Copy number and nucleotide variation of the LILR family of myelomonocytic cell activating and inhibitory receptors

Immunogenetics

Volumn 66, Issue 2, 2014, Pages 73-83

  López Álvarez, María R ^a,b   Jones, Des C ^a   Jiang, Wei ^a,b   Traherne, James A ^a,b   Trowsdale, John ^a,b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

CNV; Haplotype; ILT; LILR

Indexed keywords

IMMUNOGLOBULIN RECEPTOR; LEUKOCYTE IMMUNOGLOBULIN LIKE RECEPTOR; NUCLEOTIDE; RECEPTOR SUBTYPE; UNCLASSIFIED DRUG; LEUKOCYTE ANTIGEN; LILRA3 PROTEIN, HUMAN; LILRA6 PROTEIN, HUMAN; LILRB3 PROTEIN, HUMAN;

ALLELE; ARTICLE; CELL TYPE; CHROMOSOME; COPY NUMBER VARIATION; GENE DELETION; GENOTYPE; HAPLOTYPE; HISTOCOMPATIBILITY; HUMAN; HUMAN CELL; IMMUNOLOGICAL TOLERANCE; IMMUNORECEPTOR TYROSINE BASED ACTIVATION MOTIF; MONOCYTE; MYELOMONOCYTIC CELL; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN MOTIF; CELL LINE; CHROMOSOME 19; CYTOLOGY; DNA SEQUENCE; GENE DUPLICATION; GENE EXPRESSION; GENETIC POLYMORPHISM; GENETICS; IMMUNOLOGY; METABOLISM; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; SIGNAL TRANSDUCTION;

ALLELES; AMINO ACID MOTIFS; ANTIGENS, CD; BASE SEQUENCE; CELL LINE; CHROMOSOMES, HUMAN, PAIR 19; DNA COPY NUMBER VARIATIONS; GENE DUPLICATION; GENE EXPRESSION; HUMANS; MOLECULAR SEQUENCE DATA; MONOCYTES; POLYMORPHISM, GENETIC; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, IMMUNOLOGIC; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION; SIGNAL TRANSDUCTION;

EID: 84897018209     PISSN: 00937711     EISSN: 14321211     Source Type: Journal    
DOI: 10.1007/s00251-013-0742-5     Document Type: Article

References (44)

