Figure 2B . Confocal microscopy images of PrimPol and γH2AX ( damage control ) immunofluorescence staining in control ( UVA ) or TMP - UVA - laser irradiated ( 10 µM TMP , 2 h followed by UVA laser irradiation ) WT and PRIMPOL KO cells . Nuclear DNA is counterstained with DAPI . UVA laser path is indicated . Scale bar , 10 µm . Histograms ( right panel ) show the average percentage of PrimPol - positive cells and SD of three assays ( n ≥ 100 cells per TMP - treated conditions in each replicate ) . Circle dots in each column represent the values of individual replicates . Statistical analysis was conducted with one - way ANOVA followed by Bonferroni post - test . p - values of individual comparisons are indicated . C . Confocal microscopy images of PrimPol and γH2AX ( damage control ) immunofluorescence staining in control ( UVA ) or TMP - UVA - treated cells following control or RPA2 downregulation . Nuclear DNA is counterstained with DAPI . UVA laser path is indicated . Scale bar , 10 µm . Histograms ( right panel ) show the average PrimPol - positive cells and SD of three assays ( n ≥ 100 cells per TMP - treated conditions in each replicate ) . Circle dots in each column represent the values of individual replicates . Statistical analysis was conducted with one - way ANOVA followed by Bonferroni post - test . p - values of individual comparisons are indicated . D . Confocal microscopy images of PrimPol and γH2AX ( damage control ) immunofluorescence staining in control ( UVA ) or TMP - UVA - treated PRIMPOL KO cells stably expressing V5 - tagged WT or RPA binding domain mutant ( RBDm ) PrimPol versions . Nuclear DNA is counterstained with DAPI . UVA laser path is indicated . Scale bar , 10 µm . Histograms ( right panel ) show the average percentage of PrimPol - positive cells and SD of two assays ( n ≥ 100 cells per condition in each replicate ) . Circle dots in each column represent the values of individual replicates . Statistical analysis was conducted with one - way ANOVA followed by Bonferroni post - test . p - values of individual comparisons are indicated . E . Confocal microscopy images of PrimPol and γH2AX ( damage control ) immunofluorescence staining in control ( UVA ) or TMP - UVA - treated WT and BLM KO cells upon downregulation of TOP3A , RMI1 and RMI2 ( siTR ) when indicated . Nuclear DNA is counterstained with DAPI . UVA laser path is indicated . Scale bar , 10 µm . Histograms ( right panel ) show the average percentage of PrimPol - positive cells and SD of three assays ( n ≥ 250 cells per condition ) . Circle dots in each column represent the values of individual replicates . Statistical analysis was conducted with one - way ANOVA followed by Bonferroni post - test .

O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 2B. Confocal microscopy images of PrimPol and γH2AX (damage control) immunofluorescence staining in control (UVA) or TMP-UVA-laser irradiated (10 µM TMP, 2 h followed by UVA laser irradiation) WT and PRIMPOL KO cells. Nuclear DNA is counterstained with DAPI. UVA laser path is indicated. Scale bar, 10 µm. Histograms (right panel) show the average percentage of PrimPol-positive cells and SD of three assays (n ≥100 cells per TMP-treated conditions in each replicate). Circle dots in each column represent the values of individual replicates. Statistical analysis was conducted with one-way ANOVA followed by Bonferroni post-test. p-values of individual comparisons are indicated.C. Confocal microscopy images of PrimPol and γH2AX (damage control) immunofluorescence staining in control (UVA) or TMP-UVA-treated cells following control or RPA2 downregulation. Nuclear DNA is counterstained with DAPI. UVA laser path is indicated. Scale bar, 10 µm. Histograms (right panel) show the average PrimPol-positive cells and SD of three assays (n ≥100 cells per TMP-treated conditions in each replicate). Circle dots in each column represent the values of individual replicates. Statistical analysis was conducted with one-way ANOVA followed by Bonferroni post-test. p-values of individual comparisons are indicated.D. Confocal microscopy images of PrimPol and γH2AX (damage control) immunofluorescence staining in control (UVA) or TMP-UVA-treated PRIMPOL KO cells stably expressing V5-tagged WT or RPA binding domain mutant (RBDm) PrimPol versions. Nuclear DNA is counterstained with DAPI. UVA laser path is indicated. Scale bar, 10 µm. Histograms (right panel) show the average percentage of PrimPol-positive cells and SD of two assays (n ≥100 cells per condition in each replicate). Circle dots in each column represent the values of individual replicates. Statistical analysis was conducted with one-way ANOVA followed by Bonferroni post-test. p-values of individual comparisons are indicated.E. Confocal microscopy images of PrimPol and γH2AX (damage control) immunofluorescence staining in control (UVA) or TMP-UVA-treated WT and BLM KO cells upon downregulation of TOP3A, RMI1 and RMI2 (siTR) when indicated. Nuclear DNA is counterstained with DAPI. UVA laser path is indicated. Scale bar, 10 µm. Histograms (right panel) show the average percentage of PrimPol-positive cells and SD of three assays (n ≥250 cells per condition). Circle dots in each column represent the values of individual replicates. Statistical analysis was conducted with one-way ANOVA followed by Bonferroni post-test.


