KIR2DS4 Human

What is KIR2DS4 and what are its main structural variants?

KIR2DS4 (Killer Cell Immunoglobulin Like Receptor, Two Ig Domains And Short Cytoplasmic Tail 4) is a member of the killer cell immunoglobulin-like receptor family expressed on natural killer (NK) cells . It exists in two major allelic variants: a full-length functional receptor (KIR2DS4-fl) and a truncated version with a 22-base pair deletion (KIR2DS4-del) . The full-length variant functions as an activating receptor on NK cells, binding to specific HLA class I molecules and triggering NK cell responses . In contrast, the deleted variant produces a truncated soluble protein due to an early stop codon and lacks HLA-I binding capacity . This distinction is critical as only the full-length form can effectively transduce activating signals via association with TYRO protein tyrosine kinase binding protein, whereas the truncated form is non-functional .

The full-length KIR2DS4 receptor contains two extracellular immunoglobulin domains connected to a short cytoplasmic tail that lacks inhibitory motifs found in other KIR family members, positioning it firmly in the activating receptor category . This structural arrangement directly influences its function within the complex immune surveillance system performed by NK cells.

What is the ligand specificity of KIR2DS4?

KIR2DS4 demonstrates a unique binding profile among KIR family receptors. Unlike other KIR2D receptors that predominantly bind either C1 or C2 HLA-C allotypes, full-length KIR2DS4 binds to subsets of both C1+ and C2+ HLA-C allotypes as well as to HLA-A11 . Particularly noteworthy is its binding to HLA-A1102 but not to HLA-A1101, a distinction attributed to the substitution of lysine for glutamate at position 19 in HLA-A1102 .

Research has revealed that KIR2DS4 exhibits strong peptide selectivity, showing particular preference for rare peptides carrying a tryptophan at position 8 (p8) of 9-mer peptides bound to HLA-C05:01 . This peptide specificity is crucial for receptor function, as the complex of a peptide bound to HLA-C05:01 with a tryptophan at p8 is sufficient for activation of primary KIR2DS4+ NK cells, independent of other activation signals . Studies have also demonstrated that peptides with phenylalanine or tyrosine at p8 can stimulate KIR2DS4+ NK cells, although less effectively than those with tryptophan .

What are the genetic characteristics of KIR2DS4?

KIR2DS4 is the oldest and most prevalent KIR2DS gene, distinguished by a proline-valine motif at positions 71-72, which was introduced through gene conversion with KIR3DL2 prior to the divergence of human and chimpanzee lineages . This specific motif is largely responsible for KIR2DS4's unique HLA class I specificity, as demonstrated through site-directed swap mutagenesis . Crystallographic structure determination reveals that KIR2DS4 differs from KIR2DL receptors primarily through displacement of contact loop L2 and altered bonding potential due to substitutions at positions 71 and 72 .

KIR2DS4 is a characteristic component of the KIR A haplotype, while most other activating KIRs belong to the B haplotype . Worldwide distribution patterns show an inverse correlation between the frequencies of functional KIR2DS4 and HLA-C*05:01, suggesting a functional interaction and balancing selection between these genes . The gene is located on chromosome 19q13.4 within the leukocyte receptor complex, alongside other KIR family genes . Four genes are found in all KIR haplotypes (KIR3DL3, KIR3DP1, KIR3DL4, KIR3DL2), with KIR2DS4 being the only activating KIR carried by individuals homozygous for the A haplotype .

How does KIR2DS4 function in NK cell activation?

KIR2DS4 functions as an activating receptor on NK cells through its short cytoplasmic domain, which lacks immune tyrosine-based inhibitory motifs (ITIMs) found in inhibitory KIRs . Instead, it associates with TYRO protein tyrosine kinase binding protein to transduce activating signals, leading to NK cell degranulation and cytokine production when engaged with appropriate ligands .

A remarkable property of KIR2DS4 is that stimulation of this receptor alone can be sufficient to activate resting NK cell degranulation, without requiring synergistic stimulation of multiple receptors . When KIR2DS4+ NK cells recognize target cells expressing appropriate HLA-peptide complexes (such as HLA-C*05:01 presenting peptides with tryptophan at p8), they undergo activation resulting in cytolytic granule release and production of inflammatory cytokines including IFN-γ and TNF-α .

The activation potential of KIR2DS4 can be regulated by inhibitory receptors. NK cells expressing both KIR2DS4 and inhibitory receptors like KIR2DL1 show limited activation due to dominant inhibition by the inhibitory receptor . Consequently, the R−S4+ NK subset (cells that are unlicensed but express KIR2DS4) likely represents the major operative subset during immune responses due to their lack of inhibitory receptor expression .

What is the relationship between KIR2DS4 and HLA allotypes?

The interaction between KIR2DS4 and HLA molecules exhibits distinctive patterns that influence NK cell function. Full-length KIR2DS4 binds to specific subsets of HLA-C allotypes from both C1 and C2 groups, as well as to HLA-A11 . A critical distinction has been observed between KIR2DS4 binding to HLA-A1102 but not to HLA-A1101, attributable to a single amino acid difference - the substitution of lysine for glutamate at position 19 in HLA-A1102 .

