Journal: Human Molecular Genetics

Article Title: PD-linked CHCHD2 mutations impair CHCHD10 and MICOS complex leading to mitochondria dysfunction

doi: 10.1093/hmg/ddy413

Figure Lengend Snippet: Generation of human isogenic lines harboring PD-related CHCHD2 mutants. ( A ) PD-associated CHCHD2 mutants T61I, Q126X and R145Q on functional domains of human CHCHD2 protein. CHCH domain. ( B ) Schematic overview depicting human CHCHD2 locus and Cas9 targeting strategy with designed guide RNA recognized exon 3 sequences in human CHCHD2 locus. ( C ) Sanger sequencing chromatogram showing the heterozygous point mutation leading to Q126X+/−. Representative results from Q10 were shown. ( D ) Sanger sequencing chromatogram on the reverse DNA strand showing the heterozygous point mutation leading to R145Q+/− (R4), the homozygous point mutant leading to R145Q−/− (R17) at the targeting locus of H9 (+/+) hESCs. * the blocking nonsense mutation to enhance the specificity of Cas9 system.

Article Snippet: Non-tagged and C-terminal myc-tagged CHCHD2 plasmids were from Origene.

Techniques: Functional Assay, Sequencing, Mutagenesis, Blocking Assay

Journal: Human Molecular Genetics

Article Title: PD-linked CHCHD2 mutations impair CHCHD10 and MICOS complex leading to mitochondria dysfunction

doi: 10.1093/hmg/ddy413

Figure Lengend Snippet: CHCHD2 Q126X/R145Q mutants caused mitochondria dysfunction as transient CHCHD2 knockdown. ( A – C ) The function of mitochondria electron respiration complex was reflected by OCR on isogenic R4 (R145Q+/−) or R10, R17 (R145Q−/−) hESCs (A), on isogenic Q13, Q35 (Q126X+/−) hESCs (B) and on dopaminergic SK-N-SH cells transiently transfected with CHCHD2 siRNA (C). Quantification of basal respiration, ATP turnover, maximum respiration capacity and proton leak were shown. Representative results from independent biological replicates were shown. ( D ) The abundance of OXPHOS enzymes of H9 (+/+), Q10 (Q126X+/−), R4 (R145Q+/−) and R17 (R145Q−/−) hESCs shown by total OXPHOS antibody cocktail. Complex I–V were labeled accordingly. Equal amount of protein was loaded in each lane. ( E ) The abundance of OXPHOS enzymes of H9 (+/+), Q10 (Q126X+/−), R4 (R145Q+/−) and R17 (R145Q−/−) NPCs shown by total OXPHOS antibody cocktail. Actin served as loading control.

Article Snippet: Non-tagged and C-terminal myc-tagged CHCHD2 plasmids were from Origene.

Techniques: Transfection, Labeling

Journal: Human Molecular Genetics

Article Title: PD-linked CHCHD2 mutations impair CHCHD10 and MICOS complex leading to mitochondria dysfunction

doi: 10.1093/hmg/ddy413

Figure Lengend Snippet: Super-resolution microscope revealed CHCHD2 localized in the MICOS complex of mitochondria. ( A ) Upper panel: immunostaining of endogenous CHCHD2 (green) in SK-N-SH cells co-stained with ER marker KDEL (purple), MitoTracker (Mito, red) and DAPI (blue). Lower panel: immunostaining of overexpressed non-tagged CHCHD2 (green) in SK-N-SH cells co-stained with autophagy–lysosomal marker LAMP1 (red), MitoTracker (Mito, purple) and DAPI (blue). The boxed regions were zoomed to show the details. Scale bar, 10 μm. ( B – D ) Immunostaining of the mitochondria network of SK-N-SH cells shown by two-color STED microscopy. Endogenous CHCHD2 (green) and Mitofilin (red) was shown. The boxed region of the upper panel was enlarged and shown in the lower panel and right panel. Averaged intensity profiles for CHCHD2 (green) and Mitofilin (red) across the indicated mitochondrial tubule sections within the respective boxed area in the magnification lower panel were shown in (C) and (D). Scale bar, 5 μm (upper panel) and 1 μm (lower panel). ( E – G ) Immunostaining of the mitochondria network of SK-N-SH cells by dual-color STED microscopy. Endogenous CHCHD2 (red) and MINOS1 (green) were shown. The boxed region of the upper panel was enlarged and shown in the lower panel and right panel. Averaged intensity profiles for CHCHD2 (red) and MINOS1 (green) across the indicated mitochondrial tubule sections within the respective boxed area were shown in (F) and (G). Scale bar, 5 μm (upper panel) and 1 μm (lower panel). ( H ) Immunostaining of SK-N-SH cells transiently transfected with non-tagged CHCHD2 WT/T61I/R145Q/Q126X plasmids, co-stained with Mitofilin (red) and CHCHD2 (green) by a CHCHD2 antibody against a middle region of CHCHD2 (labeled as CHCHD2-TF). Scale bar, 10 μm.

Article Snippet: Non-tagged and C-terminal myc-tagged CHCHD2 plasmids were from Origene.

Techniques: Microscopy, Immunostaining, Staining, Marker, Transfection, Labeling

Journal: Human Molecular Genetics

Article Title: PD-linked CHCHD2 mutations impair CHCHD10 and MICOS complex leading to mitochondria dysfunction

doi: 10.1093/hmg/ddy413

Figure Lengend Snippet: PD-related CHCHD2 mutants disrupted MICOS as CHCHD2 knockdown. ( A ) Ultrastructure analysis by transmission electronic microscopy of isogenic NPCs harboring Q126X or R145Q. Representative results from H9 (+/+), Q10 (Q126X+/−), R4 (R145Q+/−) and R17 (R145Q−/−) were shown. Scale bar, 200 nm. ( B ) Ultrastructure analysis by transmission electronic microscopy of SK-N-SH cells transiently transfected with CHCHD2 siRNA and control siRNA. Scale bar, 200 nm. ( C ) Expression of CHCHD2, CHCHD10 and MICOS components Mitofilin, MINOS1 in SK-N-SH cells transiently transfected with CHCHD2 siRNA and control siRNA. Actin served as loading control. ( D – G ) Quantification of protein abundance of CHCHD2 (D), Mitofilin (E), MINOS1 (F) and CHCHD10 (G) in SK-N-SH cells transiently transfected with CHCHD2 siRNA and control siRNA. Actin served as internal control. Data are presented as mean ± SEM. n = 3. Paired t -test was used. (D), *** P = 0.0002; (E), ** P = 0.0015; (F), * P = 0.0478; (G), * P = 0.0141. ( H and I ) Expression of CHCHD2 and MICOS components in hESCs of H9, isogenic lines harboring CHCHD2 Q126X or R145Q. Actin served as loading control. CHCHD2-TF, antibody against the middle-epitope of CHCHD2; CHCHD2, antibody against C-terminus epitope of CHCHD2. ( J ) Expression of CHCHD2 and MICOS components in derived NPCs from H9, isogenic lines harboring CHCHD2 Q126X or R145Q. Actin served as loading control. Representative blots were shown.

Article Snippet: Non-tagged and C-terminal myc-tagged CHCHD2 plasmids were from Origene.

