A*01 animals as the preferred model for testing SIV vaccines.
Another avenue for increasing the number of animals available for vaccine studies is to utilize Chinese rhesus macaque in addition to the more commonly utilized Indian rhesus macaques. Both Chinese and Indian macaques are readily infected with common SIV challenge strains including SIVmac251 and SIVmac239 [13, 14]. However, the immunogenetics of Chinese macaques differ substantially from Indian macaques (unpublished data). In an analysis of over 30 Chinese macaques, no animals expressing Mamu-A*01 were detected [15], though this allele is present in over 25% of Indian rhesus macaques [5]. These differences at the MHC class I loci are supported by evidence of genetic and morphological differences between the groups [16, 17]. Therefore, using Chinese macaques for SIV research will likely necessitate a duplication of the immunogenetic work that has already been performed for Indian macaques; identifying common MHC class I alleles, defining the peptide binding motifs for these alleles, predicting CTL epitopes based on the peptide binding motifs, and finally verifying these CTL responses ex vivo from SIV-infected Chinese macaques.
Despite the need to expand the SIV-infected rhesus macaque model, the description of new CTL epitopes is impeded by financial and practical considerations. The value of ICS for epitope identification has been tempered by the cost of applying this technique to comprehensively monitor immune responses to whole viral genomes. For example, simply generating a set of overlapping 15-mers spanning each of the proteins in SIVmac239 costs approximately $80,000. This initial expenditure, plus access to flow cytometers and SIV-infected animals, places CTL epitope identification beyond the means of most non-specialist laboratories. The routine costs of CTL epitope mapping are a burden even to specialist labs that have the capacity for high-throughput ICS. A single analysis of the entire cellular immune response against SIV costs over $700 and identifies only peptide pools (approximately 10 15-mer peptides each) that are reactive. To deconvolute the pool and identify the minimal, optimal CTL epitope, another $600 in ICS tests is required, plus the synthesis of $3500 in 8-mers, 9-mers, and 10-mers that span the reactive 15-mer. Finally, the restricting element for a response can be determined by testing antigen presenting cells expressing well-defined MHC class I alleles with the reactive CTL. However, these specialized antigen presenting cell lines are time-consuming to generate and have limited utility beyond epitope mapping. In sum, the cost for mapping a single novel SIV CTL epitope is upwards of $5000 (excluding initial peptide and animal husbandry costs). The reward for this expenditure can be uncertain, as peer-reviewed journals such as the Journal of Virology have stated that "[we] will not publish papers that simply ... identify new immunodominant peptides representing T- or B- cell epitopes ... Such information or reagents must instead be used in further experimentation to test an idea or relate a clear set of novel conclusions that derive from the data [18]." Though this guideline is intended to prevent the repetitive publication of manuscripts containing new CTL epitopes, it also actively discourages the identification of new CTL epitopes by favoring in-depth analysis of previously described epitopes.
Regardless, eight new SIV and SHIV CTL epitopes have been mapped in the two years since the last sequence compendium review on this topic [19]. Epitopes that have been fully characterized, including MHC class I restriction, are subdivided into those restricted by A-loci alleles (Table I) and B-loci alleles (Table II). Responses that have not been minimally mapped or whose restriction is uncertain are shown in Table III.
