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. 2017 Oct 19;68(2):414-430.e8.
doi: 10.1016/j.molcel.2017.09.036.

Restoration of Replication Fork Stability in BRCA1- And BRCA2-Deficient Cells by Inactivation of SNF2-Family Fork Remodelers

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Free PMC article

Restoration of Replication Fork Stability in BRCA1- And BRCA2-Deficient Cells by Inactivation of SNF2-Family Fork Remodelers

Angelo Taglialatela et al. Mol Cell. .
Free PMC article

Abstract

To ensure the completion of DNA replication and maintenance of genome integrity, DNA repair factors protect stalled replication forks upon replication stress. Previous studies have identified a critical role for the tumor suppressors BRCA1 and BRCA2 in preventing the degradation of nascent DNA by the MRE11 nuclease after replication stress. Here we show that depletion of SMARCAL1, a SNF2-family DNA translocase that remodels stalled forks, restores replication fork stability and reduces the formation of replication stress-induced DNA breaks and chromosomal aberrations in BRCA1/2-deficient cells. In addition to SMARCAL1, other SNF2-family fork remodelers, including ZRANB3 and HLTF, cause nascent DNA degradation and genomic instability in BRCA1/2-deficient cells upon replication stress. Our observations indicate that nascent DNA degradation in BRCA1/2-deficient cells occurs as a consequence of MRE11-dependent nucleolytic processing of reversed forks generated by fork remodelers. These studies provide mechanistic insights into the processes that cause genome instability in BRCA1/2-deficient cells.

Keywords: BRCA1 and BRCA2; DNA replication stress; HLTF; MRE11; RAD51; SMARCAL1; ZRANB3; breast and ovarian cancer; replication fork instability; replication fork reversal.

