C , D . mouse J110 cells were transfected with either miR - 449a mimic or a negative control mimic . Whole cell extracts were subjected to immunoblot analysis to detect endogenous JAM - A and ACTIN . ACTIN was used to normalize JAM - A expression ( norm . ) as loading control . p = 0 . 04454 ( Neg . ctrol . vs . miR - 449a mimic ) ( n = 4 independent wells , 2 independent transfections ) .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

C, D. mouse J110 cells were transfected with either miR-449a mimic or a negative control mimic. Whole cell extracts were subjected to immunoblot analysis to detect endogenous JAM-A and ACTIN. ACTIN was used to normalize JAM-A expression (norm.) as loading control. p = 0.04454 (Neg. ctrol. vs. miR-449a mimic) (n = 4 independent wells, 2 independent transfections).


E , F . HeLa cells were cotransfected with either miR - 449a mimic or a negative control mimic , together with JAM - A - GFP fusion protein and GFP . Whole cell extracts were subjected to immunoblot analysis to detect GFP . GFP was used to normalize ( norm . ) by transfection efficiency as loading control . p = 0 . 001176 ( JAM - A WT Neg . ctrol . vs . miR - 449a mimic ) ( n = 9 independent wells , 4 independent transfections ) .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

E, F. HeLa cells were cotransfected with either miR-449a mimic or a negative control mimic, together with JAM-A-GFP fusion protein and GFP. Whole cell extracts were subjected to immunoblot analysis to detect GFP. GFP was used to normalize (norm.) by transfection efficiency as loading control. p = 0.001176 (JAM-A WT Neg. ctrol. vs. miR-449a mimic) (n = 9 independent wells, 4 independent transfections).


G , H . Confocal images of coronal sections from E14 brains of wild type mice stained with anti - JAM - A antibody ( green ) , phalloidin to label actin ( gray ) and DAPI to label cell nuclei ( blue ) . Scale bars : 10 μm ( G ) , 5 μm ( H ) . I . Quantification of JAM - A protein expression in the ventricular zone of E14 brain coronal sections from miR - 34 / 449 KO mice compared with littermate controls ( Het ) by immunofluorescence . ACTIN ( phalloidin signal ) was used to normalize ( norm . ) the expresion levels of JAM - A . p = 0 . 04842 ( n = 5 ( KO ) or 7 ( het ) cortices per genotype group , 3 independent litters ) .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

G, H. Confocal images of coronal sections from E14 brains of wild type mice stained with anti-JAM-A antibody (green), phalloidin to label actin (gray) and DAPI to label cell nuclei (blue). Scale bars: 10 μm (G), 5 μm (H).I. Quantification of JAM-A protein expression in the ventricular zone of E14 brain coronal sections from miR-34/449 KO mice compared with littermate controls (Het) by immunofluorescence. ACTIN (phalloidin signal) was used to normalize (norm.) the expresion levels of JAM-A. p = 0.04842 (n = 5 (KO) or 7 (het) cortices per genotype group, 3 independent litters).


A , D . Confocal time lapse images of metaphase HeLa cells stably expressing a centriole marker ( Centrin2 - GFP ; green ) , the microtubule marker ( α - tubulin - mRFP ; red ) and no extra protein ( A ) or mouse JAM - A ( D ) , 48 h after transfection of miR - 449a mimic , JAM - A siRNA , or non - targeting negative control siRNA . Scale bar , 10 μm . B , E . Quantification of spindle rotation for cells as shown in A and D . Each dot represents a single cell . Red bar indicates median . Significance was tested by Pairwise t - test with Bonferroni correction . p - value = 2e - 11 ( Neg . control versus miR449 mimic ) , p - value = 0 . 01928 ( Neg . control versus JAM - A siRNA ) , p - value = 0 . 17492 ( Neg . control versus miR449 mimic , under JAM - A overexpression ) . * indicates p ≤ 0 . 05 ; * * p ≤ 0 . 01 ; p * * * p ≤ 0 . 001 for all panels . C , F . Cumulative histograms of mitotic duration from nuclear envelope breakdown until anaphase onset , measured for cells as shown in A and D ; n ≥ 20 cells for all conditions , 2 independent replicates .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

A, D. Confocal time lapse images of metaphase HeLa cells stably expressing a centriole marker (Centrin2-GFP; green), the microtubule marker (α-tubulin-mRFP; red) and no extra protein (A) or mouse JAM-A (D), 48 h after transfection of miR-449a mimic, JAM-A siRNA, or non-targeting negative control siRNA. Scale bar, 10 μm.B, E. Quantification of spindle rotation for cells as shown in A and D. Each dot represents a single cell. Red bar indicates median. Significance was tested by Pairwise t-test with Bonferroni correction. p-value = 2e-11 (Neg. control versus miR449 mimic), p-value = 0.01928 (Neg. control versus JAM-A siRNA), p-value = 0.17492 (Neg. control versus miR449 mimic, under JAM-A overexpression). * indicates p ≤ 0.05; ** p ≤ 0.01; p*** p ≤ 0.001 for all panels.C, F. Cumulative histograms of mitotic duration from nuclear envelope breakdown until anaphase onset, measured for cells as shown in A and D; n ≥ 20 cells for all conditions, 2 independent replicates.


B . DIS3 expression in total cell lysates of control ( siCTRL ) and DIS3 U2OS silenced cells ( siDIS3 ) was analyzed by Western blot upon rescue with empty vector ( EV ) or DIS3 expressing vector ( DIS3 ) . Lamin B was used as the loading control .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

B. DIS3 expression in total cell lysates of control (siCTRL) and DIS3 U2OS silenced cells (siDIS3) was analyzed by Western blot upon rescue with empty vector (EV) or DIS3 expressing vector (DIS3). Lamin B was used as the loading control.


C . Representative images of comet assays performed under alkaline conditions in U2OS cells transfected with siCTRL or siDIS3 and then infected with a vector expressing DIS3 ( DIS3 ) or an empty vector ( EV ) . Quantitative analysis of comet tail lengths for each condition . Plots represent three biological replicates , with more than 150 cells for each point . The analysis is performed using Casplab software , error bars indicate s . e . m . ( n = 3 ) . * * * * p - value < 0 . 0001 . ns = not statistically significant , two - way ANOVA , scale bar is 200 µm .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

C. Representative images of comet assays performed under alkaline conditions in U2OS cells transfected with siCTRL or siDIS3 and then infected with a vector expressing DIS3 (DIS3) or an empty vector (EV). Quantitative analysis of comet tail lengths for each condition. Plots represent three biological replicates, with more than 150 cells for each point. The analysis is performed using Casplab software, error bars indicate s.e.m. (n=3). **** p-value < 0.0001. ns= not statistically significant, two-way ANOVA, scale bar is 200 µm.


D . Immunostaining against RPA in U2OS cells transfected with siCTRL or with siDIS3 and 48 hours later infected with a vector expressing DIS3 ( DIS3 ) or an empty vector ( EV ) . The averages of foci number per cell were calculated from three independent experiments using Cell Profiler software . At least 150 cells were counted for each point , error bars indicate s . e . m . ( n = 3 ) . * p - value < 0 . 05 . ns = not statistically significant , two - way ANOVA , scale bar is 10 µm .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

D. Immunostaining against RPA in U2OS cells transfected with siCTRL or with siDIS3 and 48 hours later infected with a vector expressing DIS3 (DIS3) or an empty vector (EV). The averages of foci number per cell were calculated from three independent experiments using Cell Profiler software. At least 150 cells were counted for each point, error bars indicate s.e.m. (n=3). * p-value < 0.05. ns= not statistically significant, two-way ANOVA, scale bar is 10 µm.


A . Immunostaining with S9 . 6 ( green ) and DAPI ( blue ) in U2OS cells , transfected for 48 hours with siCTRL or siDIS3 and then mock - treated ( UNTR ) or treated with RNase H or RNase III for 1 hour before fixation . Histograms show S9 . 6 signal intensity per cell , error bars indicate s . e . m . ( n = 3 , biological replicates ) . More than 150 cells were counted , and error bars indicate s . e . m . ( n = 3 biological replicates ) . ) . * * * * = p < 0 . 0001 , * * * = p < 0 . 001 , ns = not statistically significant , two - way ANOVA , scale bar is 10 µm .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

A. Immunostaining with S9.6 (green) and DAPI (blue) in U2OS cells, transfected for 48 hours with siCTRL or siDIS3 and then mock-treated (UNTR) or treated with RNase H or RNase III for 1 hour before fixation. Histograms show S9.6 signal intensity per cell, error bars indicate s.e.m. (n=3, biological replicates). More than 150 cells were counted, and error bars indicate s.e.m. (n=3 biological replicates).). **** = p < 0.0001, *** = p < 0.001, ns = not statistically significant, two-way ANOVA, scale bar is 10 µm.


B . Immunostaining with J2 ( green ) and DAPI ( blue ) in U2OS cells , as in panel A ) . More than 150 cells were counted , and error bars indicate s . e . m . ( n = 3 biological replicates ) . For all conditions , differences between siCTRL and siDIS3 were not statistically significant , two - way ANOVA , scale bar is 10 µm .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

B. Immunostaining with J2 (green) and DAPI (blue) in U2OS cells, as in panel A). More than 150 cells were counted, and error bars indicate s.e.m. (n=3 biological replicates). For all conditions, differences between siCTRL and siDIS3 were not statistically significant, two-way ANOVA, scale bar is 10 µm.


C . Dot blot analysis of DNA : RNA hybrids formation : serial dilutions ( 750 ng , 375 ng , 187 , 5 ng , 93 , 75 ng , 46 , 87 ng ) of genomic DNA extracted from WT or DIS3 silenced U2OS cells and pre - treated with RNase H , RNase III or mock treated , were arrayed on a membrane and probed using the S9 . 6 antibody . The histogram shows the S9 . 6 signal quantification in 3 biological replicates , error bars indicate s . e . m . , normalized on SYBR ® - Gold signal ( Adj . Vol . ) , using Image lab software . * * * = p < 0 . 001 , * * = p < 0 . 01 , ns = not statistically significant , two - way ANOVA .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

C. Dot blot analysis of DNA:RNA hybrids formation: serial dilutions (750 ng, 375 ng, 187,5 ng, 93,75 ng, 46,87 ng) of genomic DNA extracted from WT or DIS3 silenced U2OS cells and pre-treated with RNase H, RNase III or mock treated, were arrayed on a membrane and probed using the S9.6 antibody. The histogram shows the S9.6 signal quantification in 3 biological replicates, error bars indicate s.e.m., normalized on SYBR®-Gold signal (Adj. Vol.), using Image lab software. *** = p < 0.001, ** = p < 0.01, ns= not statistically significant, two-way ANOVA.


D . DRIP - qPCR analysis at four different R - loops sites , RPL13A , ACTB , ENSA , and TRIM33 in U2OS cells transduced with shScr or shDIS3 and treated or not with RNase H . Results are shown as mean + s . e . m of three independent experiments . * * * * = p < 0 . 0001 , * * * = p < 0 . 001 , * = p < 0 . 05 , two - way ANOVA .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

D. DRIP-qPCR analysis at four different R-loops sites, RPL13A, ACTB, ENSA, and TRIM33 in U2OS cells transduced with shScr or shDIS3 and treated or not with RNase H. Results are shown as mean + s.e.m of three independent experiments.**** = p < 0.0001, *** = p < 0.001, * = p < 0.05, two-way ANOVA.


