Senior Scientist
An Overview
Scientists & Staff
Office: 510-450-7649
Lab: 510-450-7634
Administrative Coordinator
Susan Camel
Office: 510-450-7992






The Trachtenberg lab has developed multiple sophisticated methods for analyzing HLA and KIR gene complexes, which in humans are found on chromosome 6 and 9, respectively. Using next-generation clonal sequencing and other state of the art molecular methods, the laboratory developed and continues to improve upon, methods that are high-throughput and capable of detecting novel variants. Her group has been awarded several patents for these methods.

Current Trachtenberg lab research projects include investigating the role of HLA and KIR in autoimmunity, with a special focus on Inflammatory Bowel Disease (Ulcerative Colitis and Crohn’s Disease). Examining the association of HLA and KIR in infectious disease, Dr. Trachtenberg has expanded her work on HLA supertype association with HIV disease progression, examining the role KIR plays in HIV infection and disease progression to AIDS.  A collaborative study on the role of KIR and HLA maternal-fetal identity and its association in susceptibility to pediatric acute lymphocytic leukemia is ongoing. Dr. Trachtenberg also collaborates on studies of HLA and KIR in stem cell transplantation, a unique environment combining individual donor and recipient immune systems. These studies illuminate the role of these important immunologic systems in health and disease. A deeper understanding of the KIR and HLA genetic determinants of disease may provide insight into immunopathology, more effective patient management and the design of clinical trials for new therapeutic interventions.

The HLA Complex

The human major histocompatibility complex (MHC), or human leukocyte antigen (HLA) complex, consists of many genetic loci, including at least seven loci that encode two distinct classes of highly polymorphic cell surface antigens that are co-expressed. These molecules bind and present processed peptide to circulating T-cell lymphocytes and are crucial to both cellular and humoral immune responses. The class I molecules, HLA-A, HLA-B and HLA-C, and the class II molecules, DR, DQ and DP, are encoded in a ~3500 kbp segment of the short arm of chromosome 6p21.31 (Figure 1). Class I antigens are presented on all nucleated cells, where they act as cell surface heterodimers that primarily present peptides derived from the cytosol (viral and self peptides) to circulating CD8+ T cells. The class I cell surface heterodimer has one highly polymorphic alpha chain, with variable residues clustering within the peptide binding cleft, which is encoded by exons 2 and 3 of the gene. The HLA class I molecules also act as ligands for killer immunoglobulin receptors (KIR), which regulate the cytotoxic activity of natural killer (NK) cells. HLA class II molecules are found on the surface of B cells, macrophages and other antigen presenting cells, where the alpha-beta heterodimer presents primarily exogenously derived peptides (bacteria and chemical toxins) to circulating CD4+ T cells. In class II molecules, the beta chain contains the highly polymorphic regions, which are localized to exon 2 of the gene and encode the peptide-binding cleft.

HLA Heterogeneity in Disease Association Research
The HLA genes are the most polymorphic in the genome. The allelic diversity of the HLA class I and class II loci is extensive, with >13,000 alleles described (Figure 1) (http://hla.alleles.org/alleles/index.html). This extensive polymorphism allows for differential binding of peptide, and is therefore functionally significant in terms of disease susceptibility and progression. The high level of HLA polymorphism is maintained in populations by balancing selection, specifically pathogen-driven selection with heterozygote advantage. Populations tend to exhibit a distribution of frequencies of alleles and extended haplotypes particular to that group. This can confound HLA disease association studies that differ with respect to ethnic groups in cases and controls, making comparisons between studies more difficult. Concordant results between studies of different ethnic groups serves to support the HLA association for both groups, and discordant results may mean that the allele is simply a marker for the actual locus, or that the different ethnic groups have different HLA disease susceptibility alleles.

Figure 1. The Human Major histocompatibility complex (MHC) aka Human Leukocyte Antigen Complex (HLA) The HLA genes are the most polymorphic in the genome. The allelic diversity of the HLA class I and class II loci is extensive, with >13,000 alleles described. (http://www.ebi.ac.uk/ipd/imgt/hla/stats.html).

