Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Resident CD49a⁺CD103⁺NKG2C⁺ NK Cells Restrict HIV Infection in Human Lymphoid Tissue Explants

ABSTRACT: Natural killer (NK) cells are pivotal effectors in antiviral immunity, yet their tissue-specific roles during acute HIV infection remain poorly defined. Using an ex vivo human tonsillar tissue model, we profile NK cell responses to early HIV infection and uncover distinct subsets with specialized functions. We identify a previously uncharacterized memory-like NK population (CD16⁺/⁻CD69⁺CD49a⁺CD103⁺NKG2C⁺) associated with reduced viral burden and enriched in cytotoxic mediators (GNLY, PRF1, GZMB), apoptotic ligands (FASLG, TRAIL), cytokine receptors (IL2RA, ILR2B, IL2RG, IL12RB2, IL18R1) and trafficking molecules (CCL3–5, CCR7, SELL). These cells coexpress NKG2A, suggesting a regulatory balance between activation and inhibition. Although functionally capable of clearing HIV-infected CD4⁺ T cells in a tissue-mimetic environment, they show impaired cytotoxicity and transcriptional signs of exhaustion after infection. Conversely, HIV drives the reprogramming of immature CD16⁻CD69⁺ NK cells toward a more cytotoxic and migratory effector phenotype. These findings reveal dynamic NK cell adaptations in lymphoid tissue during early HIV infection and highlight tissue-resident NK cells as promising targets for immunotherapeutic intervention.

ORGANISM(S): HIV-1 group M Homo sapiens

PROVIDER: GSE286121 | GEO | 2025/12/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

a26bf570-482e-435d-a268-fddc7e54b31d - samples

Project description:The dataset contains RNAseq data from 5 subsets of NK cells isolated from human lung: 1) CD69+CD49a+CD103+CD16-CD56bright NK cells 2) CD69+CD49a+CD103-CD16-CD56bright NK cells 3) CD69+CD49a-CD103-CD16-CD56bright NK cells 4) CD69-CD49a-CD103-CD16-CD56bright NK cells 5) CD56dimCD16+NKG2A+CD57- NK cells The dataset contains paired data for the subsets from 2 donors with 2 biological replicates/donor and subset.

| EGAD00001004850 | EGA

Gene expression profiling of NKG2C+ NK cells generated from inflammatory CD34+DNAM-1brCXCR4+ and Lin-CD34- CD16+CD56- blood precursors

Project description:There is limited knowledge on the origin and development of the ample spectrum of human NK cells, particularly of specialized NK subsets. Here, we characterized the NK cell progeny of CD34+DNAM-1bright CXCR4+ precursors that reside in healthy bone marrow and circulate in the peripheral blood (PB) of patients with chronic infections/inflammation. including HIV, HCV or HCMV reactivation after HSC transplantation. Unlike conventional CD34+ precursors they rapidly differentiated in vitro into cytotoxic, IFNγ-secreting CD94/NKG2C+KIR+CD57+ maturing NK cell progenies with HCMV-inhibiting activity. Progeny characterization led also to identification of an additional new PB Lin-CD56-CD16+ precursor giving rise to the same CD94/NKG2C+KIR+CD57+ maturing NK cell progenies. Microarray analysis of NK cell progenies revealed a signature compatible with maturing adaptive NK cells. In vivo circulation of multiple common lymphocyte precursors with rapid development to NKG2C+ NK cell progeny is steadily occurring and may thus be a crucial resource for the prompt control of HCMV. We used microarray to compare the transcriptional profiles of human NKG2C+ NK cells derived from i) CD34+DNAM1brightCXCR4+ precursors, ii) Lin-CD34-CD16+CD56- precursors, iii) peripheral blood.

2020-12-31 | GSE136570 | GEO

Human-induced CD49a+ NK cells promote fetal growth

Project description:CD49a+ natural killer (NK) cells are critical in promoting fetal development and maintaining immune tolerance at the maternal-fetal interface in early pregnancy. However, their tissue residency in human tissue hinder thorough studies and clinical application. How to induce functional human CD49a+ NK cells that could benefit pregnancy outcomes is still unknown. Here, we have established three no feeder cell induction systems to induce human CD49a+ NK cells from umbilical cord blood hematopoietic stem cells (HSCs), bone marrow HSCs or peripheral blood NK cells, respectively. These induced NK cells (iNKs) from three cell induction systems show high expression of CD49a, CD9, CD39, CD151, low expression of CD16, and no obvious cytotoxic capability, phenotypically and functionally similar with decidual NK cells. Furthermore, these iNKs also have high expression of growth-promoting factors and proangiogenic factors. Importantly, these iNKs have shown their capabilities to promote fetal growth and improve uterine artery blood flow in a murine pregnancy model in vivo. This research reveals properties of human-induced CD49a+ NK cells in promoting fetal growth from three cell induction systems, which may improve the feasibility of applying these iNKs to the patients having adverse pregnancy outcomes.