Figure 3H . Immunoblots showing the levels of BLM , FANCD2 and PrimPol after BLM or FANCD2 downregulation in WT and PRIMPOL KO cells for experiments in ( G ) . Ponceau - S is shown as loading control .

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Figure 3H. Immunoblots showing the levels of BLM, FANCD2 and PrimPol after BLM or FANCD2 downregulation in WT and PRIMPOL KO cells for experiments in (G). Ponceau-S is shown as loading control.


Figure 4C . Representative confocal microscopy images of EdU staining in WT and PRIMPOL KO cells , 8 h after UVA ( control ) or TMP - UVA treatment ( 2 µM TMP , 2 h followed by 5 s irradiation ) . Nuclear DNA is counterstained with DAPI . When indicated , V5 - PrimPol was reintroduced into KO cells . Scale bar , 25 µm . Dot plots indicate the distribution of nuclear EdU intensity , and the mean values are indicated by horizontal red lines . Data from the combination of three replicates ( n ≥ 200 cells per condition ) . Statistical analysis was conducted with Kruskal - Wallis test and Dunns post - test . p - values of individual comparisons are indicated .

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Figure 4C. Representative confocal microscopy images of EdU staining in WT and PRIMPOL KO cells, 8 h after UVA (control) or TMP-UVA treatment (2 µM TMP, 2 h followed by 5 s irradiation). Nuclear DNA is counterstained with DAPI. When indicated, V5-PrimPol was reintroduced into KO cells. Scale bar, 25 µm. Dot plots indicate the distribution of nuclear EdU intensity, and the mean values are indicated by horizontal red lines. Data from the combination of three replicates (n ≥200 cells per condition). Statistical analysis was conducted with Kruskal-Wallis test and Dunns post-test. p-values of individual comparisons are indicated.


Figure 5A . Confocal microscopy images of FANCD2 immunofluorescence staining in control ( UVA ) or TMP - UVA - treated ( 2 µM TMP , 2 h followed by 5 s irradiation ) WT and PRIMPOL KO cells . Nuclear DNA is counterstained with DAPI . Scale bar , 25 µm . D . Histograms show the number of chromosomal aberrations per metaphase ( average and SEM ) in each condition . Data taken from three replicates are combined ( 50 metaphases per replicate ) . Statistical analysis was conducted with one - way ANOVA followed by Bonferroni post - test . p - values of individual comparisons are indicated .

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Figure 5A. Confocal microscopy images of FANCD2 immunofluorescence staining in control (UVA) or TMP-UVA-treated (2 µM TMP, 2 h followed by 5 s irradiation) WT and PRIMPOL KO cells. Nuclear DNA is counterstained with DAPI. Scale bar, 25 µm.D. Histograms show the number of chromosomal aberrations per metaphase (average and SEM) in each condition. Data taken from three replicates are combined (50 metaphases per replicate). Statistical analysis was conducted with one-way ANOVA followed by Bonferroni post-test. p-values of individual comparisons are indicated.


