Sato K , Brandsma I , van Rossum-Fikkert SE , Verkaik N , Oostra AB , Dorsman JC , van Gent DC , Knipscheer P , Kanaar R , Zelensky AN .

	Fig.1 HSF2BP disrupts the FA pathway. (A–C) Immunoblot and clonogenic survivals of the U2OS cells stably transformed with GFP-hHSF2BP or GFP expression constructs and stably transduced with lentiviral vectors encoding anti-HSF2BP (#2, #3) or non-targeting shRNAs. Cells were treated with the indicated doses of MMC (B) or ionizing radiation (C); n = 2. Efficiency of the knockdown was assessed by immunoblotting of whole cell extracts with the indicated antibodies (A); * indicates a non-specific band. (D) Frequency of HSF2BP deletion and amplification in tumor sample sequencing data available at cBioPortal (53,54). Studies with ≥100 samples were analyzed. (E) Graphical summary of cancer samples that harbor genetic alteration in either the HSF2BP or BRCA2 gene. Alteration frequency was calculated using profiled samples (562 alterations in 55 817 profiled samples for HSF2BP, and 2945 alterations in 68 793 profiled samples for BRCA2). Each sample was colored by alteration types as indicated. (F) Example metaphase chromosomal spread from HSF2BP-overproducing cell treated overnight with 100 nM MMC. Chromatid breaks and a quadriradial chromosome are indicated with single and double arrows, respectively. (G) Quantification of chromatid breaks in HeLa cells stably transformed with HSF2BP expression vectors or control, with and without overnight 100 nM MMC treatment; 50 metaphases per condition were scored. (H) ICL repair efficiency in the presence or absence of HSF2BP. The scheme on the left shows pICL, a synthetic plasmid substrate in which the diagnostic SapI site is disrupted by a cis-platinum ICL that is restored by replication-associated repair by the FA pathway in Xenopus egg extracts (see also (Supplementary Figure S3A) for details). pICL was replicated in Xenopus egg extract that was supplemented with purified recombinant His-tagged human (h) or Xenopus (x) HSF2BP or buffer. Replication intermediates were isolated and digested with HincII, or HincII and SapI, and separated on agarose gel. Repair efficiency was calculated and plotted. As repair kinetics and absolute efficiency are highly dependent on the egg extract preparation, single experiment is plotted here, and a replica is shown in (Supplementary Figure S1L). #, SapI fragments from contaminating uncrosslinked plasmid present in varying amounts in different pICL preparations.
	Fig.2 FA pathway disruption by HSF2BP requires interaction with BRCA2. (A) ICL repair efficiency in Xenopus egg extract in the presence or absence of purified recombinant wild-type (WT) human HSF2BP or its R200T variant that cannot bind BRCA2. #, SapI fragments from contaminating uncrosslinked plasmid present in varying amounts in different pICL preparations. Repeat of this experiment is shown in (Supplementary Figure S2A). (B) Clonogenic survival of U2OS cells stably producing GFP, or GFP-tagged wild-type or non-BRCA2-binding R200T variant of HSF2BP, and exposed to the indicated doses of MMC; n = 4. (C) Schematic of a fragment of the human BRCA2 locus depicting the strategy for homozygous exon 12 excision from HeLa cells using two CRISPR/Cas9 cuts. Introns are not drawn to scale; exon phase is depicted using various shapes of the side boundaries. Genotyping primers are shown as blue arrows (see also (Supplementary Figure S2B)). Boundaries of the minimal HSF2BP-binding domain (HBD) mapped in the previous study (fragment F9 (3)) is shown with green line. (D–G) Immunoblot (D) and clonogenic survival (E and F) of the BRCA2 Δ12 and its parental HeLa cell line (wt), stably transformed with human HSF2BP expression vector (wild-type or R200T mutant) or empty vector. (D) HSF2BP is indicated with an arrow, * – non-specific band. For clonogenic survivals cells were treated with ICL-inducing agents MMC (E) and cisplatin (F), or PARPi talazoparib (G); n = 3–9.
