Transcriptomics,Genomics

Dataset Information

160

A Reproducibility-Based Computational Framework Identifies An Inducible, Enhanced Antiviral Dendritic Cell State In HIV-1 Elite Controllers (scRNA-Seq)


ABSTRACT: Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and communication could thus potentially alter host protection. Here, we explore this hypothesis by applying single-cell RNA-Seq to examine viral responses among the dendritic cells (DCs) of three elite controllers (ECs) of HIV-1 infection. We discover a highly functional antiviral DC state in ECs whose fractional abundance after in vitro exposure to HIV-1 correlates with higher CD4+ T cell counts and lower HIV-1 viral loads, and that effectively primes polyfunctional T cell responses in vitro. We identify and validate select immunomodulators that increase the fractional abundance of this state in primary peripheral blood mononuclear cells (PBMCs) from healthy individuals in vitro. Overall design: Single-cell RNA-seq profiling of HIV-1-exposed cDCs and media controls from 3 elite controllers used to identify reproducible gene expression programs associated with cell-intrinsic HIV-1 immune recognition.

INSTRUMENT(S): Illumina NextSeq 500 (Homo sapiens)

SUBMITTER: Michael B Cole  

PROVIDER: GSE80212 | GEO | 2017-12-23

SECONDARY ACCESSION(S): PRJNA318284

REPOSITORIES: GEO

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Publications

A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers.

Martin-Gayo Enrique E   Cole Michael B MB   Kolb Kellie E KE   Ouyang Zhengyu Z   Cronin Jacqueline J   Kazer Samuel W SW   Ordovas-Montanes Jose J   Lichterfeld Mathias M   Walker Bruce D BD   Yosef Nir N   Shalek Alex K AK   Yu Xu G XG  

Genome biology 20180129 1


BACKGROUND:Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and communication could thus potentially alter host protection. Here, we explore this hypothesis by applying single-cell RNA-sequencing to examine viral responses among the dendritic cells (DCs) of three elite controllers (ECs) of HIV-1 infection. RESULTS:To overcome the potentially confounding effects of donor-to-donor variability, we  ...[more]

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