Figure 6A . Kaplan - Meier survival curves of WT and PRIMPOL KO mice after the administration of a single dose of MMC ( 7 . 5 , 10 or 15 mg / kg ) . Dashed vertical lines represent median survival values for WT ( blue ) and KO ( orange ) mice . Statistical analysis was conducted with Log - rank ( Mantel - Cox ) test ; p - value for the highest dose of MMC ( 15 mg / kg ) is indicated . B . Haematoxylin - eosin ( H & E ) and Ki - 67 immunohistochemistry ( IHC ) stainings of bone marrow sections derived from WT and PRIMPOL KO mice following the administration of 10 mg / kg MMC . Control mice ( PBS ) were sacrificed when MMC - injected mice reached the humane endpoint . Scale bar , 2 . 5 mm . In each image , a relevant area is shown at higher magnification ( 10x ) .

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Figure 6A. Kaplan-Meier survival curves of WT and PRIMPOL KO mice after the administration of a single dose of MMC (7.5, 10 or 15 mg/kg). Dashed vertical lines represent median survival values for WT (blue) and KO (orange) mice. Statistical analysis was conducted with Log-rank (Mantel-Cox) test; p-value for the highest dose of MMC (15 mg/kg) is indicated.B. Haematoxylin-eosin (H&E) and Ki-67 immunohistochemistry (IHC) stainings of bone marrow sections derived from WT and PRIMPOL KO mice following the administration of 10 mg/kg MMC. Control mice (PBS) were sacrificed when MMC-injected mice reached the humane endpoint. Scale bar, 2.5 mm. In each image, a relevant area is shown at higher magnification (10x).


Figure 7E . IF detection of FANCD2 foci in WT and PRIMPOL KO cells 48 h after TMP - UVA ( 2 µM TMP , 2 h followed by 5 s irradiation ) with or without MCM3 downregulation . Nuclear DNA is counterstained with DAPI . Scale bar , 25 µm . G . Cell survival assays of WT and PRIMPOL KO cells with or without MCM3 downregulation in the presence of increasing amounts of MMC or TMP ( followed by 90 sec UVA irradiation ) for 72 h . The same control curves without MCM3 downregulation are also shown as part of Figure EV6D . Each point in the curve represents the percentage of surviving cells ( average and SD of three assays for MMC and two assays for TMP ) . Statistical analysis was conducted with two - way ANOVA followed by Bonferroni post - test . p - values of comparisons between KO and KO - siMCM3 are indicated .

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Figure 7E. IF detection of FANCD2 foci in WT and PRIMPOL KO cells 48 h after TMP-UVA (2 µM TMP, 2 h followed by 5 s irradiation) with or without MCM3 downregulation. Nuclear DNA is counterstained with DAPI. Scale bar, 25 µm.G. Cell survival assays of WT and PRIMPOL KO cells with or without MCM3 downregulation in the presence of increasing amounts of MMC or TMP (followed by 90 sec UVA irradiation) for 72 h. The same control curves without MCM3 downregulation are also shown as part of Figure EV6D. Each point in the curve represents the percentage of surviving cells (average and SD of three assays for MMC and two assays for TMP). Statistical analysis was conducted with two-way ANOVA followed by Bonferroni post-test. p-values of comparisons between KO and KO-siMCM3 are indicated.


Figure 1A ) Representative zooms of WT MEFs transfected with GFP - tagged Miro1 and Miro2 ( GFPMiro1 and GFPMiro2 ) . Control is GFP fused to the first 70 amino acids of Tom70 . Tom20 and catalase stain mitochondria and peroxisomes , respectively . Merge is of Miro ( green ) and catalase ( magenta ) with colocalisation shown as white . White arrowheads highlight an area where an isolated peroxisome is situated . B ) Quantification of the extent of GFP signal on peroxisomes . Data information : B ) One - way ANOVA with Newman - Keuls post hoc test was used for all comparisons ( n = 18 cells per condition over 3 independent experiments ) . * , * * and * * * denote p < 0 . 05 , p < 0 . 01 and p < 0 . 001 in comparison to Control , respectively , and # # and # # # denote p < 0 . 01 and p < 0 . 001 in comparison to GFPMiro1 , respectively . Data are represented as mean ± SEM . Scale bar is 5 μm . C ) Pulldown of overexpressed Pex19 in Cos7 cells with a Pex19 antibody shows interaction with full - length Miro1 , but not Miro1 lacking the transmembrane domain . E ) Representative images of Miro1 truncation constructs expressed in DKO MEFs . Mitochondria and peroxisomes are stained with Tom20 and catalase , respectively . White arrowheads highlight an area where an isolated peroxisome is situated . F . F ) Quantification of the extent of peroxisomal localisation of the Miro1 truncation constructs . Data information : F ) One - way ANOVA with Newman - Keuls post hoc test was used for all comparisons ( n = 18 cells per condition over 3 independent experiments ) . * , * * and * * * denote p < 0 . 05 , p < 0 . 01 and p < 0 . 001 in comparison to Control , respectively , and # # and # # # denote p < 0 . 01 and p < 0 . 001 in comparison to GFPMiro1 , respectively . Data are represented as mean ± SEM . Scale bar is 5 μm . G ) Co - immunoprecipation of Miro1 truncation constructs and mycPex19 following transfection into Cos7 cells . GFP - tagged Miro1 truncation constructs were pulled down with GFP - Trap agarose beads and Pex19 was probed with myc antibody .