	Fig.3 HSF2BP inhibits HR in the FA pathway. (A) HSF2BP does not inhibit ICL-induced FANCD2 ubiquitination in Xenopus egg extract. Proteins from egg extract incubated with pICL with or without the addition of recombinant human HSF2BP for the indicated periods of time were analyzed by immunoblotting with anti-Xenopus laevis FANCD2 antibody. (B and C) HSF2BP does not inhibit lesion unhooking in Xenopus egg extract. Prelabeled pICL was replicated in Xenopus egg extracts supplemented with or without recombinant human HSF2BP, and replication products were isolated, digested by HincII to generate the products shown on the scheme (B), and separated on a denaturing agarose gel (Supplementary Figure S3C). The decline of the X-structures was quantified and plotted (C). Red lines on the scheme (B) indicate the labeled parental strand. (D and E) HSF2BP does not inhibit translesion synthesis in Xenopus egg extract. pICL was replicated in Xenopus egg extracts supplemented with or without recombinant human HSF2BP in the presence of 32P-α-dCTP, and replication products were isolated, digested by HincII, or HincII and SapI, as shown on the scheme (D), and separated on a denaturing agarose gel (Supplementary Figure S3D). Extension products were quantified and plotted (E). HSF2BP-induced reduction in full-length products in the absence of SapI indicates a defect in HR. (F and G) Inhibition of HR intermediate formation by HSF2BP revealed by 2DGE. pICL was replicated in Xenopus egg extracts supplemented with or without recombinant human HSF2BP in the presence of 32P-α-dCTP, and replication products were isolated, digested by HincII, and analyzed by 2DGE. Scheme (F) shows migration patterns for various replication products. The X-arc is indicated by the blue arrows in the top right image in (G), the numbers indicate the efficiency of its formation (defined by the ratio of X-arc product intensity to total intensity).
	Fig.4 HSF2BP–BRCA2 interaction prevents RAD51 accumulation at ICL. (A and B) Stable RAD51 accumulation on pICL during repair is abrogated by wild-type human HSF2BP, but not the R200T mutant. The pICL plasmid was replicated in Xenopus egg extracts. At the indicated times, pICL was pulled down by incubation with streptavidin beads coated with biotinylated LacI (A). Presence of bound RAD51 and FANCD2 was determined by immunoblotting (B). (C and D) RAD51 focus formation after short-term (0–4 h) exposure to 1.2 μM MMC of HeLa cells stably transformed with human HSF2BP expression vector or an empty vector. Thirty minutes before fixation, EdU was added to the media to label S-phase cells. After Click-IT reaction and anti-RAD51 immunofluorescent staining, cells were imaged using confocal microscope. Representative images (C) and foci quantification (D) are shown. Foci were counted manually. The experiment was repeated two times, 50–90 nuclei per sample were analyzed, significance was determined using one-way ANOVA; scale bars = 5 μm. Experiment with chronic MMC treatment is shown in Supplementary Figure S4A. (E) Scheme of the ChIP assay. (F and G) Recombinant human HSF2BP inhibits loading of endogenous BRCA2 at the ICL in Xenopus egg extract. pICL replication samples at the indicated time points were analyzed by BRCA2 (F) and HSF2BP (G) ChIP using a primer pair for the ICL locus.
	Fig.5 HSF2BP induces ICL-dependent BRCA2 degradation. (A) Wild-type HSF2BP, but not the R200T mutant, induces BRCA2 degradation during ICL repair. pICL was replicated in Xenopus egg extracts in the presence or absence of human HSF2BP. Total extract samples were collected at the indicated time points and analyzed by immunoblotting. (B) HSF2BP-induced BRCA2 degradation is proteasome dependent. pICL was replicated in Xenopus egg extracts containing human HSF2BP in the absence or presence of proteasome inhibitor MG-132. Recombinant His-FLAG-tagged ubiquitin was added to counteract ubiquitin depletion as a result of proteasome inhibition. Total extract samples were collected at the indicated time points and analyzed by immunoblotting. (C) HSF2BP-induced BRCA2 degradation is ICL repair-dependent. Experiment as in (A) was repeated with the pControl plasmid that has the same sequence as pICL, but no crosslink. Total extract samples were collected at the indicated time points and analyzed by immunoblotting. (D) Addition of MG-132 does rescue reduced level of BRCA2 at ICLs during repair. Crosslinked plasmids were replicated in the presence or absence of purified recombinant wild-type human HSF2BP, with and without MG-132 and His-FLAG-tagged ubiquitin. Samples were analyzed by BRCA2 ChIP using a primer pair for the ICL locus. (E) HSF2BP-induced ICL repair defect is not rescued upon addition of MG-132. ICL repair efficiency in Xenopus egg extract was measured in the presence or absence of purified recombinant wild-type human HSF2BP with and without MG-132 and His-FLAG-tagged ubiquitin. #, SapI fragments from contaminating uncrosslinked plasmid present in varying amounts in different pICL preparations. (F) Schematic depiction of the model explaining HSF2BP effects on the function of BRCA2 in DSB and ICL repair.
