Targeting the Y217C missense mutation at the mouse Trp53 locus.

(A) Targeting strategy. The wildtype (WT) Trp53 gene is within a 17 kb-long EcoRI (RI) fragment (black boxes are for coding sequences and white boxes for UTRs). The targeting construct contains: (1) a 1.5 kb-long 5’ homology region; (2) a Lox-Stop-Lox (LSL) cassette with a neomycin selection gene (Neo), four transcriptional stops (STOP) and an EcoRI site, flanked by LoxP sites (arrowheads); (3) p53 coding exons, including the Y217C (YC) missense mutation in exon 6 (asterisk) and an additional BanII site; (4) a 2.8 kb-long 3’ homology region; and (5) the diphteria α-toxin (DTA) gene for targeting enrichment. Proper recombinants with a Trp53LSL-Y217C allele, resulting from the described crossing-overs, were G418 resistant. They were identified by a 2.4 kb-long band after PCR with primers a and b, and confirmed by bands of 635 and 224 bp after PCR with primers c and d and BanII digestion. They were also verified by Southern blot with the indicated probe as containing a 10.5 kb EcoRI band. Two recombinant ES clones were injected into blastocysts to generate chimeras, and germline transmission was verified by genotyping with primers c and d and BanII digestion. Excision of the LSL cassette was performed in vivo, by breeding Trp53+/LSL-Y217C male mice with females carrying the PGK-Cre transgene, to obtain mice with a Trp53Y217C allele. (B-D) Screening of recombinant ES clones (+) by PCR with primers a and b (B); PCR with primers c and d then BanII digestion (C); Southern blot (D). (E) Genotyping of mouse embryonic fibroblasts (MEFs) from an intercross of Trp53+/Y217C mice, by PCR with primers c and d and BanII digestion. (F) Trp53Y217C sequence around codon 217. The introduced Y217C missense mutation and the silent mutation creating an additional BanII restriction site are highlighted (asterisks). (G) WT and Trp53Y217C/Y217C (YC/YC) MEFs express similar p53 mRNA levels. Total RNA was extracted, then p53 mRNAs were quantified by real-time qPCR, normalized to control mRNAs and the amount in WT cells was assigned the value of 1. Primer sequences are listed in Table S8.

Trp53Y217C/Y217C cells exhibit alterations in p53 abundance and subcellular localization, defective responses to DNA damage, and increased chromosomal instability.

(A) Increased p53 protein levels in Trp53Y217C/Y217C and Trp53+/Y217C MEFs. MEFs of the indicated genotypes were treated or not with 10 μM Nutlin 3a for 24 h, then protein extracts were immunoblotted with antibodies against Mdm2, p53, p21 and actin. (B) The transactivation of classical p53 target genes Cdkn1a/p21 and Mdm2 is impaired in Trp53Y217C/Y217C cells. WT, Trp53Y217C/Y217C and Trp53-/- MEFs were treated as in (A), then (top) mRNAs were quantified in 5-6 independent experiments using real-time PCR, with results normalized to control mRNAs and mean RNA amounts in unstressed WT cells assigned a value of 1; or (bottom) ChIP assays were performed at the Cdkn1a and Mdm2 promoters in 2-3 independent experiments with an antibody against p53 or rabbit IgG as a negative control. Immunoprecipitates were quantified using real-time PCR, normalized to data over an irrelevant region, and the amount in unstressed WT cells was assigned a value of 1. (C) Assessment of p53WT and p53Y217C subcellular localization by cellular fractionation. WT and Trp53Y217C/Y217C MEFs were treated or not with 1 μM doxorubicin (Doxo) for 24 hr, submitted to cellular fractionation, then protein extracts were immunoblotted with antibodies against p53 or the fraction controls Tubulin for cytoplasm (Cp.), Nup98 for nucleoplasm (Np.) and histone H3 for chromatin (χin). (D) Assessment of p53WT and p53Y217C subcellular localization by immunofluorescence. WT, Trp53Y217C/Y217C and Trp53-/- MEFs were treated with 10 μM Nutlin 3a for 24 h, then stained with antibodies against p53 (red) or actin (green) and DNA was counterstained with DAPI (blue). (E) Absence of a cell cycle arrest response in Trp53Y217C/Y217C MEFs. Asynchronous cell populations of Trp53+/+, Trp53Y217C/Y217C and Trp53-/- MEFs were analyzed 24 hr after 0, 3 or 12 Gy ɣ-irradiation. Results from 3 independent experiments. (F) Absence of a p53-dependent apoptotic response in Trp53Y217C/Y217C thymocytes. Age-matched mice of the indicated genotypes were left untreated or submitted to 10 Gy whole-body ɣ-irradiation then sacrificed after 4 hr and their thymocytes were stained with Annexin V-FITC and analyzed by FACS, in 2 independent experiments. (G) Increased chromosomal instability in Trp53Y217C/Y217C fibroblasts. Metaphase spreads were prepared from WT, Trp53Y217C/Y217C and Trp53-/- MEFs at passage 4, then aberrant metaphases (with chromosome breaks, radial chromosomes or DMs) were scored. Left: distribution of aberrant metaphases. Data from 110 WT, 97 Trp53Y217C/Y217C or 119 Trp53-/- complete diploid metaphases, independently observed by two experimenters. Right: examples of two aberrant Trp53Y217C/Y217C metaphases: one with a double minute chromosome (DM), a chromosome break (Br) and a radial chromosome (R), the other with multiple DMs. Enlargements of regions of interest are presented between the two metaphases. Scale bars (D, G): 5 μm. ***P<0.001, **P<0.01, *P<0.05, °P=0.09, ns: non-significant by Student’s t (B, E, F) or Fischer’s (G) tests.

