Carlos Vilches

Different NK Cell Surface Phenotypes Defined by the DX9 Antibody Are Due to KIR3DL1 Gene Polymorphism

KIR3DL1 and KIR3DL2 are NK cell receptors for polymorphic HLA-B and -A determinants. The proportion of NK cells that bind anti-KIR3DL1-specific Ab DX9 and their level of binding vary between individuals. To determine whether these differences are due to KIR polymorphism, we assessed KIR3D gene diversity in unrelated individuals and families. Both KIR3DL1 and KIR3DL2 are highly polymorphic genes, with KIR3DS1 segregating like an allele of KIR3DL1. A KIR haplotype lacking KIR3DL1 and KIR3DS1 was defined. The two KIR3DL1 alleles of a heterozygous donor were expressed by different, but overlapping, subsets of NK cell clones. Sequence variation in KIR3DL1 and KIR3DL2 appear distinct; recombination is more evident in KIR3DL1, and point mutation is more evident in KIR3DL2. The KIR3DL1 genotype correlates well with levels of DX9 binding by NK cells, but not with the frequency of DX9-binding cells. Different KIR3DL1 alleles determine high, low, and no binding of DX9 Ab. Consequently, heterozygotes for high and low binding KIR3DL1 alleles have distinct subpopulations of NK cells that bind DX9 at high and low levels, giving characteristic bimodal distributions in flow cytometry. The Z27 Ab gave binding patterns similar to those of DX9. Four KIR3DL1 alleles producing high DX9 binding phenotypes were distinguished from four alleles producing low or no binding phenotypes by substitution at one or more of four positions in the encoded protein: 182 and 283 in the extracellular Ig-like domains, 320 in the transmembrane region, and 373 in the cytoplasmic tail.

KIR2DL5, a Novel Killer-Cell Receptor with a D0-D2 Configuration of Ig-Like Domains

Four novel killer-cell Ig-like receptor (KIR) genes were discovered by analysis of genomic DNA from a human donor. One gene, KIR2DL5, is expressed by subpopulations of NK cells and T cells, whereas expression of the other three genes could not be detected. KIR2DL5 has two extracellular Ig-like domains of the D0 and D2 type, a structural configuration that was previously unique to KIR2DL4. Although having a similar structure overall, the KIR2DL4 and KIR2DL5 receptors have distinctive amino acid sequences in the ligand-binding extracellular domains and differ in the transmembrane and cytoplasmic motifs that determine signal transduction. Whereas the KIR2DL4 gene is present on all KIR haplotypes and is expressed by all human NK cells, the KIR2DL5 gene is restricted to the “B” subset of KIR haplotypes and is clonally expressed by NK cells within an individual. Chimpanzee genes for KIR2DL4 and KIR2DL5 have been defined and are very similar in sequence to their human orthologs. The donor in whom KIR2DL5 was first detected bears two variants of it that differ by five nucleotide substitutions in the coding region. Although the substitutions are not predicted to affect gene expression, transcription of only one of the two KIR2DL5 variants could be detected.

Some human KIR haplotypes contain two KIR2DL5 genes: KIR2DL5A and KIR2DL5B

Abstract. Killer-cell immunoglobulin-like receptors (KIR) comprise a family of structurally diverse proteins encoded by a compact cluster of genes located in human Chromosome 19q13.4. The most recently described member of the KIR family, KIR2DL5, is represented in human populations by at least four gene variants, whose exons differ by two to eight nucleotides. We show here that these structurally similar variants are encoded by alleles of two different loci, KIR2DL5A and KIR2DL5B, which map to different regions of the KIR-gene cluster. Regarding KIR2DL5, four groups of KIR haplotypes can be distinguished: those having both KIR2DL5A and KIR2DL5B, those having either KIR2DL5A or KIR2DL5B, and those lacking KIR2DL5. Positive association between KIR2DL5A and KIR2DL5B was detected but did not reach statistical significance. These results are consistent with a model in which KIR2DL5A and KIR2DL5B are products of a gene duplication, which through the action of subsequent recombination have became separated on some haplotypes.

Gene structure and promoter variation of expressed and nonexpressed variants of the KIR2DL5 gene.

