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ATCC reference identifiers additional information cell line human u2os cells atcc htb
Reference Identifiers Additional Information Cell Line Human U2os Cells Atcc Htb, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1347 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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reference identifiers additional information cell line human u2os cells atcc htb (ATCC)

ATCC reference identifiers additional information cell line human u2os cells atcc htb
Reference Identifiers Additional Information Cell Line Human U2os Cells Atcc Htb, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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reference identifiers additional information cell line human u2os atcc htb 96 cell line (ATCC)

ATCC reference identifiers additional information cell line human u2os atcc htb 96 cell line
$Figure 1. Protein aggregation is increased following a functional loss of ataxia telangiectasia mutated (ATM), ataxia telangiectasia and Rad3-related (ATR), and upon topoisomerase poisoning. See also Figure 1—figure supplement 1. (A) In-gel Coomassie staining of indicated fractions of cell extracts of WT and ATM KO <t>U2OS</t> cells. The relative amounts of each fraction loaded are indicated. (B) Quantification of (A). Circles depict individual experiments; gray dotted lines depict matched pairs. Wilcoxon matched-pairs signed-rank test. (C) Aggregated (silver stain) and whole-cell lysate (WCL; Coomassie) fractions of HEK293T cells treated transiently with chemical agents targeting the indicating proteins (see Table 1 for drugs and doses used; for etoposide [Etop]: 3 μM; for camptothecin [CPT]: 100 nM). See also Figure 1—figure supplement 1D. (D) Quantification of (C). Circles depict individual experiments. Two-tailed Student’s t-test with Bonferroni correction. (E) Protein fractions of HEK293T cells treated transiently with increasing amounts of CPT (20–100 nM) or Etop (0.6–3 μM). (F) Quantification of (E). Two-tailed Student’s t-test with Bonferroni correction. (G) Protein fractions of HEK293T cells treated transiently with CPT (40 nM) or Etop (1.5 μM), targeting TOP1 or TOP2, respectively, 24 hr or 72 hr after treatment. (H) Quantification of (G). Two-tailed Student’s t-test with Bonferroni correction. In (B), (D), (F), and (H), the red line indicates the mean.$
Reference Identifiers Additional Information Cell Line Human U2os Atcc Htb 96 Cell Line, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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reference identifiers additional information cell line human u2os atcc htb 96 (ATCC)

ATCC reference identifiers additional information cell line human u2os atcc htb 96
$Figure 1. Protein aggregation is increased following a functional loss of ataxia telangiectasia mutated (ATM), ataxia telangiectasia and Rad3-related (ATR), and upon topoisomerase poisoning. See also Figure 1—figure supplement 1. (A) In-gel Coomassie staining of indicated fractions of cell extracts of WT and ATM KO <t>U2OS</t> cells. The relative amounts of each fraction loaded are indicated. (B) Quantification of (A). Circles depict individual experiments; gray dotted lines depict matched pairs. Wilcoxon matched-pairs signed-rank test. (C) Aggregated (silver stain) and whole-cell lysate (WCL; Coomassie) fractions of HEK293T cells treated transiently with chemical agents targeting the indicating proteins (see Table 1 for drugs and doses used; for etoposide [Etop]: 3 μM; for camptothecin [CPT]: 100 nM). See also Figure 1—figure supplement 1D. (D) Quantification of (C). Circles depict individual experiments. Two-tailed Student’s t-test with Bonferroni correction. (E) Protein fractions of HEK293T cells treated transiently with increasing amounts of CPT (20–100 nM) or Etop (0.6–3 μM). (F) Quantification of (E). Two-tailed Student’s t-test with Bonferroni correction. (G) Protein fractions of HEK293T cells treated transiently with CPT (40 nM) or Etop (1.5 μM), targeting TOP1 or TOP2, respectively, 24 hr or 72 hr after treatment. (H) Quantification of (G). Two-tailed Student’s t-test with Bonferroni correction. In (B), (D), (F), and (H), the red line indicates the mean.$
Reference Identifiers Additional Information Cell Line Human U2os Atcc Htb 96, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 99 stars, based on 1 article reviews