Figures

Figure 1
Figure 1. Analysis of nascent DNA degradation in BRCA1/2- and FANCD2-deficient cells upon SMARCAL1 depletion
(A) Detection by western blot of BRCA1 (left), BRCA2 (right) and SMARCAL1 protein levels in MCF10A cells subjected to shRNA-dependent depletion. β-actin levels are shown as loading controls. (B) Schematic of CldU/IdU pulse-labeling followed by a 5 hr hydroxyurea (HU; 2 mM) treatment (top). Representative images of CldU and IdU replication tracks in HU-treated MCF10A cells expressing the indicated shRNAs (bottom). (C) Dot plot of IdU to CldU tract length ratios for individual replication forks in HU-treated MCF10A cells expressing the indicated shRNAs with or without mirin (50 μM). The median value of 200 or more IdU and CldU tracts per experimental condition is indicated. Statistical analysis was conducted using Mann-Whitney test (n.s. not significant, **** p<0.0001). Data are representative of 3 independent experiments. (D) Schematic of CldU/IdU pulse-labeling followed by HU treatment as in (B) (top) and dot plot of IdU to CldU tract length ratios for individual replication forks in HU-treated PD20 cells with or without complementation with FANCD2 cDNA and treatment with SMARCAL1 siRNA (bottom). Data are shown and analyzed as in (C) and represent 2 independent experiments. (E) Schematic of the CldU/IdU pulse-labeling assay (top) and dot plot of IdU to CldU tract length ratios for individual replication forks in MCF10A cells with or without combined treatment with HU (2 mM) and B02 (25 μM) for 5 hrs (bottom). Data are shown and analyzed as in (C) and represent 2 independent replicates. (F) Schematic of the CldU/IdU pulse-labeling assay conducted as in (B) (top) in control and SMARCAL1 KO MCF10A cells subjected to control or BRCA1 siRNA treatment with or without expression of wild-type (WT), R764Q- or ΔN1-115-mutant SMARCAL1 proteins. Representative images of CldU (red) and IdU (green) replication tracks in the MCF10A cells indicated above after HU treatment (bottom). (G) Dot plot of IdU to CldU tract length ratios for individual replication forks in the MCF10A cells shown in (F) after HU treatment. Data are shown and analyzed as in (C) and represent 2 independent experiments. See also Figure S1.
Figure 2
Figure 2. Electron microscopy analysis of replication intermediates in BRCA1- and/or SMARCAL1-depleted cells
(A) Representative images of replication intermediates detected by electron microscopy upon a 5 hr HU treatment (2 mM) of control, BRCA1- and/or SMARCAL1-depleted MCF10A cells with or without mirin (50 μM). Replication fork arms and ssDNA gaps are indicated by numbers (i.e., 1 and 2) and arrows, respectively. (B) Bar graph representation of the percentage of replication intermediates with ssDNA regions of the indicated length in BRCA1- and/or SMARCAL1-depleted MCF10A cells treated as described in (A). 75 replication intermediates were analyzed per condition. Similar results were obtained in an independent experiment (Figure S2A). (C) Representative images of replication fork bubbles detected by electron microscopy in HU-treated control and BRCA1-depleted MCF10A cells. Replication fork arms and ssDNA gaps are indicated as in (A). See also Figure S2.
Figure 3
Figure 3. Measurement of nascent DNA degradation in BRCA1/2-deficient cells following depletion of ZRANB3 or HLTF
(A) Schematic of CldU/IdU pulse-labeling followed by a 5 hr HU treatment (2 mM) (top) and representative images of CldU and IdU replication tracks in HU-treated MCF10A expressing the indicated shRNAs (bottom). (B) Dot plot of IdU to CldU tract length ratios for individual replication forks in the HU-treated MCF10A cells shown in (A) with or without mirin (50 μM). The median value of 200 or more IdU and CldU tracts per experimental condition is indicated. P-values were calculated by Mann-Whitney test (n.s. not significant, **** p<0.0001). Data are representative of 2 independent experiments. (C) Schematic of CldU/IdU pulse-labeling followed by HU treatment as in (A) (top) and representative images of CldU and IdU replication tracks in HU-treated MCF10A expressing the indicated sh/siRNAs (bottom). (D) Dot plot of IdU to CldU tract length ratios for individual replication forks in the HU-treated MCF10A cells shown in (C). The experiment was conducted as in (B). Data are representative of 2 independent experiments and p-values were calculated as in (B). (E) Schematic of the CldU/IdU pulse-labeling assay conducted as described in (A) (top) and dot plot of IdU to CldU tract length ratios for individual replication forks in HU-treated MCF10A cells with or without BRCA1 and/or ZRANB3 siRNA-mediated depletion (bottom). ZRANB3-depleted cells were reconstituted with siRNA-resistant WT, PIP+APIM (P+A)-, NZF-zinc (NZF-z)- or K163D-mutant ZRANB3 proteins. Data are shown and analyzed as in (B) and represent 2 independent experiments. (F) Schematic of the CldU/IdU pulse-labeling assay performed as indicated in (A) (top) and dot plot of IdU to CldU tract length ratios for individual replication forks in HU-treated MCF10A cells with or without BRCA1 and/or HLTF siRNA-mediated depletion (bottom). HLTF-depleted cells were reconstituted with siRNA-resistant WT and HIRAN (HIR)-mutant HLTF proteins. Data are shown and analyzed as in (B) and represent 2 independent experiments. See also Figure S3.
Figure 4
Figure 4. Detection of MRE11 association with nascent DNA in BRCA1-deficient cells upon depletion of SMARCAL1 or ZRANB3
(A) Schematic of the proximity ligation assay (PLA) utilized to detect the association of proteins with nascent DNA, as described in the main text. (B) Representative images of PLA foci obtained in the indicated HU-treated MCF10A cells upon incubation with anti-MRE11 and anti-biotin antibodies (MRE11/Biotin; left) or with two distinct anti-biotin antibodies (Biotin/Biotin; right) according to the protocol depicted in (A). Each red spot corresponds to an interaction. DNA was stained with DAPI (blue). (C) Representation of the mean + SEM of the number of MRE11/Biotin (blue) PLA foci per cell (≥ 2 foci) in HU-treated MCF10A cells upon depletion of the factors indicated in (B). The mean + SEM of the number of Biotin/Biotin (purple) PLA foci per cell (≥ 2 foci) was used as control for the number of replication sites in each condition. 100–300 cells were analyzed per condition. Statistical analysis was conducted using one-way ANOVA on each sample relative to control samples (n.s., not significant; **** p<0.0001). Data are representative of 2 independent replicates. (D) Representative images of PLA foci obtained from HU-treated control or SMARCAL1 KO MCF10A cells as shown in (B). Cells were subjected or not to BRCA1 siRNA-mediated depletion and reconstitution with WT or R764Q-mutant SMARCAL1 proteins. (E) Representation of the mean + SEM of the number of MRE11/Biotin (blue) and Biotin/Biotin (purple) PLA foci per cell (≥ 2 foci) in HU-treated control and SMARCAL1 KO MCF10A cells, as shown in (D). 100–300 cells were analyzed per condition. Statistical analysis was conducted as in (C) (n.s. not significant; ** p<0.01; **** p<0.0001). Data are representative of 2 independent replicates. See also Figure S4.