Two variants of the novel KIR2DL5 gene (KIR2DL5.1 and .2) were identified in genomic DNA of a single donor. However, only the KIR2DL5.1 variant was transcribed in PBMC. In this study, analysis of seven additional donors reveals two new variants of the KIR2DL5 gene and indicates that transcription, or its lack, are consistently associated with particular variants of this gene. Comparison of the complete nucleotide sequences of the exons and introns of KIR2DL5.1 and KIR2DL5.2 reveals no structural abnormalities, but similar open reading frames for both variants. In contrast, the promoter region of KIR2DL5 shows a high degree of sequence polymorphism that is likely relevant for expression. Substitution within a putative binding site for the transcription factor acute myeloid leukemia gene 1 could determine the lack of expression for some KIR2DL5 variants.

Three Structurally and Functionally Divergent Kinds of Promoters Regulate Expression of Clonally Distributed Killer Cell Ig-Like Receptors (KIR), of KIR2DL4, and of KIR3DL3

The generation of killer cell Ig-like receptor (KIR) expression patterns in NK cells involves variegated silencing of KIR genes by DNA methylation. To identify regulatory elements involved in KIR gene activation, upstream regions of KIR genes were functionally characterized in NK3.3 cells as well as in primary NK cells. Three kinds of KIR promoters were defined, controlling clonally expressed KIR genes, the constitutively active KIR2DL4, and the weakly expressed KIR3DL3. Upstream of a short core promoter common to all KIR genes, a region containing functionally divergent elements was characterized. Although this region had no impact on the activity of the KIR2DL3 promoter, an inhibitory element was identified in the KIR2DL4 promoter and an activating element was found in the KIR3DL3 promoter. Upon treatment with a methyltransferase inhibitor, KIR3DL3 expression could be readily induced showing that the low levels of KIR3DL3 expression in peripheral blood are due to sustained DNA methylation of an otherwise fully functional promoter. Analysis of transcription factor binding sites identified a functional acute myeloid leukemia (AML) site common to all three KIR promoters. Mutation of this site led to a substantial increase in activity of all KIR promoters. Among the different members of the AML family, AML-2 was identified as the predominant KIR binding factor. The present study suggests that AML-2 acts as a repressor of KIR expression in mature NK cells and opens the possibility that AML factors and associated cofactors are involved in regulation of KIR expression during NK cell development.

Adaptive reconfiguration of the human NK‐cell compartment in response to cytomegalovirus: A different perspective of the host‐pathogen interaction

As discussed in this review, human cytomegalovirus (HCMV) infection in healthy individuals is associated with a variable and persistent increase of NK cells expressing the CD94/NKG2C activating receptor. The expansion of NKG2C+ NK cells reported in other infectious diseases is systematically associated with HCMV co‐infection. The functionally mature NKG2Cbright NK‐cell subset expanding in HCMV+ individuals displays inhibitory Ig‐like receptors (KIR and LILRB1) specific for self HLA class I, and low levels of NKp46 and NKp30 activating receptors. Such reconfiguration of the NK‐cell compartment appears particularly marked in immunocompromised patients and in children with symptomatic congenital infection, thus suggesting that its magnitude may be inversely related with the efficiency of the T‐cell‐mediated response. This effect of HCMV infection is reminiscent of the pattern of response of murine Ly49H+ NK cells against murine CMV (MCMV), and it has been hypothesized that a cognate interaction of the CD94/NKG2C receptor with HCMV‐infected cells may drive the expansion of the corresponding NK‐cell subset. Yet, the precise role of NKG2C+ cells in the control of HCMV infection, the molecular mechanisms underlying the NK‐cell compartment redistribution, as well as its putative influence in the response to other pathogens and tumors remain open issues.

Recognition of HLA-G by the NK cell receptor KIR2DL4 is not essential for human reproduction.

A central issue of reproductive immunology in mammals is why a semi‐allogeneic embryo is not rejected by the pregnant mother. This is particularly intriguing since, in different species, the early pregnant uterus is infiltrated by numerous maternal lymphocytes, predominantly NK cells. The human NK cell receptor KIR2DL4 has been implicated in the maternal tolerance to the embryo due to its recognition of HLA‐G, a non‐classical MHC molecule expressed preferentially in the placenta. Killer cell Ig‐like receptors (KIR) are believed to participate in the natural immunity to infection and tumors, but KIR2DL4 has unique structural, functional and genetic features that could confer it a different role. However, we demonstrate here that the KIR2DL4:HLA‐G interaction is not essential for human reproduction by showing that a multiparous woman lacks a KIR2DL4 gene.

