Study of MHC class II region polymorphism in the Filipino cynomolgus macaque population

Immunogenetics

Volumn 66, Issue 4, 2014, Pages 219-230

  Blancher, A ^a   Aarnink, A ^a   Yamada, Y ^b   Tanaka, K ^c   Yamanaka, H ^b   Shiina, T ^c  

^a UNIVERSITÉ PAUL SABATIER   (France)

^b N   (Japan)

^c TOKAI UNIVERSITY SCHOOL OF MEDICINE   (Japan)

Author keywords

Cynomolgus macaque; Haplotypes; Mafa DP; Mafa DQ; Mafa DR; Microsatellites

Indexed keywords

GENOMIC DNA; HLA DP ANTIGEN; HLA DR ANTIGEN;

ALLELE; ARTICLE; DNA POLYMORPHISM; GENETIC ASSOCIATION; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HETEROZYGOSITY; HISTOCOMPATIBILITY GENE; MACACA FASCICULARIS; MHC CLASS II GENE; MICROSATELLITE MARKER; NONHUMAN; NUCLEOTIDE SEQUENCE; PHILIPPINES; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; UNINDEXED SEQUENCE;

ANIMALIA; MACACA FASCICULARIS;

ANIMALS; DNA, COMPLEMENTARY; GENE FREQUENCY; GENES, MHC CLASS II; GENETIC ASSOCIATION STUDIES; GENETICS, POPULATION; HAPLOTYPES; HUMANS; MACACA FASCICULARIS; MICROSATELLITE REPEATS; PHILIPPINES; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC; SPECIES SPECIFICITY;

EID: 84896495296     PISSN: 00937711     EISSN: 14321211     Source Type: Journal    
DOI: 10.1007/s00251-014-0764-7     Document Type: Article

References (34)