Techniques: Transmission Assay, Microscopy, Transfection, Expressing, Derivative Assay

Journal: Human Molecular Genetics

Article Title: PD-linked CHCHD2 mutations impair CHCHD10 and MICOS complex leading to mitochondria dysfunction

doi: 10.1093/hmg/ddy413

Figure Lengend Snippet: PD-linked CHCHD2 mutants showed reduced binding to CHCHD10. ( A ) Co-immunoprecipitation of endogenous CHCHD2 by antibody against CHCHD2 in SK-N-SH cells. WCL: whole cell lysate, 5% total protein used in co-IP experiment. ( B ) Co-immunoprecipitation of endogenous CHCHD10 by antibody against CHCHD10 in SK-N-SH cells. WCL: whole cell lysate, 5% total protein used in co-IP experiment. ( C ) Co-immunoprecipitation of endogenous CHCHD2 by antibody against CHCHD2 in human brain tissue lysates. ( D ) Co-immunoprecipitation of CHCHD2 by a CHCHD2 antibody against middle region of CHCHD2 (labeled as CHCHD2-TF) in SK-N-SH cells transfected with non-tagged CHCHD2 WT/T61I/R145Q/Q126X. WCL: whole cell lysate, 5% total protein used in co-IP experiment. Lower arrow pointed to CHCHD2 Q126X and higher arrow pointed to full length CHCHD2. ( E ) Co-immunoprecipitation of CHCHD2 by a CHCHD2 antibody against middle region of CHCHD2 (labeled as CHCHD2-TF) in hESCs of H9 and isogenic lines harboring homozygous R145Q (−/−).WCL: whole cell lysate, 5% total protein used in co-IP experiment. Arrow pointed to CHCHD10. Representative results from R10 and R17 (R145Q−/−) were shown. ( F ) Quantification of protein abundance of CHCHD10 normalized with CHCHD2 on the co-immunoprecipitation complex from isogenic hESC lysates.

Article Snippet: Non-tagged and C-terminal myc-tagged CHCHD2 plasmids were from Origene.

Techniques: Binding Assay, Immunoprecipitation, Co-Immunoprecipitation Assay, Labeling, Transfection

Journal: Human Molecular Genetics

Article Title: PD-linked CHCHD2 mutations impair CHCHD10 and MICOS complex leading to mitochondria dysfunction

doi: 10.1093/hmg/ddy413

Figure Lengend Snippet: CHCHD2 and CHCHD10 maintained MICOS intergrity. ( A – C ) Immunostaining of the mitochondria by two-color super-resolution STED microscopy on of SK-N-SH cells transfected with non-tagged CHCHD2 WT (red), co-stained with CHCHD10 (green). The boxed region of the upper panel was enlarged and shown in the lower panel. Averaged intensity profiles for CHCHD10 (green) (B) and CHCHD2 (red) (C) across the indicated mitochondrial tubule sections within the respective boxed area in the magnification lower panel were shown. Scale bar, 5 μm (upper panel) and 1 μm (lower panel). ( D ) Immunostaining of CHCHD2 (red) and CHCHD10 (green) in substantial nigra (SubN) region of mouse brain slides. Boxed region was zoomed to show in right panel. Scale bar, 100 μm (left panel) and 10 μm (right panel). ( E ) Immunostaining of CHCHD2 (red) and dopaminergic neuron marker TH (green) in substantial nigra (SubN) region of mouse brain slides. Boxed region was zoomed to show in right panel. Scale bar, 100 μm (left panel) and 10 μm (right panel). ( F ) Immunostaining of CHCHD10 (red) and dopaminergic neuron marker TH (green) in substantial nigra region of mouse brain slides. Boxed region was zoomed to show as right panel. Scale bar, 100 μm (left panel) and 10 μm (right panel). (G) Ultrastructure analysis by transmission electronic microscopy of SK-N-SH cells transiently transfected with CHCHD10 siRNA and control siRNA. Scale bar, 200 nm. ( H – J ) Expression of CHCHD10 and CHCHD2 in SK-N-SH cells transiently transfected with CHCHD10 siRNA and control siRNA. The quantification of protein abundance of CHCHD10 (I) and CHCHD2 (J) were shown. Data are presented as mean ± SEM. Actin served as internal control. Results were from three independent biological replicates. Paried t -test was used. (I), * P = 0.038; (J), * P = 0.0410. ( K ) Expression of MICOS components Mitofilin, MINOS1 and CHCHD10 in SK-N-SH cells transiently transfected with CHCHD10 siRNA and control siRNA. Actin served as loading control. The blots were representative from three independent biological replicates.

Article Snippet: Non-tagged and C-terminal myc-tagged CHCHD2 plasmids were from Origene.

Techniques: Immunostaining, Microscopy, Transfection, Staining, Marker, Transmission Assay, Expressing

Journal: Human Molecular Genetics

Article Title: PD-linked CHCHD2 mutations impair CHCHD10 and MICOS complex leading to mitochondria dysfunction

doi: 10.1093/hmg/ddy413

Figure Lengend Snippet: CHCHD2 mutants reduced mitochondria transcription factor TFAM and mitochondrial targeted peptide Elamipretide/MTP-131 boosted CHCHD2 and MICOS components in isogenic R4 (R145Q+/−) NPCs. ( A and B ) Expression of TFAM and CHCHD2 in isogenic R10 (R145Q−/−), R17 (R145Q−/−) hESCs (A) and isogenic Q10 (Q126X+/−) hESCs (B). (C) Expression of CHCHD2 and TFAM in SK-N-SH cells transiently transfected with CHCHD2 siRNA and control siRNA. Actin served as loading control. Quantification of band density of TFAM normalized with Actin in SK-N-SH cells transiently transfected with CHCHD2 siRNA and control siRNA. Actin served as loading control. Data are presented as mean ± SEM. * P = 0.0121, n = 4. ( D and E ) Immunostaining of the mitochondria of SK-N-SH cells by dual-color super-resolution STED microscopy. Endogenous CHCHD2 (green) and TFAM (red) were shown in D, and endogenous CHCHD2 (green) and DNA (red) was shown in E. The boxed regions were enlarged and shown. Averaged intensity profiles for CHCHD2 (green) and TFAM/DNA (red) across the indicated mitochondrial tubule sections within the respective boxed area in the magnification lower panel were shown in (D) and (E). Scale bar, 1 μm (lower panel). ( F ) Expression of CHCHD2, CHCHD10 and MINOS1 in isogenic NPCs R4 (R145Q+/−) treated with Elamipretide/MTP-131 for 24 h. Quantification of CHCHD2 protein abundance was shown. Actin served as internal control. Data are presented as mean ± SEM. Five independent biological replicates were shown. Paired t -test was used. ** P = 0.0017; * P = 0.0368. ( G ) Expression of CHCHD2 and MINOS1 in isogenic NPCs R17 (R145Q−/−) treated with Elamipretide/MTP-131 for 24 h. Quantification of CHCHD2 protein abundance was shown. Actin served as internal control. Data are presented as mean ± SEM. Five independent biological replicates were shown. Paired t -test was used. ** P = 0. 0029; ns = not significant. ( H ) The abundance of OXPHOS enzymes on R4 (R145Q+/−) NPC cells treated with Elamipretide/MTP-131 for 24 h. Actin served as loading control. Data are presented as mean ± SEM. Representative blots from four independent biological replicates were shown. The quantification of Complex I-NDUFB8, normalized with actin was shown. * P = 0.043; ns = not significant.

Article Snippet: Non-tagged and C-terminal myc-tagged CHCHD2 plasmids were from Origene.

Techniques: Expressing, Transfection, Immunostaining, Microscopy

Journal: Human Molecular Genetics

Article Title: PD-linked CHCHD2 mutations impair CHCHD10 and MICOS complex leading to mitochondria dysfunction

doi: 10.1093/hmg/ddy413

Figure Lengend Snippet: Illustration of the pathophysiological role of CHCHD2 in MICOS. Mitochondria are separated from cytosol by mitochondria OM. Mitochondria IM separates the matrix from inter-membrane space. MICOS complex composing of Mitofilin, CHCHD3, CHCHD6 and MINOS1, was responsible for cristae morphology and maintenance in the mitochondria inner member. CHCHD2 binds to CHCHD10. However, PD-linked CHCHD2 mutants (showed in red with ‘ * ’) have impaired binding with CHCHD10, causing a reduced MICOS, with loss of mitochondria cristae, loss of mitochondria OXPHOS complexes, reduced oxygen consumption of mitochondria and decreased mitochondria transcription factor TFAM. A mitochondrial targeted peptide Elamipretide/MTP-131 was able to enhance CHCHD2, CHCHD10 and MICOS components with the abundance of mitochondria OXPHOS enzymes in cells harboring heterozygous R145Q.

Article Snippet: Non-tagged and C-terminal myc-tagged CHCHD2 plasmids were from Origene.