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$Figure 1. Protein aggregation is increased following a functional loss of ataxia telangiectasia mutated (ATM), ataxia telangiectasia and Rad3-related (ATR), and upon topoisomerase poisoning. See also Figure 1—figure supplement 1. (A) In-gel Coomassie staining of indicated fractions of cell extracts of WT and ATM KO U2OS cells. The relative amounts of each fraction loaded are indicated. (B) Quantification of (A). Circles depict individual experiments; gray dotted lines depict matched pairs. Wilcoxon matched-pairs signed-rank test. (C) Aggregated (silver stain) and whole-cell lysate (WCL; Coomassie) fractions of HEK293T cells treated transiently with chemical agents targeting the indicating proteins (see Table 1 for drugs and doses used; for etoposide [Etop]: 3 μM; for camptothecin [CPT]: 100 nM). See also Figure 1—figure supplement 1D. (D) Quantification of (C). Circles depict individual experiments. Two-tailed Student’s t-test with Bonferroni correction. (E) Protein fractions of HEK293T cells treated transiently with increasing amounts of CPT (20–100 nM) or Etop (0.6–3 μM). (F) Quantification of (E). Two-tailed Student’s t-test with Bonferroni correction. (G) Protein fractions of HEK293T cells treated transiently with CPT (40 nM) or Etop (1.5 μM), targeting TOP1 or TOP2, respectively, 24 hr or 72 hr after treatment. (H) Quantification of (G). Two-tailed Student’s t-test with Bonferroni correction. In (B), (D), (F), and (H), the red line indicates the mean.$

Journal: eLife

Article Title: Targeting DNA topoisomerases or checkpoint kinases results in an overload of chaperone systems, triggering aggregation of a metastable subproteome

doi: 10.7554/elife.70726

Figure Lengend Snippet: Figure 1. Protein aggregation is increased following a functional loss of ataxia telangiectasia mutated (ATM), ataxia telangiectasia and Rad3-related (ATR), and upon topoisomerase poisoning. See also Figure 1—figure supplement 1. (A) In-gel Coomassie staining of indicated fractions of cell extracts of WT and ATM KO U2OS cells. The relative amounts of each fraction loaded are indicated. (B) Quantification of (A). Circles depict individual experiments; gray dotted lines depict matched pairs. Wilcoxon matched-pairs signed-rank test. (C) Aggregated (silver stain) and whole-cell lysate (WCL; Coomassie) fractions of HEK293T cells treated transiently with chemical agents targeting the indicating proteins (see Table 1 for drugs and doses used; for etoposide [Etop]: 3 μM; for camptothecin [CPT]: 100 nM). See also Figure 1—figure supplement 1D. (D) Quantification of (C). Circles depict individual experiments. Two-tailed Student’s t-test with Bonferroni correction. (E) Protein fractions of HEK293T cells treated transiently with increasing amounts of CPT (20–100 nM) or Etop (0.6–3 μM). (F) Quantification of (E). Two-tailed Student’s t-test with Bonferroni correction. (G) Protein fractions of HEK293T cells treated transiently with CPT (40 nM) or Etop (1.5 μM), targeting TOP1 or TOP2, respectively, 24 hr or 72 hr after treatment. (H) Quantification of (G). Two-tailed Student’s t-test with Bonferroni correction. In (B), (D), (F), and (H), the red line indicates the mean.