Natural Killer Cells and their Killer Immunoglobulin Receptors (KIR)
NK cells are effector cells of the innate immune system that recognize the absence of HLA class I molecules from the surface of virally infected cells and target these cells for destruction through cytotoxicity and pro-inflammatory cytokine production1 (Figure 2). NK cell effector function is closely regulated through a balance of stochastically expressed activating and inhibitory KIRs that interact with specific major histocompatibility complex (MHC; HLA in humans) class I ligands present on all healthy, nucleated cells2-5. When NK cells mature, responsiveness is enhanced (or maintained) as inhibitory KIRs recognize their cognate HLA class I ligand group6,7. This HLA ligand-dependent education (licensing) process helps to confer competence and functionality on NK cells and some populations of T cells, which include γδ T cells and subsets of memory and effector αβ T cells8-10. In partnership with alternative NK receptor complexes (CD94:NKG2A), inhibitory KIR ensure that NK cells are tolerant of healthy autologous cells and responsive to cells with compromised HLA class I expression, as occurs in virus-infected and tumor cells. Although their ligands and functions are less clearly defined, the activating KIRs are hypothesized to contribute to the activation of NK cells in response to infection and malignancy

Figure 2. NK cell effector function is regulated through a balance of stochastically expressed activating and inhibitory KIRs that interact with HLA class I ligands present on healthy, nucleated cells. Here, the NK cell responds by killing the target cell because the cognate HLA ligand for the inhibitory KIR is missing. The cognate stimulatory ligand has not yet been discovered.

The KIR gene family is part of the leukocyte receptor complex (LRC), located on human chromosome 19q13.4. The KIR complex comprises a tandem array of highly homologous genes, which exhibits haplotypic variation in gene content as well as polymorphism of the individual KIR genes (Figure 3). As a consequence of these variations, unrelated individuals usually differ in KIR genotype. 
KIR haplotypes are classified into two distinct groups based on their gene content and allele combination 11-15 The group A haplotype most commonly includes five inhibitory KIR genes (KIR2DL1, KIR2DL3, KIR3DL1, KIR3DL2, KIR3DL3), with or without the activating, although often non-functional, KIR2DS4 16. The group B haplotypes have greater heterogeneity in gene content, including additional stimulatory KIR genes (KIR2DS1, KIR2DS2, KIR2DS3, KIR2DS5, KIR3DS1, and/or KIR2DS4), than the group A haplotypes (KIR2DS4 and its null allele) 12-14,17,18. KIR2DL2 and KIR2DL3 segregate as alleles, with KIR2DL3 determining the A centromeric (Cen-A) and KIR2DL2 determining the B centromeric (Cen-B) haplotype structures. The inhibitory KIR genes are highly polymorphic, with over 500 alleles discovered to date, whereas the stimulatory genes are much less polymorphic, with only 132 variants known

NK cell effector function is regulated by inhibitory KIRs that interact with HLA class I ligands. The class I HLA-C allotypes are grouped according to the presence of asparagine (HLA-C1), or lysine (HLA-C2) at residue 80 in the protein sequence, and serve as ligands for KIR2D receptors. The Bw4 antigen (with isoleucine or threonine at position 80 in the α1 domain of HLA-B; or by an arginine in position 83 for HLA-A alleles) serves as the ligand for KIR3DL1 (Figures 3 and 4)  


Figure 3. KIR haplotypes are polygenic. KIR haplotypes are classified into group A, predominately inhibitory, and group B, predominately stimulatory, haplotypes. The group A haplotype has six inhibitory genes and only one stimulatory gene (KIR2DS4). The group B haplotype has many variations, all with varying numbers of stimulatory genes, in addition to KIR2DL2. Both A and B haplotypes are divided into centromeric and telomeric ends, with considerable recombination between them creating many Cen-Tel haplotypic variants. These numerous configurations point to rapid evolution of the KIR gene cluster in humans. (Figure by Julia Udell).


Figure 4. The KIR molecules interact with polymorphic HLA class I molecules. To describe KIR-HLA ligand specificities, in this figure, the NK cell is expressing all KIR genes (A+B haplotypes), and the Target Cell is expressing all HLA class I ligands. In reality, KIRs are clonally expressed on NK cells; HLA is co-dominantly expressed. 

The highly polymorphic HLA and KIR gene families, which are located on different chromosomes, segregate independently. As a result, a diversity of receptor-ligand interactions is found within a population, with certain individuals lacking the appropriate HLA class I ligand for a particular KIR.4,5,13,19 Thus the combinatorial repertoire of KIR expressed on the NK cell surface and the particular HLA class I ligand group may result in the target cell being killed or, should inhibitory signals dominate, spared from cell death (Figure 2).