Techniques: Binding Assay

Journal: Nature Cell Biology

Article Title: RPA exhaustion activates SLFN11 to eliminate cells with heightened replication stress

doi: 10.1038/s41556-025-01852-1

Figure Lengend Snippet: a , An experimental scheme depicting how targeted CRISPR–Cas9 screens performed. Two separate screens were performed in biological triplicates utilizing pool 1 sgRNA library (1,117 genes targeted) or pool 2 sgRNA library (288 genes targeted). b , A volcano plot depicting a measure of statistical significance (−log 10 (MaGeCK score)) plotted against log 2 (fold-change) in abundance of sgRNAs targeting indicated genes in cisplatin-treated versus untreated conditions in eHAP iCas9 WT cells infected with the pool 2 sgRNA library. Labelled genes are coloured based on the DDR pathway in which they operate. c , A Venn diagram comparing genes scoring as significantly depleted in cisplatin-treated arms of the screen depicted in b performed in eHAP cells (yellow) and those in a genome-wide CRISPR–Cas9 dropout screen performed in RPE-1 p53 KO cells (blue) in ref. . d , A western blot depicting loss of PrimPol protein in an isogenic eHAP iCas9 PrimPol KO clone. e , Population doublings of eHAP iCas9 WT (grey) and PrimPol KO (red) cells plotted against time to demonstrate cell growth in the absence (squares) or presence of 450 nM (circles) or 550 nM (triangles) cisplatin. Growth curve experiments were performed in n = 2 biological replicates. Data are presented as means. f , Experimental scheme for a Cell Titer Glo viability assay to determine the cisplatin sensitivity of eHAP iCas9 WT or PrimPol KO cells complemented with WT PrimPol, PrimPol AxA (catalytic mutant Asp114Ala, Glu116Ala) or PrimPol CH (primase mutant Cys419Gly, His426Tyr). g , A western blot depicting PrimPol protein levels in eHAP iCas9 WT cells or PrimPol KO cells complemented with WT PrimPol, PrimPol AxA or PrimPol CH mutants. Exogenous protein levels were downregulated using the misFIT expression tuner system. h , Cell viability measured using the Cell Titer Glo assay on treatment of the indicated doses of cisplatin over 5 d. These experiments were performed in n = 4 biological replicates. Data are presented as mean ± s.d. i , Experimental scheme for a Cell Titer Glo assay to determine cell viability of eHAP iCas9 WT or PrimPol KO cells challenged with the indicated drugs. j , Cell viability measured after challenging eHAP iCas9 WT or PrimPol KO cells with the indicated doses of BPDE. Experiments were performed in n = 3 biological replicates. Data are presented as mean ± s.d. k , Cell viability measured after challenging eHAP iCas9 WT or PrimPol KO cells with the indicated doses of MMC. Experiments were performed in n = 3 biological replicates. Data are presented as mean ± s.d. l , A heatmap depicting sensitivity of eHAP iCas9 PrimPol KO versus WT cells to various DNA-damaging agents and inhibitors to DDR proteins. Sensitivities were determined by computing the log 2 (fold-change) between half-maximal inhibitory concentration (IC 50 ) values of PrimPol KO and WT cells. Source numerical data and unprocessed blots are available in the source data. ATMi, ataxia-telangiectasia mutated (ATM) inhibitor; ATRi, ATR inhibitor; FC, fold-change; HU, hydroxyurea; MMS, methyl methane sulfonate; Rad51i, Rad51 inhibitor; TS, template switching.

Article Snippet: PrimPol cDNA was purchased from OriGene (catalogue number SC100629).

Techniques: CRISPR, Infection, Genome Wide, Western Blot, Viability Assay, Mutagenesis, Expressing, Glo Assay, Concentration Assay

Journal: Nature Cell Biology

Article Title: RPA exhaustion activates SLFN11 to eliminate cells with heightened replication stress

doi: 10.1038/s41556-025-01852-1

Figure Lengend Snippet: ( a ) DECODR analysis of Sanger sequencing of the PRIMPOL PR sgRNA cut site in eHAP iCas9 PRIMPOL KO C1 cells showing the cells habour a -2 bp deletion. ( b ) Experimental scheme for assessing inducible Cas9 activity using a lentiviral BFP/GFP flow cytometry reporter assay. ( c ) Representative gating strategy for all flow cytometry experiments conducted in this study. ( d ) Flow cytometry of eHAP iCas9 WT or PRIMPOL KO C1 cells infected with the BFP/GFP reporter shown in (B) in the presence or absence of doxycycline. ( e ) Sanger sequencing of the PRIMPOL AxA mutant (D114A/E116A) cDNA. ( f ) Sanger sequencing of the PRIMPOL CH mutant (C419H/H426Y) cDNA. ( g ) Scheme for introducing microRNA response elements (MREs) into the 3’ UTRs of PRIMPOL expression constructs to fine-tune protein expression levels. ( h ) A Western blot showing PRIMPOL expression levels in eHAP iCas9 WT (lane 1) or PRIMPOL KO cells transiently transfected with PRIMPOL expression constructs containing indicated MREs. ( i ) Dose response curves for eHAP iCas9 WT or PRIMPOL KO cells challenged with indicated concentrations of the PARP inhibitor Olaparib. ( j ) Dose response curves for eHAP iCas9 WT or PRIMPOL KO cells challenged with indicated concentrations of the DNA polymerase inhibitor aphidicolin. ( k ) Dose response curves for eHAP iCas9 WT or PRIMPOL KO cells challenged with indicated concentrations of the DNA polymerase alpha inhibitor ST1926. ( l ) Dose response curves for eHAP iCas9 WT or PRIMPOL KO cells challenged with indicated concentrations of bleomycin. ( m ) Dose response curves for eHAP iCas9 WT or PRIMPOL KO cells challenged with indicated concentrations of the methyl methane sulfonate (MMS). ( n ) Dose response curves for eHAP iCas9 WT or PRIMPOL KO cells challenged with indicated concentrations of the RAD51 inhibitor B02. ( o ) Dose response curves for eHAP iCas9 WT or PRIMPOL KO cells challenged with indicated concentrations of the ribonucleotide reductase inhibitor hydroxyurea (HU). ( p ) Dose response curves for eHAP iCas9 WT or PRIMPOL KO cells challenged with indicated concentrations of the ATR inhibitor AZD6738. ( q ) Dose response curves for eHAP iCas9 WT or PRIMPOL KO cells challenged with indicated concentrations of the topoisomerase I inhibitor camptothecin (CPT). ( r ) Dose response curves for eHAP iCas9 WT or PRIMPOL KO cells challenged with indicated concentrations of ATM inhibitor KU-5593. All experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. Source numerical data and unprocessed blots are available in the source data.

Article Snippet: PrimPol cDNA was purchased from OriGene (catalogue number SC100629).

Techniques: Sequencing, Activity Assay, Flow Cytometry, Reporter Assay, Infection, Mutagenesis, Expressing, Construct, Western Blot, Transfection

Journal: Nature Cell Biology

Article Title: RPA exhaustion activates SLFN11 to eliminate cells with heightened replication stress

doi: 10.1038/s41556-025-01852-1

Figure Lengend Snippet: a , A volcano plot measuring statistical significance against log 2 (fold-change) in sgRNA counts in eHAP iCas9 PrimPol KO cells versus WT cells in the cisplatin-treated arm of the pool 1 sgRNA screen on day 6. Labelled genes exhibited increased sgRNA counts in PrimPol KO cells versus WT cells. b , A volcano plot measuring statistical significance against log 2 (fold-change) in sgRNA counts in eHAP iCas9 PrimPol KO cells versus WT cells in the cisplatin-treated arm of the pool 2 sgRNA screen on day 6. Genes labelled in blue exhibited increased sgRNA counts whereas genes labelled in red exhibited decreased sgRNA counts in PrimPol KO cells versus WT cells. c , A histogram of curated messenger RNA sequencing data depicting the expression of SLFN11 in human cancer cell lines curated from the DepMap repository. d , A western blot (WB) showing SLFN11 and PrimPol expression levels in HeLa, U2OS, HCT116, A549, HEK293A, DU145, eHAP and A673 cells infected with lentiviruses harbouring either Cas9–AAVS1 or Cas9–PrimPol. e , Experimental scheme showing how HeLa, U2OS, HCT116, A549, HEK293A, DU145, eHAP and A673 cells infected with Cas9–sgAAVS1 or Cas9–sgPrimPol were challenged with cisplatin and cell viability measured using the Cell Titer Glo assay. f – n , Cisplatin dose–response curves for HeLa Kyoto ( f ), U2OS ( g ), HCT116 ( h ), RPE-1 p53 KO ( i ), A549 ( j ), DU145 ( k ), HEK293A ( l ), A673 ( m ) and eHAP ( n ) cell lines harbouring Cas9–AAVS1 or Cas9–PrimPol. All experiments were performed in n = 2 biological replicates. Data are presented as means. Source numerical data and unprocessed blots are available in the source data.

