Regulation of Cellular Senescence by Polycomb Chromatin Modifiers through Distinct DNA Damage- and Histone Methylation-Dependent Pathways

Abstract

Polycomb group (PcG) factors maintain facultative heterochromatin and mediate many important developmental and differentiation processes. EZH2, a PcG histone H3 lysine-27 methyltransferase, is repressed in senescent cells. We show here that downregulation of EZH2 promotes senescence through two distinct mechanisms. First, depletion of EZH2 in proliferating cells rapidly initiates a DNA damage response prior to a reduction in the levels of H3K27me3 marks. Second, the eventual loss of H3K27me3 induces p16 (CDKN2A) gene expression independent of DNA damage and potently activates genes of the senescence-associated secretory phenotype (SASP). The progressive depletion of H3K27me3 marks can be viewed as a molecular "timer" to provide a window during which cells can repair DNA damage. EZH2 is regulated transcriptionally by WNT and MYC signaling and posttranslationally by DNA damage-triggered protein turnover. These mechanisms provide insights into the processes that generate senescent cells during aging.

Keywords: CDKN1A; CDKN2A; DNA damage response; Polycomb group; WNT pathway; cell cycle checkpoints; cellular senescence; chromatin; proinflammatory cytokines; senescence-associated secretory phenotype.

Figure 1. EZH2 Expression Decreases during Senescence, and Its Acute Downregulation Elicits Premature Senescence

(A) EZH2 mRNA levels were determined by real-time qPCR in early-passage proliferating and replicatively senescent cells of strains LF1, WI-38, and IMR90 (**p < 0.01, n = 3). (B) Early passage LF1 cells were infected with a lentivirus vector expressing HRAS(G12V) cDNA (or empty vector control), and expression of EZH2 mRNA was determined 6 days after infection. (**p < 0.01, n = 3). (C) Cells were irradiated with ionizing radiation (10 Gy) or treated with 200 ng/mL neocarzinostatin (NCS), and EZH2 mRNA levels were determined after 6 days (**p < 0.01, n = 3). (D) EZH2 protein levels and the presence of K27me3 marks on H3 were examined in LF1 cells by immunoblotting, from 18 population doublings before senescence until 8 weeks after the onset of senescence. EZH2 and H3K27me3 levels were normalized to GAPDH (green, red); H3K27me3 is also shown normalized to total H3 (blue). (E) Cells were infected with a lentivirus vector expressing shRNA 3 against EZH2 (Figure S1H). shRNA to GFP was the control. The levels of EZH2 and H3K27me3 were examined by immunoblotting. (F) EZH2 was knocked down as in (E), and proliferation was assessed by counting cell numbers (**p < 0.01, n = 3). (G) The presence of SAHF, SA-β-Gal activity, and EdU incorporation were determined 2 days after shEZH2 infection. SA-β-Gal or SAHF-positive cells were scored as percent of total cells in randomly selected fields (*p < 0.05, **p < 0.01, n = 3). (H) EZH2 was knocked down as in (E), and unsupervised hierarchical clustering of SASP gene Z scores from RNA-seq data is shown as heatmaps. Error bars represent SD. See also Figures S1 and S2 and Tables S1, S4, and S5.

Figure 2. Downregulation of EZH2 Induces DNA Damage and Senescence in a DNA Replication-Dependent Manner

(A) H3K27me3 enrichment at the CDKN2A locus was determined 4 and 8 days after shEZH2 infection using ChIP. For locations of primer pairs, see (B). Normal rabbit immunoglobulin G (IgG) was used as the immunoprecipitation (IP) control (**p < 0.01, n = 3). (B) Schematic of the CDKN2A locus. (C) The frequency of p21-expressing cells was scored by IF after knockdown of EZH2 (percent of total cells, random fields, more than 400 cells per condition, **p < 0.01). (D) The frequency of p16-expressing cells was determined as in (C) (*p < 0.05). (E) Early passage LF1 cells were grown in the presence of DZNep (5 μM), and the levels of p16, p21, and EZH2 proteins and H3K27me3 marks were examined by immunoblotting after 9 and 18 days of treatment. (F) p21 shRNAs or the empty vector were combined with an EZH2 shRNA (+) or a shGFP control (−), and SA-β-Gal-positive cells were scored 4 days after infection (*p < 0.05, **p < 0.01, n = 3). (G) 53BP1 foci were visualized by IF 4 and 8 days after EZH2 knockdown. The stacked bars depict the fraction of cells with 1 focus (blue) or 2 (red), 3 (green), and more than 4 (black) foci per nucleus (**p < 0.01, n = 4). (H) shATM and shEZH2 knockdowns were combined, and SA-β-Gal-positive cells were scored as in (F) (**p < 0.01, n = 3). (I) At the time of shEZH2 infection (time [t] = 0; Figure S1G), cells were reseeded into either normal medium (Pro, 15% FBS), quiescence-inducing medium (Qui, 0.25% FBS), or medium supplemented with thymidine (Thy). 53BP1 foci were scored after 4 days (**p < 0.01, n = 3). (J) EZH2 was knocked down as in (A), and cells were pulse-labeled with EdU for 1 hr 2 days after infection. A representative image showing colocalization of EdU (red) and 53BP1 (green) signals is shown. Right: magnified views of the indicated areas. Scale bar, 3 μm. Error bars represent SD. See also Figures S3 and S4 and Tables S1 and S2.

