Adams EJ, Parham P (2001) Species-specific evolution of MHC class I genes in the higher primates. Immunol Rev 183(1):41–64. https://doi.org/10.1034/j.1600-065x.2001.1830104.x
Article CAS PubMed Google Scholar
Arrieta-Bolaños E, Hernández-Zaragoza DI, Barquera R (2023) An HLA map of the world: a comparison of HLA frequencies in 200 worldwide populations reveals diverse patterns for class I and class II. Front Genet 14:866407. https://doi.org/10.3389/fgene.2023.866407
Article CAS PubMed PubMed Central Google Scholar
Balla-Jhagjhoorsingh SS, Koopman G, Mooij P, Haaksma TG, Teeuwsen VJ, Bontrop RE, Heeney JL (1999) Conserved CTL epitopes shared between HIV-infected human long-term survivors and chimpanzees. J Immunol (Baltimore, Md: 1950) 162(4):2308–2314
Barker DJ, Maccari G, Georgiou X, Cooper MA, Flicek P, Robinson J, Marsh SGE (2023) The IPD-IMGT/HLA Database. Nucleic Acids Res 51(D1):D1053–D1060. https://doi.org/10.1093/nar/gkac1011
Article CAS PubMed Google Scholar
Bernatchez L, Landry C (2003) MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years? J Evol Biol 16(3):363–377. https://doi.org/10.1046/j.1420-9101.2003.00531.x
Article CAS PubMed Google Scholar
Bertoni R, Sette A, Sidney J, Guidotti LG, Shapiro M, Purcell R, Chisari FV (1998) Human class I supertypes and CTL repertoires extend to chimpanzees. J Immunol 161(8):4447–4455. https://doi.org/10.4049/jimmunol.161.8.4447
Article CAS PubMed Google Scholar
Blum JS, Wearsch PA, Cresswell P (2013) Pathways of antigen processing. Annu Rev Immunol 31(1):443–473. https://doi.org/10.1146/annurev-immunol-032712-095910
Article CAS PubMed PubMed Central Google Scholar
Calis JJA, Sanchez-Perez GF, Keşmir C (2010) MHC class I molecules exploit the low G+C content of pathogen genomes for enhanced presentation. Eur J Immunol 40(10):2699–2709. https://doi.org/10.1002/eji.201040339
Chen KY, Liu J, Ren EC (2012) Structural and functional distinctiveness of HLA-A2 allelic variants. Immunol Res 53(1–3):182–190. https://doi.org/10.1007/s12026-012-8295-5
Article CAS PubMed Google Scholar
Dawkins R, Leelayuwat C, Gaudieri S, Tay G, Hui J, Cattley S, Martinez P, Kulski J (1999) Genomics of the major histocompatibility complex: haplotypes, duplication, retroviruses and disease. Immunol Rev 167(1):275–304. https://doi.org/10.1111/j.1600-065X.1999.tb01399.x
Article CAS PubMed Google Scholar
De Groot NG, Otting N, Doxiadis GGM, Balla-Jhagjhoorsingh SS, Heeney JL, Van Rood JJ, Gagneux P, Bontrop RE (2002) Evidence for an ancient selective sweep in the MHC class I gene repertoire of chimpanzees. Proc Natl Acad Sci 99(18):11748–11753. https://doi.org/10.1073/pnas.182420799
Article CAS PubMed PubMed Central Google Scholar
De Groot NG, Heijmans CMC, De Groot N, Otting N, De Vos-Rouweler AJM, Remarque EJ, Bonhomme M, Doxiadis GGM, Crouau-Roy B, Bontrop RE (2008) Pinpointing a selective sweep to the chimpanzee MHC class I region by comparative genomics. Mol Ecol 17(8):2074–2088. https://doi.org/10.1111/j.1365-294X.2008.03716.x
Article CAS PubMed Google Scholar
De Groot NG, Heijmans CMC, De Ru AH, Otting N, Koning F, Van Veelen PA, Bontrop RE (2020) The HLA A03 supertype and several Pan species major histocompatibility complex class I A allotypes share a preference for binding positively charged residues in the F pocket: implications for controlling retroviral infections. J Virology 94(9):e01960-19. https://doi.org/10.1128/JVI.01960-19
Article PubMed PubMed Central Google Scholar
Edwards BH, Bansal A, Sabbaj S, Bakari J, Mulligan MJ, Goepfert PA (2002) Magnitude of functional CD8 + T-cell responses to the gag protein of human immunodeficiency virus type 1 correlates inversely with viral load in plasma. J Virol 76(5):2298–2305. https://doi.org/10.1128/jvi.76.5.2298-2305.2002