Article Snippet: PrimPol cDNA was purchased from OriGene (catalogue number SC100629).

Techniques: RNA Sequencing, Expressing, Western Blot, Infection, Glo Assay

Journal: Nature Cell Biology

Article Title: RPA exhaustion activates SLFN11 to eliminate cells with heightened replication stress

doi: 10.1038/s41556-025-01852-1

Figure Lengend Snippet: ( a ) An experimental scheme demonstrating how viability assays were performed in indicated PRIMPOL KO cell lines. ( b ) A Western blot depicting PRIMPOL and SLFN11 protein levels in indicated cell lines and PRIMPOL KO clones. ( c ) A cisplatin dose response curve for HT-1080 ICas9 WT or PRIMPOL KO cells. Experiments were performed in N = 2 biological replicates. Data are represented as means ± SD. ( d ) Cisplatin dose response curves for NCIH-460 iCas9 WT or PRIMPOL KO clones. Experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. ( e ) A cisplatin dose response curve for A673 Cas9-AAVS1 or A673 Cas9-PRIMPOL KO clones. These experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. Source numerical data and unprocessed blots are available in the source data.

Article Snippet: PrimPol cDNA was purchased from OriGene (catalogue number SC100629).

Techniques: Western Blot, Clone Assay

Journal: Nature Cell Biology

Article Title: RPA exhaustion activates SLFN11 to eliminate cells with heightened replication stress

doi: 10.1038/s41556-025-01852-1

Figure Lengend Snippet: a , A schematic depicting how viability assays were performed. CTG, Cell Titer Glo. b , A western blot demonstrating transient knockout of SLFN11 in eHAP iCas9 WT or PrimPol KO cells. c , A dose–response curve of eHAP iCas9 WT or PrimPol KO cells in response to the indicated doses of cisplatin on loss of SLFN11. These experiments were performed in n = 3 biological replicates. Data are presented as mean ± s.d. These experiments were performed using the same WT sgNTC and PrimPol KO sgNTC samples depicted in Fig. . d , An experimental scheme for challenging eHAP iCas9 WT or PrimPol KO cells with cisplatin in the presence or absence of A-92, a chemical inhibitor of GCN2. e , A schematic depicting the signalling cascade connecting DNA damage to the ISR factor GCN2 and subsequent ribosome stalling and cell death. Inhibition of GCN2 prevents ribosome stalling and downstream cell death. f , Cisplatin dose–response curves for eHAP iCas9 WT or PrimPol KO cells in the presence or absence of 750 nM GCN2 inhibitor A-92. Experiments were performed in n = 3 biological replicates. Data are presented as mean ± s.d. g , An experimental scheme for measuring apoptosis via cleaved caspase-3 using flow cytometry. h , A bar plot depicting the percentage of cleaved caspase-3 positive cells determined using flow cytometry as shown in g . Experiments were performed in n = 3 biological replicates. Data are presented as mean ± s.d. A two-way ANOVA was performed to determine biological significance. P values: <0.0001 (WT versus PrimPol KO sgNTC + cisplatin); <0.0001 (PrimPol KO sgNTC versus PrimPol KO sgSLFN11 + cisplatin). i , An experimental scheme for measuring cell viability in response to cisplatin. j , A western blot showing SLFN11, PrimPol and GFP protein expression in SLFN11 WT, SLFN11 E209A (tRNA nuclease mutant), SLFN11 Lys652Asp (ssDNA-binding mutant) or SLFN11 Glu669Gln (helicase mutant) re-expression cell lines. k , Dose–response curves for SLFN11 re-expression cell lines challenged with cisplatin. These experiments were performed in n = 3 biological replicates. Data are presented as mean ± s.d. l , An experimental setup depicting how chromatin-fractionation immunofluorescence experiments were performed. m , The eHAP iCas9 WT or PrimPol KO cells transiently depleted of SLFN11 mock treated or treated with 450 nM cisplatin for 24 h. Representative micrographs of chromatin-bound immunofluorescence of phospho-RPA32 Ser33, DAPI or merged are shown. n , Quantification of sum focal intensity of phospho-RPA32 Ser33 in the indicated cell lines. Data were normalized in each biological replicate to untreated WT samples. These experiments were performed in n = 5 biological replicates. Data are presented as mean ± s.d. A two-way analysis of variance (ANOVA) was performed to assess biological significance. P values: 0.0004 (WT versus PrimPol KO sgNTC + cisplatin); 0.2141 (WT sgNTC versus PrimPol KO sgSLFN11 + cisplatin); 0.1980 (PrimPol KO sgNTC versus PrimPol KO sgSLFN11 + cisplatin). The pRPA S33 staining was performed as a co-stain with γH2AX phospho-Ser139 depicted in Extended Data Fig. . o , A representative western blot depicting levels of RPA phospho-Ser33, SLFN11 and GCN2 phospho-Thr899 in whole-cell extracts and chromatin fractions after treatment with 1 μM cisplatin for 24 h. This blot was performed in n = 2 biological replicates. Source numerical data and unprocessed blots are available in the source data. s.e., short exposure; l.e., long exposure.

Article Snippet: PrimPol cDNA was purchased from OriGene (catalogue number SC100629).

Techniques: Western Blot, Knock-Out, Inhibition, Flow Cytometry, Expressing, Mutagenesis, Binding Assay, Fractionation, Immunofluorescence, Staining

Journal: Nature Cell Biology

Article Title: RPA exhaustion activates SLFN11 to eliminate cells with heightened replication stress