Trp53Y217C/Y217C mice exhibit female-specific perinatal lethality.

(A) Distribution of weaned mice obtained from Trp53+/- or Trp53+/Y217C intercrosses. Obs: observed numbers of mice at weaning (P21); exp: expected numbers assuming a Mendelian distribution without sex distortion; f/m: observed female/male ratios. Consistent with previous reports, the observed distribution of weaned mice from Trp53+/- intercrosses did not conform to values expected for a Mendelian distribution without sex distortion (υ=5; χ2=16.31>15.09), indicating a significant deficit in female Trp53-/- mice (top). The distribution of weaned mice from Trp53+/Y217C intercrosses diverged even more from values for a Mendelian distribution without sex distortion (υ =5; χ2=104.23>15.09), due to a striking deficit in female Trp53Y217C/Y217C mice (bottom). Differences between the frequencies of Trp53Y217C/Y217C (4/677) and Trp53-/- (8/196) females in the progeny, or between the female to male ratios for Trp53Y217C/Y217C (4/75) and Trp53-/- (8/28) animals, are statistically significant (P=0.0012 and P=0.0087 in Fischer’s tests, respectively). (B) Exencephaly is frequently observed in p53Y217C/Y217C female embryos. Top: the distribution of E12.5-16.5 embryos from heterozygous (Trp53+/Y217C) intercrosses or heterozygous-homozygous (Trp53+/Y217C x Trp53Y217C/Y217C) crosses is shown. f or m exenc.: number of female or male embryos with exencephaly; o.a.: embryos with other abnormalities. Below, examples of female Trp53Y217C/Y217C embryos at E12.5, 13.5 and 16.5 exhibiting exencephaly (arrows) are each shown (center) together with a normal embryo from the same litter (bottom). (C) Distribution of mice at birth from the indicated crosses. Of note, out of five Trp53Y217C/Y217C females observed at birth, only one remained alive at weaning age. Thus, the female/male ratio for weaned Trp53Y217C/Y217C animals from these crosses was 1/22, a ratio similar to the one observed in A (4/75).

Oncogenic effects of the mutant protein in Trp53Y217C/Y217C male mice.

(A-B) In homozygous males, p53Y217C leads to accelerated tumor-induced death (A), and aggressive metastatic tumors (B); n=cohort size. (C) Hematoxylin and eosin (H&E) staining of sections from the lung (top) and spleen (bottom) of Trp53-/- and Trp53Y217C/Y217C male mice, showing metastases in Trp53Y217C/Y217C animals. Normal organ structures are shown, with “A” indicating pulmonary alveoli, and “WP” and “RP” standing for splenic white and red pulp, respectively. In the lung section of the Trp53Y217C/Y217C mouse, the rectangle indicates a lymphoma area. In the spleen section of the Trp53Y217C/Y217C mouse, the typical splenic structures are absent due to massive tissue homogenization of the spleen by lymphoma cells.