KIR, either alone or in combination with HLA class I, have been correlated with a variety of diseases and syndromes. These include the outcome of bone marrow transplantation, the progress and severity of virally transmitted disease, the probability of pre-eclampsia during pregnancy, and susceptibility to autoimmune diseases, such as Inflammatory Bowel Disease, psoriatic arthritis and multiple sclerosis. Collectively, these studies make a convincing case that interactions between variable HLA class I ligands and KIR have considerable impact on human health. Consequently, a better understanding of the underlying mechanisms of KIR and HLA combinatory associations could influence future clinical practice. The Trachtenberg Lab is currently examining the role of HLA and KIR in protection or susceptibility to autoimmune diseases (with special focus on IBD), infectious disease (HIV), cancer (pediatric ALL), and its role in stem cell transplantation. In these projects, particular combinations of KIRs and their HLA ligands have been found to be significantly associated with various disease states. The Trachtenberg group continues in their work to gain a deeper understanding of the KIR and HLA genetic determinants of disease, which may provide insight into immunopathology, more effective patient management and the design of clinical trials for new therapeutic interventions.

References Cited

  1. Gerosa, F., et al. Reciprocal activating interaction between natural killer cells and dendritic cells. J Exp Med 195, 327-333 (2002).
  2. Bottino, C., Vitale, M., Pende, D., Biassoni, R. & Moretta, A. Receptors for HLA class I molecules in human NK cells. Seminars in immunology 7, 67-73 (1995).
  3. Parham, P. MHC class I molecules and KIRs in human history, health and survival. Nat Rev Immunol 5, 201-214 (2005).
  4. Hiby, S.E., et al. Combinations of maternal KIR and fetal HLA-C genes influence the risk of preeclampsia and reproductive success. J Exp Med 200, 957-965 (2004).
  5. Single, R.M., et al. Global diversity and evidence for coevolution of KIR and HLA. Nat Genet 39, 1114-1119 (2007).
  6. Orr, M.T., Murphy, W.J. & Lanier, L.L. 'Unlicensed' natural killer cells dominate the response to cytomegalovirus infection. Nature immunology 11, 321-327 (2010).
  7. Elliott, J.M. & Yokoyama, W.M. Unifying concepts of MHC-dependent natural killer cell education. Trends Immunol 32, 364-372 (2011).
  8. Halary, F., et al. Control of self-reactive cytotoxic T lymphocytes expressing gamma delta T cell receptors by natural killer inhibitory receptors. Eur J Immunol 27, 2812-2821 (1997).
  9. Phillips, J.H., Gumperz, J.E., Parham, P. & Lanier, L.L. Superantigen-dependent, cell-mediated cytotoxicity inhibited by MHC class I receptors on T lymphocytes. Science 268, 403-405 (1995).
  10. Vilches, C. & Parham, P. KIR: Diverse, rapidly evolving receptors of innate and adaptive immunity. Annu Rev Immunol 20, 217-251 (2002).
  11. Gomez-Lozano, N., et al. The silent KIR3DP1 gene (CD158c) is transcribed and might encode a secreted receptor in a minority of humans, in whom the KIR3DP1, KIR2DL4 and KIR3DL1/KIR3DS1 genes are duplicated. Eur J Immunol 35, 16-24 (2005).
  12. Martin, M.P., Bashirova, A., Traherne, J., Trowsdale, J. & Carrington, M. Cutting Edge: Expansion of the KIR locus by unequal crossing over. J. Immunol. 171, 2192-2195 (2003).
  13. Norman, P.J., et al. Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes. Genome Res 19, 757-769 (2009).
  14. Norman, P.J., et al. Natural killer cell immunoglobulin-like receptor (KIR) locus profiles in African and South Asian populations. Genes and immunity 3, 86-95 (2002).
  15. Williams, F., et al. Multiple copies of KIR 3DL/S1 and KIR 2DL4 genes identified in a number of individuals. Human immunology 64, 729-732 (2003).
  16. Middleton, D., Gonzalez, A. & Gilmore, P.M. Studies on the Expression of the Deleted KIR2DS4*003 Gene Product and Distribution of KIR2DS4 Deleted and Nondeleted Versions in Different Populations. Human immunology 68, 128-134 (2007).
  17. Jiang, W., et al. 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, 1845-1854 (2012).
  18. Hollenbach, J.A., Nocedal, I., Ladner, M.B., Single, R.M. & Trachtenberg, E.A. Killer cell immunoglobulin-like receptor (KIR) gene content variation in the HGDP-CEPH populations. Immunogenetics 64, 719-737 (2012).
  19. Parham, P. & Moffett, A. Variable NK cell receptors and their MHC class I ligands in immunity, reproduction and human evolution. Nat Rev Immunol 13, 133-144 (2013).


Revised: Wednesday, October 7, 2015 1:52 PM


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