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Ablation of cDC1 development by IL-6-induced C/EBPb support in the -165 kb Zeb2 enhancer

ABSTRACT: Type 1 conventional dendritic cells (cDC1) are required for effective CD8 T cell responses to many viruses and tumors and for effective checkpoint blockade immunotherapy. Recently, cytokines produced in association with certain tumors were reported to impair anti-tumor immune responses by reducing the abundance of cDC1. However, the reported mechanism of this reduction remains unclear, attributed either to reduced cDC1 development or decreased peripheral cDC1 survival. Here we show that tumor-derived IL-6 blocks cDC1 development from both in murine and human systems. We show that mechanism of this blockade is the IL-6-dependent increase in C/EBPβ expression in the common dendritic cell progenitor (CDP). C/EBPβ and NFIL3 compete for binding to sites in the -165 kb Zeb2 enhancer, and support or repress Zeb2 expression respectively. At homeostastis, pre-cDC1 specification occurs upon Nfil3 induction and consequent Zeb2 suppression. However, IL-6 strongly induces C/EBPβ expression in CDPs, thereby preventing normal NFIL3-dependent pre-cDC1 specification. Importantly, the ability of IL-6 to block cDC1 development is dependent on the presence of C/EBPβ binding sites in the -165 kb Zeb2 enhancer, as this effect is lost in Δ1+2+3 mutnat mice in which these binding sites are mutated. These results explain how tumor-associated IL-6 suppresses cDC1 development and suggest therapeutic approaches preventing abnormal C/EBPβ induction in CDPs may help reestablish cDC1 development to enhance anti-tumor immunity.

ORGANISM(S): Mus musculus

PROVIDER: GSE215751 | GEO | 2023/06/22

REPOSITORIES: GEO

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Increased bindings of C/EBP-beta at the −165 kb Zeb2 enhancer upon systemic IL-6 exposure suppress cDC1 development

Project description:Type 1 conventional dendritic cells (cDC1) are required for effective CD8 T cell responses to many viruses and tumors and for effective checkpoint blockade immunotherapy. Recently, cytokines produced in association with certain tumors were reported to impair anti-tumor immune responses by reducing the abundance of cDC1. However, the reported mechanism of this reduction remains unclear, attributed either to reduced cDC1 development or decreased peripheral cDC1 survival. Here we show that tumor-derived IL-6 blocks cDC1 development from both in murine and human systems. We show that mechanism of this blockade is the IL-6-dependent increase in C/EBPβ expression in the common dendritic cell progenitor (CDP). C/EBPβ and NFIL3 compete for binding to sites in the -165 kb Zeb2 enhancer, and support or repress Zeb2 expression respectively. At homeostastis, pre-cDC1 specification occurs upon Nfil3 induction and consequent Zeb2 suppression. However, IL-6 strongly induces C/EBPβ expression in CDPs and increase C/EBPβ bindings at the -165 kb Zeb2 enhancer, thereby preventing normal NFIL3-dependent pre-cDC1 specification. Importantly, the ability of IL-6 to block cDC1 development is dependent on the presence of C/EBPβ binding sites in the -165 kb Zeb2 enhancer, as this effect is lost in Δ1+2+3 mutnat mice in which these binding sites are mutated. These results explain how tumor-associated IL-6 suppresses cDC1 development and suggest therapeutic approaches preventing abnormal C/EBPβ induction in CDPs may help reestablish cDC1 development to enhance anti-tumor immunity.

2023-06-22 | GSE229271 | GEO

Ablation of cDC2 development by triple mutations within the Zeb2 enhancer

Project description:The divergence of the common dendritic cell progenitor (CDP) into the conventional type 1 and type 2 dendritic cell (cDC1 and cDC2, respectively) lineages is poorly understood. Some transcription factors act in the commitment of already specified progenitors-such as BATF3, which stabilizes Irf8 autoactivation at the +32 kb Irf8 enhancer-but the mechanisms controlling the initial divergence of CDPs remain unknown. Here we report the transcriptional basis of CDP divergence and describe the first requirements for pre-cDC2 specification. Genetic epistasis analysis suggested that Nfil3 acts upstream of Id2, Batf3 and Zeb2 in cDC1 development but did not reveal its mechanism or targets. Analysis of newly generated NFIL3 reporter mice showed extremely transient NFIL3 expression during cDC1 specification. CUT&RUN and chromatin immunoprecipitation followed by sequencing identified endogenous NFIL3 binding in the -165 kb Zeb2 enhancer at three sites that also bind the CCAAT-enhancer-binding proteins C/EBPα and C/EBPβ. In vivo mutational analysis using CRISPR-Cas9 targeting showed that these NFIL3-C/EBP sites are functionally redundant, with C/EBPs supporting and NFIL3 repressing Zeb2 expression at these sites. A triple mutation of all three NFIL3-C/EBP sites ablated Zeb2 expression in myeloid, but not lymphoid progenitors, causing the complete loss of pre-cDC2 specification and mature cDC2 development in vivo. These mice did not generate T helper 2 (TH2) cell responses against Heligmosomoides polygyrus infection, consistent with cDC2 supporting TH2 responses to helminths. Thus, CDP divergence into cDC1 or cDC2 is controlled by competition between NFIL3 and C/EBPs at the -165 kb Zeb2 enhancer.

