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NKG2C and NKG2A coexpression defines a highly functional antiviral NK population in spontaneous HIV control
Nerea Sánchez-Gaona, Ana Gallego-Cortés, Antonio Astorga-Gamaza, Norma Rallón, José Miguel Benito, Ezequiel Ruiz-Mateos, Adrian Curran, Joaquin Burgos, Jordi Navarro, Paula Suanzes, Vicenç Falcó, Meritxell Genescà, Maria J. Buzon
Nerea Sánchez-Gaona, Ana Gallego-Cortés, Antonio Astorga-Gamaza, Norma Rallón, José Miguel Benito, Ezequiel Ruiz-Mateos, Adrian Curran, Joaquin Burgos, Jordi Navarro, Paula Suanzes, Vicenç Falcó, Meritxell Genescà, Maria J. Buzon
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Research Article AIDS/HIV

NKG2C and NKG2A coexpression defines a highly functional antiviral NK population in spontaneous HIV control

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Abstract

Elite controllers (ECs), a unique group of people with HIV (PWH), exhibit remarkable control of viral replication in the absence of antiretroviral therapy. In this study, we comprehensively characterized the NK cell repertoire in ECs after long-term viral control. Phenotypic profiling of NK cells revealed profound differences compared with other PWH, but marked similarities to uninfected individuals, with a distinctive prevalence of NKG2C+CD57+ memory-like NK cells. Functional analyses indicated that ECs had limited production of functional molecules upon NK stimulation and consequently reduced natural cytotoxicity against non-HIV target cells. Importantly, ECs showed an exceptional ability to kill primary HIV-infected cells by the antibody-dependent cell cytotoxicity adaptive mechanism, which was achieved by a specific memory-like NK population expressing CD16, NKG2A, NKG2C, CD57, and CXCR3. In-depth single-cell RNA-seq unveiled a unique transcriptional signature in these NK cells linked to increased cell metabolism, migration, chemotaxis, effector functions, cytokine secretion, and antiviral response. Our findings underscore a pivotal role of NK cells in the immune control of HIV and identify specific NK cells as emerging targets for immunotherapies.

Authors

Nerea Sánchez-Gaona, Ana Gallego-Cortés, Antonio Astorga-Gamaza, Norma Rallón, José Miguel Benito, Ezequiel Ruiz-Mateos, Adrian Curran, Joaquin Burgos, Jordi Navarro, Paula Suanzes, Vicenç Falcó, Meritxell Genescà, Maria J. Buzon

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Figure 5

Unique transcriptional signatures define ADCC-mediating NK cells from DC.

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Unique transcriptional signatures define ADCC-mediating NK cells from DC...
Gene expression analysis by single-cell RNA-seq. (A) UMAP visualization of NK cell populations sorted from DC individuals (NKA in red, NKB in green, NKC in blue). (B) UMAP visualization of 13 distinct NK cell clusters identified from NK cell populations sorted by unsupervised hierarchical clustering. (C) Number of cells per cluster and sample as counts (left) or proportions (right). (D) Heatmap depicting the top 5 genes most differentially expressed (upregulated) in each NK cell cluster. (E) The top panel shows a volcano plot illustrating the differentially expressed genes between NKB and NKA subsets. Genes significantly overexpressed in NKB compared with NKA are highlighted in red, while those underexpressed in NKB relative to NKA are shown in blue. The bottom panel presents representative UMAP plots depicting the expression of genes upregulated in NKA compared with NKB. (F) Significant canonical pathways predicted by Gene Ontology Biological Process analysis (GO-BP) of differentially expressed genes in NKA versus NKB. (G) The top panel presents a volcano plot illustrating the differentially expressed genes between NKC and NKA subsets. Genes significantly overexpressed in NKC relative to NKA are shown in red, while those underexpressed in NKC compared with NKA are depicted in blue. The bottom panel displays representative UMAP plots highlighting the expression of genes upregulated in NKA compared with NKC. (H) Significant canonical pathways predicted by GO-BP of differentially expressed genes in NKA relative to NKC. (I) Differentiation trajectory analysis of NK cell clusters, illustrating the progression and differentiation pathways of each population. Five distinct lineages were identified. The pseudotime inference for each NK cell cluster is presented, with UMAP plots color coded by inferred lineages. The scale indicates the maturation state, ranging from yellow (least mature) to dark blue (most mature).

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