E . Representative pictures of comet assays performed under alkaline conditions in U2OS cells transfected for 48 hours with siCTRL or siDIS3 , untreated ( UNTR ) or treated with RNase H ( RNase H ) . Tail moments analysis was performed using Casplab software , error bars indicate s . e . m . Plots represent three biological replicates , with 150 cells for each cell line . * * * * = p < 0 . 0001 , ns = not statistically significant , two - way ANOVA , scale bar is 200 µm .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

E. Representative pictures of comet assays performed under alkaline conditions in U2OS cells transfected for 48 hours with siCTRL or siDIS3, untreated (UNTR) or treated with RNase H (RNase H). Tail moments analysis was performed using Casplab software, error bars indicate s.e.m. Plots represent three biological replicates, with 150 cells for each cell line. **** = p < 0.0001, ns= not statistically significant, two-way ANOVA, scale bar is 200 µm.


A . U2OS cells were transfected with siCTRL or with siDIS3 and 48 hours later were irradiated ( IR ) or left untreated ( NO IR ) . Cells were fixed 4 hours after IR and stained for RAD51 . Histograms show foci number per cell , analyzed with Cell Profiler . The average number of foci per cell was calculated from three independent experiments . At least 200 cells were counted for each point , error bars indicate s . e . m . ( n = 3 ) . * = p < 0 . 05 , two - way ANOVA , ns = not statistically significant , scale bar is 10

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

A. U2OS cells were transfected with siCTRL or with siDIS3 and 48 hours later were irradiated (IR) or left untreated (NO IR). Cells were fixed 4 hours after IR and stained for RAD51. Histograms show foci number per cell, analyzed with Cell Profiler. The average number of foci per cell was calculated from three independent experiments. At least 200 cells were counted for each point, error bars indicate s.e.m. (n=3). * = p < 0.05, two-way ANOVA, ns= not statistically significant, scale bar is 10 µ


D . Representative pictures of alkaline comet assays performed in U2OS silenced ( siDIS3 ) or not ( siCTRL ) for DIS3 , at sequential time points after exposure to 3 Gy irradiation . Relative comet tail moments were plotted for siCTRL ( black circles ) and siDIS3 ( red circles ) . Analysis was performed using Casplab software , error bars indicate s . e . m . Plots represent three biological replicates , with more than 150 cells for each siRNA . * * * * = p < 0 . 0001 , * * = p < 0 . 001 , ns = not statistically significant , two - way ANOVA , scale bar is 20 µm .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

D. Representative pictures of alkaline comet assays performed in U2OS silenced (siDIS3) or not (siCTRL) for DIS3, at sequential time points after exposure to 3 Gy irradiation. Relative comet tail moments were plotted for siCTRL (black circles) and siDIS3 (red circles). Analysis was performed using Casplab software, error bars indicate s.e.m. Plots represent three biological replicates, with more than 150 cells for each siRNA. **** = p < 0.0001, ** = p < 0.001, ns= not statistically significant, two-way ANOVA, scale bar is 20 µm.


F . Representative images of HPRT negative mutants in HT1080 cells infected with scramble shRNA ( shScr ) or shRNA against DIS3 ( shDIS3 ) . Histograms show the mutation frequency and the deletion length of DIS3 WT ( shScr ) and DIS3 depleted cells ( shDIS3 ) after I - SceI induced DSB . Error bars represent s . e . m . ( n = 3 ) . * * * = p < 0 . 001 , ns = not statistically significant Student t - test .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

F. Representative images of HPRT negative mutants in HT1080 cells infected with scramble shRNA (shScr) or shRNA against DIS3 (shDIS3). Histograms show the mutation frequency and the deletion length of DIS3 WT (shScr) and DIS3 depleted cells (shDIS3) after I-SceI induced DSB. Error bars represent s.e.m. (n=3). *** = p < 0.001, ns= not statistically significant Student t-test.


A . U2OS cells were transfected with siCTRL or with siDIS3 and 48 hours later were 3 Gy irradiated ( IR ) or left untreated ( NO IR ) . Cells were fixed 4 hours after IR and stained for BRCA1 . Histograms show foci number per cell , analyzed with Cell Profiler . The average number of foci per cell was calculated from three independent experiments . At least 200 cells were counted for each point , error bars indicate s . e . m . ( n = 3 biological replicates ) . * * = p < 0 . 01 , ns = not statistically significant , two - way ANOVA , scale bar is 10 µm .

A. U2OS cells were transfected with siCTRL or with siDIS3 and 48 hours later were 3 Gy irradiated (IR) or left untreated (NO IR). Cells were fixed 4 hours after IR and stained for BRCA1. Histograms show foci number per cell, analyzed with Cell Profiler. The average number of foci per cell was calculated from three independent experiments. At least 200 cells were counted for each point, error bars indicate s.e.m. (n=3 biological replicates). ** = p < 0.01, ns= not statistically significant, two-way ANOVA, scale bar is 10 µm.


C . Representative images of BRCA1 staining on U2OS cells transfected with siCTRL or with siDIS3 . 48 hours after transfection cells were irradiated and 4 hours later were treated with RNase H or left untreated ( UNTR ) . Histograms show the average foci number per cell from three independent experiments analyzed with Cell Profiler . At least 200 cells were counted for each point , error bars indicate s . e . m . ( n = 3 ) . * * = p < 0 . 01 , ns = not statistically significant , one - way ANOVA , scale bar is 10 µm .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

C. Representative images of BRCA1 staining on U2OS cells transfected with siCTRL or with siDIS3. 48 hours after transfection cells were irradiated and 4 hours later were treated with RNase H or left untreated (UNTR). Histograms show the average foci number per cell from three independent experiments analyzed with Cell Profiler. At least 200 cells were counted for each point, error bars indicate s.e.m. (n=3). ** = p < 0.01, ns= not statistically significant, one-way ANOVA, scale bar is 10 µm.


D . Representative pictures of comet assays performed under alkaline conditions in U2OS cells , silenced ( siDIS3 ) or not ( siCTRL ) for DIS3 untreated ( UNTR ) or treated with RNase H ( RNase H ) . Relative comet tail moments are plotted for siCTRL ( black circles ) and siDIS3 ( red circles ) . Analysis was performed using Casplab software , error bars indicate s . e . m . Plots represent three biological replicates , with 150 cells for each siRNA . * * * * = p < 0 . 0001 , one - way ANOVA , scale bar is 20 µm .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

D. Representative pictures of comet assays performed under alkaline conditions in U2OS cells, silenced (siDIS3) or not (siCTRL) for DIS3 untreated (UNTR) or treated with RNase H (RNase H). Relative comet tail moments are plotted for siCTRL (black circles) and siDIS3 (red circles). Analysis was performed using Casplab software, error bars indicate s.e.m. Plots represent three biological replicates, with 150 cells for each siRNA. **** = p < 0.0001, one-way ANOVA, scale bar is 20 µm.


A . Representative confocal images upon irradiation with the 405nm laser . U2OS cells were presensitized with BrdU for 24 hours , micro - irradiated , fixed after 10 minutes , and stained with antibodies against γH2AX and DIS3 scale bar is 10 µm . B . Magnification image of the white box in panel A . C . Intensity profiles of γH2AX ( green ) and DIS3 signals through the yellow line in panel B . Quantification is performed with ImageJ software scale bar is 10 µm .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

A. Representative confocal images upon irradiation with the 405nm laser. U2OS cells were presensitized with BrdU for 24 hours, micro-irradiated, fixed after 10 minutes, and stained with antibodies against γH2AX and DIS3 scale bar is 10 µm. B. Magnification image of the white box in panel A. C. Intensity profiles of γH2AX (green) and DIS3 signals through the yellow line in panel B. Quantification is performed with ImageJ software scale bar is 10 µm.


A . Representative pictures of comet assays performed under alkaline conditions in DIS3 WT MM cell lines MM . 1S and RPMI - 8226 ( RPMI ) , and in DIS3 mutated MM cell lines PCM6 and OPM2 , untreated ( UNTR ) or treated with RNase H ( RNase H ) . Tail moments analysis was performed using Casplab software , error bars indicate s . e . m . Plots represent three biological replicates , with 150 cells for each cell line . * * * * = p < 0 . 0001 ns = not statistically significant , two - way ANOVA , scale bar is 20 µm .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

A. Representative pictures of comet assays performed under alkaline conditions in DIS3 WT MM cell lines MM.1S and RPMI-8226 (RPMI), and in DIS3 mutated MM cell lines PCM6 and OPM2, untreated (UNTR) or treated with RNase H (RNase H). Tail moments analysis was performed using Casplab software, error bars indicate s.e.m. Plots represent three biological replicates, with 150 cells for each cell line. **** = p < 0.0001 ns= not statistically significant, two-way ANOVA, scale bar is 20 µm.


B . Immunostaining with S9 . 6 ( green ) and DAPI ( blue ) in MM . 1S , RPMI - 8226 , PCM6 , and OPM2 cells , treated ( RNase H ) or not ( UNTR ) with RNase H for 1 hour . Histograms show S9 . 6 signal intensity per cell . More than 150 cells were counted , error bars indicate s . e . m . ( n = 3 biological replicates ) . * * * * = p < 0 . 0001 , one - way ANOVA , scale bar is 10 µm .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

B. Immunostaining with S9.6 (green) and DAPI (blue) in MM.1S, RPMI-8226, PCM6, and OPM2 cells, treated (RNase H) or not (UNTR) with RNase H for 1 hour. Histograms show S9.6 signal intensity per cell. More than 150 cells were counted, error bars indicate s.e.m. (n=3 biological replicates). **** = p < 0.0001, one-way ANOVA, scale bar is 10 µm.


A . Relative mRNA expression level of interferon genes IFI6 , ISG15 , IFITM1 , IFIT3 , IFI27 , MCL1 , cGAS , and STING in OPM2 cells infected with a vector expressing DIS3 ( DIS3 ) or an empty vector ( EV ) . Values are relative to housekeeping gene expression , normalized on EV , and represent SE of three biological replicates . * * * = p < 0 . 001 , * * = p < 0 . 01 , multiple t - tests .

A. Relative mRNA expression level of interferon genes IFI6, ISG15, IFITM1, IFIT3, IFI27, MCL1, cGAS, and STING in OPM2 cells infected with a vector expressing DIS3 (DIS3) or an empty vector (EV). Values are relative to housekeeping gene expression, normalized on EV, and represent SE of three biological replicates. *** = p < 0.001, ** = p < 0.01, multiple t-tests.


