Skip to main content
Log in

High-throughput killer cell immunoglobulin-like receptor genotyping by MALDI-TOF mass spectrometry with discovery of novel alleles

  • Original Paper
  • Published:
Immunogenetics Aims and scope Submit manuscript

Abstract

The killer cell immunoglobulin-like receptors (KIR) interact with major histocompatibility complex (MHC) class I ligands to regulate the functions of natural killer cells and T cells. Like human leukocyte antigens class I, human KIR are highly variable and correlated with infection, autoimmunity, pregnancy syndromes, and transplantation outcome. Limiting the scope of KIR analysis is the low resolution, sensitivity, and speed of the established methods of KIR typing. In this study, we describe a first-generation single nucleotide polymorphism (SNP)-based method for typing the 17 human KIR genes and pseudogenes that uses analysis by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. It is a high-throughput method that requires minute amounts of genomic DNA for discrimination of KIR genes with some allelic resolution. A study of 233 individuals shows that the results obtained by the SNP-based KIR/MALDI-TOF method are consistent with those obtained with the established sequence-specific oligonucleotide probe or sequence-specific polymerase chain reaction methods. The added sensitivity of the KIR/MALDI-TOF method allowed putative novel alleles of the KIR2DL1, KIR3DL1, KIR2DS5, and KIR2DL5 genes to be identified. Sequencing the KIR2DL5 variant proved it was a newly discovered allele, one that appears associated with Hispanic and Native American populations. This KIR/MALDI-TOF method of KIR typing should facilitate population and disease-association studies that improve knowledge of the immunological functions of KIR–MHC class I interactions.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Bottino C, Castriconi R, Moretta L, Moretta A (2005) Cellular ligands of activating NK receptors. Trends Immunol 26:221–226

    Article  PubMed  CAS  Google Scholar 

  • Carrington M, Norman PJ (2003) The KIR gene cluster. NCBI Bookshelf

  • Christiansen FT, Gaudieri S, De Santis D, Moore CB, Witt CS, James IR (2003) NK Receptor genes are predictors of HIV progression. Hum Immunol 64(Suppl 1):S12

    Article  Google Scholar 

  • Cook MA, Norman PJ, Curran MD, Maxwell LD, Briggs DC, Middleton D, Vaughan RW (2003) A multi-laboratory characterization of the KIR genotypes of 10th International Histocompatibility Workshop cell lines. Hum Immunol 64:567–571

    Article  PubMed  CAS  Google Scholar 

  • Cook MA, Milligan DW, Fegan CD, Darbyshire PJ, Mahendra P, Craddock CF, Moss PA, Briggs DC (2004) The impact of donor KIR and patient HLA-C genotypes on outcome following HLA-identical sibling hematopoietic stem cell transplantation for myeloid leukemia. Blood 103:1521–1526

    Article  PubMed  CAS  Google Scholar 

  • Crum KA, Logue SE, Curran MD, Middleton D (2000) Development of a PCR-SSOP approach capable of defining the natural killer cell inhibitory receptor (KIR) gene sequence repertoires. Tissue Antigens 56:313–326

    Article  PubMed  CAS  Google Scholar 

  • Dupont B, Selvakumar A, Steffens U (1997) The killer cell inhibitory receptor genomic region on human chromosome 19q13.4. Tissue Antigens 49:557–563

    Article  PubMed  CAS  Google Scholar 

  • Gagne K, Brizard G, Gueglio B, Milpied N, Herry P, Bonneville F, Cheneau ML, Schleinitz N, Cesbron A, Follea G, Harrousseau JL, Bignon JD (2002) Relevance of KIR gene polymorphisms in bone marrow transplantation outcome. Hum Immunol 63:271–280

    Article  PubMed  CAS  Google Scholar 

  • Garcia CA, Robinson J, Shilling HG, Guethlein LA, Parham P, Madrigal JA, Marsh SG (2004) KIR gene characterisation of HLA homozygous cell lines, HLA 2004. 13th IHWS NK/KIR Joint Report

  • Gomez-Lozano N, Vilches C (2002) Genotyping of human killer-cell immunoglobulin-like receptor genes by polymerase chain reaction with sequence-specific primers: an update. Tissue Antigens 59:184–193