doi: 10.1038/s41556-025-01852-1

Figure Lengend Snippet: ( a ) A schematic depicting how viability assays were performed. ( b ) Representative images of colony formation assays used to assess viability of eHAP iCas9 WT or PRIMPOL KO cells in response to cisplatin upon loss of SLFN11. ( c ) Quantitation of colony formation assays as depicted in (b). These experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. A two-way ANOVA was used to calculate biological significance. P -values: 0.0057 (WT sgNTC vs. PRIMPOL KO sgNTC + cisplatin). ( d ) Experimental scheme for a lentiviral-based mCherry/GFP Cas9 flow cytometry reporter. ( e ) Flow cytometry of A673 Cas9-AAVS1 C2 or A673 Cas9-PRIMPOL C2 cells showing Cas9 activity in these cells. ( f ) Experimental scheme for challenging A673 Cas9-AAVS1 C2 or A673 Cas9-PRIMPOL C2 cells transiently depleted of SLFN11 protein with cisplatin. ( g ) A Western blot showing PRIMPOL and SLFN11 protein levels in A673 Cas9-AAVS1 C2 and A673 Cas9-PRIMPOL cells transiently depleted of SLFN11 protein. ( h ) Bar blots showing cell survival of A673 Cas9-AAVS1-C2 or A673 Cas9-PRIMPOL C2 cells transiently depleted of SLFN11 protein in the presence of 58 nM cisplatin. Experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. A one-way ANOVA was performed to assess biological significance. P -values: 0.0418 (A673 Cas9-AAVS1 sgNTC vs. A673 Cas9-PRIMPOL sgNTC); 0.0214 (A673 Cas9-PRIMPOL sgNTC vs. A673-Cas9 PRIMPOL sgSLFN11). ( i ) Bar plots showing cell survival of eHAP iCas9 WT or PRIMPOL KO cells in response to treatment with 750 nM GCN2 inhibitor in the absence of cisplatin. Experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. A two-way ANOVA was performed to assess biological significance. P -values: >0.9999 (WT vs. WT + GCN2i); 0.7360 (PRIMPOL KO vs. PRIMPOL + GCN2i). ( j ) Experimental scheme for challenging eHAP iCas9 WT or PRIMPOL KO cells with cisplatin in the presence or absence of GCN2 inhibitor following transient knockout of SLFN11. ( k ) A dose response curve depicting cells with indicated genotypes challenged with cisplatin in the absence (solid lines, circles) or presence (dashed lines, triangled) of 750 nM GCN2 inhibitor. Experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. ( l ) An experimental scheme for challenging eHAP iCas9 WT, PRIMPOL KO, FANCD2 KO, or RAD18 KO cells with cisplatin in the presence or absence of 750 nM GCN2 inhibitor. ( m ) A Western blot showing PRIMPOL, FANCD2, and RAD18 protein levels in eHAP iCas9 WT, PRIMPOL KO, FANCD2 KO, and RAD18 KO cells. ( n ) A bar plot depicting cell survival of eHAP iCas9 WT, PRIMPOL KO, FANCD2 KO, and RAD18 KO cells at 450 nM cisplatin compared to an untreated control in each cell line in the absence (darker bars) or presence (lighter bars) of GCN2 inhibitor. These experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. A two-way ANOVA was performed to assess statistical significance. P -values: 0.9939 (WT vs. WT + GCN2i); 0.0006 (PRIMPOL KO vs. PRIMPOL KO + GCN2i); 0.9901 (FANCD2 KO vs. FANCD2 KO + GCN2i); 0.2275 (RAD18 KO vs. RAD18 KO + GCN2i); 0.9998 (WT + GCN2i vs. PRIMPOL KO + GCN2i); <0.0001 (WT + GCN2i vs. FANCD2 KO + GCN2i); <0.0001 (WT + GCN2i vs. RAD18 KO + GCN2i). ( o ) An experimental scheme for challenging eHAP iCas9 WT cells with cisplatin in the presence or absence of RAD51 inhibitor (B02) following transient knockout of SLFN11. ( p ) A bar plot depicting cell survival in untreated conditions in the absence or presence of RAD51 inhibitor following transient knockout of SLFN11. These experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. A two-way ANOVA was performed to assess statistical significance. P -values: >0.9999 (WT sgNTC vs. WT sgSLFN11); >0.9999 (WT sgNTC + 4.5 µM RAD51i vs. WT sgSLFN11 + 4.5 µM RAD51i); 0.9858 (WT sgNTC 9.0 µM RAD51i vs. WT sgSLFN11 + 9.0 µM RAD51i). ( q ) A bar plot depicting cell survival in cells treated with 450 nM cisplatin in the absence or presence of RAD51 inhibitor following transient knockout of SLFN11. These experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. A two-way ANOVA was performed to assess statistical significance. P -values: >0.9999 (WT sgNTC vs. WT sgSLFN11); >0.9999 (WT sgNTC + 4.5 µM RAD51i vs. WT sgSLFN11 + 4.5 µM RAD51i); 0.9982 (WT sgNTC 9.0 µM RAD51i vs. WT sgSLFN11 + 9.0 µM RAD51i). Source numerical data and unprocessed blots are available in the source data.

Article Snippet: PrimPol cDNA was purchased from OriGene (catalogue number SC100629).

Techniques: Quantitation Assay, Flow Cytometry, Activity Assay, Western Blot, Knock-Out, Control

Journal: Nature Cell Biology

Article Title: RPA exhaustion activates SLFN11 to eliminate cells with heightened replication stress

doi: 10.1038/s41556-025-01852-1

Figure Lengend Snippet: a , A schematic depicting how cell viability assays were performed in eHAP iCas9 WT or PrimPol KO cells challenged with cisplatin after transient knockout of USP1 or WDR48. b , A representative western blot depicting PrimPol, USP1 and WDR48 protein levels on loss of USP1 or WDR48. This western blot was performed in n = 2 biological replicates. c , A cisplatin dose–response curve for eHAP iCas9 WT or PrimPol cells on loss of USP1. These experiments were performed in n = 3 biological replicates. Data are presented as mean ± s.d. d , A cisplatin dose–response curve for eHAP iCas9 WT or PrimPol cells on loss of WDR48. These experiments were performed in n = 3 biological replicates. Data are presented as mean ± s.d. These experiments were performed using the same WT sgNTC and PrimPol KO sgNTC samples depicted in Fig. . e , An experimental scheme for measuring RPA exhaustion in cell pools after transient knockout of USP1 and SLFN11 using QIBC. f , A representative western blot showing USP1 and SLFN11 protein levels after transient knockout of each protein. This western blot was performed in n = 2 biological replicates. g , Representative scatter plots depicting mean ssDNA (BrdU) intensity ( y axis) plotted against mean chromatin-bound RPA32 intensity ( x axis) for each genotype and treatment depicted. The dashed boxes indicate RPA-exhausted cells where the ratio of mean ssDNA signal against mean chromatin-bound RPA32 signal has deviated from linearity (blue line). The percentage of cells undergoing RPA exhaustion in each genotype and treatment is shown. h , A bar plot depicting the percentage of cells undergoing RPA exhaustion in each genotype and treatment tested. These experiments were performed in n = 3 biological replicates. Data are presented as mean ± s.d. A two-way ANOVA was performed to assess biological significance. P values: <0.0001 (WT sgSLFN11 versus PrimPol KO sgSLFN11 + cisplatin); and <0.0001 (PrimPol KO sgSLFN11 versus PrimPol KO sgSLFN11–USP1 + cisplatin). i , An experimental scheme depicting how apoptosis (cleaved caspase-3 signal) was measured using flow cytometry in eHAP iCas9 cells after transient knockout of USP1 or SLFN11. j , A bar plot depicting the percentage of cells undergoing apoptosis, as assessed by measuring the cleaved caspase-3 signal using flow cytometry. These experiments were performed in n = 3 biological replicates. Data are presented as mean ± s.d. A two-way ANOVA was performed to assess biological significance. P values: <0.0001 (PrimPol KO sgNTC versus PrimPol KO sgUSP1 + cisplatin); <0.0001 (PrimPol KO sgNTC versus PrimPol KO sgSLFN11 + cisplatin); <0.0001 (PrimPol KO sgNTC versus PrimPol KO sgUSP1–SLFN11 + cisplatin); 0.0038 (PrimPol KO sgUSP1 versus PrimPol KO sgSLFN11 + cisplatin); and >0.9999 (PrimPol KO sgSLFN11 versus PrimPol KO sgSLFN11–USP1 + cisplatin). Source numerical data and unprocessed blots are available in the source data. DOX, doxycycline.

Article Snippet: PrimPol cDNA was purchased from OriGene (catalogue number SC100629).