Differentially expressed genes ( DEGs ) between mutant and WT samples ; p - values are from limma and false - discovery rate ( FDR ) is calculated using the Benjamini - Hochberg procedure ; FDR < 0 . 05 was used as cut off . Functional annotation analysis by IPA of the DEGs between DIS3 mutant and WT samples based on FDR cut - off . ( C ) Volcano plot of DEGs between mutant and WT samples ; labeled genes are the IFN - related genes with an FDR < 0 . 05 ( red horizontal line ) and absolute log 2 - fold change above or below 0 . 5 ( red vertical lines ) , respectively ; additional representative IFN - related genes are also labeled .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Differentially expressed genes (DEGs) between mutant and WT samples; p-values are from limma and false-discovery rate (FDR) is calculated using the Benjamini-Hochberg procedure; FDR < 0.05 was used as cut off. Functional annotation analysis by IPA of the DEGs between DIS3 mutant and WT samples based on FDR cut-off. (C) Volcano plot of DEGs between mutant and WT samples; labeled genes are the IFN-related genes with an FDR < 0.05 (red horizontal line) and absolute log 2-fold change above or below 0.5 (red vertical lines), respectively; additional representative IFN-related genes are also labeled.


( F ) Violin plot of the number of non - synonymous ( NS ) mutation load comparison between DIS3 mutant versus DIS3 WT performed on the entire CoMMpass dataset , including 853 MM patients , 88 presenting DIS3 mutations ( all samples ) and on the CoMMpass dataset , stratified according to the intensity of the IFN responsiveness ( clusters C1 , C2 , C3 ) . Wilcoxon rank - sum test was used for comparison between DIS3 mutant vs WT . * * * * = p < , * * = p < 0 . 01 , * = p < 0 . 05 . Black color dots represent the median in each group .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

(F) Violin plot of the number of non-synonymous (NS) mutation load comparison between DIS3 mutant versus DIS3 WT performed on the entire CoMMpass dataset, including 853 MM patients, 88 presenting DIS3 mutations (all samples) and on the CoMMpass dataset, stratified according to the intensity of the IFN responsiveness (clusters C1, C2, C3). Wilcoxon rank-sum test was used for comparison between DIS3 mutant vs WT. **** = p <, ** = p < 0.01, * = p < 0.05. Black color dots represent the median in each group.


( A , B ) qRT - PCR analysis of IL6 expression upon indicated stimulations in presence or absence of NOD1 ( A ) or NOD2 ( B ) . HeLa inducible NOD1 cells ( A ) or NOD2 cells ( B ) were induced in absence or presence of doxycycline overnight and afterwards stimulated with various stimuli for 4 h .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

(A, B) qRT-PCR analysis of IL6 expression upon indicated stimulations in presence or absence of NOD1 (A) or NOD2 (B). HeLa inducible NOD1 cells (A) or NOD2 cells (B) were induced in absence or presence of doxycycline overnight and afterwards stimulated with various stimuli for 4 h.


( C ) qRT - PCR analysis of Cxcl2 expression upon indicated stimulations in WT , Nod1 / 2 KO and Rip2 KO bone marrow derived macrophages ( BMDMs ) .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

(C) qRT-PCR analysis of Cxcl2 expression upon indicated stimulations in WT, Nod1/2 KO and Rip2 KO bone marrow derived macrophages (BMDMs).


ELISA analysis of IL6 in supernatants of HDFs ( E ) upon indicated stimulations for 20 h in absence or presence of the inhibitor of sphingosine kinases .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O

ELISA analysis of IL6 in supernatants of HDFs (E) upon indicated stimulations for 20 h in absence or presence of the inhibitor of sphingosine kinases.


( H ) qRT - PCR analysis of Cxcl2 expression in WT , Sphk1 KO or Sphk2 KO BMDMs upon indicated stimulations for 4 h .

O O O O O O O O O O O O O O O O O O O O O O O O O O

(H) qRT-PCR analysis of Cxcl2 expression in WT, Sphk1 KO or Sphk2 KO BMDMs upon indicated stimulations for 4 h.


( D ) Western blot analysis of MAPKs and NF - κB activation upon S1P stimulation . HeLa NOD1 or NOD2 cells were treated with cytosolic S1P ( 20 µM ) , iE - DAP ( 20 µM ) or MDP ( 20 µM ) for indicated times .

O O O O O O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O B-CONTROLLED_VAR O O O O O B-CONTROLLED_VAR I-CONTROLLED_VAR I-CONTROLLED_VAR O O O O O B-CONTROLLED_VAR O O O O O O O O

(D) Western blot analysis of MAPKs and NF-κB activation upon S1P stimulation. HeLa NOD1 or NOD2 cells were treated with cytosolic S1P (20 µM), iE-DAP (20 µM) or MDP (20 µM) for indicated times.


Multiplex analysis of CXCL2 ( I ) , CCL5 ( J ) and IL16 ( K ) production in supernatants of WT , Nod1 / 2 and Rip2 KO BMDMs upon S1P ( 10 µM ) or MDP ( 10 µM ) stimulations together with digitonin ( 2 . 5 µg / ml ) for 20 h .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B-CONTROLLED_VAR O O O O O B-CONTROLLED_VAR O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O

Multiplex analysis of CXCL2 (I), CCL5 (J) and IL16 (K) production in supernatants of WT, Nod1/2 and Rip2 KO BMDMs upon S1P (10 µM) or MDP (10 µM) stimulations together with digitonin (2.5 µg/ml) for 20 h.


( A , B ) Immunoprecipitation with various lipid - coated beads using HeLa NOD1 - GFP ( A ) and NOD2 - GFP cells ( B ) . Cell lysates of HeLa NOD1 or HeLa NOD2 cells were incubated with lipid - coated beads at room temperature for 2 h .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

(A, B) Immunoprecipitation with various lipid-coated beads using HeLa NOD1-GFP (A) and NOD2-GFP cells (B). Cell lysates of HeLa NOD1 or HeLa NOD2 cells were incubated with lipid-coated beads at room temperature for 2 h.


( E , F ) Single particle tracking of NOD1 - GFP ( E ) or NOD2 - GFP ( F ) with S1P - TAMRA . After doxycycline induction overnight , HeLa NOD1 or NOD2 cells were stimulated with S1P - TAMRA ( 20 µM ) for 1 h together with digitonin . Scale bar : 5 µm .

O O O O O O O O O O O O O O O O O O O O O O O B-MEASURED_VAR O O O O O O O O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O

(E, F) Single particle tracking of NOD1-GFP (E) or NOD2-GFP (F) with S1P-TAMRA. After doxycycline induction overnight, HeLa NOD1 or NOD2 cells were stimulated with S1P-TAMRA (20 µM) for 1 h together with digitonin. Scale bar: 5 µm.


( D ) MST analysis of direct binding of NOD1 to S1P and iE - DAP . ( E ) MST analysis of direct binding of NOD2 with S1P and MDP .

O O O O O O O O O O O B-MEASURED_VAR O B-MEASURED_VAR I-MEASURED_VAR I-MEASURED_VAR O O O O O O O O O O O O B-MEASURED_VAR O B-MEASURED_VAR O

(D) MST analysis of direct binding of NOD1 to S1P and iE-DAP. (E) MST analysis of direct binding of NOD2 with S1P and MDP.


( F ) ELISA analysis of IL8 in supernatants of HEK293T NOD1 / 2 KO cells transfected with indicated NOD1 or NOD2 mutants . After 24 h transfection , cells were stimulated with S1P ( 20 µM ) , iE - DAP ( 20 µM ) or MDP ( 20 µM ) together with digitonin for 20 h .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B-CONTROLLED_VAR O O O O O B-CONTROLLED_VAR I-CONTROLLED_VAR I-CONTROLLED_VAR O O O O O B-CONTROLLED_VAR O O O O O O B-CONTROLLED_VAR O O O O

(F) ELISA analysis of IL8 in supernatants of HEK293T NOD1/2 KO cells transfected with indicated NOD1 or NOD2 mutants. After 24 h transfection, cells were stimulated with S1P (20 µM), iE-DAP (20 µM) or MDP (20 µM) together with digitonin for 20 h.


( A , B ) MST analysis of direct binding of NOD1 ( A ) or NOD2 ( B ) with ADP in the presence of S1P ( 2 µM ) .

O O O O O O O O O O O O O O O O O O O O O B-MEASURED_VAR O O O O O O O O O O

(A, B) MST analysis of direct binding of NOD1 (A) or NOD2 (B) with ADP in the presence of S1P (2 µM).


Monocyte derived macrophages ( MDM ) were treated with 5μM etoposide ( ETO ) for 18h . Cells were stained for γH2AX and 53BP1 nuclear foci , acquired and analysed using the automated cell ‐ imaging system Hermes WiScan and ImageJ . On average 104 cells were acquired and analysed . ( n = 3 , mean ± s . e . m . ; * P ‐ value ≤ 0 . 05 ; paired t ‐ test ) . Scale bars , 10μm .

O O O O O O O O O O B-CONTROLLED_VAR O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Monocyte derived macrophages (MDM) were treated with 5μM etoposide (ETO) for 18h. Cells were stained for γH2AX and 53BP1 nuclear foci, acquired and analysed using the automated cell‐imaging system Hermes WiScan and ImageJ. On average 104 cells were acquired and analysed. (n = 3, mean ± s.e.m.; *P‐value ≤ 0.05; paired t‐test). Scale bars, 10μm.


O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O


MDM were treated with increasing concentrations of ETO and CTH for 66h . Cells were stained to distinguish between live and dead cells using LIVE / DEAD fixable Dead cell stain protocol . Percentages of live / dead cells were determined using automated cell ‐ imaging system Hermes WiScan and ImageJ . Addition of 20 % ethanol for 10min into cells treated with ETO was used as positive control . ( n = 3 , mean ± s . e . m ) .

O O O O O O O B-CONTROLLED_VAR O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O

MDM were treated with increasing concentrations of ETO and CTH for 66h. Cells were stained to distinguish between live and dead cells using LIVE/DEAD fixable Dead cell stain protocol. Percentages of live/dead cells were determined using automated cell‐imaging system Hermes WiScan and ImageJ. Addition of 20% ethanol for 10min into cells treated with ETO was used as positive control. (n = 3, mean ± s.e.m).


MDM were treated with 5μM ETO for 18h and infected in the presence of ETO with VSV - G pseudotyped HIV - 1 GFP viruses wild type ( wt ) HIV - 1 capsid mutants ( N74D or P90A ) , HIV - 2 , SIV sooty mangabey ( SIVsm E543 ) , replication competent Adenovirus type 5 AdV ( AdV ) , Semliki Forest Virus ( SFV ) and HSV - 1 . The percentages of infected cells were determined using an automated cell ‐ imaging system Hermes WiScan and ImageJ and normalized to untreated control ~ 100 % . ( n = 3 , mean ± s . e . m . ; * * P ‐ value ≤ 0 . 01 ; * * * P ‐ value ≤ 0 . 001 ; ( ns ) non ‐ significant , paired t ‐ test ) . Cells from a representative donor were used for immunoblotting .

O O O O O B-CONTROLLED_VAR O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

MDM were treated with 5μM ETO for 18h and infected in the presence of ETO with VSV-G pseudotyped HIV-1 GFP viruses wild type (wt) HIV-1 capsid mutants (N74D or P90A), HIV-2, SIV sooty mangabey (SIVsm E543), replication competent Adenovirus type 5 AdV (AdV), Semliki Forest Virus (SFV) and HSV-1. The percentages of infected cells were determined using an automated cell‐imaging system Hermes WiScan and ImageJ and normalized to untreated control ~100%. (n = 3, mean ± s.e.m.; **P‐value ≤ 0.01; ***P‐value ≤ 0.001; (ns) non‐significant, paired t‐test). Cells from a representative donor were used for immunoblotting.