    Article  PubMed  CAS  Google Scholar 

  • Gomez-Lazano N, Vilches C (2004) Erratum. Tissue Antigens 64:629

    Article  Google Scholar 

  • Gomez-Lozano N, Gardiner CM, Parham P, Vilches C (2002) Some human KIR haplotypes contain two KIR2DL5 genes: KIR2DL5A and KIR2DL5B. Immunogenetics 54:314–319

    Article  PubMed  CAS  Google Scholar 

  • Hiby SE, Walker JJ, O’Shaughnessy KM, Redman CW, Carrington M, Trowsdale J, Moffett A (2004) Combinations of maternal KIR and fetal HLA-C genes influence the risk of preeclampsia and reproductive success. J Exp Med 200:957–965

    Article  PubMed  CAS  Google Scholar 

  • Khakoo SI, Thio CL, Martin MP, Brooks CR, Gao X, Astemborski J, Cheng J, Goedert JJ, Vlahov D, Hilgartner M, Cox S, Little AM, Alexander GJ, Cramp ME, O’Brien SJ, Rosenberg WM, Thomas DL, Carrington M (2004) HLA and NK cell inhibitory receptor genes in resolving hepatitis C virus infection. Science 305:872–874

    Article  PubMed  CAS  Google Scholar 

  • Martin MP, Gao X, Lee JH, Nelson GW, Detels R, Goedert JJ, Buchbinder S, Hoots K, Vlahov D, Trowsdale J, Wilson M, O’Brien SJ, Carrington M (2002) Epistatic interaction between KIR3DS1 and HLA-B delays the progression to AIDS. Nat Genet 31:429–434

    PubMed  CAS  Google Scholar 

  • Mizuki M, Eklund A, Grunewald J (2000) Altered expression of natural killer cell inhibitory receptors (KIRs) on T cells in bronchoalveolar lavage fluid and peripheral blood of sarcoidosis patients. Sarcoidosis Vasc Diffuse Lung Dis 17:54–59

    PubMed  CAS  Google Scholar 

  • Momot T, Koch S, Hunzelmann N, Krieg T, Ulbricht K, Schmidt RE, Witte T (2004) Association of killer cell immunoglobulin-like receptors with scleroderma. Arthritis Rheum 50:1561–1565

    Article  PubMed  CAS  Google Scholar 

  • Moretta A (2002) Natural killer cells and dendritic cells: rendezvous in abused tissues. Nat Rev Immunol 2:957–964

    Article  PubMed  CAS  Google Scholar 

  • Nelson GW, Martin MP, Gladman D, Wade J, Trowsdale J, Carrington M (2004) Cutting edge: heterozygote advantage in autoimmune disease: hierarchy of protection/susceptibility conferred by HLA and killer Ig-like receptor combinations in psoriatic arthritis. J Immunol 173:4273–4276

    PubMed  CAS  Google Scholar 

  • Parham P (2003) Killer Cell Immunoglobulin like receptors: diverse species specific components of innate immunity. Immunology Suppl 110:21

    Google Scholar 

  • Parham P, McQueen KL (2003) Alloreactive killer cells: hindrance and help for haematopoietic transplants. Nat Rev Immunol 3:108–122

    Article  PubMed  CAS  Google Scholar 

  • Rajalingam R, Parham P, Abi-Rached L (2004) Domain shuffling has been the main mechanism forming new hominoid killer cell Ig-like receptors. J Immunol 172:356–369

    PubMed  CAS  Google Scholar 

  • Ruggeri L, Capanni M, Urbani E, Perruccio K, Shlomchik WD, Tosti A, Posati S, Rogaia D, Frassoni F, Aversa F, Martelli MF, Velardi A (2002) Effectiveness of donor natural killer cell alloreactivity in mismatched hematopoietic transplants. Science 295:2097–2100

    Article  PubMed  CAS  Google Scholar 

  • Selvakumar A, Steffens U, Dupont B (1997a) Polymorphism and domain variability of human killer cell inhibitory receptors. Immunol Rev 155:183–196

    Article  PubMed  CAS  Google Scholar 

  • Selvakumar A, Steffens U, Palanisamy N, Chaganti RS, Dupont B (1997b) Genomic organization and allelic polymorphism of the human killer cell inhibitory receptor gene KIR103. Tissue Antigens 49:564–573

