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Single-cell transcriptional profiling informs efficient reprogramming of human somatic cells to cross-presenting dendritic cells

Rosa, Fábio F LU ; Pires, Cristiana F LU ; Kurochkin, Ilia LU ; Halitzki, Evelyn LU ; Zahan, Tasnim LU ; Arh, Nejc LU orcid ; Zimmermannová, Olga LU ; Ferreira, Alexandra G LU orcid ; Li, Hongzhe LU and Karlsson, Stefan LU orcid , et al. (2022) In Science Immunology 7(69). p.1-18
Abstract

Type 1 conventional dendritic cells (cDC1s) are rare immune cells critical for the induction of antigen-specific cytotoxic CD8+ T cells, although the genetic program driving human cDC1 specification remains largely unexplored. We 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 efficiency. Here, we investigated single-cell transcriptional dynamics during human cDC1 reprogramming. Human induced cDC1s (hiDC1s) generated from embryonic fibroblasts gradually acquired a global cDC1 transcriptional profile and expressed antigen presentation signatures, whereas other DC subsets were not induced at the single-cell... (More)

Type 1 conventional dendritic cells (cDC1s) are rare immune cells critical for the induction of antigen-specific cytotoxic CD8+ T cells, although the genetic program driving human cDC1 specification remains largely unexplored. We 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 efficiency. Here, we investigated single-cell transcriptional dynamics during human cDC1 reprogramming. Human induced cDC1s (hiDC1s) generated from embryonic fibroblasts gradually acquired a global cDC1 transcriptional profile and expressed antigen presentation signatures, whereas other DC subsets were not induced at the single-cell level during the reprogramming process. 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 led to improvement of reprogramming efficiency by 190-fold. hiDC1s engulfed dead cells, secreted inflammatory cytokines, and performed antigen cross-presentation, key cDC1 functions. This approach allowed efficient hiDC1 generation from adult fibroblasts and mesenchymal stromal cells. Mechanistically, PU.1 showed 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 led 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.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Science Immunology
volume
7
issue
69
article number
eabg5539
pages
1 - 18
publisher
American Association for the Advancement of Science (AAAS)
external identifiers
  • scopus:85125875360
  • pmid:35245086
ISSN
2470-9468
DOI
10.1126/sciimmunol.abg5539
language
English
LU publication?
yes
id
b45ab2fd-8511-4aed-986f-a22de14a636e
date added to LUP
2022-03-17 14:52:27
date last changed
2022-08-04 22:57:50
@article{b45ab2fd-8511-4aed-986f-a22de14a636e,
  abstract     = {{<p>Type 1 conventional dendritic cells (cDC1s) are rare immune cells critical for the induction of antigen-specific cytotoxic CD8+ T cells, although the genetic program driving human cDC1 specification remains largely unexplored. We 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 efficiency. Here, we investigated single-cell transcriptional dynamics during human cDC1 reprogramming. Human induced cDC1s (hiDC1s) generated from embryonic fibroblasts gradually acquired a global cDC1 transcriptional profile and expressed antigen presentation signatures, whereas other DC subsets were not induced at the single-cell level during the reprogramming process. 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 led to improvement of reprogramming efficiency by 190-fold. hiDC1s engulfed dead cells, secreted inflammatory cytokines, and performed antigen cross-presentation, key cDC1 functions. This approach allowed efficient hiDC1 generation from adult fibroblasts and mesenchymal stromal cells. Mechanistically, PU.1 showed 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 led 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.</p>}},
  author       = {{Rosa, Fábio F and Pires, Cristiana F and Kurochkin, Ilia and Halitzki, Evelyn and Zahan, Tasnim and Arh, Nejc and Zimmermannová, Olga and Ferreira, Alexandra G and Li, Hongzhe and Karlsson, Stefan and Scheding, Stefan and Pereira, Carlos-Filipe}},
  issn         = {{2470-9468}},
  language     = {{eng}},
  number       = {{69}},
  pages        = {{1--18}},
  publisher    = {{American Association for the Advancement of Science (AAAS)}},
  series       = {{Science Immunology}},
  title        = {{Single-cell transcriptional profiling informs efficient reprogramming of human somatic cells to cross-presenting dendritic cells}},
  url          = {{http://dx.doi.org/10.1126/sciimmunol.abg5539}},
  doi          = {{10.1126/sciimmunol.abg5539}},
  volume       = {{7}},
  year         = {{2022}},
}