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.

Killer‐cell Ig‐like receptors (KIR) are structurally and functionally diverse, and enable human NK cells to survey the expression of individual HLA class I molecules, often altered in infections and tumors. Multiple events of non‐reciprocal recombination have contributed to the rapid diversification of KIR. We show that ∼4.5% of the individuals of a Caucasoid population bear a recombinant allele of KIR3DP1, officially designed KIR3DP1*004, that associates tightly with gene duplications of KIR3DP1, KIR2DL4 and KIR3DL1/KIR3DS1. The KIR3DP1 gene is normally silent, but the recombinant allele carries a novel promoter sequence and, as a consequence, is transcribed in all tested individuals. Messenger RNA of KIR3DP1*004 is made up of six exons; of these, exons 1–5 are similar to, and spliced like, those encoding the leader peptide and Ig‐domains of KIR3D. By contrast, exon 6 is homologous to no other human KIR sequence, but only to possible homologs in chimpanzees and rhesus macaques, and encodes a short hydrophilic tail. The putative KIR3DP1*004 product, like those of the related genes LAIR‐2 and LILRA3/ILT6/LIR4, is predicted to be secreted to the extracellular medium rather than anchored to the cell membrane.

Influence of congenital human cytomegalovirus infection and the NKG2C genotype on NK-cell subset distribution in children.

Human cytomegalovirus (HCMV) has been reported to reshape the NK‐cell receptor (NKR) distribution, promoting an expansion of CD94/NKG2C+ NK and T cells. The role of NK cells in congenital HCMV infection is ill‐defined. Here we studied the expression of NKR (i.e., NKG2C, NKG2A, LILRB1, CD161) and the frequency of the NKG2C gene deletion in children with past congenital infection, both symptomatic (n = 15) and asymptomatic (n = 11), including as controls children with postnatal infection (n = 11) and noninfected (n = 20). The expansion of NKG2C+ NK cells in HCMV‐infected individuals appeared particularly marked and was associated with an increased number of LILRB1+ NK cells in cases with symptomatic congenital infection. Increased numbers of NKG2C+, NKG2A+, and CD161+ T cells were also associated to HCMV infection. The NKG2C deletion frequency was comparable in children with congenital HCMV infection and controls. Remarkably, the homozygous NKG2C+/+ genotype appeared associated with increased absolute numbers of NKG2C+ NK cells. Moreover, HCMV‐infected NKG2C+/+ children displayed higher absolute numbers of NKG2A+ and total NK cells than NKG2C+/− individuals. Our study provides novel insights on the impact of HCMV infection on the homeostasis of the NK‐cell compartment in children, revealing a modulatory influence of NKG2C copy number.

Antibody-Mediated Response of NKG2Cbright NK Cells against Human Cytomegalovirus

Human CMV (HCMV) infection promotes a variable and persistent expansion of functionally mature NKG2Cbright NK cells. We analyzed NKG2Cbright NK cell responses triggered by Abs from HCMV+ sera against HCMV-infected MRC5 fibroblasts. Specific Abs promoted the degranulation (i.e., CD107a expression) and the production of cytokines (TNF-α and IFN-γ) by a significant fraction of NK cells, exceeding the low natural cytotoxicity against HCMV-infected targets. NK cell–mediated Ab-dependent cell-mediated cytotoxicity was limited by viral Ag availability and HLA class I expression on infected cells early postinfection and increased at late stages, overcoming viral immunoevasion strategies. Moreover, the presence of specific IgG triggered the activation of NK cells against Ab-opsonized cell-free HCMV virions. As compared with NKG2A+ NK cells, a significant proportion of NKG2Cbright NK cells was FcεR γ-chain defective and highly responsive to Ab-driven activation, being particularly efficient in the production of antiviral cytokines, mainly TNF-α. Remarkably, the expansion of NKG2Cbright NK cells in HCMV+ subjects was related to the overall magnitude of TNF-α and IFN-γ cytokine secretion upon Ab-dependent and -independent activation. We show the power and sensitivity of the anti-HCMV response resulting from the cooperation between specific Abs and the NKG2Cbright NK-cell subset. Furthermore, we disclose the proinflammatory potential of NKG2Cbright NK cells, a variable that could influence the individual responses to other pathogens and tumors.