The relationship between KIR2DS4 and HLA-C05:01 is particularly significant. KIR2DS4 displays strong specificity for HLA-C05:01 presenting peptides with tryptophan at position 8 . This interaction is potent enough to trigger NK cell activation independent of other stimulation signals . Population genetics studies have revealed an inverse correlation between the worldwide frequencies of functional KIR2DS4 and HLA-C*05:01, suggesting evolutionary balancing selection that maintains both genes at intermediate frequencies in human populations .

This complex relationship between KIR2DS4 and specific HLA allotypes likely contributes to the role of NK cells in various disease processes, including viral infections, autoimmunity, cancer, and disorders of pregnancy . The presence or absence of specific KIR-HLA pairs has been linked to susceptibility to numerous diseases through gene association studies .

How does KIR2DS4 expression influence NK cell function in HIV-1 infection?

Studies of HIV-1 seropositive individuals have revealed that full-length KIR2DS4 is associated with higher viral loads and lower CD4+ T-cell counts during chronic infection . This suggests that KIR2DS4 may promote HIV-1 pathogenesis rather than protection. The mechanism appears to involve the maintenance of an excessively pro-inflammatory state that benefits viral replication while contributing to CD4+ T-cell depletion .

NK cells expressing KIR2DS4 during chronic HIV-1 infection demonstrate different functional properties compared to NK cells lacking this receptor . These differences include altered patterns of degranulation and cytokine secretion, particularly IFN-γ and MIP-1β . Notably, polyfunctional NK cells (capable of performing multiple functions simultaneously) are enriched within the KIR2DS4-positive subset . This enrichment of polyfunctional cells may contribute to the pro-inflammatory environment that characterizes chronic HIV-1 infection.

Longitudinal studies using mixed models for repeated measurements on HIV-1 seropositive youth have confirmed the association between full-length KIR2DS4 and poor virologic and immunologic outcomes (p<0.01 for both viral load and CD4+ T-cell count) . These findings suggest that KIR2DS4 genotyping might provide prognostic information for HIV-1 disease progression and potentially inform personalized treatment approaches.

What peptide specificities have been identified for KIR2DS4?

KIR2DS4 exhibits remarkable peptide selectivity that distinguishes it from other KIR family receptors. Research has identified a strong preference for peptides carrying tryptophan at position 8 (p8) when presented by HLA-C05:01 . This peptide specificity is crucial for receptor function, as the complex of HLA-C05:01 with a tryptophan-containing peptide at p8 is sufficient to activate KIR2DS4+ NK cells .

Beyond tryptophan, KIR2DS4 also recognizes peptides with phenylalanine or tyrosine at p8, albeit with reduced efficacy compared to tryptophan . In contrast, peptides with valine at this position fail to stimulate KIR2DS4+ NK cells . This suggests that aromatic amino acids at position 8 are critical for KIR2DS4 recognition, with tryptophan providing optimal interaction.

A particularly significant discovery is that KIR2DS4 recognizes a highly conserved peptide sequence motif found in bacterial recombinase A (RecA) when presented by HLA-C*05:01 . This recognition enables KIR2DS4+ NK cells to respond to multiple human bacterial pathogens, including species from Helicobacter, Chlamydia, Brucella, and Campylobacter . Based on sequence conservation analysis, researchers predict that over 1,000 bacterial species could potentially activate NK cells through this KIR2DS4-mediated mechanism .

How does KIR2DS4 compare to other KIR family members?

KIR2DS4 holds a distinctive position within the KIR family due to several unique characteristics. It is distinguished from other KIR2DS receptors by the proline-valine motif at positions 71-72, which it shares with KIR3DL2 . This motif, introduced by gene conversion before the separation of human and chimpanzee lineages, is largely responsible for KIR2DS4's unique HLA class I specificity .

Unlike other KIR2D receptors that predominantly bind either C1 or C2 HLA-C allotypes, KIR2DS4 can bind to both . It also binds to HLA-A*11, further broadening its recognition spectrum beyond what is typical for other KIR family members .

From a genetic standpoint, KIR2DS4 is the oldest and most prevalent KIR2DS gene and is part of the KIR A haplotype, whereas most other activating KIRs belong to the B haplotype . For individuals homozygous for the KIR A haplotype, KIR2DS4 represents the only activating KIR they carry . This places KIR2DS4 in a potentially critical position for these individuals' NK cell responses.

Structurally, crystallographic studies have revealed that KIR2DS4 differs from KIR2DL receptors primarily through displacement of contact loop L2 and altered bonding potential due to the substitutions at positions 71 and 72 . These structural differences directly influence receptor function and ligand specificity.

How does the interaction between KIR2DS4 and bacterial epitopes influence NK cell responses?