Mark O'Connor |
Todd M. Allen |
David I. Watkins |
Bette T. Korber |
phone:608-265-3379 |
617-726-7846 |
608-265-3380 |
505-665-4453 |
fax:&608-265-8084 |
617-726-5411 |
608-263-4031 |
505-665-3493 |
Virus |
Species |
Protein |
Epitope |
Restricting |
GenBank |
References |
---|---|---|---|---|---|---|
SIVmac239 |
Rhesus |
Gag 149-157 |
LSPRTLNAW |
Mamu-A*01 |
U50836 |
11 |
SIVmac251 |
Rhesus |
Gag 181-189 |
CTPYDINQM |
Mamu-A*01 |
U50836 |
11 |
SIVmac239 |
Rhesus |
Gag 254-262 |
QNPIPVGNI |
Mamu-A*01 |
U50836 |
11 |
SIVmac239 |
Rhesus |
Gag 340-349 |
VNPTLEEMLT |
Mamu-A*01 |
U50836 |
Unpublished |
SIVmac239 |
Rhesus |
Gag 372-379 |
LAPVPIPF |
Mamu-A*01 |
U50836 |
11 |
SIVmac239 |
Rhesus |
Pol 10-20 |
EAPQFPHGSSA |
Mamu-A*01 |
U50836 |
Unpublished |
SIVmac239 |
Rhesus |
Pol 106-115 |
LGPHYTPKIV |
Mamu-A*01 |
U50836 |
11 |
SIVmac239 |
Rhesus |
Pol 110-118 |
YTPKIVGGI |
Mamu-A*01 |
U50836 |
Unpublished |
SIVmac239 |
Rhesus |
Pol 322-331 |
GSPAIFQYTM |
Mamu-A*01 |
U50836 |
Unpublished |
SIVmac239 |
Rhesus |
Pol 437-446 |
IYPGIKTKHL |
Mamu-A*01 |
U50836 |
Unpublished |
SIVmac239 |
Rhesus |
Pol 551-559 |
QVPKFHLPV |
Mamu-A*01 |
U50836 |
11 |
SIVmac251 |
Rhesus |
Pol 584-592 |
STPPLVRLV |
Mamu-A*01 |
U50836 |
11 |
SIVmac239 |
Rhesus |
Pol 655-663 |
SGPKTNIIV |
Mamu-A*01 |
U50836 |
11 |
SIVmac239 |
Rhesus |
Env 233-240 |
CAPPGYAL(L) |
Mamu-A*01 |
U50836 |
11 |
SHIV-89.6 |
Rhesus |
Env 435-443 |
YAPPISGQI |
Mamu-A*01 |
U50836 |
20 |
SIVmac239 |
Rhesus |
Env 502-510 |
ITPIGLAPT |
Mamu-A*01 |
U50836 |
Unpublished |
SIVmac239 |
Rhesus |
Env 620-628 |
TVPWPNASL |
Mamu-A*01 |
U50836 |
11 |
SIVsmE660 |
Rhesus |
Env 620-628 |
TVPWPNETL |
Mamu-A*01 |
U50836 |
21 |
SIVmac239 |
Rhesus |
Env 726-734 |
SSPPSYFQT |
Mamu-A*01 |
U50836 |
Unpublished |
SIVmac239 |
Rhesus |
Env 727-737 |
SPPSYFQTHT |
Mamu-A*01 |
U50836 |
11 |
SIVmac239 |
Rhesus |
Env 761-769 |
SWPWQIEYI |
Mamu-A*01 |
U50836 |
Unpublished |
SIVmac239 |
Rhesus |
Tat 28-35 |
STPESANL |
Mamu-A*01 |
U50836 |
11 |
SIVmac239 |
Rhesus |
Vif 14-22 |
RIPERLERW |
Mamu-A*01 |
U50836 |
Unpublished |
SIVmac239 |
Rhesus |
Vif 144-152 |
QVPSLQYLA |
Mamu-A*01 |
U50836 |
11 |
SIVmac239 |
Rhesus |
Vpx 8-18 |
IPPGNSGEETI |
Mamu-A*01 |
U50836 |
11 |
SIVmac239 |
Rhesus |
Vpx 39-48 |
HLPRELIFQV |
Mamu-A*01 |
U50836 |
Unpublished |
SIVmac239 |
Rhesus |
Vpx 102-111 |
GPPPPPPPGL |
Mamu-A*01 |
U50836 |
Unpublished |
SIVmac239 |
Rhesus |
Rev 86-95 |
DPPTNTPEAL |
Mamu-A*01 |
U50836 |
Unpublished |
SIVmac251 |
Rhesus |
Nef 159-167 |
YTSGPGIRY |
Mamu-A*02 |
U50837 |
22 |
SHIVHXBc2 |
Rhesus |
Env 99-106 |
KPCVKLTP |
Mamu-A*08 |
23 |
|
SIVmac251 |
Rhesus |
Env 305-312 |
YNLTMKCR |
Mamu-A*02 |
U50837 |
24 |
SIVmac239 |
Rhesus |
Env 495-502 |
GDYKLVEI |
Mamu-A*11 |
25-27 |
|
SIVmac32H-J5 |
Cynomolgus |
