Loss of Dnmt3a and Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR-γ
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Spain
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Spain
- Universitat Pompeu Fabra, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Spain
Figures
Figure 1 with 1 supplement
Dnmt3a loss shortens the onset of carcinogen-induced skin neoplasia, and increases tumor burden.
(A) Representative pictures of wild-type and Dnmt3a-cKO animals after 5 months of treatment with DMBA/TPA. Graph in panel A represents the percentage of animals WT (n = 6) or Dnmt3a-cKO (n = 6) that …
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Figure 1—source data 1
Data related to Figure 1B and Figure 1C.
Data showing the days from the DMBA/TPA treatment to the appearance of the first tumors in each wild type and Dnmt3a-cKO mouse (Figure 1B). Data showing the number of tumors counted on the backskin of the wild type and Dnmt3a-cKO after three or 6 months of DMBA/TPA treatment.
- https://doi.org/10.7554/eLife.21697.004
Figure 1—figure supplement 1
Dnmt3a is highly expressed in the basal cells of the interfollicular epidermis (IFE), and in the bulge of hair follicles in young mice.
(A–B) Immunofluorescence staining for Dnmt3a, Keratin 14 and Nuclei of wild type back skin (A) and tail skin (B) isolated at different ages. (C) Fpkm values of the Dnmts from RNA-seq data performed …
Figure 2 with 6 supplements
Dnmt3a and Dnmt3b double cKO animals develop more aggressive tumors than wild-type, Dnmt3a-cKO and Dnmt3b-cKO mice.
(A) Left, representative images (hematoxylin/eosin staining) of skin tumors isolated from wild type and Dnmt3b-cKO littermates after 6 months of DMBA/TPA treatment. Right, time of appearance of …
Figure 2—figure supplement 1
Deletion of Dnmt3b does not affect epidermal and hair follicle homeostasis.
Representative images (hematoxylin/eosin staining) of back skin and tail skin from wild type and Dnmt3b-cKO littermates at different ages.
Figure 2—figure supplement 2
Dnmt3b-KO and wild-type skin tumors are histologically indistinguishable.
Representative images (hematoxylin/eosin staining) of different skin tumors isolated from wild type and Dnmt3b-cKO after 6 months of DMBA/TPA treatment.
Figure 2—figure supplement 3
Dnmt3b-KO tumors do not show changes in proliferation or apoptosis compared to their wild-type counterparts.
(A) Left- Representative images of immunohistochemistry staining against the cell proliferation marker KI67 in skin tumors isolated from wild type and Dnmt3b-cKO after 6 months of DMBA/TPA …
Figure 2—figure supplement 4
The combined deletion of Dnmt3a and Dnmt3b does not affect epidermal homeostasis.
(A) Representative images (hematoxylin/eosin staining) of back skin and tail skin from adult and aged wild type and DcKO littermates. (B) Immunofluorescence staining for 5-methylcytosine and Keratin …
Figure 2—figure supplement 5
Squamous cell carcinomas in Dnmt3a/Dnmt3b double KO mice express lower levels of epithelial markers compared to wilt-type tumors.
(A) Representative confocal images for E-Cadherin, Keratin 14 and DAPI in wild type, single Dnmt3a KO and double Dnmt3a/Dnmt3b KO squamous cell carcinomas. (B) Representative confocal images for …
Figure 2—figure supplement 6
The combined deletion of Dnmt3a and Dnmt3b favors the development of skin tumors with features of spindle cell carcinomas.
(A–B) Hematoxylin/eosin staining and confocal images of two different spindle cell carcinomas developed in two DcKO animals. Representative images of immunofluorescence staining to detect the …
Figure 3 with 4 supplements
Deletion of Dnmt3a results in increased tumor heterogeneity, and upregulation of genes related to lipid metabolism.
(A) Schematic representation of FACS sorting strategy to isolate both RNA and DNA from Itga6pos cells within the tumors. (B) Heatmaps representing gene expression (rlog transformed values) of the …
Figure 3—figure supplement 1
RNA samples submitted for sequencing were obtained from tumors scored predominantly as squamous cell carcinomas in wild-type and Dnmt3a-cKO mice.
(A) Hematoxylin/eosin staining from the four wild-type tumors used for RNA-seq. (B) Hematoxylin/eosin staining from the eight Dnmt3a-cKO tumors analyzed for RNA-seq. In A and B, immunofluorescence …
Figure 3—figure supplement 2
Loss of Dnmt3a results in a reduction of apoptosis in skin tumors.
(A) Representative images for TUNEL staining to detect apoptotic cells in skin tumors isolated from wild type and Dnmt3a-cKO animals. The right graph shows the quantification of the Tunel staining …
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Figure 3—figure supplement 2—Source Data 1
Data related to Figure 3—figure supplement 2A–B.
Number of apoptotic cells (expressed in percentage of TUNEL or CASPASE-3 positive cells/DAPI positive cells) in wild-type and Dnmt3a-cKO tumors.
- https://doi.org/10.7554/eLife.21697.016
Figure 3—figure supplement 3
DMBA/TPA treatment induces an increase in cellular cell proliferation in Dnmt3a-cKO animals.
(A) Representative images of KI67 staining in treated or untreated back skin, and in skin tumors, of Dnmt3a-cKO and wild-type littermates. (B) Quantification of KI67 staining using the TMarker …
Figure 3—figure supplement 4
Dnmt3a-KO tumors express high levels of PPAR-γ.