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Figure 1A) Representative zooms of WT MEFs transfected with GFP-tagged Miro1 and Miro2 (GFPMiro1 and GFPMiro2). Control is GFP fused to the first 70 amino acids of Tom70. Tom20 and catalase stain mitochondria and peroxisomes, respectively. Merge is of Miro (green) and catalase (magenta) with colocalisation shown as white. White arrowheads highlight an area where an isolated peroxisome is situated. B) Quantification of the extent of GFP signal on peroxisomes. Data information: B) One-way ANOVA with Newman-Keuls post hoc test was used for all comparisons (n=18 cells per condition over 3 independent experiments). *, ** and *** denote p < 0.05, p < 0.01 and p < 0.001 in comparison to Control, respectively, and ## and ### denote p < 0.01 and p < 0.001 in comparison to GFPMiro1, respectively. Data are represented as mean ± SEM. Scale bar is 5 μm.C) Pulldown of overexpressed Pex19 in Cos7 cells with a Pex19 antibody shows interaction with full-length Miro1, but not Miro1 lacking the transmembrane domain.E) Representative images of Miro1 truncation constructs expressed in DKO MEFs. Mitochondria and peroxisomes are stained with Tom20 and catalase, respectively. White arrowheads highlight an area where an isolated peroxisome is situated.F.F) Quantification of the extent of peroxisomal localisation of the Miro1 truncation constructs. Data information: F) One-way ANOVA with Newman-Keuls post hoc test was used for all comparisons (n=18 cells per condition over 3 independent experiments). *, ** and *** denote p < 0.05, p < 0.01 and p < 0.001 in comparison to Control, respectively, and ## and ### denote p < 0.01 and p < 0.001 in comparison to GFPMiro1, respectively. Data are represented as mean ± SEM. Scale bar is 5 μm.G) Co-immunoprecipation of Miro1 truncation constructs and mycPex19 following transfection into Cos7 cells. GFP-tagged Miro1 truncation constructs were pulled down with GFP-Trap agarose beads and Pex19 was probed with myc antibody.


Figure 2A ) Six consecutive frames of live trafficking of peroxisomes ( pxDsRed signal at 1 . 5 seconds per frame ) . Yellow arrows show the trajectory of a fast - moving peroxisome in both WT and DKO MEFs . Scale bar is 5 μm . B ) Blind scoring of the number of long - range peroxisomal trafficking events in WT , Miro1KO and Miro2KO and DKO MEFs ( n = 42 cells over six independent experiments . Two different MEFs lines were used for each genotype ) . Data information : For B ) a Kruskall - Wallis with a Dunn ' s correction posthoc test was used to test for significance . For B ) no statistical difference between conditions was observed , unless stated . Data are represented as mean ± SEM . C ) and D ) Quantification of individual track length and velocity , respectively ( n = 24 cells over three independent experiments ) . Data information : Analysis for C ) , D ) is a one - way ANOVA with Newman - Keuls post - hoc test . * * denotes p < 0 . 01 . For C ) , D ) no statistical difference between conditions was observed , unless stated . Data are represented as mean ± SEM . E ) Representative blots of Miro1 , Miro2 and actin from whole cell lysates of wild - type and Miro1 - floxed ERT Cre - recombinase MEFs treated with and without 4 - OH tamoxifen for 48 hours . Lysates were taken one day after the end of treatment . F ) Quantification of long - range peroxisomal trafficking events by blind scoring of pxDsRed signal from a two - minute movie ( n = 18 cells per condition over three independent experiments ) . Data information : Statistical significance in F ) was calculated by two - way ANOVA . For F ) no statistical difference between conditions was observed , unless stated . Data are represented as mean ± SEM . G ) Representative blot of Miro1 and Miro2 following knockdown of either Miro1 or Pex14 in HeLa cells . H ) Quantification of long - range peroxisomal trafficking events ( visualised with pxGFP ) in HeLa cells transfected with scrambled , Miro1 and Pex14 siRNA , by blind scoring of a five - minute movie ( n = 18 cells over three independent experiments ) . Data information : For H ) is a one - way ANOVA with Newman - Keuls post - hoc test . * * denotes p < 0 . 01 . For H ) , no statistical difference between conditions was observed , unless stated . Data are represented as mean ± SEM .