1. Anderson KJ, Allen RL (2009) Regulation of T-cell immunity by leucocyte immunoglobulin-like receptors: innate immune receptors for self on antigen-presenting cells. Immunology 127:8-17
2. Barrow AD, Trowsdale J (2008) The extended human leukocyte receptor complex: diverse ways of modulating immune responses. Immunol Rev 224:98-123
3. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acid Res 27(2):573-580
4. Borges L, Hsu ML, Fanger N, Kubin M, Cosman D (1997) A family of human lymphoid and myeloid Ig-like receptors, some of which bind to MHC class I molecules. J Immunol 159:5192-5196 (Pubitemid 127470042)
5. Brown D, Trowsdale J, Allen R (2004) The LILR family: modulators of innate and adaptive immune pathways in health and disease. Tissue Antigens 64(3):215-225 (Pubitemid 39120446)
6. Brown DP, Jones DC, Anderson KJ et al (2009) The inhibitory receptor LILRB4 (ILT3) modulates antigen presenting cell phenotype and, along with LILRB2 (ILT4), is upregulated in response to Salmonella infection. BMC Immunol 10:56
7. Cao W, Bover L, Cho M et al (2009) Regulation of TLR7/9 responses in plasmacytoid dendritic cells by BST2 and ILT7 receptor interaction. J Exp Med 206(7):1603-1614
8. Chang CC, Ciubotariu R, Manavalan JS et al (2002) Tolerization of dendritic cells by T(S) cells: the crucial role of inhibitory receptors ILT3 and ILT4. Nat Immunol 3(3):237-243 (Pubitemid 34218114)
9. Chang CC, Liu Z, Vlad G et al (2009) Ig-like transcript 3 regulates expression of proinflammatory cytokines and migration of activated T cells. J Immunol 182:5208-5216
10. Colonna M, Navarro F, Bellon T et al (1997) A common inhibitory receptor for major histocompatibility complex class I molecules on human lymphoid and myelomonocytic cells. J Exp Med 186:1809-1818 (Pubitemid 27524591)
11. Colonna M, Samaridis J, Cella M et al (1998) Human myelomonocytic cells express an inhibitory receptor for classical and nonclassical MHC class I molecules. J Immunol 160:3096-3100 (Pubitemid 28164696)
12. Colonna M, Nakajima H, Navarro F, Lopez-Botet M (1999) A novel family of Ig-like receptors for HLA class I molecules that modulate function of lymphoid and myeloid cells. J Leukoc Biol 66:375-381 (Pubitemid 29439243)
13. Fanger NA, Cosman D, Peterson L, Braddy SC, Maliszewski CR, Borges L (1998) The MHC class I binding proteins LIR-1 and LIR-2 inhibit Fc receptor-mediated signaling in monocytes. Eur J Immunol 28:3423-3434 (Pubitemid 28510753)
14. Huynh OA, Hampartzoumian T, Arm JP et al (2007) Down-regulation of leucocyte immunoglobulin-like receptor expression in the synovium of rheumatoid arthritis patients after treatmentwith disease-modifying antirheumatic drugs. Rheumatology (Oxford) 46(5):742-751 (Pubitemid 47061702)
15. Jeffreys AJ, Holloway JK, Kauppi L et al (2004) Meiotic recombination hot spots and human DNA diversity. Philos Trab R Soc London B Biol 59(1441):141-152 (Pubitemid 38106457)
16. Jiang W, Johnson C, Jayaraman J et al (2012) Copy number variation leads to considerable diversity for B but not A haplotypes of the human KIR genes encoding NK cell receptors. Genome Res 22(10):1845-1854
17. Jones DC, Edgar RS, Ahmad T et al (2006) Killer Ig-like receptor (KIR) genotype and HLA ligand combinations in ulcerative colitis susceptibility. Genes Immun 7(7):576-582 (Pubitemid 44614872)
18. Jones DC, Roghanian A, Brown DP et al (2009) Alternative mRNA splicing creates transcripts encoding soluble proteins from most LILR genes. Eur J Immunol 39(11):3195-3206
19. Kabalak G, Dobberstein SB, Matthias T, Reuter S, The YH, Dörner T, Schmidt RE, Witte T (2009) Association of immunoglobulin-like transcript 6 deficiency with Sjögren's syndrome. Arthritis Rheum 60(10):2923-2925
20. + T suppressor cells. J Immunol 176(5):2790-2798
21. Koch S, Goedde R, Nigmatova V et al (2005) Association of multiple sclerosis with ILT6 deficiency. Genes Immun 6:445-447 (Pubitemid 43090521)
22. Kuroki K, Tsuchiya N, Shiroishi M et al (2005) Extensive polymorphisms of LILRB1 (ILT2, LIR1) and their association with HLA-DRB1 shared epitope negative rheumatoid arthritis. Hum Mol Genet 14(16):2469-2480 (Pubitemid 41418008)
23. Lee DJ, Sieling PA, Ochoa MT et al (2007) LILRA2 activation inhibits dendritic cell differentiation and antigen presentation to T cells. J Immunol 179(12):8128-8136
24. Liu P, Carvalho CM, Hastings PJ, Lupski JR (2012) Mechanisms for recurrent and complex human genomic rearrangements. Curr Opin Genet Dev 22(3):211-220
25. Manavalan JS, Rossi PC, Vlad G et al (2003) High expression of ILT3 and ILT4 is a general feature of tolerogenic dendritic cells. Transpl Immunol 11(3-4):245-258 (Pubitemid 37120544)
26. Nakajima H, Samaridis J, Angman L, Colonna M (1999) Human myeloid cells express an activating ILT receptor (ILT1) that associates with Fc receptor gamma-chain. J Immunol 162(1):5-8 (Pubitemid 29018897)
27. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3(5):418-426 (Pubitemid 16010523)
28. Ordóñez D, Sánchez AJ, Martínez- Rodríguez JE et al (2009) Multiple sclerosis associates with LILRA3 deletion in Spanish patients. Genes Immun 10(6):579-585
29. Park S, Yang JS, Kim J et al (2012) Evolutionary history of human disease genes reveals phenotypic connections and comorbidity among genetic diseases. Sci Rep 2:757
30. Pilsbury LE, Allen RL, Vordermeier M (2010) Modulation of Toll-like receptor activity by leukocyte Ig-like receptors and their effects during bacterial infection. Mediat Inflamm 2010:536478
31. Robinson J, Mistry K, McWilliam H, Lopez R, Marsh SG (2010) IPD - the Immuno Polymorphism Database. Nucleic Acids Res 38:D863-D869
32. Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 3:1101-1108 (Pubitemid 351818697)
33. Sudmant PH, Kitzman JO, Antonacci F et al (2010) Diversity of human copy number variation and multicopy genes. Science 330(6004):641-646
34. Tavano B, Galao RP, Graham DR et al (2013) Ig-like transcript 7, but not bone marrow stromal cell antigen 2 (also known as HM1.24, tetherin, or CD317), modulates plasmacytoid dendritic cell function in primary human blood leukocytes. J Immunol 190(6):2622-2630
35. Torkar M, Haude A, Milne S, Beck S, Trowsdale J, Wilson MJ (2000) Arrangement of the ILT gene cluster: a common null allele of the ILT6 gene results from a 6.7-kbp deletion. Eur J Immunol 30:3655-3662 (Pubitemid 32005239)
36. Traherne JA, Horton R, Roberts AN et al (2006) Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history. PLoS Genet 2(1):e9
37. Traherne JA, Martin M, Ward R et al (2010) Mechanisms of copy number variation and hybrid gene formation in the KIR immune gene complex. Hum Mol Genet 19(5):737-751
38. Willcox BE, Thomas LM, Bjorkman PJ (2003) Crystal structure of HLA-A2 bound to LIR-1, a host and viral major histocompatibility complex receptor. Nat Immunol 4(9):913-919 (Pubitemid 37098663)
39. Wiśniewski A, Wagner M, Nowak I et al (2013) 6.7-kbp deletion in LILRA3 (ILT6) gene is associated with later onset of the multiple sclerosis in a Polish population. Hum Immunol 74(3):353-357
40. Yang Z, Bjorkman PJ (2008) Structure of UL18, a peptide-binding viral MHC mimic, bound to a host inhibitory receptor. Proc Natl Acad Sci U S A 105(29):10095-10100
41. Yang ZH, Nielsen R, Goldman N, Pedersen AMK (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449 (Pubitemid 30257141)
42. Zhang J, Kumar S, Nei M (1997) Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes.Mol Biol Evol 14(12):1335-1338
43. Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, Yu J (2006) KaKs-Calculator: calculating Ka and Ks through model selection and model averaging. Genomics ProteomE Bioinforma 4(4):259-263 (Pubitemid 46771391)
44. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31(13):3406-3415