2022-04-19 | GSE188579 | GEO

Ablation of cDC2 specification by triple mutations in the Zeb2 enhancer [ChIP-Seq]

Project description:The divergence of the common dendritic cell progenitor (CDP) into specified progenitors for the cDC1 and cDC2 dendritic cells subsets is poorly understood. Some transcription factors (TFs) act in commitment of already specified progenitors, such as Batf3 which stabilizes Irf8 autoactivation at the +32 kb Irf8 enhancer, but the mechanism of CDP divergence remains unknown. Here, we report the transcriptional basis of CDP divergence and describe the first requirements for pre-cDC2 specification. Genetic epistasis analysis suggested that Nfil3 acts upstream of Id2, Batf3, and Zeb2 in cDC1 development but has not revealed its mechanism or targets. Analysis of newly generated NFIL3 reporter mice showed extremely transient NFIL3 expression during cDC1 specification. CUT&RUN and ChIP-seq analysis identified endogenous NFIL3 binding in the –165 kb Zeb2 enhancer at three sites that also bind CCAAT-enhancer-binding proteins C/EBPa and C/EBPb. In vivo mutational analysis using CRISPR/Cas9 targeting showed that these NFIL3/C/EBP sites are functionally redundant, with C/EBPs supporting and NFIL3 repressing Zeb2 expression at these sites, respectively. Mutation of all three NFIL3/C/EBP sites ablated Zeb2 expression in myeloid, but not lymphoid progenitors, causing complete loss of pre-cDC2 specification and mature cDC2 development in vivo. These mice failed to generate TH2 responses against H. polygyrus infection, consistent with cDC2 supporting TH2 responses to helminths. Thus, CDP divergence is controlled by competition between NFIL3 and C/EBPs at the –165 kb Zeb2 enhancer.

2022-04-19 | GSE174108 | GEO

Ablation of cDC2 specification by triple mutations in the Zeb2 enhancer [CUT&RUN]

2022-04-19 | GSE188482 | GEO

Ablation of cDC2 specification by triple mutations in the Zeb2 enhancer [RNA-seq]

2022-04-19 | GSE188564 | GEO

An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development (RNA-Seq)

Project description:Classical type 1 dendritic cells (cDC1s) are required for anti-viral and anti-tumor immunity, which has motivated a need to understand their development. The development of the cDC1 progentitor requires an E protein–dependent enhancer located 41 kilobases downstream of the transcription start site of the transcription factor IRF8 (+41 kb Irf8 enhancer) but its maturation instead requires the BATF3-dependent +32 kb Irf8 enhancer. To understand this switch, we performed single-cell RNA sequencing of the common dendritic cell progenitor (CDP) and identified a cluster of cells that expressed transcription factors that influence cDC1 development, such as Nfil3, Id2, and Zeb2. Genetic epistasis among these factors revealed that Nfil3 expression is required for the transition from Zeb2hi and Id2lo CDPs to Zeb2lo and Id2hi CDPs, which represent the earliest committed cDC1 progenitors. This genetic circuit blocks E protein activity to exclude plasmacytoid DC potential and explains the switch in Irf8 enhancer usage during cDC1 development.

2019-06-23 | GSE132770 | GEO

An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development

Project description:An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development

| PRJNA509877 | ENA

An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development (RNA-Seq)

Project description:An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development (RNA-Seq)

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Hi-C2 of mouse splenic macrophages and pDCs

Project description:The transcriptional repressor Zeb2 regulates development of many cell fates among somatic, neural and hematopoietic lineages, but the basis for its requirement in these diverse linages is unclear. Our recent study uncovered a mutually repressive regulatory circuit between Id2 and Zeb2, and predicted that Zeb2 should be positively regulated by members of the E protein family of transcription factors. Here, we identified a 400bp enhancer region located 165 kilobases (kb) upstream of the Zeb2 transcriptional start site (TSS) that binds the E proteins E2A and E2-2 at several E-box motifs and is active in hematopoietic lineages. Germline deletion of this 400bp region (Zeb2 –165–/– mice) specifically prevented Zeb2 expression in hematopoietic stem cell (HSC) derived lineages. Zeb2 –165–/– mice lacked development of pDCs, monocytes, and B cells. Surprisingly, all macrophages in Zeb2 –165–/– mice were exclusively of embryonic origin. Using single-cell chromatin profiling, we identified a second Zeb2 enhancer located at +164kb that is selectively active in embryonically derived lineages, but not in lineages derived from HSCs. Thus, Zeb2 expression in adult, but not embryonic, hematopoiesis is selectively controlled by the –165kb Zeb2 enhancer.

2021-11-10 | GSE171564 | GEO

Hi-C sequencing data of WT and Zeb2 enhancer mutant splenic CD8+ T cells

Project description:To evaluate the impact of -165-kb Zeb2 enhancer deletion on 3D chromatin structure, we performed in situ Hi-C analysis of WT and Zeb2 –165–/– splenic CD8+ T cells, which showed no significant global changes on the structure of chromosome 2

2021-11-10 | GSE171103 | GEO

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