MDM were treated with 5μM ETO for 18h and infected in the presence of ETO with VSV - G pseudotyped HIV - 1 GFP . 104 cells were recorded and analysed for GFP expression 48h post - infection using an automated cell ‐ imaging system Hermes WiScan and ImageJ . ( n = 4 , mean ± s . e . m ; * * * P ‐ value ≤ 0 . 001 , paired t ‐ test ) .

O O O O O B-CONTROLLED_VAR O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

MDM were treated with 5μM ETO for 18h and infected in the presence of ETO with VSV-G pseudotyped HIV-1 GFP. 104 cells were recorded and analysed for GFP expression 48h post-infection using an automated cell‐imaging system Hermes WiScan and ImageJ. (n = 4, mean ± s.e.m; ***P‐value ≤ 0.001, paired t‐test).


MDM were treated with 5μM ETO for 18h and infected in the presence of ETO with full - length replication competent macrophage tropic HIV - 1 virus BaL . Cells were stained for intracellular p24 and the percentage of infected cells was quantified 48 h post ‐ infection by FACS ( n = 3 , mean ± s . e . m ; * * * P ‐ value ≤ 0 . 001 , paired t ‐ test ) .

MDM were treated with 5μM ETO for 18h and infected in the presence of ETO with full-length replication competent macrophage tropic HIV-1 virus BaL. Cells were stained for intracellular p24 and the percentage of infected cells was quantified 48 h post‐infection by FACS (n = 3, mean ± s.e.m; ***P‐value ≤ 0.001, paired t‐test).


G - I MDM were treated with 5μM ETO for 18h and infected in the presence of ETO with HIV - 1 BaL and DNA isolated 18 h post ‐ infection for qPCR . Late viral RT products . AZT : MDM treated with 20μM AZT , a reverse - transcriptase inhibitor , were used as control . ( n = 3 , mean ± s . e . m . ; ( ns ) non ‐ significant , paired t ‐ test ) .

O O O O O O O O B-CONTROLLED_VAR O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O B-CONTROLLED_VAR O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

G-I MDM were treated with 5μM ETO for 18h and infected in the presence of ETO with HIV-1 BaL and DNA isolated 18 h post‐infection for qPCR.  Late viral RT products. AZT: MDM treated with 20μM AZT, a reverse-transcriptase inhibitor, were used as control. (n = 3, mean ± s.e.m.; (ns) non‐significant, paired t‐test).


G - I MDM were treated with 5μM ETO for 18h and infected in the presence of ETO with HIV - 1 BaL and DNA isolated 18 h post ‐ infection for qPCR . 2LTR circles . ( n = 3 , mean ± s . e . m . ; * P ‐ value ≤ 0 . 05 , paired t ‐ test ) .

O O O O O O O O B-CONTROLLED_VAR O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

G-I MDM were treated with 5μM ETO for 18h and infected in the presence of ETO with HIV-1 BaL and DNA isolated 18 h post‐infection for qPCR.2LTR circles. (n = 3, mean ± s.e.m.; *P‐value ≤ 0.05, paired t‐test).


G - I MDM were treated with 5μM ETO for 18h and infected in the presence of ETO with HIV - 1 BaL and DNA isolated 18 h post ‐ infection for qPCR . Integrated copies of viral DNA , Alu - Gag qPCR . ( n = 3 , mean ± s . e . m . ; * * * P ‐ value ≤ 0 . 001 , paired t ‐ test ) .

O O O O O O O O B-CONTROLLED_VAR O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

G-I MDM were treated with 5μM ETO for 18h and infected in the presence of ETO with HIV-1 BaL and DNA isolated 18 h post‐infection for qPCR.Integrated copies of viral DNA, Alu-Gag qPCR. (n = 3, mean ± s.e.m.; ***P‐value ≤ 0.001, paired t‐test).


MDM were treated with 5μM ETO for 18h and infected with HIV - 1 BaL ( 3 , 6 , 12 ffu / cell ) . Cells were stained for intracellular p24 and the percentage of infected cells was quantified 48 h post ‐ infection by FACS ( n = 3 , mean ± s . e . m ; * * P ‐ value ≤ 0 . 01 ; * * * P ‐ value ≤ 0 . 001 , paired t ‐ test ) .

O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

MDM were treated with 5μM ETO for 18h and infected with HIV-1 BaL (3, 6, 12 ffu/cell). Cells were stained for intracellular p24 and the percentage of infected cells was quantified 48 h post‐infection by FACS (n = 3, mean ± s.e.m; ** P‐value ≤ 0.01; ***P‐value ≤ 0.001, paired t‐test).


MDM were treated with 5μM ETO for 18h , infected with HIV - 1 BaL ( 3 , 6 , 12 ffu / cell ) and DNA isolated 18 h post ‐ infection for qPCR . ( n = 3 , mean ± s . e . m . ; ( ns ) non ‐ significant , paired t ‐ test ) .

O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

MDM were treated with 5μM ETO for 18h, infected with HIV-1 BaL (3, 6, 12 ffu/cell) and DNA isolated 18 h post‐infection for qPCR. (n = 3, mean ± s.e.m.; (ns) non‐significant, paired t‐test).


MDM were treated with 5μM ETO for 18h , infected with HIV - 1 BaL and DNA isolated 4 , 6 , and 18 h post ‐ infection for qPCR . ( n = 3 , mean ± s . e . m . ; ( ns ) non ‐ significant , paired t ‐ test ) .

O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

MDM were treated with 5μM ETO for 18h, infected with HIV-1 BaL and DNA isolated 4, 6, and 18 h post‐infection for qPCR. (n = 3, mean ± s.e.m.; (ns) non‐significant, paired t‐test).


MDM were transfected with control or pool of SAMHD1 ( KD ) siRNA and 3 days later treated with 5μM ETO and infected in the presence of ETO with VSV ‐ G pseudotyped HIV ‐ 1 GFP 18h later . Cells from a representative donor were used for immunoblotting . The percentage of infected cells was quantified by the automated cell ‐ imaging system Hermes WiScan and ImageJ 48h post - infection . ( n = 3 , mean ± s . e . m . ; * * P ‐ value ≤ 0 . 01 ; ( ns ) non ‐ significant , paired t ‐ test ) .

O O O O O O O O O O O O O O O O O O O O B-CONTROLLED_VAR O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

MDM were transfected with control or pool of SAMHD1 (KD) siRNA and 3 days later treated with 5μM ETO and infected in the presence of ETO with VSV‐G pseudotyped HIV‐1 GFP 18h later. Cells from a representative donor were used for immunoblotting. The percentage of infected cells was quantified by the automated cell‐imaging system Hermes WiScan and ImageJ 48h post-infection. (n = 3, mean ± s.e.m.; **P‐value ≤ 0.01; (ns) non‐significant, paired t‐test).


MDM were treated with 5μM ETO for 18h and co ‐ infected in the presence of ETO with VSV ‐ G HIV ‐ 1 GFP and SIVmac virus ‐ like particles containing Vpx / Vpr ( SIV VLP ) . Cells from a representative donor were used for immunoblotting . The percentage of infected cells was quantified by the Hermes WiScan and ImageJ 48h post - infection . ( n = 3 , mean ± s . e . m . ; * * P ‐ value ≤ 0 . 01 ; ( ns ) non ‐ significant , paired t ‐ test ) .

O O O O O B-CONTROLLED_VAR O O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

MDM were treated with 5μM ETO for 18h and co‐infected in the presence of ETO with VSV‐G HIV‐1 GFP and SIVmac virus‐like particles containing Vpx/Vpr (SIV VLP). Cells from a representative donor were used for immunoblotting. The percentage of infected cells was quantified by the Hermes WiScan and ImageJ 48h post-infection. (n = 3, mean ± s.e.m.; **P‐value ≤ 0.01; (ns) non‐significant, paired t‐test).


MDM were treated with 5μM ETO for 18h and co ‐ infected in the presence of ETO with VSV ‐ G HIV ‐ 1 GFP and SIVmac virus ‐ like particles containing Vpx / Vpr ( SIV VLP ) or deleted for Vpx ( SIV VLP del Vpx ) or deleted for Vpr ( SIV VLP del Vpr ) . Cells from a representative donor were used for immunoblotting . The percentage of infected cells was quantified by the automated cell ‐ imaging system Hermes WiScan and ImageJ 48h post - infection . ( n = 4 , mean ± s . e . m . ; * * P ‐ value ≤ 0 . 01 ; ( ns ) non ‐ significant , paired t ‐ test ) .

O O O O O B-CONTROLLED_VAR O O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

MDM were treated with 5μM ETO for 18h and co‐infected in the presence of ETO with VSV‐G HIV‐1 GFP and SIVmac virus‐like particles containing Vpx/Vpr (SIV VLP) or deleted for Vpx (SIV VLP del Vpx) or deleted for Vpr (SIV VLP del Vpr). Cells from a representative donor were used for immunoblotting. The percentage of infected cells was quantified by the automated cell‐imaging system Hermes WiScan and ImageJ 48h post-infection. (n = 4, mean ± s.e.m.; **P‐value ≤ 0.01; (ns) non‐significant, paired t‐test).


D - F . MDM were treated with 5μM ETO for 18h and co ‐ infected in the presence of ETO with HIV - 1 BaL and SIVmac virus ‐ like particles containing Vpx / Vpr ( SIV VLP ) . DNA was isolated 18 h post ‐ infection for qPCR quantification of F . Late RT products ; G . 2LTR circles ; H integrated viral DNA . Late viral RT products . AZT : MDM treated with 20μM AZT , a reverse - transcriptase inhibitor , were used as control . ( n = 3 , mean ± s . e . m . ; ( ns ) non ‐ significant , paired t ‐ test ) .

O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B-CONTROLLED_VAR O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

D-F. MDM were treated with 5μM ETO for 18h and co‐infected in the presence of ETO with HIV-1 BaL and SIVmac virus‐like particles containing Vpx/Vpr (SIV VLP). DNA was isolated 18 h post‐infection for qPCR quantification of F. Late RT products; G. 2LTR circles; H integrated viral DNA.Late viral RT products. AZT: MDM treated with 20μM AZT, a reverse-transcriptase inhibitor, were used as control. (n = 3, mean ± s.e.m.; (ns) non‐significant, paired t‐test).


D - F . MDM were treated with 5μM ETO for 18h and co ‐ infected in the presence of ETO with HIV - 1 BaL and SIVmac virus ‐ like particles containing Vpx / Vpr ( SIV VLP ) . DNA was isolated 18 h post ‐ infection for qPCR quantification of F . Late RT products ; G . 2LTR circles ; H integrated viral DNA . 2LTR circles . ( n = 3 , mean ± s . e . m . ; ( ns ) non ‐ significant ; * P ‐ value ≤ 0 . 05 , paired t ‐ test ) .

