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Series GSE162650 Query DataSets for GSE162650
Status Public on Mar 05, 2022
Title Single-cell transcriptional profiling informs efficient reprogramming of human somatic cells to cross-presenting dendritic cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Type-1 conventional dendritic cells (cDC1s) are rare immune cells critical for the induction of antigen-specific cytotoxic CD8+ T-cells. The genetic program driving human cDC1 specification remains largely unexplored. We have previously identified PU.1, IRF8 and BATF3 transcription factors as sufficient to induce cDC1 fate in mouse fibroblasts but reprogramming of human somatic cells was limited by low efficiencies. Here, we investigated single-cell transcriptional dynamics during human cDC1 reprogramming. Human induced cDC1s (hiDCs) generated from embryonic fibroblasts gradually acquire a global cDC1 transcriptional profile and activate antigen presentation signatures. Importantly, other DC subsets are not induced at the single-cell level. We extracted gene modules associated with successful reprogramming and identified inflammatory signaling and the cDC1-inducing transcription factor network as key drivers of the process. Combining IFN-γ, IFN-β and TNF-α with constitutive expression of cDC1-inducing transcription factors lead to improvement of reprogramming efficiency by 190-fold. hiDCs uptake dead cells, secrete inflammatory cytokines and perform antigen cross-presentation, a key cDC1 function. This approach allowed efficient hiDC1 generation from adult fibroblasts and mesenchymal stromal cells. Mechanistically, PU.1 shows dominant and independent chromatin targeting at early phases of reprogramming, recruiting IRF8 and BATF3 to shared binding sites. The cooperative binding at open enhancers and promoters leads to silencing of fibroblast genes and activation of a cDC1 program. These findings provide mechanistic insights into human cDC1 specification and reprogramming and represent a platform for generating patient-tailored cDC1s, a long-sought DC subset for vaccination strategies in cancer immunotherapy.
Overall design RNAseq profiling on single cells, generated after transduction of human embryonic fibroblasts (HEFs) or human dermal fibroblasts (HDFs) with PU.1, IRF8, BATF3, at day 3 and day 9, generated in the presence or absence of IFN-γ, IFN-β and TNF-α. Single cell RNAseq profiling of HEFs, HDFs, and freshly isolated peripheral blood Dendritic cells type 1 (HLA-DR+CD11C+CD141+), Dendritic cells type 2 (HLA-DR+CD11C+CD141-CD1C+) and plasmacytoid dendritic cells (HLA-DR+CD11C-CD123+) were used as controls.
Contributor(s) Rosa FF, Pires CF, Kurochkin I, Pereira C
Citation(s) 35245086
Submission date Dec 04, 2020
Last update date Nov 01, 2022
Contact name Ilia Kurochkin
Organization name Lund University
Street address BMC A12, Sölvegatan 17
City Lund
State/province Skane
ZIP/Postal code 221 84
Country Sweden
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (35)
GSM4956203 HEF donor A rep1
GSM4956204 hiDC d3 donor A rep1
GSM4956205 hiDC d9 CD45+HLA-DR+ donor A rep1
BioProject PRJNA682551
SRA SRP295851

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Supplementary file Size Download File type/resource
GSE162650_hdf_idc_cdc1_counts.txt.gz 9.9 Mb (ftp)(http) TXT
GSE162650_hef_all_counts.txt.gz 98.9 Mb (ftp)(http) TXT
GSE162650_hef_idc_cdc1_counts.txt.gz 8.0 Mb (ftp)(http) TXT
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