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Figure 2A) Six consecutive frames of live trafficking of peroxisomes (pxDsRed signal at 1.5 seconds per frame). Yellow arrows show the trajectory of a fast-moving peroxisome in both WT and DKO MEFs. Scale bar is 5 μm.B) Blind scoring of the number of long-range peroxisomal trafficking events in WT, Miro1KO and Miro2KO and DKO MEFs (n=42 cells over six independent experiments. Two different MEFs lines were used for each genotype). Data information: For B) a Kruskall-Wallis with a Dunn's correction posthoc test was used to test for significance. For B) no statistical difference between conditions was observed, unless stated. Data are represented as mean ± SEM.C) and D) Quantification of individual track length and velocity, respectively (n=24 cells over three independent experiments). Data information: Analysis for C), D) is a one-way ANOVA with Newman-Keuls post-hoc test. ** denotes p < 0.01. For C), D) no statistical difference between conditions was observed, unless stated. Data are represented as mean ± SEM.E) Representative blots of Miro1, Miro2 and actin from whole cell lysates of wild-type and Miro1-floxed ERT Cre-recombinase MEFs treated with and without 4-OH tamoxifen for 48 hours. Lysates were taken one day after the end of treatment.F) Quantification of long-range peroxisomal trafficking events by blind scoring of pxDsRed signal from a two-minute movie (n=18 cells per condition over three independent experiments). Data information: Statistical significance in F) was calculated by two-way ANOVA. For F) no statistical difference between conditions was observed, unless stated. Data are represented as mean ± SEM.G) Representative blot of Miro1 and Miro2 following knockdown of either Miro1 or Pex14 in HeLa cells.H) Quantification of long-range peroxisomal trafficking events (visualised with pxGFP) in HeLa cells transfected with scrambled, Miro1 and Pex14 siRNA, by blind scoring of a five-minute movie (n=18 cells over three independent experiments). Data information: For H) is a one-way ANOVA with Newman-Keuls post-hoc test. ** denotes p < 0.01. For H), no statistical difference between conditions was observed, unless stated. Data are represented as mean ± SEM.


Figure 3A ) Representative images of WT , Miro1KO , Miro2KO and DKO MEFs seeded onto Y - shaped fibronectin micropatterns stained for mitochondria ( Tom20 in red ) and peroxisomes ( Catalase in white ) . Scale bar represents 10 μm . Data information : n = 60 cells over three independent experiments . B ) Normalised cumulative distribution of mitochondria in WT , Miro1KO , Miro2KO and DKO MEFs . C ) Distance at which 95 % of mitochondria are distributed ( Mito95 ) for all four genotypes of MEF . Data information : n = 60 cells over three independent experiments . For C ) one - way ANOVA with Newman - Keuls post - hoc test was used to test for statistical significance . * * * represents p < 0 . 001 . Data are represented as mean ± SEM . D ) Normalised cumulative distribution curves comparing the peroxisomal distribution from the centre of the cell to the periphery of WT , Miro1KO , Miro2KO and DKO MEFs . E ) Bar graph comparing the average distance at which 95 % of the peroxisomal signal is distributed ( Perox95 ) . Data information : n = 60 cells over three independent experiments . For E ) a one - way ANOVA with Newman - Keuls post - hoc test was used to test for statistical significance . * * * represents p < 0 . 001 . Data are represented as mean ± SEM .