2022-02-23 | GSE184719 | GEO

RNA sequencing of NK cells in human lung

Project description:Human lung tissue-resident NK cells (trNK cells) are likely to play important roles in viral infections, inflammation and cancer. However, knowledge about lung trNK cells is lacking but is fundamental for exploiting these cells in therapeutic approaches. Here we analysed the transcriptome of CD69+CD49a+CD103+CD16-CD56bright, CD69+CD49a+CD103-CD16-CD56bright, CD69+CD49a-CD103-CD16-CD56bright, CD69-CD49a-CD103-CD16-CD56bright, and CD56dimCD16+NKG2A+CD57- NK cells isolated from human lung.

| EGAS00001003544 | EGA

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

Project description: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.

2024-11-29 | GSE273423 | GEO

Role of NKG2a/c + CD8 + T cells in pathogenic versus non-pathogenic SIV infections

Project description:Some viruses have established an equilibrium with their host. African green monkeys (AGM) display persistent high viral replication in blood and intestine during Simian immunodeficiency virus (SIV) infection but resolve systemic inflammation after acute infection and lack intestinal immune or tissue damage during chronic infection. We show that NKG2 a/c + CD8 + T cells increase in blood and intestine of AGM in response to SIVagm infection in contrast to SIVmac infection in macaques, the latter modeling HIV infection. NKG2 a/c + CD8 + T cells were not expanded in lymph nodes and CXCR5 + NKG2 a/c + CD8 + T cell frequencies further decreased after SIV infection. Genome-wide transcriptome analysis of NKG2 a/c + CD8 + T cells from AGM revealed the expression of NK cell receptors, and of molecules with cytotoxic effector, gut homing, immunoregulatory and gut barrier function, including CD73. NKG2 a/c + CD8 + T cells correlated negatively with IL-23 in the intestine during SIVmac infection. The data suggest a potential regulatory role of NKG2 a/c + CD8 + T cells in intestinal inflammation during SIV/HIV infections.

2021-03-11 | E-MTAB-8664 | biostudies-arrayexpress

HIV/HBV co-infection remodels the immune landscape and Natural Killer cell functional responses

Project description:Background: Hepatitis B (HBV) and human immunodeficiency virus (HIV) co-infection is a common occurrence globally, with significant morbidity and mortality. Both viruses lead to dysregulated immune responses including changes in natural killer (NK) cells, a key component of antiviral defense and a promising target for HBV cure strategies. In this study we used high-throughput single cell analysis to explore the immune cell landscape in people with HBV mono-infection and HIV/HBV co-infection, on antiviral therapy, with emphasis on identifying the distinctive characteristics of NK cell subsets. Results: Our data show striking differences in the transcriptional programs of NK cells. HIV/HBV co-infection was characterized by an overrepresentation of adaptive, KLRC2 expressing NK cells, including a higher abundance of a chemokine enriched (CCL3/CCL4) adaptive cluster. The NK cell remodeling in HIV/HBV co-infection was reflected in enriched activation pathways shared with T cells, including CD3 phosphorylation and ZAP-70 translocation that can mediate stronger ADCC responses and a bias towards chemokine/cytokine signaling. By contrast HBV mono-infection imposed a stronger cytotoxic profile on NK cells and a more prominent signature of exhaustion with higher circulating levels of HBsAg. Mirroring the transcriptomic analysis, phenotypic alterations in the NK cell pool in co-infection were consistent with increased ‘adaptiveness’ and better capacity for ADCC compared to HBV mono-infection. Overall an adaptive NK cell signature correlated inversely with circulating levels of HBsAg and HBV-RNA in our cohort. Conlcusions: This study provides new insights into the differential transcriptional signature and functional profile of NK cells in HBV and HIV/HBV co-infection, highlighting new pathways that can be manipulated to tailor NK cell-focused approaches to advance cure strategies in the different population groups.

2024-08-01 | GSE241183 | GEO

CD49a+ and CD49a- NK cells from human livers

Project description:Purified NK cells from human liver tissues were first enriched by MACS using NK Cell Isolation Kit (Miltenyi Biotec, German) and CD49a+/- hepatic NK cells were isolated by FACS Aria cell sorter (BD Biosciences, United States) to attain a purity greater than 95%.

2020-07-07 | GSE109198 | GEO

Quantitative proteomics of cytokine-induced memory-like (CIML) NK cells

Project description:NK cells from healthy donors were isolated from peripheral blood and stimulated overnight with IL-12/15/18 to induce a memory-like phenotype. After 7 days of culture, the phenotype and degranulation potential of CIML NK cells was characterized in two distinct NK cell subsets: CD16+/CD56+ and CD16−/CD56. Finally, NK cell subsets were purified using fluorescence-activated cell sorting (FACS) and subjected to high-throughput multiplexed quantitative proteomics.

2025-07-14 | PXD059190 | Pride

RNA-seq of NK cells from blood samples of HV and AML patients

Project description:CD56neg CD16+ Natural Killer (NK) cells have been reported to expand in chronic diseases and acute myeloid leukemia (AML). However, their biological role is still unclear. Using bulk RNA-sequencing, we compared gene expression profile of CD56neg CD16+ NK cells with conventional CD56bright, CD56dim CD16- and CD56dim CD16+ NK cells from blood samples of HV and AML patients. RNA-seq unveiled that CD56neg CD16+ NK cells were mature circulating NK cells with functional capacities. Taken together, our results suggest that CD56neg CD16+ NK cells are a relevant target for future NK-cell-based immunotherapies.

2024-12-20 | E-MTAB-14569 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data