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. 2016 Feb 4;61(3):419-433.
doi: 10.1016/j.molcel.2015.12.010. Epub 2016 Jan 7.

FBXW7 Facilitates Nonhomologous End-Joining via K63-Linked Polyubiquitylation of XRCC4

Qiang Zhang  1 , David Karnak  1 , Mingjia Tan  1 , Theodore S Lawrence  1 , Meredith A Morgan  2 , Yi Sun  3
Affiliations

FBXW7 Facilitates Nonhomologous End-Joining via K63-Linked Polyubiquitylation of XRCC4

Qiang Zhang et al. Mol Cell. .

Abstract

FBXW7 is a haploinsufficient tumor suppressor with loss-of-function mutations occurring in human cancers. FBXW7 inactivation causes genomic instability, but the mechanism remains elusive. Here we show that FBXW7 facilitates nonhomologous end-joining (NHEJ) repair and that FBXW7 depletion causes radiosensitization. In response to ionizing radiation, ATM phosphorylates FBXW7 at serine 26 to recruit it to DNA double-strand break (DSB) sites, whereas activated DNA-PKcs phosphorylates XRCC4 at serines 325/326, which promotes binding of XRCC4 to FBXW7. SCF(FBXW7) E3 ligase then promotes polyubiquitylation of XRCC4 at lysine 296 via lysine 63 linkage for enhanced association with the Ku70/80 complex to facilitate NHEJ repair. Consistent with these findings, a small-molecule inhibitor that abrogates XRCC4 polyubiquitylation reduces NHEJ repair. Our study demonstrates one mechanism by which FBXW7 contributes to genome integrity and implies that inactivated FBXW7 in human cancers could be a strategy for increasing the efficacy of radiotherapy.