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Figure 3A) Representative images of WT, Miro1KO, Miro2KO and DKO MEFs seeded onto Y-shaped fibronectin micropatterns stained for mitochondria (Tom20 in red) and peroxisomes (Catalase in white). Scale bar represents 10 μm. Data information: n = 60 cells over three independent experiments.B) Normalised cumulative distribution of mitochondria in WT, Miro1KO, Miro2KO and DKO MEFs. C) Distance at which 95% of mitochondria are distributed (Mito95) for all four genotypes of MEF. Data information: n = 60 cells over three independent experiments. For C) one-way ANOVA with Newman-Keuls post-hoc test was used to test for statistical significance. *** represents p < 0.001. Data are represented as mean ± SEM.D) Normalised cumulative distribution curves comparing the peroxisomal distribution from the centre of the cell to the periphery of WT, Miro1KO, Miro2KO and DKO MEFs. E) Bar graph comparing the average distance at which 95% of the peroxisomal signal is distributed (Perox95). Data information: n = 60 cells over three independent experiments. For E) a one-way ANOVA with Newman-Keuls post-hoc test was used to test for statistical significance. *** represents p < 0.001. Data are represented as mean ± SEM.


Figure 4A ) Snapshots and tracks of pxDsRed signal in WT , Miro1KO , Miro2KO and DKO MEFs following live imaging at 1 . 5 seconds per frame for two minutes . B ) Quantification of median net displacement of individual peroxisomes ( pxDsRed signal ) for WT , Miro1KO , Miro2KO and DKO MEFs ( n = 42 cells over six independent experiments . Two different MEFs lines were used for each genotype ) . Data information : For multiple comparisons in B ) a one - way ANOVA with Newman - Keuls post - hoc test was used to test for statistical significance . C ) Still images every 30 seconds of ER and peroxisomes ( ER - DsRed pseudo - coloured to green and pxGFP pseudo - coloured to magenta , respectively ) in WT and DKO MEFs taken from two - minute movies by live - cell spinning - disk microscopy . Arrows track individual peroxisomes associated with an ER tubule . Scale bar is 5 μm . D ) Quantification of the relative ER displacement over a two - minute movie using ER - DsRed signal in WT and DKO MEFs ( n = 20 cells per condition over three independent experiments ) . Data information : Student ' s t - test was used to calculate statistical significance . * and * * * represent p < 0 . 05 and p < 0 . 001 , respectively . Data are represented as mean ± SEM . E ) Median net displacement of peroxisomes in WT and DKO MEFs . n = 20 cells per condition over three independent experiments . F ) Median net displacement of peroxisomes in DKO MEFs with and without myc - tagged variant 4 of Miro1 ( mycv4 ) ( n = 12 cells per condition over three independent experiments ) . Data information : Student ' s t - test was used to calculate statistical significance . * and * * * represent p < 0 . 05 and p < 0 . 001 , respectively . Data are represented as mean ± SEM .

O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 4A) Snapshots and tracks of pxDsRed signal in WT, Miro1KO, Miro2KO and DKO MEFs following live imaging at 1.5 seconds per frame for two minutes. B) Quantification of median net displacement of individual peroxisomes (pxDsRed signal) for WT, Miro1KO, Miro2KO and DKO MEFs (n=42 cells over six independent experiments. Two different MEFs lines were used for each genotype). Data information: For multiple comparisons in B) a one-way ANOVA with Newman-Keuls post-hoc test was used to test for statistical significance.C) Still images every 30 seconds of ER and peroxisomes (ER-DsRed pseudo-coloured to green and pxGFP pseudo-coloured to magenta, respectively) in WT and DKO MEFs taken from two-minute movies by live-cell spinning-disk microscopy. Arrows track individual peroxisomes associated with an ER tubule. Scale bar is 5 μm.D) Quantification of the relative ER displacement over a two-minute movie using ER-DsRed signal in WT and DKO MEFs (n=20 cells per condition over three independent experiments). Data information: Student's t-test was used to calculate statistical significance. * and *** represent p<0.05 and p<0.001, respectively. Data are represented as mean ± SEM.E) Median net displacement of peroxisomes in WT and DKO MEFs. n=20 cells per condition over three independent experiments.F) Median net displacement of peroxisomes in DKO MEFs with and without myc-tagged variant 4 of Miro1 (mycv4) (n=12 cells per condition over three independent experiments). Data information: Student's t-test was used to calculate statistical significance. * and *** represent p<0.05 and p<0.001, respectively. Data are represented as mean ± SEM.