Article CAS PubMed PubMed Central Google Scholar
Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the Author, Department of Genome Sciences, University of Washington, Seattle
Hans JB, Bergl RA, Vigilant L (2017) Gorilla MHC class I gene and sequence variation in a comparative context. Immunogenetics 69(5):303–323. https://doi.org/10.1007/s00251-017-0974-x
Article CAS PubMed PubMed Central Google Scholar
Hatcher EL, Zhdanov SA, Bao Y, Blinkova O, Nawrocki EP, Ostapchuck Y, Schäffer AA, Brister JR (2017) Virus variation resource – improved response to emergent viral outbreaks. Nucleic Acids Res 45(D1):D482–D490. https://doi.org/10.1093/nar/gkw1065
Article CAS PubMed Google Scholar
Hoof I, Peters B, Sidney J, Pedersen LE, Sette A, Lund O, Buus S, Nielsen M (2009) NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics 61(1):1–13. https://doi.org/10.1007/s00251-008-0341-z
Article CAS PubMed Google Scholar
Hunter JD (2007) Matplotlib: a 2D graphics environment. Computing in Science & Engineering 9(3):90–95. https://doi.org/10.1109/MCSE.2007.55
Hurley CK, Kempenich J, Wadsworth K, Sauter J, Hofmann JA, Schefzyk D, Schmidt AH, Galarza P, Cardozo MBR, Dudkiewicz M, Houdova L, Jindra P, Sorensen BS, Jagannathan L, Mathur A, Linjama T, Torosian T, Freudenberger R, Manolis A, Dehn J (2020) Common, intermediate and well-documented HLA alleles in world populations: CIWD version 3.0.0. HLA 95(6):516–531. https://doi.org/10.1111/tan.13811
Article CAS PubMed PubMed Central Google Scholar
Jurtz V, Paul S, Andreatta M, Marcatili P, Peters B, Nielsen M (2017) NetMHCpan-4.0: improved peptide–MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data. J Immunol 199(9):3360–3368. https://doi.org/10.4049/jimmunol.1700893
Article CAS PubMed Google Scholar
Kiepiela P, Ngumbela K, Thobakgale C, Ramduth D, Honeyborne I, Moodley E, Reddy S, De Pierres C, Mncube Z, Mkhwanazi N, Bishop K, Van Der Stok M, Nair K, Khan N, Crawford H, Payne R, Leslie A, Prado J, Prendergast A, Goulder P (2007) CD8+ T-cell responses to different HIV proteins have discordant associations with viral load. Nature Medicine 13(1):46–53. https://doi.org/10.1038/nm1520
Article CAS PubMed Google Scholar
Košmrlj A, Read EL, Qi Y, Allen TM, Altfeld M, Deeks SG, Pereyra F, Carrington M, Walker BD, Chakraborty AK (2010) Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection. Nature 465(7296):350–354. https://doi.org/10.1038/nature08997
Article CAS PubMed PubMed Central Google Scholar
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948. https://doi.org/10.1093/bioinformatics/btm404
Article CAS PubMed Google Scholar
Lawlor DA, Warren E, Ward FE, Parham P (1990) Comparison of class I MHC alleles in humans and apes. Immunol Rev 113(1):147–185. https://doi.org/10.1111/j.1600-065X.1990.tb00040.x
Article CAS PubMed Google Scholar
Lawlor DA, Warren E, Taylor P, Parham P (1991) Gorilla class I major histocompatibility complex alleles: Comparison to human and chimpanzee class I. J Exp Med 174(6):1491–1509. https://doi.org/10.1084/jem.174.6.1491
Article CAS PubMed Google Scholar
Letunic I, Bork P (2024) Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res gkae268. https://doi.org/10.1093/nar/gkae268
Lighten J, Papadopulos AST, Mohammed RS, Ward BJ, Paterson GI, Baillie L, Bradbury IR, Hendry AP, Bentzen P, Van Oosterhout C (2017) Evolutionary genetics of immunological supertypes reveals two faces of the Red Queen. Nat Commun 8(1):1294. https://doi.org/10.1038/s41467-017-01183-2
留言 (0)