SAMHD1 Promotes DNA End Resection to Facilitate DNA Repair by Homologous Recombination

Abstract

DNA double-strand break (DSB) repair by homologous recombination (HR) is initiated by CtIP/MRN-mediated DNA end resection to maintain genome integrity. SAMHD1 is a dNTP triphosphohydrolase, which restricts HIV-1 infection, and mutations are associated with Aicardi-Goutières syndrome and cancer. We show that SAMHD1 has a dNTPase-independent function in promoting DNA end resection to facilitate DSB repair by HR. SAMHD1 deficiency or Vpx-mediated degradation causes hypersensitivity to DSB-inducing agents, and SAMHD1 is recruited to DSBs. SAMHD1 complexes with CtIP via a conserved C-terminal domain and recruits CtIP to DSBs to facilitate end resection and HR. Significantly, a cancer-associated mutant with impaired CtIP interaction, but not dNTPase-inactive SAMHD1, fails to rescue the end resection impairment of SAMHD1 depletion. Our findings define a dNTPase-independent function for SAMHD1 in HR-mediated DSB repair by facilitating CtIP accrual to promote DNA end resection, providing insight into how SAMHD1 promotes genome integrity.

Keywords: AGS; CLL; CtIP; DNA damage response; DNA end resection; DNA repair; HIV; autoimmune; dNTP; homologous recombination.

Figure 1. SAMHD1 Functions in DNA DSB Repair

(A) U2OS cells transfected with indicated siRNA were seeded for colony formation, treated with indicated doses of IR, and assayed for surviving colonies 12 days (d) later. Percent surviving colonies is shown. (B–C) U2OS cells transfected with NT or SAMHD1 siRNA were treated with indicated doses of CPT (B) or etoposide (C) for 72 hours (h) and assayed for cell viability using AlamarBlue. (D) Western blot analysis showing SAMHD1 knockdown in U2OS cells at 72 h. (E) MCF7 cells transfected with indicated siRNAs and plasmids were treated with 200 nM CPT for 72 h and assayed for viability with AlamarBlue. Treated to untreated viability relative to NT siRNA is shown. (F) Western blot analysis in MCF7 cells demonstrating SAMHD1 knockdown and expression of SAMHD1-GFP. (G–H) U2OS cells transfected with indicated siRNAs were synchronized by mimosine arrest for 16 h, released into S-phase, and exposed to 10 Gy IR. DNA damage was analyzed by neutral comet assay. (G) Dot plot with median of comet tail moment is shown. (H) Representative images of comet tails are shown. For (A–C), (E), and (G), mean and standard error of the mean (SEM) from at least three independent replicas is shown. * p < 0.05, ** p < 0.01, *** p < 0.001. See also Figure S1.

Figure 2. SAMHD1 Localizes to DSBs in Response to DNA Damage

(A–C) HeLa cells were treated with 2 μM CPT for 4 h, fixed, and processed for immunofluorescence with indicated antibodies. (A) Percent cells with SAMHD1 foci are shown. (B–C) Representative immunofluorescence images of SAMHD1 co-localizing with γH2AX or RAD51 after DNA damage are shown. (D) U2OS cells expressing SAMHD1-GFP were microirradiated, fixed after 1 min, and processed for immunofluorescence with anti-RPA70 antibodies. (E–F) U2OS cells were treated with 0.1 μM CPT and 10 μM EdU for 1 h, washed, and processed 1 h for immunofluorescence with click chemistry and anti-SAMHD1 and CtIP antibodies. Quantitation (E) and representative SR images (F) of co-localization between nascent DNA (naDNA via EdU) and SAMHD1 or CtIP showing increased association upon CPT damage. For (A) and (E), mean and SEM from at least three independent replicas is shown. *** p < 0.001, **** p < 0.0001. See also Figure S2.

Figure 3. SAMHD1 Functions in DSB Repair by Facilitating HR

(A) U2OS cells transfected with NT or SAMHD1 siRNA were treated with indicated doses of Veliparib and assayed for surviving colonies 12 d later. Percent surviving colonies is shown. (B) MCF7 cells transfected with indicated siRNAs and plasmids were treated with 50 μM Veliparib for 72 h and assayed for viability with AlamarBlue. Treated to untreated viability relative to NT siRNA is shown. (C) U2OS cells integrated with a DR-GFP HR reporter substrate were transfected with indicated siRNAs and I-SceI, fixed, and analyzed for HR by GFP expression using flow cytometry. (D) Cell cycle profile of U2OS cells depleted for SAMHD1 was determined by flow cytometry. (E) Quantitation of cell cycle profile shown. (F–G) HeLa cells transfected with SAMHD1 or NT siRNA were treated with 2 μM CPT for 4 h, fixed, and processed for immunofluorescence with indicated antibodies. Representative images (F) and quantitation (G) of relative percent γH2AX positive cells with RAD51 foci is shown. (H) Western blot analysis showing SAMHD1 knockdown in HeLa cells at 72 h. For (A–C), (E), and (G), mean and SEM from at least three replicas is shown. ** p < 0.01, *** p < 0.001. See also Figure S3.

