The BRAF oncoprotein functions through the transcriptional repressor MAFG to mediate the CpG Island Methylator phenotype

Abstract

Most colorectal cancers (CRCs) containing activated BRAF (BRAF[V600E]) have a CpG island methylator phenotype (CIMP) characterized by aberrant hypermethylation of many genes, including the mismatch repair gene MLH1. MLH1 silencing results in microsatellite instability and a hypermutable phenotype. Through an RNAi screen, here we identify the transcriptional repressor MAFG as the pivotal factor required for MLH1 silencing and CIMP in CRCs containing BRAF(V600E). In BRAF-positive human CRC cell lines and tumors, MAFG is bound at the promoters of MLH1 and other CIMP genes, and recruits a corepressor complex that includes its heterodimeric partner BACH1, the chromatin remodeling factor CHD8, and the DNA methyltransferase DNMT3B, resulting in hypermethylation and transcriptional silencing. BRAF(V600E) increases BRAF/MEK/ERK signaling resulting in phosphorylation and elevated levels of MAFG, which drives DNA binding. Analysis of transcriptionally silenced CIMP genes in KRAS-positive CRCs indicates that different oncoproteins direct the assembly of distinct repressor complexes on common promoters.

Figure 1. An RNAi Screen to Identify Mediators of MLH1 Transcriptional Silencing

(A) Schematic of the shRNA screen. (B) qRT-PCR analysis monitoring MLH1 expression in parental RKO cells, or MLH1 and Blast^Rexpression in RKO/pMLH¹-Blast^R cells, following treatment with either DMSO or 5-aza-2’-deoxycytidine (5-AZA). The results were normalized to that observed upon DMSO treatment, which was set to 1. (C) Viability of RKO or RKO/pMLH1-Blast^R cells treated with DMSO or 5-AZA for 3 days and then 0, 1, 2 or 5 µM blasticidin for 6 days. Cells were stained with crystal violet. (D) Bisulfite sequencing analysis of the endogenous MLH1 promoter in parental RKO cells or the pMLH1-Blast^R reporter in RKO/pMLH1-Blast^R cells treated in the absence or presence of 5-AZA. (Top) Schematic of the MLH1 promoter; positions of CpGs are shown to scale by vertical lines. (Bottom) Each circle represents a methylated (black) or unmethylated (white) CpG dinucleotide. Each row represents a single clone. (E) qRT-PCR analysis monitoring MLH1 expression in RKO cells expressing a non-silencing (NS) shRNA or an shRNA against one of the 16 candidates. The results were normalized to that observed with the NS shRNA, which was set to 1. Data are represented as mean ± SD. *P ≤0.05, **P≤0.01. (F) Immunoblot analysis monitoring MLH1 levels in RKO cells upon knockdown of each of the 16 candidates. α-tubulin (TUBA) was monitored as a loading control. See also Figure S1.

Figure 2. A MAFG-Directed Corepressor Complex Mediates MLH1 Transcriptional Silencing

(A) qRT-PCR analysis monitoring MLH1 expression in RKO cells expressing a NS, BACH1, BACH2 or NFE2L1 shRNA. (B) qRT-PCR analysis monitoring MLH1 expression in RKO cells expressing a NS, DNMT1, DNMT3A or DNMT3B shRNA. (C) Bisulfite sequencing analysis of the MLH1 promoter in RKO cells expressing a NS, MAFG, BACH1, CHD8 or DNMT3B shRNA. Decreased promoter methylation in the presence of 5-AZA is shown as a control. (D) ChIP analysis monitoring binding of MAFG, BACH1, CHD8 and DNMT3B to the MLH1 promoter or, as a control, an irrelevant DNA region (negative control [NC] DNA) in RKO cells. The results were normalized to that obtained with IgG, which was set to 1. (E) ChIP analysis monitoring binding of MAFG, BACH1, CHD8 and DNMT3B to the MLH1 promoter in RKO cells expressing a NS, MAFG, BACH1, CHD8 or DNMT3B shRNA. Data are represented as mean ± SD. *P≤0.05, **P≤0.01. (F) Co-immunoprecipitation analysis. RKO cell extracts were immunoprecipitated with a MAFG, BACH1, CHD8, DNMT3B or control (IgG) antibody, and the immunoprecipitate was analyzed for MAFG, BACH1, CHD8 or DNMT3B by immunoblotting. See also Figure S2.