Evidence of inflammation in Trp53Y217C/Y217C mice.

(A-B) RNAseq analysis of thymi from Trp53Y217C/Y217C (n=3) and Trp53-/- (n=3) 8 weeks-old male mice. Volcano plot (A), with differentially expressed genes (DEGs), downregulated (blue) or upregulated (red) in Trp53Y217C/Y217C cells. Unsupervised clustering heat-map plot (B), with 192 DEGs ranked according to log2 fold changes. (C) Gene Ontology (GO) analysis of DEGs. Out of 192 DEGs, 141 are associated with at least one GO term, according to the Gene Ontology enRIchment anaLysis and visuaLizAtion tool (GOrilla). For each GO term, enrichment was calculated by comparing with the full list of 19759 genes associated with a GO term, and results are presented here with a color scale according to P-value of enrichment. This analysis mainly revealed an enrichment for genes associated with white blood cell chemotaxis/migration and inflammation, as shown here. Complete results of the analysis are presented in Figure S11. (D) RT-qPCR analysis of the indicated genes in thymi from 8 weeks-old Trp53+/+, Trp53Y217C/Y217C and Trp53-/- male mice. Means + s.e.m. (n=3 per genotype). ***P<0.001, **P<0.01, *P<0.05, °P<0.075 by Student’s t test. (E) Gene set enrichment analysis (GSEA) of transcriptomes from Trp53Y217C/Y217C and Trp53-/- thymic cells. GSEA identified 13 gene sets enriched in Trp53Y217C/Y217C cells with normalized enrichment scores (NES) > 2. Nominal p-values (NOM p-val) and false discovery rate q-values (FDR q-val) are indicated. (F) GSEA provides evidence of increased NC-NF-kB signaling in Trp53Y217C/Y217C male thymocytes. Results are presented as in E. (G) Supformin (LCC-12), an anti-inflammatory molecule, increases the female to male ratio in Trp53Y217C/Y217C weaned pups. Trp53+/Y217C females were mated with Trp53Y217C/Y217C males, then oral gavage of pregnant females with 5 mg/kg supformin was performed on the 10th and 11th days post-coitum, and their progeny was genotyped at weaning. The female to male (f/m) ratio for Trp53Y217C/Y217C weaned pups that were exposed to supformin in utero (+) was compared to the f/m ratios for Trp53-/- or Trp53Y217C/Y217C weaned pups never exposed to supformin (-). Exposure to supformin led to a five-fold increase in the proportion of Trp53Y217C/Y217C weaned females. **P<0.01, °P=0.056, ns: non-significant by Fischer’s test.

Protein sequence alignment showing homology between mouse p53 Tyrosine 217 and human p53 Tyrosine 220.

Portions of the DNA binding domains from the mouse (residues 208-228) and human (residues 211-231) p53 proteins are shown, with identical residues in bold, and mouse Tyrosine 217 and human Tyrosine 220 in red.

Uncropped images of the western blot presented in Figure 2A.

All images are from the same blot, cut in two below the 35 kDa marker before incubation with the indicated antibodies.

Uncropped images of the fractionation assays presented in Figure 2C.

Chemiluminescence and colorimetric scans obtained with a ChemiDoc imaging system (Bio-Rad) were superposed to show the entire membranes, ladder lanes (λ), and chemiluminescence signals from subcellular fractions.

Cell cycle arrest responses of Trp53+/+, Trp53Y217C/Y217C and Trp53-/- mouse embryonic fibroblasts.

Asynchronous MEFs were exposed to 0-12 Gy ɣ-irradiation, then after 24 hr cells were labelled with BrdU for 1 hr and analyzed by FACS. A typical experiment for cells of each genotype and condition is shown, with % cells in G1, S or G2/M mentioned in each panel.

Apoptotic responses of Trp53+/+, Trp53-/- and Trp53Y217C/Y217C thymocytes.