O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

D-F. MDM were treated with 5μM ETO for 18h and co‐infected in the presence of ETO with HIV-1 BaL and SIVmac virus‐like particles containing Vpx/Vpr (SIV VLP). DNA was isolated 18 h post‐infection for qPCR quantification of F. Late RT products; G. 2LTR circles; H integrated viral DNA.2LTR circles. (n = 3, mean ± s.e.m.; (ns) non‐significant; *P‐value ≤ 0.05, paired t‐test).


D - F . MDM were treated with 5μM ETO for 18h and co ‐ infected in the presence of ETO with HIV - 1 BaL and SIVmac virus ‐ like particles containing Vpx / Vpr ( SIV VLP ) . DNA was isolated 18 h post ‐ infection for qPCR quantification of F . Late RT products ; G . 2LTR circles ; H integrated viral DNA . Integrated copies of viral DNA , Alu - Gag qPCR . ( n = 3 , mean ± s . e . m . ; ( ns ) non ‐ significant ; * * P ‐ value ≤ 0 . 01 , paired t ‐ test ) .

O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

D-F. MDM were treated with 5μM ETO for 18h and co‐infected in the presence of ETO with HIV-1 BaL and SIVmac virus‐like particles containing Vpx/Vpr (SIV VLP). DNA was isolated 18 h post‐infection for qPCR quantification of F. Late RT products; G. 2LTR circles; H integrated viral DNA.Integrated copies of viral DNA, Alu-Gag qPCR. (n = 3, mean ± s.e.m.; (ns) non‐significant; **P‐value ≤ 0.01, paired t‐test).


The percentage of infected cells was quantified by Hermes WiScan and ImageJ 48h post - infection . ( n = 3 , mean ± s . e . m . ; ( ns ) non ‐ significant ; * * P ‐ value ≤ 0 . 01 , paired t ‐ test ) .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

The percentage of infected cells was quantified by Hermes WiScan and ImageJ 48h post-infection. (n = 3, mean ± s.e.m.; (ns) non‐significant; **P‐value ≤ 0.01, paired t‐test).


A - B . MDM were treated with 5μM ETO for 18h and co ‐ infected in the presence of ETO with VSV ‐ G HIV ‐ 1 GFP and SIVmac virus ‐ like particles containing Vpx wild type ( WT ) / Vpr or Vpx Q76A mutant / Vpr ( SIV VLP Q76A ) . ( n = 3 , mean ± s . e . m . ; ( ns ) non ‐ significant ; * P ‐ value ≤ 0 . 05 ; * * P ‐ value ≤ 0 . 01 , paired t ‐ test ) . MDM were differentiated and cultured in Human serum instead of FCS .

O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

A-B. MDM were treated with 5μM ETO for 18h and co‐infected in the presence of ETO with VSV‐G HIV‐1 GFP and SIVmac virus‐like particles containing Vpx wild type (WT)/Vpr or Vpx Q76A mutant/Vpr (SIV VLP Q76A). (n = 3, mean ± s.e.m.; (ns) non‐significant; *P‐value ≤ 0.05; **P‐value ≤ 0.01, paired t‐test).MDM were differentiated and cultured in Human serum instead of FCS.


A - B . MDM were treated with 5μM ETO for 18h and co ‐ infected in the presence of ETO with VSV ‐ G HIV ‐ 1 GFP and SIVmac virus ‐ like particles containing Vpx wild type ( WT ) / Vpr or Vpx Q76A mutant / Vpr ( SIV VLP Q76A ) . ( n = 3 , mean ± s . e . m . ; ( ns ) non ‐ significant ; * P ‐ value ≤ 0 . 05 ; * * P ‐ value ≤ 0 . 01 , paired t ‐ test ) . MDM were differentiated and cultured in FCS . A standard culture condition used in all experiments . See Materials and Methods .

O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

A-B. MDM were treated with 5μM ETO for 18h and co‐infected in the presence of ETO with VSV‐G HIV‐1 GFP and SIVmac virus‐like particles containing Vpx wild type (WT)/Vpr or Vpx Q76A mutant/Vpr (SIV VLP Q76A). (n = 3, mean ± s.e.m.; (ns) non‐significant; *P‐value ≤ 0.05; **P‐value ≤ 0.01, paired t‐test).MDM were differentiated and cultured in FCS. A standard culture condition used in all experiments. See Materials and Methods.


C - F . MDM we treated with 5μM ETO for 18h and co ‐ infected in the presence of ETO with HIV - 1 BaL and SIV VLP Q76A . DNA was isolated 18 h post ‐ infection for qPCR quantification of D . Late RT products ; E . 2LTR circles ; F . integrated viral DNA . The percentage of infected cells was quantified by the automated cell ‐ imaging system Hermes WiScan and ImageJ 48h post - infection . Cells from a representative donor were used for immunoblotting . ( n = 3 , mean ± s . e . m . ; * P ‐ value ≤ 0 . 05 ; * * P ‐ value ≤ 0 . 01 , paired t ‐ test ) .

O O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

C-F. MDM we treated with 5μM ETO for 18h and co‐infected in the presence of ETO with HIV-1 BaL and SIV VLP Q76A. DNA was isolated 18 h post‐infection for qPCR quantification of D. Late RT products; E. 2LTR circles; F. integrated viral DNA.  The percentage of infected cells was quantified by the automated cell‐imaging system Hermes WiScan and ImageJ 48h post-infection. Cells from a representative donor were used for immunoblotting. (n = 3, mean ± s.e.m.; *P‐value ≤ 0.05; **P‐value ≤ 0.01, paired t‐test).


C - F . MDM we treated with 5μM ETO for 18h and co ‐ infected in the presence of ETO with HIV - 1 BaL and SIV VLP Q76A . DNA was isolated 18 h post ‐ infection for qPCR quantification of D . Late RT products ; E . 2LTR circles ; F . integrated viral DNA . Late viral RT products . AZT : MDM treated with 20μM AZT , a reverse - transcriptase inhibitor , were used as control . ( n = 3 , mean ± s . e . m . ; ( ns ) non ‐ significant ; * P ‐ value ≤ 0 . 05 , paired t ‐ test ) .

O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B-CONTROLLED_VAR O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

C-F. MDM we treated with 5μM ETO for 18h and co‐infected in the presence of ETO with HIV-1 BaL and SIV VLP Q76A. DNA was isolated 18 h post‐infection for qPCR quantification of D. Late RT products; E. 2LTR circles; F. integrated viral DNA.Late viral RT products. AZT: MDM treated with 20μM AZT, a reverse-transcriptase inhibitor, were used as control. (n = 3, mean ± s.e.m.; (ns) non‐significant; *P‐value ≤ 0.05, paired t‐test).


C - F . MDM we treated with 5μM ETO for 18h and co ‐ infected in the presence of ETO with HIV - 1 BaL and SIV VLP Q76A . DNA was isolated 18 h post ‐ infection for qPCR quantification of D . Late RT products ; E . 2LTR circles ; F . integrated viral DNA . 2LTR circles . ( n = 3 , mean ± s . e . m . ; ( ns ) non ‐ significant ; * P ‐ value ≤ 0 . 05 , paired t ‐ test ) .

O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

C-F. MDM we treated with 5μM ETO for 18h and co‐infected in the presence of ETO with HIV-1 BaL and SIV VLP Q76A. DNA was isolated 18 h post‐infection for qPCR quantification of D. Late RT products; E. 2LTR circles; F. integrated viral DNA.2LTR circles. (n = 3, mean ± s.e.m.; (ns) non‐significant; *P‐value ≤ 0.05, paired t‐test).


C - F . MDM we treated with 5μM ETO for 18h and co ‐ infected in the presence of ETO with HIV - 1 BaL and SIV VLP Q76A . DNA was isolated 18 h post ‐ infection for qPCR quantification of D . Late RT products ; E . 2LTR circles ; F . integrated viral DNA . Integrated copies of viral DNA , Alu - Gag qPCR . ( n = 3 , mean ± s . e . m . ; * P ‐ value ≤ 0 . 05 ; * * P ‐ value ≤ 0 . 01 , paired t ‐ test ) .

O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

C-F. MDM we treated with 5μM ETO for 18h and co‐infected in the presence of ETO with HIV-1 BaL and SIV VLP Q76A. DNA was isolated 18 h post‐infection for qPCR quantification of D. Late RT products; E. 2LTR circles; F. integrated viral DNA.Integrated copies of viral DNA, Alu-Gag qPCR. (n = 3, mean ± s.e.m.; *P‐value ≤ 0.05; **P‐value ≤ 0.01, paired t‐test).


MDM were treated with 5μM ETO for 18h , 3μg / ml cGAMP and 10ng / ml IFNβfor 18h . RNA was isolated and qPCR performed for selected genes using TaqMan assays . Expression levels of target genes were normalised to GAPDH . ( n = 3 , mean ± s . e . m . ; * P ‐ value ≤ 0 . 05 ; ( ns ) non ‐ significant , paired t ‐ test ) .

O O O O O B-CONTROLLED_VAR O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

MDM were treated with 5μM ETO for 18h, 3μg/ml cGAMP and 10ng/ml IFNβfor 18h. RNA was isolated and qPCR performed for selected genes using TaqMan assays. Expression levels of target genes were normalised to GAPDH. (n = 3, mean ± s.e.m.; *P‐value ≤ 0.05; (ns) non‐significant, paired t‐test).


MDM were treated with 5μM ETO or cGAMP for 18h or 100ng / ml LPS for 2h . Cells were stained and analysed for IRF3 translocation into nucleus . Scale bars : 10μm .

O O O O O B-CONTROLLED_VAR O B-CONTROLLED_VAR O O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O

MDM were treated with 5μM ETO or cGAMP for 18h or 100ng/ml LPS for 2h. Cells were stained and analysed for IRF3 translocation into nucleus. Scale bars: 10μm.


Quantification of nuclei positive for IRF3 staining . ( n = 3 , mean ± s . e . m . ) .

O O O O O O O O O O O O O O O O O O O O O O O

Quantification of nuclei positive for IRF3 staining. (n = 3, mean ± s.e.m.).


MDM were treated with increasing concentrations of ETO and CTH . Cells were stained for MCM2 expression , acquired and analysed using the automated cell ‐ imaging system Hermes WiScan and ImageJ . On average 104 cells were acquired . ( n = 3 , mean ± s . e . m . ) .

O O O O O O O B-CONTROLLED_VAR O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

MDM were treated with increasing concentrations of ETO and CTH. Cells were stained for MCM2 expression, acquired and analysed using the automated cell‐imaging system Hermes WiScan and ImageJ. On average 104 cells were acquired. (n = 3, mean ± s.e.m.).


MDM were treated with 5μM ETO , lysed and immunoblotting performed to detect cell cycle / cell cycle arrest and DNA damage associated proteins .

O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O

MDM were treated with 5μM ETO, lysed and immunoblotting performed to detect cell cycle/cell cycle arrest and DNA damage associated proteins.


MDM were treated with 5μM ETO or 0 . 01μM CTH for 18h , lysed and immunoblotting performed to detect cell cycle / cell cycle arrest and DNA damage associated proteins .

O O O O O B-CONTROLLED_VAR O O O O O O O O O O O O O O O O O O O O O O O O O O

MDM were treated with 5μM ETO or 0.01μM CTH for 18h, lysed and immunoblotting performed to detect cell cycle/cell cycle arrest and DNA damage associated proteins.