Techniques: Knock-Out, Western Blot, Flow Cytometry

Journal: Nature Cell Biology

Article Title: RPA exhaustion activates SLFN11 to eliminate cells with heightened replication stress

doi: 10.1038/s41556-025-01852-1

Figure Lengend Snippet: ( a ) Representative flow cytometry experiments depicting cleaved caspase-3 signal plotted against forward scatter area. Cleaved caspase-3 positive cells were gated and quantitated as depicted. ( b ) A scheme depicting how apoptosis was measured in eHAP iCas9 WT or PRIMPOL KO cells using cleaved caspase-3 positive cells in flow cyomtetry experiments. ( c ) Representative dot plots depicting how the percentage of cleaved caspase-3 positive cells were determined using flow cytometry after challenge with cisplatin in the absence or presence of 650 nM GCN2 inhibitor. ( d ) A bar plot depicting the percentage of cleaved caspase-3 positive cells in each indicated genotype following challenge with cisplatin in the absence or presence of GCN2 inhibitor determined using flow cytometry in (b). These experiments were performed in N = 4 biological replicates. Data represented as means ± SD. A two-way ANOVA was performed to assess biological significance P -values: 0.0003 (WT sgNTC vs. PRIMPOL KO sgNTC + cisplatin); >0.9999 (WT sgSLFN11 vs. PRIMPOL KO sgSLFN11 + cisplatin); 0.0002 (PRIMPOL KO sgNTC vs. PRIMPOL KO sgSLFN11 + cisplatin). ( e ) Representative Western blots demonstrating induction of DNA damage response markers in eHAP iCas9 WT or PRIMPOL KO cells in response to indicated doses of cisplatin for 24 or 48 h. ( f ) Experimental setup of measuring chromatin-bound phospho-gamma H2AX serine 139 using immunofluorescence in eHAP iCas9 WT or PRIMPOL KO cells depleted of SLFN11 protein (top). ( g ) eHAP iCas9 WT or PRIMPOL KO Cells transiently depleted of SLFN11 were mock treated or treated with 450 nM cisplatin for 24 h. Representative micrographs of chromatin-bound immunofluorescence of γH2AX phospho serine 139, DAPI, or merged are shown. ( h ) Bar plots showing phospho-gamma H2AX serine 139 foci signal normalised to WT untreated cells in eHAP iCas9 WT or PRIMPOL KO cells depleted of SLFN11 protein. Experiments were performed in N = 5 biological replicates. Data are represented as means ± SD. A two-way ANOVA was used to assess biological significance. P -values: >0.9999 (WT sgNTC vs. PRIMPOL KO sgNTC + cisplatin); 0.4353 (PRIMPOL KO sgNTC vs. PRIMPOL KO sgSLFN11 + cisplatin); 0.2441 (WT sgNTC vs. PRIMPOL KO sgSLFN11). γH2AX phospho serine 139 staining was performed as a co-stain with pRPA S33 depicted in Fig. . ( i ) eHAP iCas9 WT or PRIMPOL KO Cells transiently depleted of SLFN11 were mock treated or treated with 450 nM cisplatin for 24 h. Representative micrographs of chromatin-bound immunofluorescence of RAD51, DAPI, or merged are shown ( j ) Quantification of RAD51 foci in indicated cell lines. These experiments were performed in N = 5 biological replicates. Data are represented as means ± SD. A two-way ANOVA was performed to assess biological significance. P -values: 0.0050 (WT sgNTC vs. PRIMPOL KO sgNTC + cisplatin); 0.0013 (PRIMPOL KO sgNTC vs. PRIMPOL KO sgSLFN11 + cisplatin); 0.9994 (WT sgNTC vs. PRIMPOL KO sgSLFN11 + cisplatin). Source numerical data and unprocessed blots are available in the source data.

Article Snippet: PrimPol cDNA was purchased from OriGene (catalogue number SC100629).

Techniques: Flow Cytometry, Western Blot, Immunofluorescence, Staining

Journal: Nature Cell Biology

Article Title: RPA exhaustion activates SLFN11 to eliminate cells with heightened replication stress

doi: 10.1038/s41556-025-01852-1

Figure Lengend Snippet: a , A diagram depicting how ssDNA was measured by detecting incorporated BrdU under non-denaturing conditions. b , An experimental scheme for measuring RPA exhaustion in eHAP iCas9 WT or PrimPol KO cells in which SLFN11 has been transiently knocked out using QIBC. c , Representative scatter plots depicting mean BrdU signal intensity per cell ( y axis) plotted against mean chromatin-bound RPA32 ( x axis). The linear relationship between BrdU and RPA32 signals is depicted as a light-blue line. Cells undergoing RPA exhaustion are depicted within the dashed box and coloured red. The percentage of cells undergoing RPA exhaustion is indicated in each panel. d , A bar plot depicting the percentage of cells undergoing RPA exhaustion in the experiments shown in a and b . These experiments were performed in n = 3 biological replicates. Data are presented as mean ± s.d. A two-way ANOVA was performed to assess biological significance. P values: 0.0009 (WT sgNTC versus PrimPol KO sgNTC + cisplatin); <0.0001 (WT sgSLFN11 versus PrimPol KO sgSLFN11 + cisplatin); and 0.0009 (PrimPol KO sgNTC versus PrimPol KO sgSLFN11 + cisplatin). e , Representative scatter plots depicting mean γH2AX–pSer139 signal intensity per cell ( y axis) plotted against mean chromatin-bound RPA32 ( x axis). Cells with high RPA32 and γH2AX–pSer139 signals are coloured in red. The percentage of cells with high RPA32 and γH2AX–pSer139 signals is indicated in each panel. f , A bar plot depicting the percentage of cells exhibiting high RPA32–γH2AX–pSer139 signals in the experiments shown in a and e . These experiments were performed in n = 3 biological replicates. Data are presented as mean ± s.d. A two-way ANOVA was performed to assess biological significance. P values: 0.0023 (WT sgNTC versus PrimPol KO sgNTC + cisplatin); 0.0003 (WT sgSLFN11 versus PrimPol KO sgSLFN11 + cisplatin); and 0.0001 (PrimPol KO sgNTC versus PrimPol KO sgSLFN11 + cisplatin). g , Experimental scheme for challenging eHAP iCas9 WT or PrimPol KO cells with cisplatin in the presence or absence of GCN2i after siRNA knockdown of RPA2. h , A western blot depicting RPA2, PrimPol, vinculin and total protein levels in eHAP iCas9 WT or PrimPol KO cells after transient knockdown of RPA2. i , A dose–response curve depicting cell survival in eHAP iCas9 WT or PrimPol KO cells (normalized to untransfected cells) after siRNA knockdown of RPA at indicated concentrations in the presence or absence of cisplatin and GCN2i. This experiment was performed in n = 3 biological replicates. Data are presented mean ± s.d. j , An experimental scheme for challenging eHAP iCas9 WT or PrimPol KO cells with two fixed doses of cisplatin in the presence or absence of DNA-PK inhibitor (DNA-PKi) after transient knockout of SLFN11. k , A bar plot depicting cell survival in the presence of 450 nM cisplatin with or without treatment with DNA-PKi. The experiments were performed in n = 3 biological replicates. Data are presented as mean ± s.d. A two-way ANOVA was performed to assess statistical significance. P value: <0.0001 (PrimPol KO sgNTC versus PrimPol KO sgSLFN11 + cisplatin). l , A bar plot depicting cell survival in the presence of 1.5 μM cisplatin with or without treatment with DNA-PKi. The experiments shown were performed in n = 3 biological replicates. Data are presented as mean ± s.d. A two-way ANOVA was performed to assess statistical significance. P values: 0.0423 (WT sgNTC − DNA-PKi versus WT sgNTC + DNA-PKi); <0.0001 (WT sgSLFN11 − DNA-PKi versus WT sgSLFN11 + DNA-PKi); <0.0001 (PrimPol KO sgSLFN11 − DNA-PKi versus PrimPol sgSLFN11 + DNA-PKi).

Article Snippet: PrimPol cDNA was purchased from OriGene (catalogue number SC100629).

Techniques: Knockdown, Western Blot, Knock-Out

Journal: Nature Cell Biology

Article Title: RPA exhaustion activates SLFN11 to eliminate cells with heightened replication stress

doi: 10.1038/s41556-025-01852-1

Figure Lengend Snippet: ( a ) Representative micrographs depicting BrdU, RPA, and DAPI signals generated in QIBC experiments shown in Fig. . ( b ) Representative micrographs depicting γH2AX pS139, RPA, and DAPI signals generated in QIBC experiments shown in Fig. . ( c ) A dose response curve depicting cell viability in eHAP iCas9 WT or PRIMPOL KO cells treated with indicated doses of siRNA targeting the RPA2 gene in the presence or absence of 750 nM GCN2 inhibitor. These experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. Source numerical data are available in the source data.

