Silencing of the DNA mismatch repair gene MLH1 induced by hypoxic stress in a pathway dependent on the histone demethylase LSD1

Abstract

Silencing of MLH1 is frequently seen in sporadic colorectal cancers. We show here that hypoxia causes decreased histone H3 lysine 4 (H3K4) methylation at the MLH1 promoter via the action of the H3K4 demethylases LSD1 and PLU-1 and promotes durable long-term silencing in a pathway that requires LSD1. Knockdown of LSD1 or its corepressor, CoREST, also prevents the resilencing (and associated cytosine DNA methylation) of the endogenous MLH1 promoter in RKO colon cancer cells following transient reactivation by treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-aza-dC). The results demonstrate that hypoxia is a driving force for silencing of MLH1 and that the LSD1/CoREST complex is necessary for this process. The results reveal a mechanism by which hypoxia promotes cancer cell evolution to drive malignant progression through epigenetic modulation. Our findings suggest that LSD1/CoREST acts as a colon cancer oncogene by epigenetically silencing MLH1 and also identify the LSD1/CoREST complex as a potential target for therapy.

Fig. 1. Hypoxia-induced histone modifications at the MLH1 promoter, accompanied by down-regulated MLH1 expression

MCF-7 cells were exposed to normoxia (N) or to hypoxia at 0.01% O₂ (H) for various times. Cells were collected for quantitative ChIP analyses using specific antibodies to determine H3K4 methylation levels and H3K9 acetylation and methylation levels at the MLH1 promoters. (A) Decreased H3K4 methylation levels at the MLH1 promoter in response to 48 h of hypoxia. Specific antibodies were used to determine specific H3K4 methylation forms. Relative promoter occupancies (% input) are shown with error bars based on standard errors (SEs) calculated from at least three replicates. The input signal is set as 100% (not depicted in graphs) for each assay. (B) Time-course assay of H3K4 methylation changes at the MLH1 promoter. MCF-7 cells placed under hypoxia were collected at the indicated times for qChIP analysis. Promoter occupancy levels are expressed as the fold change relative to normoxia, based on three independent ChIP assays, with error bars based on SEs. Significant differences were identified as p<0.05 (as indicated by *) or p<0.01 (as indicated by **) compared to normoxic levels. (C) Hypoxia increases H3K9 methylation and decreases H3K9 acetylation at the MLH1 promoter. qChIP analysis of H3K9 acetylation (left) and methylation (right) levels at the MLH1 promoter after 48 h normoxia or hypoxia exposure. Relative promoter occupancies (% input) are shown with error bars calculated as above. (D) Time course of hypoxia-induced H3K9 acetylation (left) and methylation (right) at the MLH1 promoter by qChIP analysis. MCF-7 cells were exposed to normoxia or hypoxia for the indicated times, and H3K9 acetylation and methylation levels at the MLH1 promoter were analyzed as above. (E) Time-course of MLH1 expression at the protein level determined by western blot analysis in MCF-7 cells. Cells were exposed to normoxia (N) or hypoxia (H) for the indicated times, and were collected for western blot analysis. (F) Time-course of MLH1 mRNA expression by quantitative real-time PCR analysis (qRT-PCR). mRNA levels are expressed as the fold change relative to those of the corresponding normoxic control cells at each time point.

Fig. 2. The histone demethylases, LSD1 and PLU-1, and the LSD1 partner CoREST, together mediate hypoxia-induced H3K4 demethylation at the MLH1 promoter

SW480 cells with LSD1 knockdown, with PLU-1 knockdown, or with double knockdown of both LSD1 and PLU-1 were established using lentiviral shRNAs constructs targeting LSD1 or PLU-1. Control cells were transduced with a lentiviral expression construct for a GFP shRNA. (A) Western blot analyses to determine LSD1 and PLU-1 expression levels in the SW480-GFPsh, SW480-LSD1sh, SW480-PLU-1sh and double knockdown SW480-LSD1-PLU-1sh cells under normoxic and hypoxic conditions. (B) qChIP analyses of H3K4 methylation levels at the MLH1 promoter following 48 h exposure to normoxia or hypoxia in SW480-GFPsh cells; SW480-LSD1sh cells; SW480-PLU-1sh cells; and double knockdown SW480-LSD1-PLU-1sh cells (indicated as SW-L1P2). Promoter occupancy levels are expressed as the fold change relative to the normoxic control SW480 GFPsh cells. Standard errors are indicated. (C). Quantitative real-time PCR analysis of MLH1 mRNA levels in SW480 GFPsh, SW480 LSD1sh, SW480 PLU-1sh and SW480 LSD1-PLU-1sh cells after 48 h of normoxic or hypoxic exposure. mRNA levels are expressed as the fold change relative to normoxic control SW480 GFPsh cells. (D). Western blot analysis of MLH1 protein levels in the same cell lines as in (C), above, after 48 h of normoxic or hypoxic exposure (E). CoREST also plays a role in hypoxia-induced H3K4 demethylation at the MLH1 promoter in SW480 cells. Quantification of ChIP analyses of H3K4 methylation levels at the MLH1 promoter following 48 h exposure to normoxia or hypoxia in the SW480 GFPsh cells compared to the SW480 CoRESTsh cells. Promoter occupancy levels are expressed as the fold change relative to the normoxic SW480 GFPsh cells, based on three independent ChIP assays with error bars based on SEs.