( F ) Representative images of germ cells immunostained for SYCP3 ( green ) , DMC1 ( red ) , and DDX4 ( magenta ) at each meiotic sub - stage . Nuclear DAPI staining is shown in white . The sub - stages of meiosis were defined based on the staining patterns of SYCP3 , DMC1 , and DAPI as described in Materials and Methods . ( G ) Percentages of germ cells at each meiotic sub - stage as defined in Fig 1F . The average percentages in the outer or inner ovarian cortex on each meiotic sub - stage were calculated from at least three fetal ovaries [ 8 wpf ( n = 4 ) , 10 / 12 / 14 / 16 / 18 wpf ( n = 3 ) ] .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

(F) Representative images of germ cells immunostained for SYCP3 (green), DMC1 (red), and DDX4 (magenta) at each meiotic sub-stage. Nuclear DAPI staining is shown in white. The sub-stages of meiosis were defined based on the staining patterns of SYCP3, DMC1, and DAPI as described in Materials and Methods. (G) Percentages of germ cells at each meiotic sub-stage as defined in Fig 1F. The average percentages in the outer or inner ovarian cortex on each meiotic sub-stage were calculated from at least three fetal ovaries [8 wpf (n=4), 10/12/14/16/18 wpf (n=3)].


( C ) IF for oogonia ( POU5F1 , TFAP2C ) , meiotic ( SYCP3 , SYCP1 ) , and oogenic ( ZP3 , TP63 ) markers in the transplanted cy rOvaries . Germ cells and nuclei were marked with DDX4 ( magenta ) and DAPI ( white ) , respectively . The upper - right magnified images of each panel show the expression of each marker ( green ) co - stained with DDX4 ( magenta ) . The lower - right magnified images of each panel show DDX4 expression ( magenta ) co - stained with DAPI ( white ) . The numbers written in the upper - left corner indicate weeks after transplantation ( w - ptp ) . Scale bar = 20 μm . ( D ) Percentages of cells positive for individual markers among DDX4 + germ cells from the IF of cy rOvaries at 3 − 15 w - ptp [ 3 w - ptp ( n = 3 ) , 6 / 9 / 12 w - ptp ( n = 4 ) , 15 w - ptp ( n = 6 ) ] . The average values with SDs are shown . ( E ) H & E staining of transplanted cy rOvaries at 21 w - ptp . Dashed lines indicate the transplanted cy rOvaries beneath the kidney capsule of KSN / Slc mice . K , mouse kidney . Scale bars = 200 μm ( left ) and 100 μm ( right ) .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

(C) IF for oogonia (POU5F1, TFAP2C), meiotic (SYCP3, SYCP1), and oogenic (ZP3, TP63) markers in the transplanted cy rOvaries. Germ cells and nuclei were marked with DDX4 (magenta) and DAPI (white), respectively. The upper-right magnified images of each panel show the expression of each marker (green) co-stained with DDX4 (magenta). The lower-right magnified images of each panel show DDX4 expression (magenta) co-stained with DAPI (white). The numbers written in the upper-left corner indicate weeks after transplantation (w-ptp). Scale bar = 20 μm. (D) Percentages of cells positive for individual markers among DDX4+ germ cells from the IF of cy rOvaries at 3−15 w-ptp [3 w-ptp (n=3), 6/9/12 w-ptp (n=4), 15 w-ptp (n=6)]. The average values with SDs are shown. (E) H&E staining of transplanted cy rOvaries at 21 w-ptp. Dashed lines indicate the transplanted cy rOvaries beneath the kidney capsule of KSN/Slc mice. K, mouse kidney. Scale bars = 200 μm (left) and 100 μm (right).


( E ) IF analyses of key markers as described in Fig 1E in the cultured cy rOvaries . Germ cells and nuclei were marked with DDX4 ( magenta ) and DAPI ( white ) , respectively . The upper - right magnified images of each panel show the expression of key markers ( green ) co - stained with DDX4 ( magenta ) . The lower - right magnified images of each panel show DDX4 expression ( magenta ) co - stained with DAPI ( white ) . The numbers written in the upper - left corner indicate the period of IVC ( w - ivc ) . Scale bar = 20 μm . ( F ) Percentages of cells positive for individual markers among DDX4 + germ cells from the IF of cy rOvaries at 3 - 15 w - ivc [ 3 / 6 / 9 / 12 w - ivc ( n = 3 ) , 15 w - ivc ( n = 3 or 4 ) ] .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

(E) IF analyses of key markers as described in Fig 1E in the cultured cy rOvaries. Germ cells and nuclei were marked with DDX4 (magenta) and DAPI (white), respectively. The upper-right magnified images of each panel show the expression of key markers (green) co-stained with DDX4 (magenta). The lower-right magnified images of each panel show DDX4 expression (magenta) co-stained with DAPI (white). The numbers written in the upper-left corner indicate the period of IVC (w-ivc). Scale bar = 20 μm. (F) Percentages of cells positive for individual markers among DDX4+ germ cells from the IF of cy rOvaries at 3-15 w-ivc [3/6/9/12 w-ivc (n=3), 15 w-ivc (n=3 or 4)].


( A ) Gross appearance ( a ) , H & E staining ( b ) , and IF ( c ) for FOXL2 / DDX4 / DAPI of the human in vivo female gonads ( 11W , left column ) and the cultured rOvaries at 7 and 14 w - ivc . FOXL2 , granulosa cell marker ; DDX4 , germ cell marker ; DAPI , nucleus . Scale bars = 1 mm ( a , left ) , 200 μm ( a , middle / right ) , 50 μm ( b ) , and 20 μm ( c ) . g . a . , gestational age .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

(A) Gross appearance (a), H&E staining (b), and IF (c) for FOXL2/DDX4/DAPI of the human in vivo female gonads (11W, left column) and the cultured rOvaries at 7 and 14 w-ivc. FOXL2, granulosa cell marker; DDX4, germ cell marker; DAPI, nucleus. Scale bars = 1 mm (a, left), 200 μm (a, middle/right), 50 μm (b), and 20 μm (c). g.a., gestational age.


IF for oogonia ( POU5F1 ) , cell proliferation ( Ki67 ) , meiotic ( SYCP3 , DMC1 , γH2AX , SYCP1 ) , and oogenic ( ZP3 , TP63 ) markers for human in vivo female gonad ( 11W , B ) Germ cells and nuclei were marked with DDX4 ( magenta ) and DAPI ( white ) , respectively . The upper right magnified images of each panel show the expression of key markers ( green ) co - stained with DDX4 ( magenta ) . The lower right magnified images of each panel show DDX4 expression ( magenta ) co - stained with DAPI ( white ) .

IF for oogonia (POU5F1), cell proliferation (Ki67), meiotic (SYCP3, DMC1, γH2AX, SYCP1), and oogenic (ZP3, TP63) markers for human in vivo female gonad (11W, B) Germ cells and nuclei were marked with DDX4 (magenta) and DAPI (white), respectively. The upper right magnified images of each panel show the expression of key markers (green) co-stained with DDX4 (magenta). The lower right magnified images of each panel show DDX4 expression (magenta) co-stained with DAPI (white).


IF for oogonia ( POU5F1 ) , cell proliferation ( Ki67 ) , meiotic ( SYCP3 , DMC1 , γH2AX , SYCP1 ) , and oogenic ( ZP3 , TP63 ) markers human in vitro cultured rOvaries at 14 w - ivc ( C ) . Germ cells and nuclei were marked with DDX4 ( magenta ) and DAPI ( white ) , respectively . The upper right magnified images of each panel show the expression of key markers ( green ) co - stained with DDX4 ( magenta ) . The lower right magnified images of each panel show DDX4 expression ( magenta ) co - stained with DAPI ( white ) .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

IF for oogonia (POU5F1), cell proliferation (Ki67), meiotic (SYCP3, DMC1, γH2AX, SYCP1), and oogenic (ZP3, TP63) markers human in vitro cultured rOvaries at 14 w-ivc (C). Germ cells and nuclei were marked with DDX4 (magenta) and DAPI (white), respectively. The upper right magnified images of each panel show the expression of key markers (green) co-stained with DDX4 (magenta). The lower right magnified images of each panel show DDX4 expression (magenta) co-stained with DAPI (white).


( D ) Percentages of cells positive for individual markers among DDX4 + germ cells from the IF of human in vivo female gonads ( 11W ) and human cultured rOvaries at 7 and 14 w - ivc . The mean values from two biological replicates are shown .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

(D) Percentages of cells positive for individual markers among DDX4+ germ cells from the IF of human in vivo female gonads (11W) and human cultured rOvaries at 7 and 14 w-ivc. The mean values from two biological replicates are shown.


Analyses for human germ cells by SC3 - seq . ( E ) UHC for human germ cells in vivo and in rOvaries with all expressed genes ( 20 , 048 genes ) and a heatmap of the expression levels of selected marker genes . Color bars under the dendrogram show the in vivo stage ( 1st bar ) , the period of IVC ( 2nd bar ) , and the cell type ( 3rd bar ) . The heatmap color - coding is as indicated . The color coding in bars is as indicated in Fig 5F .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Analyses for human germ cells by SC3-seq. (E) UHC for human germ cells in vivo and in rOvaries with all expressed genes (20,048 genes) and a heatmap of the expression levels of selected marker genes. Color bars under the dendrogram show the in vivo stage (1st bar), the period of IVC (2nd bar), and the cell type (3rd bar). The heatmap color-coding is as indicated. The color coding in bars is as indicated in Fig 5F.


Analyses performed by 10X scRNA - seq . ( A ) UMAP plot of germ cells from six 10X scRNA - seq datasets ( two for humans [ this study and ( Chitiashvili et al . , 2020 ) ] , one for monkeys [ this study ] , and three for mice [ ( Ge et al . , 2021 , Niu & Spradling , 2020 , Zhao et al . , 2020 ) ] ) integrated by CCA . Meiotic sub - stages were defined after CCA followed by Louvain clustering . Colors indicate the computationally assigned meiotic sub - stages defined by the expression levels of key meiotic markers conserved in all three species ( see Materials and Methods ) . The color - coding is as indicated . M , mitotic ; PL , pre - leptotene ; L , leptotene ; Z , zygotene ; P , pachytene ; D , diplotene . ( B ) The UMAP plot highlighting cells from each dataset . The color - coding for each developmental stage is as indicated .

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Analyses performed by 10X scRNA-seq. (A) UMAP plot of germ cells from six 10X scRNA-seq datasets (two for humans [this study and (Chitiashvili et al., 2020)], one for monkeys [this study], and three for mice [(Ge et al., 2021, Niu & Spradling, 2020, Zhao et al., 2020)]) integrated by CCA. Meiotic sub-stages were defined after CCA followed by Louvain clustering. Colors indicate the computationally assigned meiotic sub-stages defined by the expression levels of key meiotic markers conserved in all three species (see Materials and Methods). The color-coding is as indicated. M, mitotic; PL, pre-leptotene; L, leptotene; Z, zygotene; P, pachytene; D, diplotene. (B) The UMAP plot highlighting cells from each dataset. The color-coding for each developmental stage is as indicated.