    PubMed  CAS  Google Scholar 

  • Shilling HG, Lienert-Weidenbach K, Valiante NM, Uhrberg M, Parham P (1998) Evidence for recombination as a mechanism for KIR diversification. Immunogenetics 48:413–416

    Article  PubMed  CAS  Google Scholar 

  • Shilling HG, Guethlein LA, Cheng NW, Gardiner CM, Rodriguez R, Tyan D, Parham P (2002) Allelic polymorphism synergizes with variable gene content to individualize human KIR genotype. J Immunol 168:2307–2315

    PubMed  CAS  Google Scholar 

  • Shilling HG, McQueen KL, Cheng NW, Shizuru JA, Negrin RS, Parham P (2003) Reconstitution of NK cell receptor repertoire following HLA-matched hematopoietic cell transplantation. Blood 101:3730–3740

    Article  PubMed  CAS  Google Scholar 

  • Trachtenberg E, Korber B, Sollars C, Kepler TB, Hraber PT, Hayes E, Funkhouser R, Fugate M, Theiler J, Hsu YS, Kunstman K, Wu S, Phair J, Erlich H, Wolinsky S (2003) Advantage of rare HLA supertype in HIV disease progression. Nat Med 9:928–935

    Article  PubMed  CAS  Google Scholar 

  • Trachtenberg EA, Sollars C, Korber B, Erlich EH, Wolinsky S, Kepler T (2004) Natural killer cell immunogloblin-like receptors (KIR) are associated with protective effect in HIV-1 transmission and disease progression in the Chicago Multicenter AIDS Cohort Study (MACS). 8th Annual Meeting for the Society of Natural Immunity and the 20th International Natural Killer Cell Workshop, Noordwijkerhout, The Netherlands

  • Uhrberg M, Valiante NM, Shum BP, Shilling HG, Lienert-Weidenbach K, Corliss B, Tyan D, Lanier LL, Parham P (1997) Human diversity in killer cell inhibitory receptor genes. Immunity 7:753–763

    Article  PubMed  CAS  Google Scholar 

  • Valiante NM, Lienert K, Shilling HG, Smits BJ, Parham P (1997) Killer cell receptors: keeping pace with MHC class I evolution. Immunol Rev 155:155–164

    Article  PubMed  CAS  Google Scholar 

  • van der Slik AR, Koeleman BP, Verduijn W, Bruining GJ, Roep BO, Giphart MJ (2003) KIR in type 1 diabetes: disparate distribution of activating and inhibitory natural killer cell receptors in patients versus HLA-matched control subjects. Diabetes 52:2639–2642

    Article  PubMed  Google Scholar 

  • Vilches C, Rajalingam R, Uhrberg M, Gardiner CM, Young NT, Parham P (2000) KIR2DL5, a novel killer-cell receptor with a D0–D2 configuration of Ig-like domains. J Immunol 164:5797–5804

    PubMed  CAS  Google Scholar 

  • Witt CS, Dewing C, Sayer DC, Uhrberg M, Parham P, Christiansen FT (1999) Population frequencies and putative haplotypes of the killer cell immunoglobulin-like receptor sequences and evidence for recombination. Transplantation 68:1784–1789

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We wish to express our gratitude to Drs. Derek Middleton and Carlos Vilches and their laboratories for their generosity and gracious sharing of expertise. Finally, we are grateful for the technical and administrative contributions from J Agraz, K Saeteurn, N Bose, E Sanseau, K Guttierrez, J-C Cossec, and M Vinson. This work was supported by grants R21 AI 65254-01A1, P01 CA 111412, and UO1 AI067068-01 from the National Institutes of Health and the My Brother Joey Foundation to Elizabeth Trachtenberg. The MALDI-TOF MassARRAY system was acquired through NIH-NCRR #1S10RR 16703-01. The investigation was conducted at the Children’s Hospital and Research Center Oakland in facilities constructed with support from Research Facilities Improvement Program Grant Number CO6RR-16226 from the National Center for Research Resources, National Institutes of Health.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Elizabeth A. Trachtenberg.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Houtchens, K.A., Nichols, R.J., Ladner, M.B. et al. High-throughput killer cell immunoglobulin-like receptor genotyping by MALDI-TOF mass spectrometry with discovery of novel alleles. Immunogenetics 59, 525–537 (2007). https://doi.org/10.1007/s00251-007-0222-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00251-007-0222-x

Keywords

Navigation