Mice were ɣ-irradiated (or not) and their thymocytes were recovered and analyzed by FACS after annexin V-FITC staining. A typical experiment for cells of each genotype and condition is shown. Numbers indicate % cells either alive (live), early apoptotic (early) or mid to late apoptotic (mid+late).

Comparison of stress responses in WT, Trp53+/Y217C and Trp53+/- cells.

(A) Transactivation of the classical p53 target genes Cdkn1a/p21, Mdm2 and Pmaip1/Noxa in response to Nutlin or Doxorubicin. WT, Trp53+/Y217C and Trp53+/- MEFs were treated or not with 10 μM Nutlin 3a (Nut) or 1 μM Doxorubicin (Doxo) for 24 h, then mRNAs were quantified in ≥ 4 independent experiments using real-time PCR, with results normalized to control mRNAs and mean RNA amounts in unstressed WT cells assigned a value of 1. For each condition and gene, a DNE would lead to significant decrease in transactivation in Trp53+/Y217C MEFs compared to both WT and Trp53+/- MEFs, a result that was not observed. (B) Cell cycle arrest responses to ɣ-irradiation. Asynchronous cell populations of WT, Trp53+/Y217C and Trp53+/- MEFs were analyzed 24 hr after 0, 3 or 12 Gy ɣ-irradiation, in 3 independent experiments. The comparison of cells submitted to identical irradiation doses revealed similar arrest responses in cells of all genotypes. (C) Apoptotic responses to ɣ-irradiation. WT, Trp53+/Y217C and Trp53+/- MEFs age-matched mice were left untreated or submitted to 10 Gy whole-body ɣ-irradiation, then sacrificed after 4 hr and their thymocytes were stained with Annexin V-FITC and analyzed by FACS, in 2 independent experiments. The percentage of apoptotic cells was significantly higher in irradiated WT thymocytes compared to irradiated Trp53+/Y217C or Trp53+/- cells, whereas Trp53+/Y217C and Trp53+/- cells were not significantly different. **P<0.01, *P<0.05, ns: non-significant by Student’s t test.

Evidence of aberrant chromosome X inactivation in Trp53Y217C/Y217C and Trp53-/- female embryos.

The expression of Xist and 3 X-linked genes (Maob, Usp9x and Pls3) was quantified in neurospheres from 2 Trp53+/+, 5 Trp53Y217C/Y217C and 3 Trp53-/- female embryos by using real-time PCR, with results normalized to control mRNAs and mean RNA amounts in WT neurospheres assigned a value of 1. *P<0.05, °P=0.09, ns: non-significant by Student’s t tests.

Trp53+/Y217C and Trp53+/- mice exhibit similar tumor onset and spectra.

No significant difference was observed between heterozygous Trp53+/- and Trp53+/Y217C mice, neither in spontaneous tumor onset and survival (A), nor in tumor spectra (B); n=cohort size. Mice of both sexes were included in this study.

Example of a Trp53Y217C/Y217C mouse with a thymic lymphoma and lymphomatous infiltrates in the liver and kidney.

H&E staining of sections from the thymus (top), liver (middle) and kidney (bottom) of a Trp53Y217C/Y217C male mouse, showing tumor lymphocytes (TL) in the thymus and lymphocyte infiltrates (LI) in the liver and kidney, near blood vessels (BV). Hepatocytes (H), kidney tubules (TB) and a glomerulus (G) are also indicated.

RNA-seq analysis from the thymi of 8 weeks-old Trp53+/+, Trp53Y217C/Y217C and Trp53-/- male mice.

(A) Heat-Map plot, with 717 differentially expressed genes suggestive of a loss of function (LOF), a separation of function (SOF) or a gain of function (GOF) for the p53Y217C mutant, ranked according to log2 fold change (n=number of genes). (B) Evidence of LOF in Trp53Y217C/Y217C cells for genes encoding Puma, p21 and Zmat3. Data from 3 mice per genotype. ***P<0.001, **P<0.01, *P<0.05, °P=0.07, ns: non-significant by Student’s t tests.

Gene ontology analysis of differentially expressed genes.