Article Snippet: DOI: https://doi.org/10.7554/eLife.70726 18 of 29 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Cell line (human) U2OS ATCC HTB- 96 Cell line (human) U2OS ATM KO This study See ‘Mammalian cell culture’ Cell line (human) U2OS + HSPB5 This study See ‘Mammalian cell culture’ Cell line (human) U2OS ATM KO + HSPB5 This study See ‘Mammalian cell culture’ Cell line (human) Phoenix- Ampho ATCC RRID:CVCL_H716 Retrovirus packaging cell line Antibody GFP (mouse, monoclonal) Takara Bio Clontech 632380 WB (1:5000) Antibody ATM (mouse, monoclonal) Santa Cruz Sc- 23921 WB (1:200) Antibody HSPB5 (mouse, monoclonal) StressMarq SMC- 159 WB (1:2000) Antibody HSPB5 (mouse, monoclonal) StressMarq SMC- 165 IF (1:200) Antibody GAPDH (mouse, monoclonal) Fitzgerald 10R- G109a WB (1:10,000) Antibody TUB (mouse, monoclonal) Sigma- Aldrich T5138 WB (1:4000) Antibody HDAC1 (mouse, monoclonal) DSHB PCPR- HDAC1- 2E12 WB (0.5 μg/ml) Antibody MCM7 (Mmouse, monoclonal) Santa Cruz 47DC141 WB (1:100) Antibody TUBA1A (mouse, monoclonal) Sigma- Aldrich T5168 WB (1:2000) Antibody FUS (mouse, monoclonal) Santa Cruz Sc- 47711 IF (1:200) Antibody 53BP1 (rabbit, monoclonal) Santa Cruz Sc- 22760 IF (1:150) Antibody 53BP1 (rabbit, monoclonal) Bethyl A300- 272A IF (1:500) Antibody HSP70 (mouse, monoclonal) StressMarq SMC- 104A IF (1:100) Antibody HSP90 (mouse, monoclonal) StressMarq SMC- 149 IF (1:100) Recombinant DNA reagent pQCXIN–HSPB5 (plasmid) PMID:20843828 Recombinant DNA reagent ATM CRISPR/Cas9 KO (plasmid) Santa Cruz sc- 400192 Recombinant DNA reagent ATM HDR (plasmid) Santa Cruz sc- 400192- HDR Sequence- based reagent HEK293Q71F (forward primer) This study PCR primer GAGTCC CTCAAG TCCTTCC Sequence- based reagent HEK293Q71R (reverse primer) This study PCR primer AAACGG GCCCTC TAGACTC Commercial assay or kit Silver stain kit Pierce (Thermo Scientific) 24612 Commercial assay or kit Allprep DNA/RNA isolation mini kit QIAGEN 80004 Commercial assay or kit S- trap micro Protifi K02- micro- 10 Commercial assay or kit Masterpure Complete DNA and RNA purificiation kit Epicentre (supplied through Lucigen) MC85200 Commercial assay or kit QuantSeq 3’ mRNA- Seq library prep kit (FWD) Lexogen 015.96 Chemical compound, drug Camptothecin Selleckchem S1288 See Table 1 Chemical compound, drug Etoposide Sigma- Aldrich E1383 See Table 1 Chemical compound, drug TDP1 inhibitor Merck 532177 See Table 1 Continued Continued on next page Huiting et al. eLife 2022;11:e70726.

Techniques: Functional Assay, Staining, Silver Staining, Two Tailed Test

$Figure 2. Camptothecin (CPT) and ataxia telangiectasia mutated (ATM) loss drives aggregation in a cell-type-dependent manner. See also Figure 2— figure supplement 1. (A) Volcano plot of label-free quantification (LFQ) MS/MS analysis of the aggregated fractions of DMSO and CPT-treated HEK293T cells. n = 4. Only proteins identified in >1 repeats of either case or control are shown. (B) Volcano plot of LFQ MS/MS analysis of the aggregated fractions of DMSO and ATM inhibitor-treated HEK293T cells. n = 4. Only proteins identified in >1 repeats of either case or control are shown. (C) Venn diagram showing overlap between U2OS and HEK293T increased aggregation, after the indicated treatments. (D) Western blot using the indicated antibodies on the aggregated and whole-cell lysate (WCL) fractions of drug-treated and ATM KO HEK293 cells, and wild-type U2OS cells. n = 2. (E) GO term analysis (Function) of the increased aggregation in CPT- or ATM-inhibitor-treated HEK293T cells. (F) Venn diagram showing overlap between increased aggregation after the indicated treatments in HEK293T cells and baseline aggregation in U2OS cells. (G) Aggregated (silver stain) and WCL (Coomassie) fractions of untreated HEK293T and U2OS cells. n = 2.$

