@article{nemec_kapatos_holmes_hess_2018, title={The prevalent Boxer MHC class Ia allotype dog leukocyte antigen (DLA)-88*034:01
 preferentially binds nonamer peptides with a defined motif}, volume={92}, ISSN={2059-2302}, url={http://dx.doi.org/10.1111/tan.13398}, DOI={10.1111/tan.13398}, abstractNote={Development of effective immunotherapy for chemoresistant malignancies can be advanced by studies in spontaneous cancer models, such as the dog. A crucial first step, T‐cell epitope discovery, can be assisted by determination of binding motifs of common dog leukocyte antigen (DLA) class Ia allotypes. Boxers are popular, inbred dogs with increased risks of relevant target cancers and restricted MHC diversity. We sought to identify the motif of DLA‐88*034:01, a breed‐dominant allotype, to assist peptide prediction from tumor antigens. Mass spectrometry of eluted peptides showed a preference for nonamers with conserved amino acid preferences: basic at position (P)1; hydrophobic at P2; acidic at P4; histidine at P6; and phenylalanine at P9. This data should expedite finding epitopes restricted by this DLA‐88 allotype.}, number={6}, journal={HLA}, publisher={Wiley}, author={Nemec, Paige S. and Kapatos, Alexander and Holmes, Jennifer C. and Hess, Paul R.}, year={2018}, month={Nov}, pages={403–407} }
 @article{gojanovich_ross_holmer_holmes_hess_2013, title={Characterization and allelic variation of the transporters associated with antigen processing (TAP) genes in the domestic dog (Canis lupus familiaris)}, volume={41}, ISSN={0145-305X}, url={http://dx.doi.org/10.1016/j.dci.2013.07.011}, DOI={10.1016/j.dci.2013.07.011}, abstractNote={The function of the transporters associated with antigen processing (TAP) complex is to shuttle antigenic peptides from the cytosol to the endoplasmic reticulum to load MHC class I molecules for CD8+ T-cell immunosurveillance. Here we report the promoter and coding regions of the canine TAP1 and TAP2 genes, which encode the homologous subunits forming the TAP heterodimer. By sampling genetically divergent breeds, polymorphisms in both genes were identified, although there were few amino acid differences between alleles. Splice variants were also found. When aligned to TAP genes of other species, functional regions appeared conserved, and upon phylogenetic analysis, canine sequences segregated appropriately with their orthologs. Transfer of the canine TAP2 gene into a murine TAP2-defective cell line rescued surface MHC class I expression, confirming exporter function. This data should prove useful in investigating the association of specific TAP defects or alleles with immunity to intracellular pathogens and cancer in dogs.}, number={4}, journal={Developmental & Comparative Immunology}, publisher={Elsevier BV}, author={Gojanovich, Gregory S. and Ross, Peter and Holmer, Savannah G. and Holmes, Jennifer C. and Hess, Paul R.}, year={2013}, month={Dec}, pages={578–586} }
 @article{holmes_holmer_ross_buntzman_frelinger_hess_2013, title={Polymorphisms and tissue expression of the feline leukocyte antigen class I loci FLAI-E, FLAI-H, and FLAI-K}, volume={65}, ISSN={0093-7711 1432-1211}, url={http://dx.doi.org/10.1007/s00251-013-0711-z}, DOI={10.1007/s00251-013-0711-z}, abstractNote={Cytotoxic CD8+ T-cell immunosurveillance for intracellular pathogens, such as viruses, is controlled by classical major histocompatibility complex (MHC) class Ia molecules, and ideally, these antiviral T-cell populations are defined by the specific peptide and restricting MHC allele. Surprisingly, despite the utility of the cat in modeling human viral immunity, little is known about the feline leukocyte antigen class I complex (FLAI). Only a few coding sequences with uncertain locus origin and expression patterns have been reported. Of 19 class I genes, three loci—FLAI-E, FLAI-H, and FLAI-K—are predicted to encode classical molecules, and our objective was to evaluate their status by analyzing polymorphisms and tissue expression. Using locus-specific, PCR-based genotyping, we amplified 33 FLAI-E, FLAI-H, and FLAI-K alleles from 12 cats of various breeds, identifying, for the first time, alleles across three distinct loci in a feline species. Alleles shared the expected polymorphic and invariant sites in the α1/α2 domains, and full-length cDNA clones possessed all characteristic class Ia exons. Alleles could be assigned to a specific locus with reasonable confidence, although there was evidence of potentially confounding interlocus recombination between FLAI-E and FLAI-K. Only FLAI-E, FLAI-H, and FLAI-K origin alleles were amplified from cDNAs of multiple tissue types. We also defined hypervariable regions across these genes, which permitted the assignment of names to both novel and established alleles. As predicted, FLAI-E, FLAI-H, and FLAI-K fulfill the major criteria of class Ia genes. These data represent a necessary prerequisite for studying epitope-specific antiviral CD8+ T-cell responses in cats.}, number={9}, journal={Immunogenetics}, publisher={Springer Science and Business Media LLC}, author={Holmes, Jennifer C. and Holmer, Savannah G. and Ross, Peter and Buntzman, Adam S. and Frelinger, Jeffrey A. and Hess, Paul R.}, year={2013}, month={Jun}, pages={675–689} }
 @article{ross_holmes_gojanovich_hess_2012, title={A cell-based MHC stabilization assay for the detection of peptide binding to the canine classical class I molecule, DLA-88}, volume={150}, ISSN={["0165-2427"]}, url={http://europepmc.org/articles/PMC3494747}, DOI={10.1016/j.vetimm.2012.08.012}, abstractNote={Identifying immunodominant CTL epitopes is essential for studying CD8+ T-cell responses in populations, but remains difficult, as peptides within antigens typically are too numerous for all to be synthesized and screened. Instead, to facilitate discovery, in silico scanning of proteins for sequences that match the motif, or binding preferences, of the restricting MHC class I allele - the largest determinant of immunodominance - can be used to predict likely candidates. The high false positive rate with this analysis ideally requires binding confirmation, which is obtained routinely by an assay using cell lines such as RMA-S that have defective transporter associated with antigen processing (TAP) machinery, and consequently, few surface class I molecules. The stabilization and resultant increased life-span of peptide-MHC complexes on the cell surface by the addition of true binders validates their identity. To determine whether a similar assay could be developed for dogs, we transfected a prevalent class I allele, DLA-88*50801, into RMA-S. In the BARC3 clone, the recombinant heavy chain was associated with murine β2-microglobulin, and importantly, could differentiate motif-matched and -mismatched peptides by surface MHC stabilization. This work demonstrates the potential to use RMA-S cells transfected with canine alleles as a tool for CTL epitope discovery in this species.}, number={3-4}, journal={VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY}, author={Ross, Peter and Holmes, Jennifer C. and Gojanovich, Gregory S. and Hess, Paul R.}, year={2012}, month={Dec}, pages={206–212} }