Research has revealed that KIR2DS4 recognizes a highly conserved peptide sequence motif in bacterial recombinase A (RecA) when presented by HLA-C*05:01 . This discovery expands our understanding of NK cell function beyond their traditional role in viral and cancer immunity, suggesting a significant contribution to antibacterial defense.

The interaction between KIR2DS4 and RecA epitopes presented by HLA-C*05:01 triggers robust NK cell activation, including degranulation and production of pro-inflammatory cytokines such as IFN-γ and TNF-α . This activation occurs in a peptide-specific manner, with strongest responses to peptides containing tryptophan at position 8 . The bacterial RecA epitope has been identified in multiple human pathogens, including species from Helicobacter, Chlamydia, Brucella, and Campylobacter, suggesting a broad role for KIR2DS4 in antibacterial immunity .

Based on sequence conservation analysis, researchers predict that over 1,000 bacterial species could potentially activate NK cells through this KIR2DS4-mediated mechanism . This suggests that KIR2DS4 may serve as a pattern recognition receptor for a conserved bacterial epitope, providing NK cells with the ability to respond to bacterial infections in a manner analogous to, but distinct from, toll-like receptors and other innate immune pattern recognition receptors.

The ability of KIR2DS4 to recognize bacterial epitopes may have evolutionary implications, potentially explaining the maintenance of this receptor throughout human evolution despite its association with increased HIV-1 pathogenesis . The balance between protective antibacterial immunity and detrimental effects in viral infections may represent an evolutionary trade-off that has shaped the distribution of KIR2DS4 alleles in human populations.

What are the implications of KIR2DS4-mediated activation in unlicensed NK cells?

A remarkable feature of KIR2DS4 is its ability to potently activate unlicensed NK cells (R− NK cells that lack inhibitory receptors for self-MHC) . This phenomenon challenges the traditional licensing paradigm, which holds that NK cells without self-MHC-specific inhibitory receptors remain hyporesponsive to ensure self-tolerance.

When unlicensed NK cells expressing KIR2DS4 encounter appropriate ligands (such as HLA-C*05:01 presenting peptides with tryptophan at p8), they demonstrate activation comparable to licensed NK cells . This suggests that KIR2DS4 stimulation can override the lack of licensing, providing a mechanism for activating NK cells that would otherwise remain functionally quiescent.

What methodologies are appropriate for studying KIR2DS4 genotyping and function?

Several complementary methodologies have been developed and validated for studying KIR2DS4 at both genetic and functional levels:

For genotyping, genomic DNA extraction followed by PCR-based methods represents the standard approach . Generic KIR typing can be performed by PCR amplification using primers targeted to regions specific for each KIR gene . To distinguish between expressed and non-expressed allotypes of KIR2DS4, allele-specific primers have been developed that differentiate between full-length and deleted variants . Pyrosequencing techniques can provide additional resolution for complex KIR regions . Intermediary-resolution HLA typing via sequence-specific oligonucleotide probes (PCR-SSOP) is also important for understanding KIR-HLA interactions .

For functional studies, several experimental approaches have proven valuable:

• Cell-based assays measuring NK cell degranulation (typically by flow cytometric detection of CD107a expression) in response to target cells expressing specific HLA-peptide complexes

• Cytokine production assays measuring IFN-γ and TNF-α through intracellular cytokine staining

• Redirected antibody-mediated degranulation assays using FcR+ P815 cells to study individual receptor contributions

• Peptide loading assays, where cells are incubated with specific synthetic peptides to study peptide specificity

Crystallographic structure determination has provided valuable insights into the structural basis of KIR2DS4's unique binding properties . Additionally, site-directed swap mutagenesis has been used to identify key residues responsible for receptor specificity .

For population studies, mixed models for repeated longitudinal measurements have been successfully employed to assess the impact of KIR2DS4 variants on disease outcomes over time .

How might KIR2DS4 contribute to the pathogenesis of infectious diseases beyond HIV-1?

While the role of KIR2DS4 in HIV-1 pathogenesis has been established, its contribution to other infectious diseases remains an area of active investigation. Based on current evidence, several mechanisms can be proposed:

For bacterial infections, KIR2DS4 recognition of the conserved RecA epitope presented by HLA-C*05:01 enables NK cells to respond to multiple human bacterial pathogens . This recognition has been demonstrated for species from Helicobacter, Chlamydia, Brucella, and Campylobacter, with predictions suggesting over 1,000 bacterial species could potentially activate NK cells through this mechanism . This broad recognition pattern suggests KIR2DS4 may function as a pattern recognition receptor for bacterial infections.

The ability of KIR2DS4 to activate unlicensed NK cells expands the pool of responsive NK cells during infection . This may be particularly important for responding to pathogens that downregulate MHC class I expression to evade T cell recognition.

The genetic variability of KIR2DS4 (full-length vs. deleted variants) likely influences susceptibility to various infectious diseases beyond HIV-1 . Population-based studies examining associations between KIR2DS4 variants and infectious disease outcomes could provide valuable insights into these relationships.

Table: KIR2DS4 Variants and Their Functional Properties