( I ) IF analyses of CLGN with TP63 ( oogenic marker ) and DDX4 ( germ cell marker ) in a 13 - year - old human oocyte of a primordial follicle . Nuclear DAPI staining is shown in white .

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(I) IF analyses of CLGN with TP63 (oogenic marker) and DDX4 (germ cell marker) in a 13-year-old human oocyte of a primordial follicle. Nuclear DAPI staining is shown in white.


( C ) The Chr . 10 : A and X : A ratios ( top ) , and XIST expression ( bottom ) in human female germ cells in vivo and in cultured rOvaries analyzed by SC3 - seq .

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(C) The Chr.10:A and X:A ratios (top), and XIST expression (bottom) in human female germ cells in vivo and in cultured rOvaries analyzed by SC3-seq.


A HeLa cells expressing LAMP1 - RFP were treated with vehicle alone ( control ) or LLOMe for 1 h to induce lysosome damage . Cells were fixed 2 h after washout , stained with p62 and galectin - 3 ( Gal3 ) antibodies , and analyzed by confocal microscopy .

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A HeLa cells expressing LAMP1-RFP were treated with vehicle alone (control) or LLOMe for 1 h to induce lysosome damage. Cells were fixed 2 h after washout, stained with p62 and galectin-3 (Gal3) antibodies, and analyzed by confocal microscopy.


B p97 translocates to ruptured lysosomes . Cells co - expressing LAMP1 - RFP and GFP - p97 were treated as in ( A ) and stained with the pan - ubiquitin antibody FK2 ( Ub ) . Percentage of cells showing recruitment of p97 in three independent experiments ( mean ± SD ) .

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B p97 translocates to ruptured lysosomes. Cells co-expressing LAMP1-RFP and GFP-p97 were treated as in (A) and stained with the pan-ubiquitin antibody FK2 (Ub). Percentage of cells showing recruitment of p97 in three independent experiments (mean ± SD).


C Immunodetection of endogenous p97 after LLOMe treatment as in ( A ) . Percentage of cells showing recruitment of p97 in three independent experiments ( mean ± SD ) .

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C Immunodetection of endogenous p97 after LLOMe treatment as in (A). Percentage of cells showing recruitment of p97 in three independent experiments (mean ± SD).


D Clearance of damaged lysosomes depends on p97 . Cells were transfected with control ( Ctrl ) or p97 siRNA oligos , fixed at indicated time points after LLOMe washout and stained for endogenous Gal3 . Quantification of the number of Gal3 - positive vesicles per cell . Data represent mean ± SD of four independent experiments with ≥ 30 cells quantified per condition ( one - sided Welch ' s unequal variances t - tests comparing the siCtrl with sip97 ) .

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D Clearance of damaged lysosomes depends on p97. Cells were transfected with control (Ctrl) or p97 siRNA oligos, fixed at indicated time points after LLOMe washout and stained for endogenous Gal3. Quantification of the number of Gal3-positive vesicles per cell. Data represent mean ± SD of four independent experiments with ≥30 cells quantified per condition (one-sided Welch's unequal variances t-tests comparing the siCtrl with sip97).


E Cells were chased after LLOMe treatment for 12 h with vehicle alone ( DMSO ) , bortezomib ( Btz , 10 nM ) , NH4Cl ( 20 mM ) or the p97 inhibitor NMS - 873 ( 5 µM ) , and Gal3 vesicles quantified . Data represent mean ± SEM of three independent experiments with ≥ 30 cells quantified per condition ( one - sided Welch ' s t - tests ) .

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E Cells were chased after LLOMe treatment for 12 h with vehicle alone (DMSO), bortezomib (Btz, 10 nM), NH4Cl (20 mM) or the p97 inhibitor NMS-873 (5 µM), and Gal3 vesicles quantified. Data represent mean ± SEM of three independent experiments with ≥30 cells quantified per condition (one-sided Welch's t-tests).


F p97 is essential for cell survival after lysosome rupture . Cells were transfected with control ( Ctrl ) , p97 or SEL1L siRNA oligos and treated with indicated concentrations of LLOMe for 12 h . Cell viability was measured using the MTS assay . Data represent mean ± SD of three independent experiments .

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F p97 is essential for cell survival after lysosome rupture. Cells were transfected with control (Ctrl), p97 or SEL1L siRNA oligos and treated with indicated concentrations of LLOMe for 12 h. Cell viability was measured using the MTS assay. Data represent mean ± SD of three independent experiments.


G Taufibrils are endocytosed and induce lysosomal damage . Taufibrils were generated in vitro , fluorescently labelled by Dylight488 and fragmented by sonication ( 488 - labelled tau ) . HeLa cells expressing mCherry - Gal3 were incubated with 300 nM taufibrils for 24 h . Arrows indicate compartments that contain 488 - labelled tau and are positive for mCherry - Gal3 indicating lysosome rupture . Percentage of cells with Gal3 - positive vesicles was quantified from three independent experiments ( mean ± SD ) .

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G Taufibrils are endocytosed and induce lysosomal damage. Taufibrils were generated in vitro, fluorescently labelled by Dylight488 and fragmented by sonication (488-labelled tau). HeLa cells expressing mCherry-Gal3 were incubated with 300 nM taufibrils for 24 h. Arrows indicate compartments that contain 488-labelled tau and are positive for mCherry-Gal3 indicating lysosome rupture. Percentage of cells with Gal3-positive vesicles was quantified from three independent experiments (mean ± SD).


H Accumulation of tau - induced lysosomal damage upon p97 depletion . Cells transfected with control ( Ctrl ) or p97 siRNA oligos were treated as in ( G ) . Percentage of cells with Gal3 - positive vesicles was quantified from three independent experiments ( mean ± SD ) . * = p < 0 . 05 ; * * = p < 0 . 01 ; * * * = p < 0 . 001 . Scale bars , 10 µm .

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H Accumulation of tau-induced lysosomal damage upon p97 depletion. Cells transfected with control (Ctrl) or p97 siRNA oligos were treated as in (G). Percentage of cells with Gal3-positive vesicles was quantified from three independent experiments (mean ± SD). * = p < 0.05; ** = p < 0.01; *** = p < 0.001. Scale bars, 10 µm.


A Impaired clearance of damaged lysosomes in cells expressing a p97 disease - mutant . Wild - type and p97R155H / + MEFs were LLOMe - treated for 1 h and released for indicated times . Percentage of cells with Gal3 - positive vesicles was quantified from three independent experiments ( mean ± SD , Student ' s unpaired t - test ) . Scale bar , 25 µm .

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A Impaired clearance of damaged lysosomes in cells expressing a p97 disease-mutant. Wild-type and p97R155H/+MEFs were LLOMe-treated for 1 h and released for indicated times. Percentage of cells with Gal3-positive vesicles was quantified from three independent experiments (mean ± SD, Student's unpaired t-test). Scale bar, 25 µm.


B Stable U2OS cell lines were doxycycline - induced to express myc - tagged p97 wild - type or disease - mutants as indicated . Induced parental cells served as control ( U2OS - ) . Cells were treated with LLOMe for 1h and chased for indicated time before fixation . Percentage of cells with Gal3 - positive vesicles was quantified from three independent experiments . Comparable expression levels were verified ( see Figure EV2A ) .

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B Stable U2OS cell lines were doxycycline-induced to express myc-tagged p97 wild-type or disease-mutants as indicated. Induced parental cells served as control (U2OS -). Cells were treated with LLOMe for 1h and chased for indicated time before fixation. Percentage of cells with Gal3-positive vesicles was quantified from three independent experiments. Comparable expression levels were verified (see Figure EV2A).


C Stable U2OS cell lines described in ( B ) were treated with LLOMe for 1 h and chased for indicated time . LC3 and GAPDH levels were analyzed by immunoblotting . Quantification is shown in Figure EV2B .

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C Stable U2OS cell lines described in (B) were treated with LLOMe for 1 h and chased for indicated time. LC3 and GAPDH levels were analyzed by immunoblotting. Quantification is shown in Figure EV2B.


D Accumulation of damaged lysosomes in affected p97 patient skeletal muscle . Patient biopsies immunostained for Gal3 and caveolin - 3 ( Cav3 ) . Quantification from 4 random 10X fields for each biopsy and means for controls and patients , respectively . Patients carry p97 mutations R155H ( # 1 - 3 ) or R93C for ( # 4 ) . Patients # 2 and # 3 are cousins . Scale bar , 100 µm .

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D Accumulation of damaged lysosomes in affected p97 patient skeletal muscle. Patient biopsies immunostained for Gal3 and caveolin-3 (Cav3). Quantification from 4 random 10X fields for each biopsy and means for controls and patients, respectively. Patients carry p97 mutations R155H (#1-3) or R93C for (#4). Patients #2 and #3 are cousins. Scale bar, 100 µm.


A Candidate screen for p97 cofactors involved in autophagy of damaged lysosomes . HeLa cells were transfected with indicated siRNA oligos and LLOMe - treated for 1 h . Cells were chased for 12 h , fixed and stained for Gal3 . See Figure EV3 for depletion efficiency . B Quantification of the percentage of cells with more than three Gal3 vesicles per cell for each condition . This threshold was chosen so that less than 1 % of untreated cells were considered positive . Data represent mean ± SEM of three independent experiments with ≥ 30 cells quantified per condition . * = p < 0 . 05 ; * * = p < 0 . 01 ; * * * = p < 0 . 001 ( one - sided Welch ' s t - tests ) .

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A Candidate screen for p97 cofactors involved in autophagy of damaged lysosomes. HeLa cells were transfected with indicated siRNA oligos and LLOMe-treated for 1 h. Cells were chased for 12 h, fixed and stained for Gal3. See Figure EV3 for depletion efficiency.B Quantification of the percentage of cells with more than three Gal3 vesicles per cell for each condition. This threshold was chosen so that less than 1% of untreated cells were considered positive. Data represent mean ± SEM of three independent experiments with ≥30 cells quantified per condition. * = p < 0.05; ** = p < 0.01; *** = p < 0.001 (one-sided Welch's t-tests).


C YOD1 , UBXD1 and PLAA are translocated along with p97 to ruptured lysosomes . Cells expressing indicated tagged proteins were LLOMe - treated for 1 h or with vehicle alone ( control ) , fixed 2 h after washout , and stained for endogenous LAMP1 and , in the case of PLAA , with Alexa - 488 conjugated anti - HA antibodies . See Figure EV3B for quantification .

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C YOD1, UBXD1 and PLAA are translocated along with p97 to ruptured lysosomes. Cells expressing indicated tagged proteins were LLOMe-treated for 1 h or with vehicle alone (control), fixed 2 h after washout, and stained for endogenous LAMP1 and, in the case of PLAA, with Alexa-488 conjugated anti-HA antibodies. See Figure EV3B for quantification.


D An ATP - stabilized complex of p97 containing both UBXD1 and PLAA . Stable HEK293 cell lines were doxycycline - induced to express p97 wild - type ( wt ) or the ATPase - mutant E578Q ( EQ ) at near endogenous level . Endogenous UBXD1 was immunoprecipitated and associated proteins detected by immunoblotting with indicated antibodies . Arrowheads indicate endogenous ( lower band ) and induced p97 ( upper band ) .