	Figure 1. HSF2BP disrupts the FA pathway. (A–C) Immunoblot and clonogenic survivals of the U2OS cells stably transformed with GFP-hHSF2BP or GFP expression constructs and stably transduced with lentiviral vectors encoding anti-HSF2BP (#2, #3) or non-targeting shRNAs. Cells were treated with the indicated doses of MMC (B) or ionizing radiation (C); n = 2. Efficiency of the knockdown was assessed by immunoblotting of whole cell extracts with the indicated antibodies (A); * indicates a non-specific band. (D) Frequency of HSF2BP deletion and amplification in tumor sample sequencing data available at cBioPortal (53,54). Studies with ≥100 samples were analyzed. (E) Graphical summary of cancer samples that harbor genetic alteration in either the HSF2BP or BRCA2 gene. Alteration frequency was calculated using profiled samples (562 alterations in 55 817 profiled samples for HSF2BP, and 2945 alterations in 68 793 profiled samples for BRCA2). Each sample was colored by alteration types as indicated. (F) Example metaphase chromosomal spread from HSF2BP-overproducing cell treated overnight with 100 nM MMC. Chromatid breaks and a quadriradial chromosome are indicated with single and double arrows, respectively. (G) Quantification of chromatid breaks in HeLa cells stably transformed with HSF2BP expression vectors or control, with and without overnight 100 nM MMC treatment; 50 metaphases per condition were scored. (H) ICL repair efficiency in the presence or absence of HSF2BP. The scheme on the left shows pICL, a synthetic plasmid substrate in which the diagnostic SapI site is disrupted by a cis-platinum ICL that is restored by replication-associated repair by the FA pathway in Xenopus egg extracts (see also (Supplementary Figure S3A) for details). pICL was replicated in Xenopus egg extract that was supplemented with purified recombinant His-tagged human (h) or Xenopus (x) HSF2BP or buffer. Replication intermediates were isolated and digested with HincII, or HincII and SapI, and separated on agarose gel. Repair efficiency was calculated and plotted. As repair kinetics and absolute efficiency are highly dependent on the egg extract preparation, single experiment is plotted here, and a replica is shown in (Supplementary Figure S1L). #, SapI fragments from contaminating uncrosslinked plasmid present in varying amounts in different pICL preparations.
	Figure 2. FA pathway disruption by HSF2BP requires interaction with BRCA2. (A) ICL repair efficiency in Xenopus egg extract in the presence or absence of purified recombinant wild-type (WT) human HSF2BP or its R200T variant that cannot bind BRCA2. #, SapI fragments from contaminating uncrosslinked plasmid present in varying amounts in different pICL preparations. Repeat of this experiment is shown in (Supplementary Figure S2A). (B) Clonogenic survival of U2OS cells stably producing GFP, or GFP-tagged wild-type or non-BRCA2-binding R200T variant of HSF2BP, and exposed to the indicated doses of MMC; n = 4. (C) Schematic of a fragment of the human BRCA2 locus depicting the strategy for homozygous exon 12 excision from HeLa cells using two CRISPR/Cas9 cuts. Introns are not drawn to scale; exon phase is depicted using various shapes of the side boundaries. Genotyping primers are shown as blue arrows (see also (Supplementary Figure S2B)). Boundaries of the minimal HSF2BP-binding domain (HBD) mapped in the previous study (fragment F9 (3)) is shown with green line. (D–G) Immunoblot (D) and clonogenic survival (E and F) of the BRCA2 Δ12 and its parental HeLa cell line (wt), stably transformed with human HSF2BP expression vector (wild-type or R200T mutant) or empty vector. (D) HSF2BP is indicated with an arrow, * – non-specific band. For clonogenic survivals cells were treated with ICL-inducing agents MMC (E) and cisplatin (F), or PARPi talazoparib (G); n = 3–9.