The 192 differentially expressed genes (DEGs) between Trp53-/- and Trp53Y217C/Y217C thymocytes (Fig. 5A) were analyzed with the Gene Ontology enRIchment anaLysis and visuaLizAtion tool (GOrilla). Out of 192 genes, 141 were associated with a GO term. For each GO term, enrichment was calculated by comparing with the full list of 19759 genes associated with a GO term. For example, genes with GO term #0071621 (granulocyte chemotaxis) represent 79/19759 genes associated with a GO term, but 8/141 of the identified DEGs, which represents a 14.19-fold enrichment.

Gene set enrichment analysis (GSEA) of transcriptomes from Trp53Y217C/Y217C (Y220C) and Trp53-/- (KO) thymic cells: examples of GSEA enrichment plots.

Examples of GSEA enrichment plots indicating differences in immune responses (A), mitochondrial function (B) and chromatin plasticity (C) are shown.

GSEA enrichment plot showing increased NC-NF-kB signaling in Trp53Y217C/Y217C cells.

Transcriptomes from Trp53Y217C/Y217C (Y220C) and Trp53-/- (KO) thymic cells were compared by Gene Set Enrichment Analysis.

Viability of Mdm2 or Mdm4 loss in a Trp53Y217C/Y217C background.

Mouse distributions from the indicated crosses were determined at weaning. As for Trp53+/Y217C intercrosses, these crosses yielded a deficit in weaned Trp53Y217C/Y217C females compared to Trp53Y217C/Y217C males (4/75 from Trp53+/Y217C intercrosses (Figure 3A); 0/9 from crosses between Mdm4+/- Trp53+/Y217C and Mdm4+/- Trp53Y217C/Y217C mice; and 0/5 from mating Mdm2+/- Trp53+/Y217C mice with Mdm2+/- Trp53Y217C/Y217C or Mdm2-/- Trp53Y217C/Y217C animals). Trp53Y217C/Y217C females over Mdm4 or Mdm2 deficient or haplo-insufficient backgrounds were also less frequent than their male counterparts, but the female/male ratio for Trp53Y217C/Y217C mice over a Mdm4+/- background (4/15) was significantly increased (P=0.04 when 4/75 and 4/15 ratios are compared in a Fischer’s test). Whether or not the female/male ratios for Trp53Y217C/Y217C mice were significantly increased over Mdm4-/- (1/6), Mdm2-/- (1/11) or Mdm2+/- (1/11) backgrounds remained uncertain due to limited animal numbers.

Evidence of dystocia in pregnant Trp53Y217C/Y217C females.

Results of the mating of two (a and b) Trp53 Y217C/Y217C females (F) with a Trp53+/Y217C male (M) are shown. Both females were rapidly pregnant after encountering a male, but had to be sacrificed due to extended labor and pain during their first (female a) or third (female b) delivery.

Differentially expressed genes between WT, Trp53Y217C/Y217C (YC) and Trp53-/- (KO) thymocytes from age-matched animals.

Most differentially expressed genes correspond to a loss of function (LOF) in the p53Y217C mutant (categories 1 and 2, see Figure S10A), but genes corresponding to a separation of function (SOF, categories 3 and 4) or a gain of function (GOF, categories 5 and 6) were also observed.

A De-Seq analysis of RNA seq data from Trp53-/- (KO) and Trp53Y217C/Y217C (YC) thymi revealed 192 differentially expressed genes.

As shown in Figure 5B, 107 genes (in bold) were less expressed and 85 genes were more expressed in Trp53Y217C/Y217C cells compared to Trp53-/- cells.

Ccl17, Ccl9, Ccr3, Cxcl10, S100a8 and S100a9 are associated with GO terms of white blood cell migration/chemotaxis and inflammation.

Distribution of weaned pups after mating Trp53+/Y217C females with Trp53Y217C/Y217C males and oral gavage of pregnant females with supformin.

Due to the gavage of pregnant mothers, all the pups born in this experiment were exposed to supformin in utero (SIU+).

Effects of the Trp53Y217C mutation: a summary.

The comparison between Trp53-/- and Trp53Y217C/Y217C mice is presented. The phenotypes observed in Trp53-/- male (M) and female (F) mice result from p53 loss of function (LOF), whereas those observed in Trp53Y217C/Y217C mice result from p53 LOF as well as additional effects (gain of function (GOF) in red). The + signs denote the presence of a phenotype. Xi: X chromosome inactivation.

Primers used in this study.