1. Aarnink A, Estrade L, Apoil PA, Kita YF, Saitou N, Shiina T, Blancher A (2010) Study of cynomolgus monkey (Macaca fascicularis) DRA polymorphism in four populations. Immunogenetics 62(3):123-136. doi: 10.1007/s00251-009-0421-8
2. Aarnink A, Bonhomme M, Blancher A (2013) Positive selection in the major histocompatibility complex class III region of cynomolgus macaques (Macaca fascicularis) of the Philippines origin. Tissue Antigens 81(1):12-18. doi: 10.1111/tan.12028
3. Arikata M, Itoh Y, Okamatsu M, Maeda T, Shiina T, Tanaka K, Suzuki S, Nakayama M, Sakoda Y, Ishigaki H, Takada A, Ishida H, Soda K, Pham VL, Tsuchiya H, Nakamura S, Torii R, Shimizu T, Inoko H, Ohkubo I, Kida H, Ogasawara K (2012) Memory immune responses against pandemic (H1N1) 2009 influenza virus induced by a whole particle vaccine in cynomolgus monkeys carrying Mafa-A1052:02. PLoS ONE 7(5):e37220. doi: 10.1371/journal.pone.0037220
4. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004) GENETIX Version 4.05, Logiciel sous Windows TM pour la génétique des Populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000. France: Université Montpellier II, Montpellier
5. Bigaud M, Wieczorek G, Beerli C, Audet M, Blancher A, Heusser C, Morris RE, Wagner J (2012) Sotrastaurin (AEB071) alone and in combination with cyclosporine A prolongs survival times of non-human primate recipients of life-supporting kidney allografts. Transplantation 93(2):156-164. doi: 10.1097/TP.0b013e31823cf92f
6. Blancher A, Tisseyre P, Dutaur M, Apoil PA, Maurer C, Quesniaux V, Raulf F, Bigaud M, Abbal M (2006) Study of cynomolgus monkey (Macaca fascicularis) MhcDRB (Mafa-DRB) polymorphism in two populations. Immunogenetics 58(4):269-282. doi: 10.1007/s00251-006-0102-9
7. Blancher A, Bonhomme M, Crouau-Roy B, Terao K, Kitano T, Saitou N (2008) Mitochondrial DNA sequence phylogeny of 4 populations of the widely distributed cynomolgus macaque (Macaca fascicularis fascicularis). J Hered 99(3):254-264. doi: 10.1093/jhered/esn003
8. Blancher A, Aarnink A, Tanaka K, Ota M, Inoko H, Yamanaka H, Nakagawa H, Apoil PA, Shiina T (2012) Study of cynomolgus monkey (Macaca fascicularis) Mhc DRB gene polymorphism in four populations. Immunogenetics 64(8):605-614. doi: 10.1007/s00251-012-0613-5
9. Bonhomme M, Blancher A, Crouau-Roy B (2005) Multiplexed microsatellites for rapid identification and characterization of individuals and populations of Cercopithecidae. Am J Primatol 67(3):385-391. doi: 10.1002/ajp.20193
10. Bonhomme M, Blancher A, Jalil MF, Crouau-Roy B (2007) Factors shaping genetic variation in the MHC of natural non-human primate populations. Tissue Antigens 70(5):398-411. doi: 10.1111/j.1399-0039.2007.00925.x
11. Creager HM, Becker EA, Sandman KK, Karl JA, Lank SM, Bimber BN, Wiseman RW, Hughes AL, O'Connor SL, O'Connor DH (2011) Characterization of full-length MHC class II sequences in Indonesian and Vietnamese cynomolgus macaques. Immunogenetics 63(9):611-618. doi: 10.1007/s00251-011-0537-5
12. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14(6):1188-1190. doi: 10.1101/gr.849004
13. Cullen M, Perfetto SP, Klitz W, Nelson G, Carrington M (2002) High-resolution patterns of meiotic recombination across the human major histocompatibility complex. Am J Hum Genet 71(4):759-776. doi: 10.1086/342973
14. Daza-Vamenta R, Glusman G, Rowen L, Guthrie B, Geraghty DE (2004) Genetic divergence of the rhesus macaque major histocompatibility complex. Genome Res 14(8):1501-1515. doi: 10.1101/gr.2134504
15. de Groot NG, Otting N, Robinson J, Blancher A, Lafont BA, Marsh SG, O'Connor DH, Shiina T, Walter L, Watkins DI, Bontrop RE (2012) Nomenclature report on the major histocompatibility complex genes and alleles of Great Ape, Old and New World monkey species. Immunogenetics 64(8):615-631. doi: 10.1007/s00251-012-0617-1
16. Garcia-Boronat M, Diez-Rivero CM, Reinherz EL, Reche PA (2008) PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery. Nucleic Acids Res 36(Web Server issue):W35-W41. doi: 10.1093/nar/gkn211