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Figures

Figure 1
Figure 1. ATM-dependent recruitment of FBXW7α to DNA damage sites
(A) MiaPaCa-2 cells transfected with Flag-FBXW7α were exposed to IR (7.5 Gy) and fixed for immunofluorescence 15 minutes post-IR. Cells were co-stained for Flag-FBXW7 (red) and 53BP1 (green). (B) Accumulation of GFP-FBXW7α fusion protein along DNA damage ‘tracks’ after UVA laser microirradiation (microIR). (C) Flag-FBXW7α transfected MiaPaCa-2 cells were irradiated (7.5 Gy) and collected for immunoprecipitation (IP) and immunoblot (IB) with Flag and pS/TQ antibodies, respectively. (D) Cells were treated with DMSO, Nu7441 (1 μM, DNA-PKcs inhibitor), KU55933 (10 μM, ATM inhibitor) or VE-821 (10 μM, ATR inhibitor) for 1 hour pre- and 15 minutes post-IR and then collected for IP/IB as indicated. (E) GFP-FBXW7α accumulation at DNA damage sites after laser microIR was measured in AT fibroblasts. (F) MiaPaCa-2 cells were transiently transfected with Flag-FBXW7α-WT, S26A or S72A, followed by IP/IB after IR. (G) Localization of GFP-FBXW7α WT and mutants at DNA damage sites 15 minutes after microIR. Scale bars are 10 μm. (See also Figure S1.)
Figure 2
Figure 2. Depletion of FBXW7 leads to persistent γH2AX, impaired NHEJ, and radiosensitization
(A, B) FBXW7 isogenic HCT116 (A) or MiaPaCa-2 cells transfected with either non-specific (siNS) or FBXW7 siRNA (siFBXW7; two independent siRNAs) (B) were analyzed at the indicated times post-IR (6 Gy) for γH2AX positivity by flow cytometry. (C–D) MiaPaCa-2 and Panc-1 cells stably expressing the DR-GFP HR reporter were transfected with the indicated siRNAs and infected with adenovirus expressing I-SceI. The percentage of GFP-positive cells, indicating HR repair, was analyzed by flow cytometry (n = 2 independent experiments). (E) MiaPaCa-2 cells were transfected with siNS or siFBXW7. Forty-eight hours post-transfection, cells were further transfected with linearized-pEYFP plasmid for 12 hours, followed by harvesting for qPCR to detect the ligated EYFP region, normalized to an uncut flanking DNA sequence. (F) Cells stably expressing the I-SceI NHEJ reporter were transfected with siNS or siFBXW7, infected with I-SceI expressing adenovirus, and analyzed for GFP positivity by flow cytometry. (G) Cell extracts were incubated with linearized (by EcoRI for a 2 hour digestion producing 5′ overhangs) pBlueScript vector. End-joining products appear as higher molecular weight bands. (H) NHEJ activity was assessed in FBXW7 isogenic HCT116 cells stably expressing FBXW7α WT or S26A mutant as described in panel E. (I, J) FBXW7 isogenic HCT116 (I) or MiaPaCa-2 cells transfected with siRNA (J) were treated with IR and processed for clonogenic survival 24 hours post-IR. The radiation enhancement ratio (RER) and surviving fraction are the mean ± SD/SE of 2–3 independent experiments. (K–L) MEF cells (wild type and FBXW7 null) were serum starved (24 hours) and then assessed for λH2AX foci by immunofluorescence at the indicated times post-IR (2 Gy). Scale bar, 5 μm. Similar results were observed with 6 Gy radiation (data not shown). (M–N) NHEJ activity was assessed in serum starved (24 hours) normal fibroblasts HFF (M) and MRC5 (N) with FBXW7 or XRCC4 depletion. (A–B, E–F, H–J, M–N) Data are the mean ± SE of 3 independent experiments. *p<0.05, **p<0.01, ***p<0.001. (See also Figure S2.)
Figure 3
Figure 3. SCFFBXW7α promotes XRCC4 polyubiquitylation via K63-linkage
(A) FBXW7α interacts with XRCC4, LigIV, XLF, and UBC13, but not MDC1 and 53BP1 endogenously in MiaPaCa-2 cells. IgG was used as the IP control. (B) MiaPaCa-2 cells were harvested for immunoprecipitation with XRCC4 antibody at the indicated times post-IR, followed by immunoblotting for the indicated proteins. (C) XRCC4 mutation in the FBXW7 binding motif (S325/326A) reduces FBXW7α-XRCC4 association. MiaPaCa-2 cells co-transfected with Flag-FBXW7α and XRCC4 WT or S325/326A mutant were irradiated and then collected for IP/IB. (D) FBXW7α promotes XRCC4 polyubiquitylation in response to radiation. MiaPaCa-2 cells transfected with various constructs were harvested 15 minutes post-IR (7.5 Gy) for IP with HA antibody, followed by IB with XRCC4 antibody. (E) XRCC4 polyubiquitylation is via K63-ubiquitin linkage. Wild type or mutant (K48R, K63R) HA-tagged ubiquitin (HA-Ub) were used to define the type of ubiquitin linkage. (F) K63-only, but not K48-only ubiquitin mutant mediates XRCC4 polyubiquitylation upon IR treatment in MiaPaCa-2 cells. (G) MiaPaCa-2 cells transfected with non-specific, UBC5 or UBC13 siRNA were further transfected with the indicated constructs and harvested 15 minutes post-IR for in vivo ubiquitylation assays. (H) MiaPaCa-2 cells stably expressing an NHEJ reporter were transfected with non-specific, UBC5 or UBC13 siRNA and NHEJ repair efficiency was measured as described in Figure 2F (n = 2 independent experiments). (See also Figure S3.)
Figure 4
Figure 4. SCFFBXW7α ubiquitylates XRCC4 at Lys296 in an ATM- and DNA-PKcs-dependent manner
