Nuclear receptor corepressor 1 controls regulatory T cell subset differentiation and effector function
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Austria
- Medical University of Vienna, Vienna, Department of Medicine I, Laboratory of Infection Biology, Austria
- CeMM Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Austria
- Medical University of Vienna, Department of Laboratory Medicine, Austria
- Medical University of Vienna, Center for Medical Statistics, Informatics, and Intelligent Systems, Institute of Artificial Intelligence, Austria
- Medical University of Vienna, Department of Internal Medicine III, Division of Gastroenterology and Hepatology, Hans Popper Laboratory of Molecular Hepatology, Austria
- Medical University of Vienna, Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Austria
Figures
Figure 1 with 3 supplements
Loss of NCOR1 leads to a relative increase in CD44hiCD62L– effector Treg cells.
(a) Flow cytometric analysis of splenocytes isolated from wild-type (WT) and NCOR1-cKO mice showing CD44 and CD62L expression in CD4+FOXP3+ cells at steady-state. (b) Diagrams showing the percentage …
Figure 1—figure supplement 1
Effector markers are upregulated in NCOR1-deficient Treg cells.
(a) Diagrams showing a summary of the percentage of CD44hiCD62L– (left) and CD44loCD62L+ (right) CD4+FOXP3+ cells from lymph nodes (LNs) of wild-type (WT) and NCOR1-cKO mice. (b) Diagrams showing a …
Figure 1—figure supplement 2
Characterization of FOXP3+ Treg cells isolated from NCOR1-cKO mice.
(a) Flow cytometric analysis of wild-type (WT) and NCOR1-cKO splenocytes showing expression of Ki67 in CD4+ FOXP3+ cells at steady state. (b) Summary showing percentage (left) and expression (gMFI) …
Figure 1—figure supplement 3
Gating strategies for flow cytometric analysis.
(a) Gating strategy for identification of effector (CD44hiCD62L–) and naïve (CD44loCD62L+) Treg cells: After exclusion of debris (FSC-A/ SSC-A), doublets (FSC-H/ FSC-W) and dead cells (using …
Figure 2
NCOR1 controls effector features in murine and human iTreg cells.
(a,b) Naïve wild-type (WT) and NCOR1-cKO CD4+ T cells were activated with anti-CD3/anti-CD28 for 3 days in the presence of TGFβ and IL2. (a) Diagrams show the summary of the percentages of WT and …
Figure 3 with 1 supplement
NCOR1 regulates the ratio of naive to effector Treg cells in a Treg cell-intrinsic manner.
(a) Experimental strategy for generating bone marrow (BM) chimeric mice. (b) Flow cytometric analysis showing the distribution of CD45.1+ and CD45.2+ cells as well as the expression of FOXP3, CD44 …
Figure 3—figure supplement 1
Treg cell-specific deletion of NCOR1 results in enhanced CD44hiCD62L– effector Treg cell subsets.
(a) Representative agarose gel picture showing Ncor1 deletion PCR in WT tail samples and FACS-sorted WT CD4+ splenocytes (left panel), TCRß+, CD8+, CD4+YFP–, and CD4+YFP+ cells isolated from the …
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Figure 3—figure supplement 1—source data 1
Raw, uncropped agarose gel picture showing Ncor1 deletion PCR indicating Ncor1 deletion.
Representative agarose gel picture showing Ncor1 deletion PCR results in WT tail samples and FACS-sorted WT CD4+ splenocytes (left panel), TCRß+, CD8+, CD4+YFP–, and CD4+YFP+ cells isolated from the spleen of NCOR1-cKOFoxp3 mice (middle panel) and CD4+YFP– and CD4+YFP+ cells isolated from the thymus (right panel) of NCOR1-cKOFoxp3 mice. Two mice were pooled for sorting. Size of floxed PCR fragment: 346bp. Size Δ fragment: 246bp.
- https://cdn.elifesciences.org/articles/78738/elife-78738-fig3-figsupp1-data1-v1.tiff
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Figure 3—figure supplement 1—source data 2
Raw, uncropped agarose gel picture showing Ncor1 deletion PCR indicating Ncor1 deletion.
Representative agarose gel picture showing Ncor1 deletion PCR results in wild-type (WT) tail samples and FACS-sorted WT CD4+ splenocytes (left panel), TCRß+, CD8+, CD4+YFP–, and CD4+YFP+ cells isolated from the spleen of NCOR1-cKOFoxp3 mice (middle panel) and CD4+YFP– and CD4+YFP+ cells isolated from the thymus (right panel) of NCOR1-cKOFoxp3 mice. Two mice were pooled for sorting. Size of floxed PCR fragment: 346bp. Size Δ fragment: 246bp. The black rectangle framed section in the blot shows the cropped area of the final picture in Figure 3—figure supplement 1. Band sizes are indicated on the left side of the picture. Floxed/ delta fragments are indicated on the right side of the picture. The samples are indicated in the lower part of the picture.
- https://cdn.elifesciences.org/articles/78738/elife-78738-fig3-figsupp1-data2-v1.pdf
Figure 4 with 1 supplement
NCOR1 is essential for Treg cell-mediated protection in adoptive CD4+ T cell transfer colitis.
(a) Experimental protocol for adoptive transfer colitis. Control groups received naïve CD4+ T cells only or no cells at all (not shown). (b) Weight scores in percentages of initial body weight …
Figure 4—figure supplement 1
In vitro characterization of wild-type (WT) and NCOR1-cKO Treg cells.