Article Snippet: PrimPol cDNA was purchased from OriGene (catalogue number SC100629).

Techniques: Generated

Journal: Nature Cell Biology

Article Title: RPA exhaustion activates SLFN11 to eliminate cells with heightened replication stress

doi: 10.1038/s41556-025-01852-1

Figure Lengend Snippet: ( a ) An experimental schematic describing how cell viability assays were performed in the presence of cisplatin and ML323 (USP1 inhibitor). ( b ) A cisplatin dose response curve for eHAP iCas9 WT or PRIMPOL KO cells with or without 4.5 μM ML323. These experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. ( c ) A bar plot showing how eHAP iCas9 WT (gray bars) or PRIMPOL KO cells (red bars) respond to 4.5 μM ML323. Survival is normalised to untreated conditions within each genotype. These experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. A two-way ANOVA was performed to assess statistical significance. P -values: 0.4946 (WT vs. WT + USP1i); 0.7018 (PRIMPOL KO vs. PRIMPOL KO + USP1i). ( d ) A schematic showing how cell viability experiments were performed in A673 Cas9-AAVS1 or A673 Cas9-PRIMPOL cells in the presence of cisplatin and ML323 (16.5 μM). ( e ) A bar blot depicting cell survival for A673 Cas9-AAVS1 or A673 Cas9-PRIMPOL cells in the presence of 200 nM cisplatin -/+ 16.5 μM ML323. These experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. A two-way ANOVA was performed to assess statistical significance. P -values: 0.9925 (WT vs. WT + USP1i); 0.0203 (PRIMPOL KO vs. PRIMPOL KO + USP1i). ( f ) An experimental scheme depicting how cell viability was measured after challenging cells with cisplatin and USP1 inhibitor (ML323) in eHAP iCas9 cells with indicated genotypes. ( g ) A bar plot depicting cell survival of eHAP iCas9 WT or PRIMPOL KO cells following challenge with 670 nM cisplatin in the absence (darker bars) or presence (light bars) of 4.5 μM USP1 inhibitor following transient knockout of SLFN11. These experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. A two-way ANOVA was performed to assess statistical significance. P -values: >0.9999 (WT sgNTC vs. WT sgNTC + USP1i); >0.9999 (WT sgSLFN11 vs. WT sgSLFN11 + USP1i); 0.0032 (PRIMPOL KO sgNTC vs. PRIMPOL KO sgNTC + USP1i); 0.8134 (PRIMPOL KO sgSLFN11 vs. PRIMPOL KO sgSLFN11 + USP1i); 0.8522 (WT sgNTC vs. WT sgSLFN11); <0.0001 (PRIMPOL KO sgNTC vs. PRIMPOL KO sgSLFN11); 0.8160 (WT sgNTC + USP1i vs. PRIMPOL KO sgNTC + USP1i). Source numerical data are available in the source data.

Article Snippet: PrimPol cDNA was purchased from OriGene (catalogue number SC100629).

Techniques: Knock-Out

Journal: Nature Cell Biology

Article Title: RPA exhaustion activates SLFN11 to eliminate cells with heightened replication stress

doi: 10.1038/s41556-025-01852-1

Figure Lengend Snippet: ( a ) A schematic showing how RAD18 or FANCL was knocked out in eHAP iCas9 WT or PRIMPOL KO cells and subsequently challenged with cisplatin. ( b ) A Western blot showing PRIMPOL and RAD18 protein levels in eHAP iCas9 WT or PRIMPOL KO cells upon loss of RAD18 (R18). ( c ) A cisplatin dose response curve for eHAP iCas9 WT or PRIMPOL cells upon loss of RAD18. These experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. These experiments were performed using the same WT sgNTC and PRIMPOL KO sgNTC samples depicted in (m). ( d ) A Western blot showing PRIMPOL and FANCL protein levels in eHAP iCas9 WT or PRIMPOL KO cells upon loss of FANCL (FL). ( e ) A cisplatin dose response curve for eHAP iCas9 WT or PRIMPOL KO cells upon loss of FANCL. eHAP iCas9 WT and PRIMPOL KO curves are the same as those shown in (d), as these experiments were performed at the same time. These experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. ( f ) A series of Western blots showing indicated protein levels in eHAP iCas9 WT or PRIMPOL cells upon loss of USP1 and/or RAD18 (R18). ( g ) A series of Western blots showing indicated protein levels in eHAP iCas9 WT or PRIMPOL KO cells upon loss of USP1 and/or FANCL (FL). ( h ) An experimental scheme for how USP1/RAD18/FANCL proteins were knocked out in eHAP iCas9 WT or PRIMPOL KO cells and subsequently challenged with cisplatin in a colony formation assay. ( i ) Representative images of colony formation assays in indicated cell backgrounds in untreated conditions or upon treatment with 450 nM cisplatin. ( j ) Quantification of colony survival in the colony formation assays represented in (d) normalised to untreated samples within each genotype. These experiments were performed in N = 3 biological replicates. Data are represented as means ± SD. A two-way ANOVA was performed to test statistical significance. P -values: 0.9964 (WT sgNTC vs. WT sgUSP1); 0.0098 (WT sgRAD18/NTC vs. WT sgRAD18/sgUSP1); 0.9998 (WT sgFANCL/sgNTC vs. WT sgFANCL/USP1); 0.0012 (PRIMPOL KO sgNTC vs. PRIMPOL KO sgUSP1); <0.0001 (PRIMPOL KO sgRAD18/NTC vs. PRIMPOL KO sgRAD18/USP1); >0.9999 (PRIMPOL KO sgFANCL/NTC vs. PRIMPOL KO sgFANCL/USP1). ( k ) An experimental schematic describing how chromatin-bound immunofluorescence was performed. ( l ) Representative micrographs depicting DNA staining (DAPI), FANCD2 staining, and a merged image of DAPI/FANCD2 staining. ( m ) A bar plot showing chromatin-bound FANCD2 foci numbers in eHAP iCas9 WT or PRIMPOL KO cells treated with 450 nM cisplatin. These experiments were performed in N = 5 biological replicates. Data are represented as means ± SD. A two-way ANOVA was performed to assess statistical significance. P-values: 0.0071 (WT + cisplatin vs. PRIMPOL KO + cisplatin). Source numerical data and unprocessed blots are available in the source data.

Article Snippet: PrimPol cDNA was purchased from OriGene (catalogue number SC100629).

Techniques: Western Blot, Colony Assay, Immunofluorescence, Staining

Journal: Nature Cell Biology

Article Title: RPA exhaustion activates SLFN11 to eliminate cells with heightened replication stress

doi: 10.1038/s41556-025-01852-1

Figure Lengend Snippet: a , An experimental scheme depicting how cell viability was measured in indicated cell lines after transient knockout of SLFN11 and challenge with DNA polymerase α inhibitor (ST1926). b , A western blot depicting SLFN11 protein levels after transient knockout of SLFN11 in the indicated cell lines. c – g , Dose–response curves of HeLa Kyoto iCas9 ( c ), HT-1080 iCas9 ( d ), TOV112D iCas9 ( e ), A673 iCas9 ( f ) and eHAP iCas9 ( g ) cells challenged with the indicated doses of DNA polymerase α inhibitor (ST1926). Experiments were performed in n = 3 biological replicates. Data are presented as mean ± s.d. h , In WT cells expressing SLFN11 (blue panel), PrimPol repriming activity restricts accumulation of ssDNA at cisplatin-stalled replication forks caused by uncoupling of the helicase and DNA polymerase, thereby preventing SLFN11 activation and cell death. Similarly, inhibition of DNA polymerase α uncouples DNA replication on each strand to drive ssDNA accumulation at forks in a PrimPol-independent manner. In PrimPol-deficient cells (green panel), cisplatin-induced DNA damage drives accumulation of ssDNA at replication forks in a USP1-dependent manner, leading to RPA exhaustion and SLFN11 activation. USP1-dependent downregulation of the FA pathway allows for full SLFN11 activation and subsequent ribosome stalling, ISR activation and cell death, as previously described . In SLFN11-deficient cells (red panel), cisplatin-induced DNA damage or inhibition of DNA polymerase α causes ssDNA accumulation at forks and RPA exhaustion. Loss of SLFN11 prevents signal transduction through ribosome stalling and GCN2, preventing SLFN11-dependent cell death. Instead, prolonged RPA exhaustion leads to fork breakage and replication catastrophe as previously described , leading to DSBs that are repaired by the NHEJ pathway, leading to cell death. Source numerical data and unprocessed blots are available in the source data. PolAi, Pol A inhibitor.