Journal: eLife

Article Title: Targeting DNA topoisomerases or checkpoint kinases results in an overload of chaperone systems, triggering aggregation of a metastable subproteome

doi: 10.7554/elife.70726

Figure Lengend Snippet: Figure 2. Camptothecin (CPT) and ataxia telangiectasia mutated (ATM) loss drives aggregation in a cell-type-dependent manner. See also Figure 2— figure supplement 1. (A) Volcano plot of label-free quantification (LFQ) MS/MS analysis of the aggregated fractions of DMSO and CPT-treated HEK293T cells. n = 4. Only proteins identified in >1 repeats of either case or control are shown. (B) Volcano plot of LFQ MS/MS analysis of the aggregated fractions of DMSO and ATM inhibitor-treated HEK293T cells. n = 4. Only proteins identified in >1 repeats of either case or control are shown. (C) Venn diagram showing overlap between U2OS and HEK293T increased aggregation, after the indicated treatments. (D) Western blot using the indicated antibodies on the aggregated and whole-cell lysate (WCL) fractions of drug-treated and ATM KO HEK293 cells, and wild-type U2OS cells. n = 2. (E) GO term analysis (Function) of the increased aggregation in CPT- or ATM-inhibitor-treated HEK293T cells. (F) Venn diagram showing overlap between increased aggregation after the indicated treatments in HEK293T cells and baseline aggregation in U2OS cells. (G) Aggregated (silver stain) and WCL (Coomassie) fractions of untreated HEK293T and U2OS cells. n = 2.

Techniques: Quantitative Proteomics, Tandem Mass Spectroscopy, Control, Western Blot, Silver Staining

$Figure 5. The lowered aggregation threshold caused by topoisomerase poisoning or a loss of ataxia telangiectasia mutated (ATM) is accompanied by a rewiring and aggregation of known interacting (co)chaperones. See also Figure 5—figure supplements 1 and 2. (A) Presence of (co)chaperones in the aggregated protein fractions in HEK293T cells. Left panel: Venn diagram showing the overlap in aggregating chaperones. Right panel: graph depicting the overlap in aggregating chaperones in detail. (B) Pie charts showing the presence of HSPA1A and HSPA8 clients in aggregated protein fractions compared to clients present in both NIA fractions. See text for reference; only clients identified in at least two out of three repeats in Lee et al. were taken into account here. (C) Table showing the number of (co)chaperones logged in BioGRID as interacting with NIA and aggregating protein fractions. (D) See also (A): only (co)chaperones aggregating in both HEK293T experimental set-ups or significantly more in one of them are shown here. BioGRID (co)chaperone interactions with the aggregated proteins identified in this study, per (co)chaperone. Darker colors represent a higher percentage of proteins with a reported binding to that (co)chaperone. See Figure 5—figure supplement 2 for a complete overview. (E) Volcano plot showing protein levels of (co)chaperones in camptothecin (CPT)-treated HEK293T cells compared to DMSO-treated cells. (F) Differentially expressed (co)chaperones in CPT-treated HEK293T cells compared to DMSO-treated cells based on RNAseq data. (G) Western blot analysis using the indicated antibodies on the whole-cell lysate (WCL) fractions of HEK293T cells after the indicated time and treatment. HS, heat shock (2 hr at 43°C incubator). n = 2. (H) Graph showing (co)chaperones whose genes show a differential expression in both CPT-treated HEK293T cells compared to DMSO-treated HEK293T cells and in untreated U2OS compared to untreated HEK293T cells.$

Journal: eLife

Article Title: Targeting DNA topoisomerases or checkpoint kinases results in an overload of chaperone systems, triggering aggregation of a metastable subproteome

doi: 10.7554/elife.70726

Figure Lengend Snippet: Figure 5. The lowered aggregation threshold caused by topoisomerase poisoning or a loss of ataxia telangiectasia mutated (ATM) is accompanied by a rewiring and aggregation of known interacting (co)chaperones. See also Figure 5—figure supplements 1 and 2. (A) Presence of (co)chaperones in the aggregated protein fractions in HEK293T cells. Left panel: Venn diagram showing the overlap in aggregating chaperones. Right panel: graph depicting the overlap in aggregating chaperones in detail. (B) Pie charts showing the presence of HSPA1A and HSPA8 clients in aggregated protein fractions compared to clients present in both NIA fractions. See text for reference; only clients identified in at least two out of three repeats in Lee et al. were taken into account here. (C) Table showing the number of (co)chaperones logged in BioGRID as interacting with NIA and aggregating protein fractions. (D) See also (A): only (co)chaperones aggregating in both HEK293T experimental set-ups or significantly more in one of them are shown here. BioGRID (co)chaperone interactions with the aggregated proteins identified in this study, per (co)chaperone. Darker colors represent a higher percentage of proteins with a reported binding to that (co)chaperone. See Figure 5—figure supplement 2 for a complete overview. (E) Volcano plot showing protein levels of (co)chaperones in camptothecin (CPT)-treated HEK293T cells compared to DMSO-treated cells. (F) Differentially expressed (co)chaperones in CPT-treated HEK293T cells compared to DMSO-treated cells based on RNAseq data. (G) Western blot analysis using the indicated antibodies on the whole-cell lysate (WCL) fractions of HEK293T cells after the indicated time and treatment. HS, heat shock (2 hr at 43°C incubator). n = 2. (H) Graph showing (co)chaperones whose genes show a differential expression in both CPT-treated HEK293T cells compared to DMSO-treated HEK293T cells and in untreated U2OS compared to untreated HEK293T cells.