Figure 3. BRAF(V600E)-Mediated Upregulation of MAFG is Required for Transcriptional Silencing of MLH1

(A) qRT-PCR analysis monitoring MLH1 expression in RKO cells following treatment with PLX4720 or U0126. (B) Immunoblot analysis monitoring MLH1, MAFG, phosphorylated ERK1/2 (p-ERK1/2) and total ERK1/2 (t-ERK1/2) levels in RKO cells treated with DMSO, PLX4720 or U0126. (C) qRT-PCR analysis monitoring MLH1 expression in RKO cells expressing a NS or BRAF shRNA. (D) Bisulfite sequencing analysis of the MLH1 promoter in RKO cells expressing a NS or BRAF shRNA. (E) Immunoblot analysis monitoring MLH1, MAFG, p-ERK1/2 and t-ERK1/2 levels in PFFs expressing BRAF(V600E) or MAFG. (F) qRT-PCR analysis monitoring MLH1 expression in PFFs expressing BRAF(V600E) or MAFG. The results were normalized to that obtained with a vector control, which was set to 1. (G) qRT-PCR analysis monitoring MAFG expression in PFFs expressing BRAF(V600E) or MAFG. (H) Immunoblot analysis showing MAFG levels in RKO cells treated with 0–8 µM MG132 for 4 hours. (I) In vivo phosphorylation assay. 293T cells were transfected with myc-tagged MAFG-wild-type (WT), -T3A or -S124A in the presence or absence of an ERK1-expression plasmid. Cell lysate was immunoprecipitated with a myc antibody and immunoprecipitates were analyzed by immunoblotting with a phosphorylated-(S/T)P antibody. (J) RKO cells were transfected with myc-tagged MAFG-WT, -T3A or –S124A and treated in the presence or absence of PLX4720, and analyzed as described in (I). (K) In vitro kinase assay. GST-tagged MAFG-WT, -T3A or -S124A peptides were incubated in the presence or absence of ERK1 and γ-ATP and analyzed for incorporation of the radiolabel by autoradiography. (L) HA-ubiquitination pull-down assay. Extracts from RKO cells expressing HA-tagged ubiquitin and myc-tagged MAFG-WT, -T3A or -S124A and treated in the presence or absence of PLX4720 were immunoprecipitated using an HA antibody, and the immunoprecipitate was analyzed by immunoblotting using a myc antibody. (M) ChIP analysis monitoring binding of MAFG, BACH1, CHD8 and DNMT3B to the MLH1 promoter in RKO cells expressing a NS or BRAF shRNA or treated with DMSO, PLX4720 or U0126. Data are represented as mean ± SD. *P≤0.05, **P≤0.01. See also Figure S3.

Figure 4. Validation of the Role of MAFG and its Corepressors in MLH1 Silencing in Other CRC cell lines and BRAF-Positive Human Tumor Samples

(A) ChIP analysis monitoring binding of MAFG, BACH1, CHD8 and DNMT3B to the MLH1 promoter or, as a control, an irrelevant DNA region (NC DNA) in VACO432 cells. (B) qRT-PCR analysis monitoring MLH1 expression in VACO432 cells expressing an NS, MAFG, BACH1, CHD8 or DNMT3B shRNA. (C) qRT-PCR analysis monitoring MLH1 expression (left) or immunoblot analysis monitoring MLH1 levels (right) in VACO432 cells treated with DMSO or 1 or 5 µM PLX4720 or U0126. (D) ChIP analysis monitoring binding of MAFG, BACH1, CHD8 and DNMT3B to the MLH1 promoter or, as a control, an irrelevant DNA region (NC DNA) in SW48 cells. (E) qRT-PCR analysis monitoring MLH1 expression in SW48 cells expressing an NS, MAFG, BACH1, CHD8 or DNMT3B shRNA. (F) qRT-PCR analysis monitoring MLH1 expression (left) or immunoblot analysis monitoring MLH1 levels (right) in SW48 cells treated with DMSO or 1 or 5 µM gefitinib (Selleck) or U0126 for 24 hours. (G) PAT-ChIP analysis monitoring binding of MAFG to the MLH1 promoter in matched adjacent normal (N) and BRAF-positive CRC human tumor (T) samples. Data are represented as mean ± SD. *P≤0.05, **P≤0.01. (H) Immunoblot analysis monitoring MAFG levels in samples described in (G). See also Figure S4.