Figure 4. SAMHD1 Facilitates HR and ATR Activation by Promoting DNA End Resection

(A) U2OS cells transfected with SAMHD1 or NT siRNA were treated with 2 μM CPT for 4 h, harvested, run on SDS-PAGE, and probed with indicated antibodies. (B–C) U2OS cells transfected with SAMHD1 or NT siRNA were treated with 2 μM CPT for 4 h, fixed, and processed for immunofluorescence with indicated antibodies. Representative images (B) and quantitation (C) of relative percent γH2AX positive cells with RPA70 foci is shown. (D) Representative images of GFP-RPA70 expressing U2OS cells transfected with NT or SAMHD1 siRNA, subjected to laser micro-irradiation, fixed 5 min after damage, and processed for immunofluorescence with anti-γH2AX antibodies. (E–F) U2OS cells stably transfected with GFP-ATRIP were treated with 2 μM CPT for 4 h, fixed, and processed for immunofluorescence with anti-γH2AX antibodies. Representative images (E) and quantitation (F) of relative percent γH2AX positive cells with GFP-ATRIP foci is shown. (G) HCT-116 cells transfected with SAMHD1 or NT siRNA were treated with 2 μM CPT for 4 h, harvested, run on SDS-PAGE, and probed with indicated antibodies. (H–I) SAMHD1 depleted U2OS cells were treated with 30 μM BrdU for 36 h followed by 3 μM CPT treatment for 4 h. Cells were fixed under non-denaturing conditions and processed for immunofluorescence using anti-BrdU (ssDNA) and γH2AX antibodies. Representative images (H) and quantitation (I) of relative percent γH2AX positive cells with BrdU foci is shown. For (C), (F), and (I), mean and SEM from three independent replicas is shown. *** p < 0.001. See also Figure S4.

Figure 5. SAMHD1 Promotes HR and DNA End Resection Independent of its dNTPase Activity and Complexes with CtIP in Response to DNA Damage

(A) U2OS cells integrated with a DR-GFP HR reporter substrate were transfected with indicated siRNAs, cDNAs, and I-SceI, and fixed. RFP positive cells were gated and analyzed for HR by GFP expression using flow cytometry. (B) Western blot analysis in U2OS cells demonstrating SAMHD1 knockdown and expression of SAMHD1-RFP. (C) U2OS cells were transfected with indicated siRNAs and cDNA, treated with 10 Gy IR, and processed 4 h later for immunofluorescence with indicated antibodies. Quantitation of percent γH2AX positive cells with RPA70 foci that are HA-SAMHD1 positive for complemented cells is shown. (D) 293T cells were transfected with GFP-CtIP and SAMHD1-HA, treated with 10 Gy IR, harvested 4 h later, IP’d with anti-HA antibodies, run on SDS-PAGE, and immunoblotted with indicated antibodies. (E) 293T cells were transfected with CtIP-FLAG and SAMHD1-RFP, treated with 10 Gy IR, harvested 4 h later, IP’d with anti-flag antibodies, run on SDS-PAGE, and immunoblotted with indicated antibodies. (F) Endogenous SAMHD1 was IP’d from lysate from HCT-116 cells treated with or without IR, washed, separated by SDS-PAGE, and immunoblotted with indicated antibodies. (G) Recombinant GST-CtIP and SAMHD1 purified from E. coli was pulled down with an anti-SAMHD1 antibody, washed, separated by SDS-PAGE, and immunoblotted with indicated antibodies. (H–I, K) 293T cells were transfected with SAMHD1-HA WT and deletion or point mutants and GFP-CtIP, treated with 10 Gy, IR, harvested 4 h later, IP’d with anti-HA antibodies, run on SDS-PAGE, and immunoblotted with indicated antibodies. Domain mapping analysis indicates that aa 115–562 is sufficient for interaction with CtIP (H) and aa 465–562 is necessary for interaction with CtIP (I). (J) Schematic representation of SAMHD1 structural domains and evolutionary conservation of CtIP interaction domain. (K) A naturally occurring cancer-associated SAMHD1 mutation (K484T) impairs the interaction of SAMHD1 with CtIP. For (A) and (C), mean and SEM from three independent replicas is shown. ** p < 0.01, *** p < 0.001. See also Figure S5.