(a) Flow cytometric analysis of splenocytes isolated from WT and NCOR1-cKO mice showing expression of TGFβ in CD4+FOXP3+ Treg cells after stimulation with PMA/ ionomycin for 4hr. (b) Summary showing …
Figure 5 with 1 supplement
Similar frequencies and numbers of wild-type (WT) and NCOR1-cKO Treg cells within small intestinal intraepithelial lymphocyte (SI-IEL) and lamina propria cell (SI-LP) populations in adoptive CD4+ T cell transfer colitis.
(a) Flow cytometric analysis of SI-LP cells isolated from recipient Rag2–/– mice injected with WT CD45.1+CD4+ T cells only (top panel) or with WT CD45.1+CD4+ T cells together with either WT (middle …
Figure 5—figure supplement 1
IFNγ and IL17A expression in CD4+ T cells co-transferred with either wild-type (WT) of NCOR1-cKO Treg cells.
(a) Flow cytometric analysis showing IFNγ and IL17A expression in CD45.1+ CD4+ T cells isolated from small intestinal intraepithelial lymphocytes (SI-IEL), small intestinal lamina propria cells …
Figure 6 with 1 supplement
NCOR1 controls transcriptional states in naïve and effector Treg cells.
(a) Contour plots show the gating strategy for the isolation of Treg cells for RNA-sequencing. Cells from spleen and lymph nodes of WT.DEREG and NCOR1-cKO.DEREG mice were isolated and EGFP+ (i.e. …
Figure 6—figure supplement 1
Deletion of NCOR1 leads to an upregulation of cholesterol pathways.
(a) Diagram showing top five pathways which are up- or downregulated in naïve (left) and effector (right) NCOR1-cKO Treg cells, as revealed by Ingenuity Pathway Analysis (QIAGEN Inc). The lower …
Figure 7 with 4 supplements
NCOR1 controls the ratio of naïve to effector Treg cells in an LXRß-independent manner.
(a) Contour plots show FOXP3 and CD4 expression in splenic TCRβ+CD4+ cells of mice of the indicated genotype. (b) Percentages of FOXP3+ CD4+ T cells of all mice analyzed as described in (a). (c) …
Figure 7—figure supplement 1
LXRβ agonist-treatment of WT iTreg cells leads to a small increase in CD44hi Treg cells.
(a) Summary showing the expression levels (values shown as fragments per kilobase of transcript per million mapped reads; FPKM) of Nr1h3 (LXRα) and Nr1h2 (LXRβ) in naïve and effector WT and …
Figure 7—figure supplement 2
Phenotypic characterization of NCOR1/LXRß-cDKO mice.
(a) Contour plots show TCRß expression on and cell size (forward-scatter; FSC) of splenocytes from mice of the indicated genotype. (b) Diagram indicates the frequency of TCRß+ cells as well as of …
Figure 7—figure supplement 3
MYC protein expression levels in NCOR1-cKO, LXRβ-cKO and NCOR1-LXRβ-cDKO Treg cell subsets and in human NCOR1-knockout CD4+ T cells cultured under iTreg cell differentiation conditions.
(a) Diagram indicates MYC expression levels (geometric mean fluorescence intensity; gMFI) in naïve (CD44loCD62+) and effector (CD44hiCD62L–) Treg cells of the indicated genotype. For gMFI …
Figure 7—figure supplement 4
NCOR1 positively regulates FOXP3+ Treg cell differentiation and controls naïve and effector Treg cell subset integrity.
NCOR1 promotes FOXP3+ Treg differentiation, since Treg cell frequencies within the CD4+ T cell population are decreased in the absence of NCOR1. In contrast, LXRß restrains Treg cell …
Author response image 1
(a) Flow cytometry analysis of CD4 and CD11c expression in co-cultures of splenic dendritic cells (DCs) with either WT of NCOR1-cKO Treg cells after 24 hours.
DC and Treg cells were cocultured in the presence of anti-CD3. (b) Flow cytometry analysis of CD80, CD86 and MHCII expression in DCs from co-cultures as described in (a). The 1st row displays DC …
Author response image 2
Summary showing the expression levels (values showing as fragments per kilobase of transcript per million mapped reads; FPKM) of the indicated genes in naive and effector WT and NCOR1-cKO Treg cells as determined by RNA-seq.
Each bar represents 3 mice per group. Mean ±}SD is shown. *P <0.05, **P < 0.01, and ***P < 0.001 (unpaired 2-tailed Student’s t test).
Author response image 3
Summary showing the expression levels (values showing as fragments per kilobase of transcript per million mapped reads; FPKM) of the indicated genes in naïve and effector WT and NCOR1cKO Treg cells as determined by RNA-seq.
Each symbol represents one sample (2 mice per sample, 3 independent sample preparations steps).
Additional files
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Supplementary file 1
Bioinformatic analysis tables of WT and NCOR1-cKO Treg cells.
(a) List of differentially expressed genes (DEG) between NCOR1-cKO and WT naive Treg cells. FDR <0.05. (b) DEG between NCOR1-cKO and WT effector Treg cells. FDR <0.05. (c). Gene Set Enrichment Analysis (GSEA) hallmark gene sets enriched between NCOR1-cKO and WT naïve Treg cells. (d) GSEA hallmark gene sets enriched between NCOR1-cKO and WT effector Treg cells. (e) Top 50 Canonical Pathways (identified by Ingenuity Pathways Analysis) between NCOR1-cKO and WT naive Treg cells. (f) Top 50 Canonical Pathways (identified by Ingenuity Pathways Analysis) between NCOR1-cKO and WT effector Treg cells. (g) Naive and effector Treg cell gene sets. The lists show the 100 most DEG between naive and effector WT Treg cells.
- https://cdn.elifesciences.org/articles/78738/elife-78738-supp1-v1.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/78738/elife-78738-mdarchecklist1-v1.docx