Fig. 3. Hypoxia induces silencing of the MLH1 promoter in a pathway dependent on LSD1

(A) Schematic of the MLH1-TK-Blast^R dNheI pDisplay construct used to select for clones undergoing MLH1 promoter silencing. (B) Frequency of ganciclovir (GCV)-resistant clones (indicative of silencing of MLH1-TK-Blast^R expression) following exposure of RKO cells to normoxia or hypoxia (1% O₂) for the indicated number of days. Selection in the presence of GCV was performed under normoxic conditions for 10 additional days. Error bars represent SEs from three replicates. (C) Image of representative cell culture wells showing differential GCV-resistant colony formation following growth in normoxia or hypoxia and subsequent GCV selection. (D) Treatment of MLH1-silenced clones with the DNA methylation inhibitor, 5-azadC, reactivates the silenced MLH1 promoters to yield GCV sensitivity (due to reactivated TK expression) and blasticidin resistance (due to Blast^R expression). GCV-resistant clones induced by hypoxia were pooled and treated with DMSO, 0.2 μm 5-aza-dC, or 0.3 μm 5-aza-dC for 48 h. Colony formation in the presence of GCV (blue bar) or blasticidin (red bar) was quantified relative to the DMSO control as shown. (E) Knockdown of LSD1 inhibits the hypoxia-induced silencing of the MLH1 promoter construct. RKO cells containing the MLH1- TK^R-Blast^R construct and expressing shRNA to either GFP or LSD1 were exposed to normoxia or 1% O₂ for 35 days and then selected in GCV for 10 additional days under normoxic conditions. The frequency of the resulting GCV resistant clones indicative of MLH1 promoter silencing is shown.

Fig. 4. LSD1 and CoREST are required for MLH1 re-silencing in RKO cells following reactivation by transient 5-aza-dC exposure

RKO GFPsh cells, RKO LSD1sh cells, RKO PLU-1sh cells and RKO CoRESTsh cells were treated with 5-aza-dC at 5 μm for 8 days. The cells were then placed in standard conditions for 42 additional days. MLH1 expression was analyzed at the indicated times. (A) Western blot analyses to determine MLH1 expression levels in RKO GFPsh cells, RKO LSD1sh cells, and RKO PLU-1sh immediately after 8 days of 5-azadC treatment (indicated as D-8) or after replacement in standard medium without of 5-aza-dC for 27 days (indicated as R-27), or 33 days (indicated as R-33) or 42 days (indicated as R-42). (B) Western blot analyses to determine MLH1 expression levels in RKO GFPsh cells, RKO CoRESTsh cells immediately after 5-aza-dC treatment for 8 days (indicated as D-8) or after replacement in standard medium for 15 days (indicated as R-15), 28 days (indicated as R-28) or 38 days (indicated as R-38). (C) Western blot analyses to determine LSD1 expression levels in RKO GFPsh, RKO LSD1sh, and RKO CoRESTsh cells. (D) Western blot analyses to determine CoREST expression levels in RKO GFPsh and RKO CoRESTsh cells.

Fig. 5. The histone demethylase, LSD1, mediates H3K4 demethylation at the MLH1 promoter during MLH1 silencing in RKO cells

RKO GFPsh and RKO LSD1sh cells were treated with 5-aza-dC at 5 μm for 8 days. The cells were then replaced in normal culture medium for 28 additional days. ChIP analyses were performed to determine H3K4 methylation and H3K9 acetylation levels at the MLH1 promoter at the indicated times. (A) Agarose gel image of ChIP analyses of H3K4 methylation and H3K9 acetylation levels at the MLH1 promoter following 8 days (D-8) of 5-aza-dC treatment in RKO GFPsh cells and RKO LSD1sh cells. PCR amplification products corresponding to the MLH1 promoter region are shown. (B) Quantification of H3K4 methylation and H3K9 acetylation levels by real-time PCR at the MLH1 promoter under the same conditions as in (A). Relative promoter occupancies (% input) are shown with error bars based on standard errors (SEs) calculated from at least three replicates. (C) Agarose gel image of ChIP analyses of H3K4 methylation and H3K9 acetylation levels at the MLH1 following 28 days recovery (R-28) after 5-aza-dC treatment in RKO GFPsh cell line versus RKO LSD1sh cell line. (D) Quantification of H3K4 methylation and H3K9 acetylation levels by real-time PCR at the MLH1 promoter in the same condition as (C).

Fig. 6. LSD1 and CoREST prevent MLH1 promoter re-methylation after cessation of 5-aza-dC treatment in RKO cells

RKO GFPsh, RKO LSD1sh, and RKO CoRESTsh cells were treated with 5-aza-dC at 5 μm for 8 days. Then cells were released from 5-aza-dC by placement in standard culture medium for 20 or 30 additional days. Real-time PCR to quantify DNA methylation levels at MLH1 promoter was performed using the Methylight assay. PMR (Percentage of Methylation Reference) value was used to quantify the methylation levels at MLH1 promoter. (A) Methylight analysis of DNA methylation levels in the MLH1 promoter in RKO-GFPsh cells immediately after 5-aza-dC treatment (indicated as D-8), 20 days post treatment (indicated as R20), or 30 days post treatment (indicated as R30). (B) Methylight analysis of DNA methylation levels at the MLH1 promoter in RKO-LSD1sh cells as above. (C) Methylight analysis of DNA methylation levels at the MLH1 promoter in RKO-CoRESTsh cells. (D) Graphical summary of the data in (A), (B), and (C).