(A) CPM (Count per Million Read) values of the mRNA encoding for PPAR-γ obtained from the RNA-sequencing of the 12 tumors studied. (B) Representative immunofluorescence staining for DAPI, PPAR-γ and …
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Figure 3—figure supplement 4—Source Data 1
Data related to Figure 3—figure supplement 4B.
Number of proliferative cells (expressed as the percentage of KI67+/all nuclei) in the untreated epidermis, DMBA-treated epidermis, and in the tumors, from wild-type and Dnmt3a-cKO mice.
- https://doi.org/10.7554/eLife.21697.019
Figure 4 with 1 supplement
Dnmt3a binds a subset of enhancers in tumor cells.
(A) Schematic representation of a short treatment of DMBA/TPA in wild-type and Dnmt3a-cKO animals. (B) Genomic localizations of Dnmt3a determined by ChIP-seq of Dnmt3a in epidermal cells isolated …
Figure 4—figure supplement 1
Deletion of Dnmt3a alters the expression of genes involved in proliferation, lipid metabolism, epidermal differentiation, and Wnt signaling, after 6 weeks of DMBA/TPA treatment.
(A) Left panel, heatmaps representing gene expression (rlog transformed values) of the 498 genes in sorted bulge hair follicle stem cells (Bulge) (Itga6bright/CD34pos) that were differentially …
Figure 5 with 1 supplement
Depletion of Dnmt3a leads to loss of DNA methylation and hydroxymethylation around its target enhancers.
(A) Relative methylation score (CpG count) measured around 363 enhancers bound by Dnmt3a (–5 kb, +5 kb) from independent biological replicates of FACS sorted tumor cells from wild type (n = 2) and …
Figure 5—figure supplement 1
MeDIP-seq and hMeDIP-seq analysis from sorted tumor cells.
(A) CpG count reads versus theoretical distribution in MeDIP and hMeDIP samples from wild type and Dnmt3a-cKO tumors. (B) MeDIP-seq signals around active and non-active TSSs in wild-type Itga6bright …
Figure 6
Dnmt3a binds and methylates a subset of promoters of genes involved in lipid metabolism in DMBA/TPA-treated epidermal cells.
(A) Relative methylation score (CpG count) measured around active and silenced promoters bound by Dnmt3a (–5 kb, +5 kb) from independent biological replicates of FACS-sorted tumor cells from wild …
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Figure 6—source data 1
Data related to Figure 6G.
RNA-sequencing CPM values (Counts por Million Reads) of Pparg expression in the DMBA/TPA epidermis and in the tumors from wild-type and Dnmt3a-cKO mice.
- https://doi.org/10.7554/eLife.21697.025
Figure 7 with 1 supplement
PPAR-γ inhibition revert the tumor initiation phenotype of the Dnmt3a-cKO.
(A) Schematic representation of the DMBA/TPA orthotopic treatment together PPAR-γ inhibitor (Sigma GW9662) treatment onto wild-type and Dnmt3a-cKO animals. (B) Time of appearance, expressed in …
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Figure 7—source data 1
Data related to Figure 7C.
Data showing the number of tumors counted on the backskin of the wild-type and Dnmt3a-cKO mice after 120 days of DMBA/TPA plus vehicle or plus GW9662 (PPAR-G inhibitor).
- https://doi.org/10.7554/eLife.21697.027
Figure 7—figure supplement 1
The mRNA of Dnmt3a is downregulated in human cutaneous squamous cell carcinomas compared to normal human epidermis.
MRNA expression of Dnmt3a in human healthy epidermis compared to actinic keratoses and Squamous Cell Carcinomas (SCC) quantified using GEO2R platform of the published databases (GSE2503, GSE42677, …
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Figure 7—figure supplement 1—source data 1
Data related to Figure 7—figure supplement 1.
Dnmt3a mRNA expression obtained using the online platform GEO2R from four published datasets of human healthy epidermis, actinic keratosis and squamous cell carcinomas samples.
- https://doi.org/10.7554/eLife.21697.029
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Additional files
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Supplementary file 1
This file contains information related to Figure 3.
It shows the fold change difference of all RefSeq genes between Dnmt3a-cKO and wild type tumors in integrin alpha6-purified tumor cells. Please note that the negative values represent the genes that are expressed at higher levels in the Dnmt3a-cKO tumor cells.
- https://doi.org/10.7554/eLife.21697.030
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Supplementary file 2
This file contains information related to Figure 4 and Figure 4—figure supplement 1.
It shows the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values of all RefSeq genes obtained by RNA-sequencing in bulge cells (integrin alpha6bright/CD34+, BULGE) and interfollicular epidermis basal cells (integrin alpha6bright/CD34-, IFE) purified cells from Dnmt3a-cKO and wild type epidermis after 6 weeks of DMBA/TPA treatment.
- https://doi.org/10.7554/eLife.21697.031
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Supplementary file 3
This file contains information related to Figure 4, Figure 5 and Figure 6.
Spreadsheet1 contains the genomic coordinates and the related annotations of the Chip-Seq peaks of Dnmt3a in precancerous epidermis (after 6 weeks of DMBA/TPA treatment). Spreadsheet2 contains the list of genes bound at their promoter by Dnmt3a in precancerous epidermis. Spreadsheet3 contains the genomic coordinates of the active enhancers not bound by Dnmt3a in precancerous epidermis. Spreadsheet4 contains the genomic coordinates of the promoters not bound by Dnmt3a in precancerous epidermis. Spreadsheet5 contains the genomic coordinates of the active enhancers bound by Dnmt3a in precancerous epidermis.
- https://doi.org/10.7554/eLife.21697.032