	Figure 3. HSF2BP inhibits HR in the FA pathway. (A) HSF2BP does not inhibit ICL-induced FANCD2 ubiquitination in Xenopus egg extract. Proteins from egg extract incubated with pICL with or without the addition of recombinant human HSF2BP for the indicated periods of time were analyzed by immunoblotting with anti-Xenopus laevis FANCD2 antibody. (B and C) HSF2BP does not inhibit lesion unhooking in Xenopus egg extract. Prelabeled pICL was replicated in Xenopus egg extracts supplemented with or without recombinant human HSF2BP, and replication products were isolated, digested by HincII to generate the products shown on the scheme (B), and separated on a denaturing agarose gel (Supplementary Figure S3C). The decline of the X-structures was quantified and plotted (C). Red lines on the scheme (B) indicate the labeled parental strand. (D and E) HSF2BP does not inhibit translesion synthesis in Xenopus egg extract. pICL was replicated in Xenopus egg extracts supplemented with or without recombinant human HSF2BP in the presence of 32P-α-dCTP, and replication products were isolated, digested by HincII, or HincII and SapI, as shown on the scheme (D), and separated on a denaturing agarose gel (Supplementary Figure S3D). Extension products were quantified and plotted (E). HSF2BP-induced reduction in full-length products in the absence of SapI indicates a defect in HR. (F and G) Inhibition of HR intermediate formation by HSF2BP revealed by 2DGE. pICL was replicated in Xenopus egg extracts supplemented with or without recombinant human HSF2BP in the presence of 32P-α-dCTP, and replication products were isolated, digested by HincII, and analyzed by 2DGE. Scheme (F) shows migration patterns for various replication products. The X-arc is indicated by the blue arrows in the top right image in (G), the numbers indicate the efficiency of its formation (defined by the ratio of X-arc product intensity to total intensity).
	Figure 4. HSF2BP–BRCA2 interaction prevents RAD51 accumulation at ICL. (A and B) Stable RAD51 accumulation on pICL during repair is abrogated by wild-type human HSF2BP, but not the R200T mutant. The pICL plasmid was replicated in Xenopus egg extracts. At the indicated times, pICL was pulled down by incubation with streptavidin beads coated with biotinylated LacI (A). Presence of bound RAD51 and FANCD2 was determined by immunoblotting (B). (C and D) RAD51 focus formation after short-term (0–4 h) exposure to 1.2 μM MMC of HeLa cells stably transformed with human HSF2BP expression vector or an empty vector. Thirty minutes before fixation, EdU was added to the media to label S-phase cells. After Click-IT reaction and anti-RAD51 immunofluorescent staining, cells were imaged using confocal microscope. Representative images (C) and foci quantification (D) are shown. Foci were counted manually. The experiment was repeated two times, 50–90 nuclei per sample were analyzed, significance was determined using one-way ANOVA; scale bars = 5 μm. Experiment with chronic MMC treatment is shown in Supplementary Figure S4A. (E) Scheme of the ChIP assay. (F and G) Recombinant human HSF2BP inhibits loading of endogenous BRCA2 at the ICL in Xenopus egg extract. pICL replication samples at the indicated time points were analyzed by BRCA2 (F) and HSF2BP (G) ChIP using a primer pair for the ICL locus.
	Figure 5. HSF2BP induces ICL-dependent BRCA2 degradation. (A) Wild-type HSF2BP, but not the R200T mutant, induces BRCA2 degradation during ICL repair. pICL was replicated in Xenopus egg extracts in the presence or absence of human HSF2BP. Total extract samples were collected at the indicated time points and analyzed by immunoblotting. (B) HSF2BP-induced BRCA2 degradation is proteasome dependent. pICL was replicated in Xenopus egg extracts containing human HSF2BP in the absence or presence of proteasome inhibitor MG-132. Recombinant His-FLAG-tagged ubiquitin was added to counteract ubiquitin depletion as a result of proteasome inhibition. Total extract samples were collected at the indicated time points and analyzed by immunoblotting. (C) HSF2BP-induced BRCA2 degradation is ICL repair-dependent. Experiment as in (A) was repeated with the pControl plasmid that has the same sequence as pICL, but no crosslink. Total extract samples were collected at the indicated time points and analyzed by immunoblotting. (D) Addition of MG-132 does rescue reduced level of BRCA2 at ICLs during repair. Crosslinked plasmids were replicated in the presence or absence of purified recombinant wild-type human HSF2BP, with and without MG-132 and His-FLAG-tagged ubiquitin. Samples were analyzed by BRCA2 ChIP using a primer pair for the ICL locus. (E) HSF2BP-induced ICL repair defect is not rescued upon addition of MG-132. ICL repair efficiency in Xenopus egg extract was measured in the presence or absence of purified recombinant wild-type human HSF2BP with and without MG-132 and His-FLAG-tagged ubiquitin. #, SapI fragments from contaminating uncrosslinked plasmid present in varying amounts in different pICL preparations. (F) Schematic depiction of the model explaining HSF2BP effects on the function of BRCA2 in DSB and ICL repair.

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