Gag 242-250 |
SVDEQIQWM |
Mafa-A*02 |
28 |
Virus |
Species |
Protein |
Epitope |
RestrictingAlleles |
GenBank |
References |
---|---|---|---|---|---|---|
SIVmac251 |
Rhesus |
Env 501-509 |
EITPIGLAP |
Mamu-B*01 |
U42837 |
29 |
SIVmac239 |
Rhesus |
Nef 136-146 |
ARRHRILDMYL |
Mamu-B*03 |
U41825 |
25-27 |
SIVmac239 |
Rhesus |
Env 573-581 |
KRQQELLRL |
Mamu-B*03 |
U41825 |
25-27 |
SIVmac239 |
Rhesus |
Nef 62-69 |
QGQYMNTP |
Mamu-B*04 |
U41826 |
25-27 |
SHIVHXBc2 |
Rhesus |
Env 553-561 |
NNLLRAIEA |
Mamu-B*12 |
23 |
|
SIVmac239 |
Rhesus |
Nef 165-173 |
IRYPKTFGW |
Mamu-B*17 |
25-27 |
Virus |
Species |
Protein |
Epitope |
References |
---|---|---|---|---|
SIVmac251 |
Rhesus |
Gag 35-59 |
VWAANELDRFGLAESLLENKEGCQK |
30 |
SIVmac251 |
Rhesus |
Gag 246-281 |
QIQWMYRQQNPIPVGNIYRRWIQLGLQKCVRMYNPT |
31-34 |
SIVmac251 |
Cynomolgus |
Gag 296-315 |
SYVDRFYKSLRAEQTDAAYK |
35 |
SIVmac251 |
Rhesus |
Env 21-30 |
YCTLYVTVFY |
Unpublished |
SIVmac239 |
Rhesus |
Env 113-121 |
CNKSETDRW |
36 |
SIVmac251 |
Rhesus |
Env 262-281 |
SCTRMMETQTSTWFGFNGTR |
Unpublished |
SIVmac251 |
Rhesus |
Env 292-301 |
GRDNRTIISL |
Unpublished |
SIVmac251 |
Rhesus |
Env 312-331 |
RRPGNKTVLPVTIMSGLVFH |
Unpublished |
SIVmac251 |
Rhesus |
Nef 108-123 |
LRAMTYKLAIDMSHFI |
31-34, 42 |
SIVmac251 |
Rhesus |
Nef 128-137 |
GLEGIYYSAR |
31-34 |
SIVmac251 |
Rhesus |
Nef 155-169 |
DWQDYTSGPGIRYPK |
31-34 |
SIVmac251 |
Rhesus |
Nef 164-178 |
GIRYPKTFGWLWKLV |
26, 31-34 |
SIVmac251 |
Rhesus |
Nef 171-179 |
FGWLWKLVP |
27 |
SIVmac251 |
Rhesus |
Nef 201-225 |
SKWDDPWGEVLAWKFDPTLAYTYEA |
31-34 |
SIVmac239 |
Rhesus |
Nef 157-167 |
QDYTSGPGIRY |
37 |
SIVmac239 |
Sooty mangabey |
Nef 20-28 |
LLRARGETY |
37 |
SIVmac239 |
Rhesus |
Vpr 74-81 |
RGGCIHSR |
Unpublished |
SIVmac239 |
Rhesus |
Nef 45-53 |
GLDKGLSSL |
Unpublished |
SIVmac251 |
Rhesus |
Nef 169-178 |
KTFGWLWKLV |
38 |
SIVmac251 |
Rhesus |
Nef 211-225 |
LAWKFDPTLAYTYEA |
38 |
SIVmac251 |
Rhesus |
Nef 112-119 |
SYKLAIDM |
38, 42 |
SIVmac251 |
Rhesus |
Nef 120-135 |
SHFKEKGGLEGIYYS |
42 |
SIVmac251 |
Rhesus |
Nef 125-138 |
EKGGLELIYYSARR |
42 |
SHIV-HXBc2 |
Rhesus |
Gag 321-340 |
TLLIQNANPDCKLVLKGLGV |
39 |
SHIV-HXBc2 |
Rhesus |
Gag 421-440 |
DHVMAKCPDRQAGFLGLGPW |
39 |
SIVNef 239 |
Rhesus |
Env 484-492 |
AEVAELYRL |
40 |
SIVmac239 |
Sooty mangabey |
Gag 196-205 |
HQAAMQIIRD |
41 |
SIVmac239 |
Sooty mangabey |
Env 429-437 |
YVPCHIRQI |
41 |
Naturally-infected |
Sooty mangabey |
Env 428-437 |
NYVPCHIRQI |
41 |
SIVmac239 |
Sooty mangabey |
Env 339-363 |
PKQAWCWFGGKWKDAIKEVKQTIVK |
41 |
SIVmac239 |
Sooty mangabey |
Nef 21-30 |
LRARGETYGR |
41 |
SIVmac239 |
Sooty mangabey |
Nef 20-30 |
LLRARGETYGR |
41 |
Naturally-infected |
Sooty mangabey |
Nef 21-32 |
LRARGETYGRLL |
41 |
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