(A) In vitro ubiquitylation assays were performed by incubating purified XRCC4 with ATP, ubiquitin, E1, and E2 in the presence or absence of E2, immunoprecipitated Flag-FBXW7 or XRCC4 followed by IB. Ub (K63R) and XRCC4 S325/326A were used as negative controls. (B) Pharmacological inhibition of DNA-PKcs or ATM by Nu7441 or KU55933, respectively inhibits XRCC4 ubiquitylation. MiaPaCa-2 cells transfected with the indicated constructs were pre-treated with inhibitors (1 hour) and irradiated (7.5 Gy). XRCC4 ubiquitylation was examined by IP with HA antibody, followed by IB for the indicated proteins. (C) Depletion of DNA-PKcs or ATM impairs XRCC4 polyubiquitylation. XRCC4 polyubiquitylation was assessed in cells treated with non-specific, DNA-PKcs, or ATM siRNAs. (D) K296 on XRCC4 is the ubiquitylation site of FBXW7α. Ubiquitylation of four XRCC4 lysine mutants (K271R, K285R, K296R, and K308R) was measured as described in Figure 3D. (See also Figure S4.)
Figure 5
Figure 5. FBXW7α-mediated XRCC4 polyubiquitylation facilitates NHEJ complex formation
(A–B) FBXW7 isogenic HCT116 cells were irradiated (7.5 Gy) and collected for co-IP assays with XRCC4 or Ku80 antibody, followed by IB for NHEJ proteins. (C) K296 of XRCC4 is required for association with Ku70/80. XRCC4 WT and K296R mutants were expressed in MiaPaCa-2 cells and their interaction with endogenous NHEJ proteins after IR was examined by XRCC4 IP. (D) Purified GST-Ku70/K80 heterodimer proteins from Sf9 cells were incubated with agarose beads conjugated with tetra-ubiquitin K48 or K63, as indicated. Ku70/80 and tetra-ubiquitin chains were eluted by SDS sample buffer, followed by immunoblotting for GST. (See also Figure S5.)
Figure 6
Figure 6. Ubiquitylation at K296 promotes XRCC4 chromatin association, NHEJ repair, and radiation survival
(A) GFP-XRCC4 localization along microIR DNA damage sites was monitored and quantified post-microIR in FBXW7 isogenic HCT116 cells. Data are plotted as the percentage increase in fluorescence (arbitrary units) at the site of microIR and are the mean ± SD of 5 cells. (B) K296R mutation impairs the recruitment of GFP-XRCC4 to DNA damage sites. GFP-XRCC4 WT or K296R were expressed in MiaPaCa-2 cells and their localization to microIR DNA damage sites was monitored post-microIR. (C) XRCC4 isogenic HCT116 cells, XRCC4 WT and K296R stable cells were treated with or without IR (6 Gy) and harvested at various time points for the isolation of non-chromatin and chromatin fraction, followed by immunoblot analysis. (D) NHEJ activity was assessed in XRCC4 isogenic HCT116 cells stably expressing XRCC4 WT or S325/326 or K296R mutants as described in Figure 2D (Data are the mean ± SE of 3 independent experiments) (E) XRCC4 isogenic HCT116 cells, as well as derived XRCC4 WT, S325/326A, and K296R stable cells were irradiated and 24 hours later processed for clonogenic survival. Data are presented as mean ± SD of 4 repeats. Scale bars are 10 μm. *p<0.05, ***p<0.001. (See also Figure S6.)
Figure 7
Figure 7. Pharmacological inhibition of SCFFBXW7 causes NHEJ inhibition
(A) MiaPaCa-2 cells transfected with WT, K48R or K63R HA-ubiquitin were pre-treated with MLN4924 (300 nM) for 6 hours, followed by IR (6 Gy) and collection for IP (15 minutes post-IR) with HA antibody, followed by IB. (B) MiaPaCa-2 cells were treated with drugs for the indicated times, followed by cell-free extract preparation. Linearized-pBlueScript vector (by EcoRI digestion) was incubated with the extracts for 2 hours. Reactions were subjected to agarose gel electrophoresis. (C) Cells stably expressing I-SceI NHEJ reporter were pre-treated for 1 hour with MLN4924, followed by infection with adenovirus expressing I-SceI and continued MLN4924 treatment for 24 hours. GFP positive cells, indicative of NHEJ repair, were quantitated by flow cytometry. (D) Cells were pre-treated with drugs for 1 hour, then transfected with linearized-pEYFP plasmid (by NheI digestion), and analyzed by qPCR 12 hours later for the ligated pEYFP region normalized to an uncut flanking DNA sequence. (E) MiaPaCa-2 cells expressing the I-SceI NHEJ reporter were treated with non-specific (siNS) or FBXW7 siRNA and MLN4924. Data are the normalized mean percentage of MLN4924 inhibition for each RNAi condition. siFBXW7 alone caused 30% NHEJ inhibition relative to siNS. Data are the mean ± SD/SE of 2 (E) or 3 (C, D) independent experiments. *p<0.05, **p<0.01, ***p<0.001. (See also Figure S7.) (F) Proposed model for FBXW7 regulation of NHEJ. In response to radiation-induced DSBs, FBXW7α is phosphorylated (at S26) by ATM, leading to its recruitment to DSB sites. Locally enriched FBXW7 recognizes phosphorylated XRCC4 (by DNA-PKcs at S325/326) and together with other components of the SCF E3 ubiquitin ligase promotes K63-linked polyubiquitylation of XRCC4 at K296. Polyubiquitylated XRCC4 facilitates the association of XRCC4 (and LigIV/XLF) with the Ku70/80 heterodimer and DSBs to form an active NHEJ complex for effective repair. Pharmacologic (by MLN4924) or genetic (siRNA or genome deletion) inactivation of FBXW7α inhibits this pathway resulting in impaired NHEJ, persistent DSBs and increased radiation sensitivity. (See also Figure S7.)
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