Figure 3. Inhibition of EZH2 Activity Induces Senescence in the Absence of DNA Damage by Depleting H3K27me3 Marks and Activating p16 and SASP Genes

(A) Early passage LF1 cells were grown continuously in the presence of GSK126, and levels of EZH2 protein and H3K27me3 marks were examined by immunoblotting. (B and C) Cells were treated with GSK126 as in (A), and proliferation (B) or SA-β-Gal staining (C) were determined (**p < 0.01, n = 3). (D and E) Cells were treated as in (A), and the frequency of p21-positive (D) and p16-positive (E) cells was scored by IF (percent of total cells, random fields, more than 400 cells per condition, *p < 0.05, **p < 0.01). (F) Cells were treated with GSK126 for 8 days and examined for 53BP1 foci as in Figure 2G (n = 3). (G) Cells were infected with lentivirus vectors expressing EZH2 cDNA, EZH2 with an in-frame deletion of the SET domain (EZH2ΔSET), or empty vector control, and expression of the indicated genes was determined by real-time qPCR 9 days after infection. Data are represented as heatmaps relative to control cells (n = 3). (H) Cells were treated with GSK126 (5 μM), JQ1 (100 nM), or both, and expression of the indicated genes was determined by real-time qPCR after 10 days. Data are represented as heatmaps relative to DMSO-treated cells (n = 3). (I) Cytokine array analysis of conditioned medium from cells treated with GSK126 (5 μM) or GSK126 plus JQ1 (100 nM) for 17 days. For comparison, cells were infected with shRNAs against EZH2 (shEZH2) or GFP (control [CTR]) for 8 days. IL1A and IL1B were secreted at undetectable levels, as reported previously (Orjalo et al., 2009), because they remain cell surface-associated. Data are represented as heatmaps relative to CTR (n = 2). See Table S3 for the measured cytokine concentrations. (J) Cells were treated with GSK126 (5 μM) or DMSO for 10 days, and H3K27me3 and H3K27ac enrichment at the IL1A-IL1B-IL37 loci was determined by ChIP-qPCR. Primer pairs were chosen in regions of putative enhancers, and their locations are shown in the schematic as red bars. H3K27ac and H3K4me1 tracks were obtained from ENCODE (GEO: GSM469966 and GSM521895). Normal rabbit IgG was used as the IP control (*p < 0.05, **p < 0.01, n = 3). Error bars represent SD. See also Figure S5 and Tables S1, S2, and S3.

Figure 4. Expression of EZH2 Opposes Entry into OIS and Induction of SASP

(A) LF1 cells were engineered using lentivirus vectors to stably express EZH2 cDNA and a 4-OHT-inducible ER:RAS(G12V) protein. Control cell lines were constructed using empty vectors. Cells were treated with 4-OHT (200 nM) or vehicle (ethanol) for the indicated times, and the levels of EZH2 and ER:RAS proteins were determined by immunoblotting. (B) Proliferation in the experiment shown in (A) was assessed by counting cell numbers (*p < 0.05, **p < 0.01, n = 3). (C) SA-β-Gal-positive cells were scored after 12 days of 4-OHT treatment in the experiment shown in (A) (**p < 0.01, n = 3). (D) p16 mRNA expression was determined by real-time qPCR as in (C) (**p < 0.01, n = 3). (E) Expression of the indicated SASP genes was determined by real-time qPCR as in (C) (*p < 0.05, **p < 0.01, n = 3). Error bars represent SD. See also Table S1.