17. Giraldo-Vela JP, Rudersdorf R, Chung C, Qi Y, Wallace LT, Bimber B, Borchardt GJ, Fisk DL, Glidden CE, Loffredo JT, Piaskowski SM, Furlott JR, Morales-Martinez JP, Wilson NA, Rehrauer WM, Lifson JD, Carrington M, Watkins DI. (2008) The major histocompatibility complex class II alleles Mamu-DRB11003 and -DRB10306 are enriched in a cohort of simian immunodeficiency virus-infected rhesus macaque elite controllers. J Virol. 82(2):859-70
18. Li W, Wang T, Ling F, Zhao H, Wei L, Zhuo M, Du H, Wang X (2012) Identification of MhcMafa-DRB alleles in a cohort of cynomolgus macaques of Vietnamese origin. Am J Primatol 74(10):958-966. doi: 10.1002/ajp.22048
19. Ling F, Zhuo M, Ni C, Zhang GQ, Wang T, Li W, Wei LQ, Du HL, Wang JF, Wang XN (2012) Comprehensive identification of high-frequency and co-occurring Mafa-B, Mafa-DQB1, and Mafa-DRB alleles in cynomolgus macaques of Vietnamese origin. Hum Immunol 73(5):547-553. doi: 10.1016/j.humimm.2012.02.003
20. Menninger K, Wieczorek G, Riesen S, Kunkler A, Audet M, Blancher A, Schuurman HJ, Quesniaux V, Bigaud M (2002) The origin of cynomolgus monkey affects the outcome of kidney allografts under neoral immunosuppression. Transplant Proc 34(7):2887-2888
21. O'Connor SL, Blasky AJ, Pendley CJ, Becker EA, Wiseman RW, Karl JA, Hughes AL, O'Connor DH (2007) Comprehensive characterization of MHC class II haplotypes in Mauritian cynomolgus macaques. Immunogenetics 59(6):449-462. doi: 10.1007/s00251-007-0209-7
22. Otting N, de Groot N, de Vos-Rouweler AJ, Louwerse A, Doxiadis GG, Bontrop RE (2012) Multilocus definition of MHC haplotypes in pedigreed cynomolgus macaques (Macaca fascicularis). Immunogenetics 64(10):755-765. doi: 10.1007/s00251-012-0632-2
23. Raymond M, Rousset F (1995) Genepop (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248-249
24. Reche PA, Reinherz EL (2003) Sequence variability analysis of human class I and class II MHC molecules: functional and structural correlates of amino acid polymorphisms. J Mol Biol 331(3):623-641
25. Robinson J, Halliwell JA, McWilliam H, Lopez R, Marsh SG (2013a) IPD - the immuno polymorphism database. Nucleic Acids Res 41(Database issue):D1234-D1240. doi: 10.1093/nar/gks1140
26. Robinson J, Halliwell JA, McWilliam H, Lopez R, Parham P, Marsh SG (2013b) The IMGT/HLA database. Nucleic Acids Res 41(Database issue):D1222-D1227. doi: 10.1093/nar/gks949
27. Schneider TD, Stephens RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18(20):6097-6100
28. Shiina T, Tanaka K, Katsuyama Y, Otabe K, Sakamoto K, Kurata M, Nomura M, Yamanaka H, Nakagawa H, Inoko H, Ota M (2010) Mitochondrial DNA diversity among three subpopulations of cynomolgus macaques (Macaca fascicularis) originating from the Indochinese region. Exp Anim / Jpn Assoc Lab Anim Sci 59(5):567-578
29. Smith DG, McDonough JW, George DA (2007) Mitochondrial DNA variation within and among regional populations of longtail macaques (Macaca fascicularis) in relation to other species of the fascicularis group of macaques. Am J Primatol 69(2):182-198. doi: 10.1002/ajp.20337
30. Tosi AJ, Morales JC, Melnick DJ (2002) Y-chromosome and mitochondrial markers in Macaca fascicularis indicate introgression with indochinese M. mulatta and a biogeographic barrier in the isthmus of Kra. Int J Primatol 23:161-178
31. Walsh GP, Tan EV, dela Cruz EC, Abalos RM, Villahermosa LG, Young LJ, Cellona RV, Nazareno JB, Horwitz MA (1996) The Philippine cynomolgus monkey (Macaca fasicularis) provides a new nonhuman primate model of tuberculosis that resembles human disease. Nat Med 2(4):430-436
32. Wieczorek G, Bigaud M, Menninger K, Riesen S, Quesniaux V, Schuurman HJ, Audet M, Blancher A, Mihatsch MJ, Nickeleit V (2006) Acute and chronic vascular rejection in nonhuman primate kidney transplantation. Am J Transplant 6(6):1285-1296
33. Willer DO, Guan Y, Luscher MA, Li B, Pilon R, Fournier J, Parenteau M, Wainberg MA, Sandstrom P, MacDonald KS (2010) Multi-low-dose mucosal simian immunodeficiency virus SIVmac239 challenge of cynomolgus macaques immunized with "hyperattenuated" SIV constructs. J Virol 84(5):2304-2317. doi: 10.1128/JVI.01995-09
34. Wiseman RW, Wojcechowskyj JA, Greene JM, Blasky AJ, Gopon T, Soma T, Friedrich TC, O'Connor SL, O'Connor DH (2007) Simian immunodeficiency virus SIVmac239 infection of major histocompatibility complex-identical cynomolgus macaques from Mauritius. J Virol 81(1):349-361. doi: 10.1128/JVI.01841-06