Techniques: Binding Assay, Western Blot, Quantitative Proteomics

$Figure 6. Protein aggregation triggered by genotoxic stress is amenable to modulation by chaperones. See also Figure 6—figure supplements 1 and 2. (A) Western blot of whole-cell lysate (WCL) and aggregated proteins isolated from HEK293T cells treated transiently with DMSO or camptothecin (CPT), followed by treatment with the VER-155008 HSP70 inhibitor (10 μM), probed with the indicated antibodies. n = 3. (B) Aggregated (silver stain) and WCL (Coomassie) fractions of U2OS wild-type and ATM KO cells, with or without overexpression of HSPB5. (C) Quantification of (B). (D) Representative immunofluorescence pictures of U2OS wild-type and ATM KO cells stably overexpressing HSPB5 or not, stained with ProteoStat (red) and Hoechst (blue). (E) Quantification of aggresome signatures in (D). (F). Representative immunofluorescence pictures of U2OS wild-type and ATM KO cells stably overexpressing HSPB5 or not, stained with anti-FUS (green) and Hoechst (blue). (G) Quantification of extranuclear FUS inclusions in (F). (H) Aggregated (silver stain) and WCL (Coomassie) fractions of HEK293 cells stably overexpressing HSPB5 or not, treated transiently with DMSO or CPT. Three technical repeats are shown here. (I) Quantification of three independent biological repeats of (H). In (C), (E), (G), and (I), squares represent independent biological repeats, bars represent mean ± SEM. p-Values are obtained by two-tailed Student’s t-tests followed by a Bonferroni correction for multiple comparisons.$

Journal: eLife

Article Title: Targeting DNA topoisomerases or checkpoint kinases results in an overload of chaperone systems, triggering aggregation of a metastable subproteome

doi: 10.7554/elife.70726

Figure Lengend Snippet: Figure 6. Protein aggregation triggered by genotoxic stress is amenable to modulation by chaperones. See also Figure 6—figure supplements 1 and 2. (A) Western blot of whole-cell lysate (WCL) and aggregated proteins isolated from HEK293T cells treated transiently with DMSO or camptothecin (CPT), followed by treatment with the VER-155008 HSP70 inhibitor (10 μM), probed with the indicated antibodies. n = 3. (B) Aggregated (silver stain) and WCL (Coomassie) fractions of U2OS wild-type and ATM KO cells, with or without overexpression of HSPB5. (C) Quantification of (B). (D) Representative immunofluorescence pictures of U2OS wild-type and ATM KO cells stably overexpressing HSPB5 or not, stained with ProteoStat (red) and Hoechst (blue). (E) Quantification of aggresome signatures in (D). (F). Representative immunofluorescence pictures of U2OS wild-type and ATM KO cells stably overexpressing HSPB5 or not, stained with anti-FUS (green) and Hoechst (blue). (G) Quantification of extranuclear FUS inclusions in (F). (H) Aggregated (silver stain) and WCL (Coomassie) fractions of HEK293 cells stably overexpressing HSPB5 or not, treated transiently with DMSO or CPT. Three technical repeats are shown here. (I) Quantification of three independent biological repeats of (H). In (C), (E), (G), and (I), squares represent independent biological repeats, bars represent mean ± SEM. p-Values are obtained by two-tailed Student’s t-tests followed by a Bonferroni correction for multiple comparisons.

Techniques: Western Blot, Isolation, Silver Staining, Over Expression, Immunofluorescence, Stable Transfection, Staining, Two Tailed Test