Immunogenetics (2005) 57: 53–68 DOI 10.1007/s00251-004-0749-z ORIGINAL PAPER Alessandro Sette . John Sidney . Huynh-Hoa Bui . Marie-France del Guercio . Jeff Alexander . John Loffredo . David I. Watkins . Bianca R. Mothé Characterization of the peptide-binding specificity of Mamu-A*11 results in the identification of SIV-derived epitopes and interspecies cross-reactivity Received: 5 September 2004 / Revised: 10 November 2004 / Published online: 4 March 2005 # Springer-Verlag 2005 Abstract The SIV-infected Indian rhesus macaque is the most established model of HIV infection, providing insight into pathogenesis and a system for testing novel vaccines. However, only a limited amount of information is avail- able regarding the peptide-binding motifs and epitopes bound by their class I and class II MHC molecules. In this study, we utilized a library of over 1,000 different peptides and a high throughput MHC-peptide binding assay to de- tail the binding specificity of the rhesus macaque class I molecule Mamu-A*11. These studies defined the fine specificity of primary anchor positions, and dissected the role of secondary anchors, for peptides of 8–11 residues in length. This detailed information was utilized to develop size-specific polynomial algorithms to predict Mamu-A*11 binding capacity. Testing SIV mac 239-derived Mamu-A*11 binding peptides for recognition by peripheral blood mono- nuclear cells (PBMC) from Mamu-A*11-positive, SIV- infected macaques, identified five novel SIV-derived Mamu-A*11 epitopes. Finally, we detected extensive cross- reactivity at the binding level between Mamu-A*11 and the mouse H-2 class I molecule K k . Further experiments revealed that three out of four Mamu-A*11 binding peptides which bound K k and were immunogenic in K k mice were also recognized in Mamu-A*11-infected macaques. This is the first detailed description of mouse-macaque interspecies cross-reactivity, potentially useful in testing novel vaccines in mice and macaques. Keywords AIDS . SIV . MHC . Epitope . Macaque Introduction Rhesus macaques represent an important animal model for many infectious diseases, including HIV and biodefense pathogens. This model provides key insights into disease pathogenesis, and allows for the evaluation of novel vaccine concepts. Several independent observations have impli- cated cellular immunity, specifically cytotoxic T-lympho- cyte (CTL) responses, in the control of SIV and HIV viral replication (Brander and Walker 1999; Goulder et al. 1997; Letvin et al. 1999). Recently, a renewed interest in Cate- gory A-C pathogens has revitalized efforts for developing analytical methods to rigorously analyze both cellular and humoral immune responses in non-human primates, in a number of different disease models. The immunogenetics of rhesus macaques has only re- cently been explored in detail. A series of studies focused on the Mamu-A*01 class I molecule, led to the identification of its peptide-binding specificity and characterized 14 differ- ent SIV-derived CTL epitopes (Allen et al. 2001; Sidney et al. 2000). More recently, Mamu-B*17, another high- frequency allele in rhesus macaques, has been studied. The identification of the peptide-binding specificity of Mamu- B*17 resulted in the determination of 15 new SIV-derived CTL epitopes (Mothe et al. 2002b). These studies were instrumental in the synthesis of the first macaque tetramer (Kuroda et al. 1998) and enabled several different studies addressing viral evasion from CTL responses, during both the acute and chronic phases of SIV/SHIV infection (Allen et al. 2000a; Barouch et al. 2000, 2003; Chen et al. 2000; O’Connor et al. 2002; Subbramanian et al. 2003; Vogel et al. 2002). The peptide-binding specificity of other molecules, A. Sette . J. Sidney . H.-H. Bui La Jolla Institute for Allergy and Immunology, San Diego, CA 92121, USA M.-F. del Guercio . J. Alexander Epimmune, Inc, San Diego, CA 92121, USA J. Loffredo . D. I. Watkins Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA B. R. Mothé (*) Department of Biological Sciences, California State University, San Marcos, San Marcos, CA 92096, USA e-mail: bmothe@csusm.edu Tel.: +1-760-7503063 Fax: +1-760-7504637