Article Snippet: PrimPol cDNA was purchased from OriGene (catalogue number SC100629).

Techniques: Knock-Out, Western Blot, Expressing, Activity Assay, Activation Assay, Inhibition, Transduction

Journal: eBioMedicine

Article Title: Exercise-derived peptide protects against pathological cardiac remodeling

doi: 10.1016/j.ebiom.2022.104164

Figure Lengend Snippet: The primers used in this study.

Article Snippet: The concentrations of CCDC80tide in EVs were measured by ELISA (Human CCDC80 ELISA Kit, EK1962, Boster Bio, USA) combined with immunoblotting assay.

Techniques:

Journal: eBioMedicine

Article Title: Exercise-derived peptide protects against pathological cardiac remodeling

doi: 10.1016/j.ebiom.2022.104164

Figure Lengend Snippet: CCDC80 is a potential exerkine involved in cardiovascular pathophysiology . a. Circos plot visualizes the overlap between upregulated gene lists from three databases, and the blue curves link genes that belong to the same enriched GO term. b. Pie charts represent the network of enriched terms in upregulated genes. Each circle node represents an enriched term and is clustered by its identity, where the size of a slice represents the percentage of genes under the term that originated from the corresponding database. c. Heatmap of enriched terms across the three upregulated gene lists, colored by p -values. d. Heatmap of enrichment analysis in DisGeNET, colored by p-values. e. Circos plot displays the overlap between upregulated gene lists, and the purple curves link identical genes. The five genes within the black box represent the genes with significant upregulation throughout the three databases. f. RT-PCR analysis of the expression levels of CCDC80 in various tissues of mice. g, h. After overexpression of PGC-1α in C2C12 cells, the expressions of Pgc-1α (g) and Ccdc80 (h) was determined by qPCR. i, j and k. Eight-week-old male mice were forced to swim 5 days per week for 3 months. Control groups mice were raised normally without swimming training. After complete swimming training, the skeletal muscles of mice were collected for western blot analysis of CCDC80 and PGC-1α ( n= 7). Data are presented as the average of four biological replicates (n = 4) ± SD. Statistical significance was determined using Student's t-test, *** p < 0.001.

Article Snippet: The concentrations of CCDC80tide in EVs were measured by ELISA (Human CCDC80 ELISA Kit, EK1962, Boster Bio, USA) combined with immunoblotting assay.

Techniques: Reverse Transcription Polymerase Chain Reaction, Expressing, Over Expression, Control, Muscles, Western Blot

Journal: eBioMedicine

Article Title: Exercise-derived peptide protects against pathological cardiac remodeling

doi: 10.1016/j.ebiom.2022.104164

Figure Lengend Snippet: CCDC80 generates a peptide encapsulated in EVs in response to PGC-1α overexpression . a. The cell lysates and culture supernatants collected from vehicle- or Flag-PGC-1α-overexpressing C2C12 cells (treated or not with BFA, 1 μg/mL, 16 h) were prepared and analyzed for CCDC80 protein levels by WB. N= 3 b. The supernatants of CCDC80-EGFP-overexpressing C2C12 cells were harvested and filtered through a sterile 0.22-μm filter and then added to H9c2 cells. After 12-h incubation, the cell fluorescence was detected. The fluorescent spots indicated by white arrows were supposedly EVs. N= 3 c, d, e. The supernatants of CCDC80-overexpressing C2C12 cells were collected, and EVs were extracted for TEM (c), NTA (d), and EVs markers (e) determinations. N= 3. WCL: whole cell lysates. f. The cell lysates and EVs isolated from the supernatants of vehicle- or CCDC80-HA-overexpressing C2C12 cells were prepared and analyzed for CCDC80 protein levels by WB. g. The schematic diagram of CCDC80tide in CCDC80.

Article Snippet: The concentrations of CCDC80tide in EVs were measured by ELISA (Human CCDC80 ELISA Kit, EK1962, Boster Bio, USA) combined with immunoblotting assay.

Techniques: Over Expression, Sterility, Incubation, Fluorescence, Isolation

Journal: Journal of Cell Science

Article Title: BAR-SH3 sorting nexins are conserved interacting proteins of Nervous wreck that organize synapses and promote neurotransmission

doi: 10.1242/jcs.178699

Figure Lengend Snippet: Synaptic growth is not altered in SH3PX1 mutants. (A–F) Confocal images of NMJ 6/7 (A,C,E) and NMJ 4 (B,D,F) preparations labeled for Bruchpilot (green) and Cy3-conjugated HRP in control (A,B), SH3PX1 10A /Df(3L)BSC392 (C,D; 10A/Df ) and SH3PX1 10A /SH3PX1 C1 (E,F; 10A/C1 ) larvae. (G,H) Scatter plots of the number of boutons in control and SH3PX1 mutants at NMJ 6/7, segments A2 and A3 (G), and NMJ 4 (H). Control: n =19 NMJ 6/7, 50 NMJ 4; SH3PX1 10A /Df(3L)BSC392 : n =17 NMJ 6/7, 43 NMJ 4; SH3PX1 10A /SH3PX1 C1 : n =20 NMJ 6/7, 53 NMJ 4. n.s., not significant compared to control; ANOVA followed by post-hoc tests with Šidák correction. Error bars represent s.e.m., line represents mean. (I–J″) Confocal images of control and SH3PX1 10A /Df(3L)BSC392 boutons labeled with antibodies against Bruchpilot (I,J) and GluRIIC (I′,J′); (I″,J″) merged images of Bruchpilot and GluRIIC labelling. (K–P) Confocal images of control and SH3PX1 10A /SH3PX1 C1 boutons labeled with antibodies against Nwk (K,L), active zone cytomatrix component Rim-binding Protein (RBP; M,N) and the vesicular glutamate transporter VGlut (O,P). wt , wild type. Scale bars: 20 µm (A–F), 5 µm (I–P).

Article Snippet: The following antibodies were used: mouse monoclonal anti-α-tubulin (western blotting, 1:40,000; Sigma-Aldrich #T9026), mouse monoclonal anti-BRP (immunofluorescence, 1:200; nc82, Erich Buchner, from the Developmental Studies Hybridoma Bank, Iowa City, IA), rabbit polyclonal anti-DsRed (western blotting, 1:1000; #632496, Clontech, Mountain View, CA), mouse monoclonal anti-FLAG (M2) (immunofluorescence, 1:500; western blotting, 1:4000; #F1804, Sigma-Aldrich, St Louis, MO), chicken polyclonal anti-GFP (western blotting, 1:5000, #13970 AbCam, Cambridge, UK), rabbit polyclonal anti-GFP (immunofluorescence, 1:1000, Life Technologies #A11122), rabbit anti-GluRIIC (immunofluorescence, 1:1000) , monoclonal anti-hemagglutinin (HA) (western blotting, 1:3000; #3724, Cell Signaling Technologies, Danvers, MA), chicken polyclonal anti-NWK2 (western blotting, 1:1000; #6509, ProSci, Poway, CA), rabbit polyclonal anti-Nwk (immunofluorescence, 1:1000) , rabbit anti-RIM-binding protein (immunofluorescence, 1:500) , rabbit polyclonal anti-SH3PX1 (immunofluorescence, 1:500; western blotting, 1:2000) , mouse monoclonal anti-synapsin1 (immunofluorescence, 1:500; Synaptic Systems #106001) and rabbit anti- Drosophila -VGlut (immunofluorescence, 1:10,000) ( ).

Techniques: Labeling, Binding Assay