Figure 6. SAMHD1 Recruits CtIP to DNA Damage Sites and Chromatin in Response to DNA Damage and Promotes DNA End Resection through its Interaction with CtIP

(A–B) U2OS cells were treated with 0.1 μM CPT and 10 μM EdU for 1 h, washed, and processed 1 h for immunofluorescence with click chemistry and anti-SAMHD1 and CtIP antibodies. (A) Quantitation of co-localization of SAMHD1 and CtIP upon CPT damage. (B) Representative SR images of a single foci showing SAMHD1/CtIP co-localization in cells also labeled for naDNA. (C) U2OS cells integrated with a DR-GFP HR reporter substrate were transfected with indicated siRNAs and I-SceI, fixed, and analyzed for HR by GFP expression using flow cytometry. (D) U2OS cells transfected with CtIP, SAMHD1, or NT siRNA were treated with 2 μM CPT for 4 h, fixed, and processed for immunofluorescence with indicated antibodies. Quantitation of relative percent γH2AX positive cells with RPA70 foci is shown. (E) Representative images of GFP-CtIP expressing U2OS cells transfected with NT or SAMHD1 siRNA, subjected to laser micro-irradiation, fixed 5 min after damage, and processed for immunofluorescence with anti-γH2AX antibodies. (F) HCT-116 cells transfected with SAMHD1 or NT siRNA were treated with 10 Gy IR and harvested 1 h later for biochemical fractionation. Chromatin bound proteins were run on SDS-PAGE and immunoblotted with indicated antibodies. NS indicates non-specific band as loading control. (G) Representative images of U2OS SAMHD1 WT and KO cells expressing RFP-SAMHD1 and GFP-CtIP, subjected to laser micro-irradiation, fixed 5 min after damage, and processed for immunofluorescence with anti-γH2AX antibodies. (H) U2OS cells were transfected with indicated siRNAs and cDNA, treated with 10 Gy IR, and processed 4 h later for indirect immunofluorescence with anti-RPA70, HA, and γH2AX antibodies. Quantitation of percent γH2AX positive cells with RPA70 foci that are SAMHD1-GFP positive for complemented cells, from 3 independent replicas of 60 cells counted each is shown. (I) U2OS cells transfected with indicated siRNAs and plasmids were treated with 200 nM CPT for 72 h prior to assaying for viability with AlamarBlue. Treated to untreated viability relative to NT siRNA is shown. (J) Western blot analysis showing expression of SAMHD1-GFP and endogenous SAMHD1 in U2OS cells 72 h after siRNA transfection and 48 h after cDNA transfection. The higher levels of SAMHD1 in the SAMHD1-GFP transfected cells likely represents exogenous SAMHD1 cleaved from SAMHD-GFP. For (A), (C–D), (H), and (I), mean and SEM from three independent replicas is shown. ** p < 0.01, **** p < 0.0001. See also Figure S6.

Figure 7. Targeting SAMHD1 with Virus Like Particles Containing Vpx Sensitizes Cancer Cells to DSB-Inducing Agents

(A) Western blot analysis showing SAMHD1 degradation in U2OS cells treated with VLPs containing Vpx or no Vpx for 48 h. (B–C) U2OS cells were treated with VLPs containing Vpx or no Vpx for 48 h followed by indicated doses of CPT (B) or veliparib (C) for 72 h and assayed for cell viability using AlamarBlue. (D) U2OS cells transfected with or without SAMHD-GFP were treated with VLPs containing Vpx or no Vpx for 48 h followed by 50 nM CPT for 72 h and assayed for cell viability using AlamarBlue. (E) Western blot analysis showing expression of SAMHD1-GFP and endogenous SAMHD1 in U2OS cells 72 h after transfection and 48 after treatment with VLPs containing Vpx or no Vpx at which time cells were treated in (D). The higher levels of SAMHD1 in the SAMHD1-GFP transfected and Vpx treated cells (lower band in 3^rd lane) likely results from a combination of endogenous SAMHD1 and exogenous SAMHD1 cleaved from SAMHD-GFP that has not been degraded. (F) Model showing SAMHD1 function in DNA end resection to facilitate DSB repair by HR. In response to DSB-inducing agents, SAMHD1 interacts with CtIP/MRN in a damage-regulated manner and recruits CtIP to DSBs to promote DNA end resection, facilitating DSB repair by HR. For (B–C) and (D), mean and SEM from three independent replicas is shown. ** p < 0.01, *** p < 0.001.