Figure 5. DNA Damage-Mediated Degradation of EZH2

(A) LF1 cells were treated with etoposide (40 μM) for 8 hr and immunostained with antibodies to phospho-ATM (S1981, green) or EZH2 (red). Nuclei were counterstained with DAPI (blue). The same image is shown in the three channels. Scale bar, 10 μm. (B) Cells were treated with etoposide for 20 hr, stained as in (A), and scored for EZH2 intensity and the number of phospho-ATM (S1981) foci per nucleus (random fields, more than 200 cells per condition). (C) Cells were treated with etoposide (Eto) plus the ATM inhibitor KU-55933 (10 μM) or carrier (DMSO), and the levels of EZH2 protein were determined by immunoblotting. (D) Cells infected with lentivirus vectors expressing shRNA against ATM (or empty vector as control) were treated for 8 hr with etoposide (+) or DMSO vehicle (−). Cell lysates were immunoprecipitated with anti-EZH2 antibody, followed by immunoblotting analysis with anti-phospho-serine or anti-EZH2 antibodies. Aliquots of whole cell lysates (WCLs) were immunoblotted for GAPDH to verify equivalent total protein input. (E) Cells engineered using lentivirus vectors to stably express EZH2 or EZH2(S652A/S734A) mutant cDNAs were processed and analyzed as in (D). (F) EZH2 or EZH2(S652A/S734A) mutant cDNA-expressing cells were treated with etoposide and cycloheximide (CHX, 50 μg/mL), and the levels of EZH2 protein were determined by immunoblotting. (G) Cells were treated with etoposide in a time course, and the relative levels of EZH2 mRNA and EZH2 protein were determined by real-time qPCR and immunoblotting, respectively. The p values shown are pairwise comparisons with the zero time point (*p < 0.05, **p < 0.01, n = 3). Error bars represent SD. See also Figure S6 and Table S1.

Figure 6. EZH2 Is Required for Senescence Induced by Downregulation of WNT or MYC Signaling

(A) WNT2 and MYC mRNA levels were determined by real-time qPCR in early-passage proliferating and replicatively senescent (2 weeks, Figure 1D) LF1 fibroblasts (**p < 0.01, n = 3). (B) LF1 cells were infected with lentivirus vectors expressing shRNAs against WNT2 or MYC, and SA-β-Gal-positive cells were scored 4 days after infection. shGFP was used as the control (**p < 0.01, n = 3). (C) MYC enrichment at the promoter region of the EZH2 gene was determined by ChIP after knockdown of WNT2 or MYC as in (B). Locations of primer pairs are shown on the left. Normal rabbit IgG was used as the IP control (*p < 0.05, **p < 0.01, n = 3). (D) Cells were infected with shRNA (#1) targeting MYC as in (B), and the levels of MYC, EZH2, SUZ12, and EED proteins were determined by immunoblotting. (E) Cells were infected with shRNA (#1) against WNT2 as in (B), and the levels of active β-catenin (ABC), EZH2, SUZ12, and EED proteins were examined by immunoblotting. (F) Cells were infected with a lentivirus vector expressing MYC cDNA, and the levels of EZH2 and MYC proteins were determined by immunoblotting. Empty pLX vector (–) was used as the control. (G) Cells were treated for 8 days with the indicated concentrations of the GSK3 inhibitor CHIR99021, and the levels of EZH2 and ABC proteins were determined by immunoblotting. (H) Ectopic expression of EZH2 cDNA was combined with a shRNA knockdown of WNT2. Controls were empty pLX vector for EZH2 (–) and shGFP for WNT2. The levels of p16, p21, and EZH2 proteins were determined by immunoblotting. Note that, although endogenous EZH2 expression is effectively downregulated by shWNT2 (lane 3; see also E), ectopic expression is maintained by the pLX-EZH2 vector (lane 4). (I) p21 mRNA expression was determined by real-time qPCR in the experiment shown in (H) (*p < 0.05, n = 3). (J) The frequency of SA-β-Gal-positive cells was scored in the experiment shown in (H) (*p < 0.05, **p < 0.01, n = 3). (K) The double intervention shown in (H) was performed with MYC shRNA (instead of WNT2 shRNA), and the levels of p16, p21, and EZH2 proteins were examined. Note again that, although endogenous EZH2 expression is effectively downregulated by shMYC (lane 3; see also D), ectopic expression is maintained by the pLX-EZH2 vector (lane 4). (L) p21 mRNA expression was determined in the experiment shown in (K) (**p < 0.01, n = 3). (M) SA-β-Gal-positive cells were quantified in the experiment shown in (K). Error bars represent SD. See also Figure S6 and Tables S1 and S2.