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D An ATP-stabilized complex of p97 containing both UBXD1 and PLAA. Stable HEK293 cell lines were doxycycline-induced to express p97 wild-type (wt) or the ATPase-mutant E578Q (EQ) at near endogenous level. Endogenous UBXD1 was immunoprecipitated and associated proteins detected by immunoblotting with indicated antibodies. Arrowheads indicate endogenous (lower band) and induced p97 (upper band).


E Stable HEK293 cells treated as in ( D ) and transiently expressing GFP - tagged YOD1 - wt or the YOD1 - C160S catalytic mutant ( CS ) were processed for co - immunoprecipitation with GFP nanobodies . Asterisk , unspecific band . Note that the YOD1 - CS mutant stabilized p97 binding and , in the p97 - EQ background , also associated with UBXD1 and PLAA .

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E Stable HEK293 cells treated as in (D) and transiently expressing GFP-tagged YOD1-wt or the YOD1-C160S catalytic mutant (CS) were processed for co-immunoprecipitation with GFP nanobodies. Asterisk, unspecific band. Note that the YOD1-CS mutant stabilized p97 binding and, in the p97-EQ background, also associated with UBXD1 and PLAA.


F Control ( IgG ) and UBXD1co - immunoprecipitation with indicated associated proteins from HeLa cells expressing GFP - YOD1 - CS after formaldehyde cross - linking . Ufd1 served as a negative control . Scale bars , 10 µm .

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F Control (IgG) and UBXD1co-immunoprecipitation with indicated associated proteins from HeLa cells expressing GFP-YOD1-CS after formaldehyde cross-linking. Ufd1 served as a negative control. Scale bars, 10 µm.


A K63 - and K48 - ubiquitination of damaged lysosomes . Untransfected HeLa cells , or cells expressing mCherry - Gal3 ( Ch - Gal3 ) were LLOMe - treated for 1 h . 2 h after washout , cells were stained with antibodies specific for K63 or K48 chains , and LAMP1 or p62 as indicated . Percentage of K63 - or K48 - ubiquitinated LAMP1 vesicles and percentage of p62 - positive K63 or K48 vesicles were quantified from three independent experiments ( mean ± SD , Student ' s unpaired t - test for LAMP1 ) . * = p < 0 . 05 .

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A K63- and K48-ubiquitination of damaged lysosomes. Untransfected HeLa cells, or cells expressing mCherry-Gal3 (Ch-Gal3) were LLOMe-treated for 1 h. 2 h after washout, cells were stained with antibodies specific for K63 or K48 chains, and LAMP1 or p62 as indicated. Percentage of K63- or K48-ubiquitinated LAMP1 vesicles and percentage of p62-positive K63 or K48 vesicles were quantified from three independent experiments (mean ± SD, Student's unpaired t-test for LAMP1). * = p < 0.05.


B Colocalization of K63 - and K48 - linked ubiquitin conjugates on individual lysosomes . Cells expressing GFP - TAB2 - NZF ( K63 - sensor ) were treated as in ( A ) and stained for K48 chains and LAMP1 . Note that the apparent nuclear localization of the sensor is a consequence of the extraction procedure ( van Wijk et al . , 2012 ) .

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B Colocalization of K63- and K48-linked ubiquitin conjugates on individual lysosomes. Cells expressing GFP-TAB2-NZF (K63-sensor) were treated as in (A) and stained for K48 chains and LAMP1. Note that the apparent nuclear localization of the sensor is a consequence of the extraction procedure (van Wijk et al., 2012).


C Cells expressing GFP - p97 - EQ were treated as in ( A ) and stained with antibodies as indicated . D Quantification of the total number of K63 - or K48 - ubiquitinated vesicles per cell , and number of p97 - EQ positive K63 - or K48 - ubiquitinated vesicles ( mean ± SD ) . E Percentage of GFP - p97 - EQ vesicles positive for K63 or K48 chains was determined ( mean ± SD ) .

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C Cells expressing GFP-p97-EQ were treated as in (A) and stained with antibodies as indicated.D Quantification of the total number of K63- or K48-ubiquitinated vesicles per cell, and number of p97-EQ positive K63- or K48-ubiquitinated vesicles (mean ± SD).E Percentage of GFP-p97-EQ vesicles positive for K63 or K48 chains was determined (mean ± SD).


F ELDR components target K48 - conjugates on lysosomes . Detection of GFP - YOD1 - CS or UBXD1 - GFP alone , or co - transfected with PLAA - HA and GFP - p97 - EQ , 2 h after LLOMe washout and co - stained with indicated antibodies .

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F ELDR components target K48-conjugates on lysosomes. Detection of GFP-YOD1-CS or UBXD1-GFP alone, or co-transfected with PLAA-HA and GFP-p97-EQ, 2 h after LLOMe washout and co-stained with indicated antibodies.


A Time course of K63 - and K48 - ubiquitination . Control - depleted cells were fixed at indicated time points after LLOMe washout and stained with chain - specific antibodies and LAMP1 . Automated quantification of LAMP1 vesicles positive for K63 or K48 chains . Data represent mean ± SD of three independent experiments . B Depletion of p97 or YOD1 results in increase and persistence of K48 chains on damaged lysosomes . Experiment and quantification as in ( A ) in cells treated with p97 or YOD1 siRNA oligos .

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A Time course of K63- and K48-ubiquitination. Control-depleted cells were fixed at indicated time points after LLOMe washout and stained with chain-specific antibodies and LAMP1. Automated quantification of LAMP1 vesicles positive for K63 or K48 chains. Data represent mean ± SD of three independent experiments.B Depletion of p97 or YOD1 results in increase and persistence of K48 chains on damaged lysosomes. Experiment and quantification as in (A) in cells treated with p97 or YOD1 siRNA oligos.


C The p97 - EQ mutant stabilizes K48 - conjugates . Lysosome damage was induced as in ( A ) in cells transfected with GFP - tagged p97 - wt or p97 - EQ . Cells were chased after washout for 12 h and stained for K48 chains . D Quantification of K48 - positive lysosomes 2 h and 12 h after damage in cells treated as in ( A ) . Data represent mean ± SD of three independent experiments .

C The p97-EQ mutant stabilizes K48-conjugates. Lysosome damage was induced as in (A) in cells transfected with GFP-tagged p97-wt or p97-EQ. Cells were chased after washout for 12 h and stained for K48 chains.D Quantification of K48-positive lysosomes 2 h and 12 h after damage in cells treated as in (A). Data represent mean ± SD of three independent experiments.


E The catalytically - inactive mutant of YOD1 stabilizes K48 - conjugates . Cells transfected with GFP - tagged YOD1 - wt or the YOD1 - CS were treated and stained as in ( C ) . F Quantification as in ( D ) of cells treated as in ( E ) . * * = p < 0 . 01 * * * = p < 0 . 001 ( Student ' s unpaired t - test ) . ns , not significant . Scale bars , 10 µm .

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E The catalytically-inactive mutant of YOD1 stabilizes K48-conjugates. Cells transfected with GFP-tagged YOD1-wt or the YOD1-CS were treated and stained as in (C).F Quantification as in (D) of cells treated as in (E). ** = p < 0.01 *** = p < 0.001 (Student's unpaired t-test). ns, not significant. Scale bars, 10 µm.


A YOD1 can link p97 to ubiquitin . Ubiquitin - GST ( Ub - GST ) or GST alone was incubated with the indicated purified proteins and isolated . Co - isolated proteins ( pulldown ) were detected in SDS - gels . Note binding of p97 and YOD1 to Ub - GST only in combination .

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A YOD1 can link p97 to ubiquitin. Ubiquitin-GST (Ub-GST) or GST alone was incubated with the indicated purified proteins and isolated. Co-isolated proteins (pulldown) were detected in SDS-gels. Note binding of p97 and YOD1 to Ub-GST only in combination.


B The S2 site of YOD1 is critical for ubiquitin binding . Experiments as in ( A ) with indicated combinations of p97 and YOD1 - wt or the ubiquitin - binding mutant , MutS2 .

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B The S2 site of YOD1 is critical for ubiquitin binding. Experiments as in (A) with indicated combinations of p97 and YOD1-wt or the ubiquitin-binding mutant, MutS2.


C Reconstitution of a complex of ELDR components on ubiquitin . Experiments as in ( A ) with combinations of p97 - wt or p97 - EQ , YOD1 , PLAA and UBXD1 as indicated . Note that PLAA associates with p97 and YOD1 on ubiquitin only in the case of p97 - EQ .

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C Reconstitution of a complex of ELDR components on ubiquitin. Experiments as in (A) with combinations of p97-wt or p97-EQ, YOD1, PLAA and UBXD1 as indicated. Note that PLAA associates with p97 and YOD1 on ubiquitin only in the case of p97-EQ.


D Translocation of YOD1 to lysosomes depends on ubiquitin binding by the S2 site . LLOMe - treated cells expressing GFP - YOD1 - CS or the double mutant GFP - YOD1 - CS - MutS2 were chased for 2 h and stained for K48 chains and LAMP1 . Ratio of GFP signal on K48 vesicles to GFP signal in the whole cell was determined .

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D Translocation of YOD1 to lysosomes depends on ubiquitin binding by the S2 site. LLOMe-treated cells expressing GFP-YOD1-CS or the double mutant GFP-YOD1-CS-MutS2 were chased for 2 h and stained for K48 chains and LAMP1. Ratio of GFP signal on K48 vesicles to GFP signal in the whole cell was determined.


E The S2 site is essential for K48 - conjugate removal . GFP - YOD1 - wt or GFP - YOD1 - MutS2 overexpressing cells treated as in ( D ) were stained for K48 chains . Quantification of the number of K48 - positive vesicles per cell . Data represent mean ± SD of three independent experiments . * * = p < 0 . 01 ( Student ' s unpaired t - test ) . Scale bars , 10 µm .

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E The S2 site is essential for K48-conjugate removal. GFP-YOD1-wt or GFP-YOD1-MutS2 overexpressing cells treated as in (D) were stained for K48 chains. Quantification of the number of K48-positive vesicles per cell. Data represent mean ± SD of three independent experiments. ** = p < 0.01 (Student's unpaired t-test). Scale bars, 10 µm.


A Largely mutually exclusive localization of LC3 and K48 chains . GFP - LC3 expressing HeLa cells were fixed 2 h after LLOMe washout and stained for endogenous LAMP1 and K48 or K63 chains . Correlation coefficients were calculated for colocalization of LC3 with K63 or K48 . The whiskers represent 10th and 90th percentile . Points below and above the whiskers are drawn as individual dots . The single line indicates the median . * * * = p < 0 . 001 ( Mann - Whitney - U test ) .

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A Largely mutually exclusive localization of LC3 and K48 chains. GFP-LC3 expressing HeLa cells were fixed 2 h after LLOMe washout and stained for endogenous LAMP1 and K48 or K63 chains. Correlation coefficients were calculated for colocalization of LC3 with K63 or K48. The whiskers represent 10th and 90th percentile. Points below and above the whiskers are drawn as individual dots. The single line indicates the median. *** = p < 0.001 (Mann-Whitney-U test).