Figure 5
Figure 5. Nucleolytic activity of MRE11 on reversed fork structures
(A) Representative images of reversed fork intermediates detected by electron microscopy upon a 5 hr HU treatment (2 mM) of control and BRCA1-depleted MCF10A cells with or without mirin (50 μM). Parental and reversed fork arms are indicated by numbers (i.e., 1 and 2) and arrows, respectively. (B) Representation of the percentage of reversed fork intermediates detected by electron microscopy in HU-treated BRCA1- and/or SMARCAL1-depleted MCF10A cells with or without mirin treatment, as described in (A). 75 replication intermediates were analyzed per condition. Similar results were obtained in an independent experiment (Figure S5B). (C) Schematic of the fork reversal and degradation assay utilized to monitor the activity of MRN or MR complexes on reversed fork structures generated on a plasmid-sized replication fork (pRF) by SMARCAL1 or ZRANB3, as described in the main text. (D) Fork reversal and degradation assay conducted upon incubation of the pRF substrate with wild-type (WT, 50 nM) or helicase-dead (HD, 50 nM) SMARCAL1 proteins for 5 min with or without subsequent addition of MRN complex (50 nM) for 2 hrs. Quantification of the BamHI digestion of reversed fork products is shown underneath each lane. The asterisk indicates a non-specific band. Similar results were obtained in an independent experiment. (E–F) Fork reversal and degradation assay conducted upon incubation of the pRF substrate with ZRANB3 or SMARCAL1 proteins (50 nM) for 5 min with or without subsequent addition of WT or nuclease deficient (MH129L,D130VRN) MRN or MR complex (50 nM) for 2 hrs. dsDNA corresponding to the BamHI digestion product of pRF was utilized as a marker in (E). Detection and quantification of BamHI digestion products was conducted as in (D). Data are representative of 3 or more independent experiments.
Figure 6
Figure 6. Effects of the depletion of SNF2-family members on genomic stability in BRCA1/2-deficient cells
(A) Dot plot of neutral comet tail moments detected in MCF10A cells expressing the indicated shRNAs following a 100 nM camptothecin (CPT) treatment for 5 hrs. Data are represented as the mean ± SEM of 75 or more comet tails per indicated condition. P-values were calculated by one-way ANOVA (n.s. not significant, **** p<0.0001). Data are representative of 2 independent experiments. (B) Representative images of neutral comet tails from CPT-treated MCF10A cells expressing the indicated shRNAs. (C) Dot plot of neutral comet tail moments detected upon a 5 hr CPT treatment (100 nM) of control or SMARCAL1 KO MCF10A cells with or without BRCA1 siRNA-mediated depletion and reconstitution with WT, R764Q- or ΔN1-115-mutant SMARCAL1 proteins. Data are shown and analyzed as in (A) and represent 2 independent replicates. (D) Dot plot of neutral comet tail moments upon a 5 hr CPT treatment (100 nM) of MCF10A cells with or without BRCA1 and/or ZRANB3 siRNA-mediated depletion and reconstitution with siRNA-resistant WT, PIP+APIM (P+A)-, NZF-zinc (NZF-z)- or K163D-mutant ZRANB3 proteins. Data are shown and analyzed as in (A) and represent 2 independent experiments. (E) Analysis of chromosomal aberrations in MCF10A cells expressing the indicated shRNAs upon a 100 nM CPT treatment for 5 hrs. Data are represented as the mean ± SEM of 25 or more metaphases per indicated condition. P-values were calculated by one-way ANOVA (n.s. not significant, ** p<0.01, *** p<0.001, **** p<0.0001). Data are representative of 2 independent experiments. (F) Representative images of metaphase spreads from CPT-treated MCF10A cells expressing the indicated shRNAs. Chromosomal aberrations are indicated by arrows. See also Figure S6.
Figure 7
Figure 7. Analysis of cell survival in BRCA1-deficient breast cancer cells upon SMARCAL1 depletion
(A) Western blot showing BRCA1 and SMARCAL1 protein levels in MDA-MB-231 cells transfected with the indicated siRNAs. GAPDH levels are shown as loading controls. (B) Survival analysis in MDA-MB-231 cells subjected to BRCA1 and/or SMARCAL1 depletion with two independent siRNAs, as indicated in (A), upon treatment with olaparib (left) or cisplatin (right). Cell survival is expressed as percentage relative to the untreated control and data represent the mean ± SD of at least 3 replicates per condition. Asterisks indicate p-values that are significant for both SMARCAL1/BRCA1 co-depleted samples (#1 and #2) relative to their corresponding BRCA1-depleted sample (unpaired Student’s t-test; * p<0.05; ** p<0.01). Data are representative of 2 independent experiments. (C) Survival analysis in BRCA1-mutant MDA-MB-436 cells subjected to SMARCAL1 depletion with 2 independent siRNAs upon treatment with olaparib (left) or cisplatin (right). Data are represented as in (B). Asterisks indicate p-values that are significant for both SMARCAL1-depleted samples (#1 and #2) relative to their corresponding control (unpaired Student’s t-test; * p<0.05; ** p<0.01). Data are representative of 2 independent experiments. (D) Schematic of the CldU/IdU pulse-labeling assay (top) and dot plot of IdU to CldU tract length ratios for individual replication forks in MDA-MB-231 cells treated with HU (2 mM for 5 hrs) and the indicated siRNAs (bottom). The median value of 200 or more IdU and CldU tracts per experimental condition is indicated. Statistical analysis was conducted using Mann-Whitney test (**** p<0.0001). Data are representative of 2 independent experiments. See also Figure S7.

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