Figure 5. MAFG and its Corepressors Mediate CIMP in BRAF-Positive RKO Cells

(A and B) qRT-PCR analysis monitoring expression of CIMP genes in RKO cells expressing a MAFG or CHD8 shRNA (A) or a BACH1 or DNMT3B shRNA (B). The results were normalized to that obtained with the NS control, which was set to 1. (C) Bisulfite sequencing analysis of representative CIMP genes in RKO cells expressing a NS, MAFG, CHD8, BACH1 or DNMT3B shRNA. (D) ChIP analysis monitoring binding of MAFG, BACH1, CHD8 and DNMT3B on representative CIMP gene promoters in RKO cells. Data are represented as mean ± SD. *P≤0.05, **P≤0.01. See also Figure S5.

Figure 6. MAFG and its Corepressors Mediate CIMP in Other CRC Cell Lines and BRAF-Positive Human Tumor Samples

(A) ChIP analysis monitoring binding of MAFG, BACH1, CHD8 and DNMT3B to representative CIMP gene promoters in VACO432 (left) and SW48 (right) cells. (B) qRT-PCR analysis monitoring expression of representative CIMP genes in VACO432 (left) or SW48 (right) cells expressing a NS, MAFG, BACH1, CHD8 or DNMT3B shRNA. (C) PAT-ChIP analysis monitoring binding of MAFG to representative CIMP gene promoters in matched adjacent normal (N) and BRAF-positive CRC human tumor (T) samples. (D) Soft agar assay measuring colony formation of RKO cells expressing a NS, MAFG or CHD8 shRNA. (E) Tumor formation assay. RKO cells expressing a NS, MAFG or CHD8 shRNA were subcutaneously injected into the flanks of nude mice (n=3), and tumor formation was measured. Data are represented as mean ± SD. *P≤0.05, **P≤0.01. See also Figure S6.

Figure 7. Oncogenic BRAF and KRAS Direct the Assembly of Distinct Repressor Complexes on Common CIMP Gene Promoters

(A and B) qRT-PCR analysis monitoring CIMP gene expression in RKO (A) and DLD-1 (B) cells expressing a NS, MAFG, CHD8, ZNF304 or KAP1 shRNA. Comparable analysis of BACH1, DNMT3B, SETDB1 and DNMT1 shRNAs is shown in Figures S7B and S7D. (C and D) ChIP analysis monitoring binding of MAFG, CHD8, ZNF304 and KAP1 on CIMP gene promoters in RKO (C) and DLD-1 (D) cells. Comparable analysis of BACH1, DNMT3B, SETDB1 and DNMT1 is shown in Figures S7E and S7F. (E and F) ChIP analysis monitoring binding of DNMT3B to CIMP gene promoters in RKO cells (E) and binding of DNMT1 to CIMP gene promoters in DLD-1 cells (F) expressing a NS, MAFG, CHD8, ZNF304 or KAP1 shRNA. Comparable analysis of BACH1, DNMT3B, SETDB1 and DNMT1 is shown in Figures S7G and S7H. Data are represented as mean ± SD. *P≤0.05, **P≤0.01. (G) Model for BRAF(V600E)-directed recruitment of MAFG and its corepressors to MLH1 and CIMP gene promoters. See also Figure S7.