Figure 5A ) Representative images of catalase staining ( peroxisomes ) in WT , Miro1KO , Miro2KO and DKO MEFs . B ) Bar graph comparing average peroxisomal area of WT Miro1KO , Miro2KO and DKO MEFs ( n = 60 cells per condition over three independent experiments ) . Data information : Calculation of statistical significance in B ) was a one - way ANOVA with Newman - Keuls post - hoc . * , * * and * * * denote p < 0 . 05 , p < 0 . 01 and p < 0 . 001 , respectively . Data are represented as mean ± SEM . Scale bar is 10 μm . Scale bar in zooms is 5 μm . C ) Comparison of total peroxisomal number between WT , Miro1KO , Miro2KO and DKO MEFs . n = 60 cells per condition over three independent experiments . Data information : Calculation of statistical significance in C ) was a one - way ANOVA with Newman - Keuls post - hoc . * , * * and * * * denote p < 0 . 05 , p < 0 . 01 and p < 0 . 001 , respectively . Data are represented as mean ± SEM . Scale bar is 10 μm . Scale bar in zooms is 5 μm . D ) Representative images of Control ( GFP - tagged 1 - 70 of Tom70 ) , GFPMiro1 and GFPMiro2 in WT MEFs stained with catalase ( peroxisomes ) . E ) Representative images of Pex14 ( peroxisomes ) in DKO MEFs expressing either GFP ( control ) or GFP - tagged variant 4 of Miro1 ( GFPv4 ) . F ) Bar graph comparing average peroxisomal area of Control , GFPMiro1 and GFPMiro2 overexpressing WT MEFs ( n = 60 cells per condition over three independent experiments ) . Data information : Calculation of statistical significance in F ) was a one - way ANOVA with Newman - Keuls post - hoc . * , * * and * * * denote p < 0 . 05 , p < 0 . 01 and p < 0 . 001 , respectively . Data are represented as mean ± SEM . Scale bar is 10 μm . Scale bar in zooms is 5 μm . G ) Comparison of average area of individual peroxisomes between DKO MEFs expressing either GFP ( control ) or GFP - tagged variant 4 of Miro1 ( GFPv4 ) ( n = 30 cells per condition over three independent experiments ) . Data information : Statistical test used in G ) was a two - tailed Student ' s t test . * , * * and * * * denote p < 0 . 05 , p < 0 . 01 and p < 0 . 001 , respectively . Data are represented as mean ± SEM . Scale bar is 10 μm . Scale bar in zooms is 5 μm .

O B-PANEL_START O O O O O O O O O O O O O O O O O O O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O 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-PANEL_START O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 5A) Representative images of catalase staining (peroxisomes) in WT, Miro1KO, Miro2KO and DKO MEFs.B) Bar graph comparing average peroxisomal area of WT Miro1KO, Miro2KO and DKO MEFs ( n = 60 cells per condition over three independent experiments). Data information: Calculation of statistical significance in B) was a one-way ANOVA with Newman-Keuls post-hoc. *, ** and *** denote p < 0.05, p < 0.01 and p < 0.001, respectively. Data are represented as mean ± SEM. Scale bar is 10 μm. Scale bar in zooms is 5 μm.C) Comparison of total peroxisomal number between WT, Miro1KO, Miro2KO and DKO MEFs. n = 60 cells per condition over three independent experiments. Data information: Calculation of statistical significance in C) was a one-way ANOVA with Newman-Keuls post-hoc. *, ** and *** denote p < 0.05, p < 0.01 and p < 0.001, respectively. Data are represented as mean ± SEM. Scale bar is 10 μm. Scale bar in zooms is 5 μm.D) Representative images of Control (GFP-tagged 1-70 of Tom70), GFPMiro1 and GFPMiro2 in WT MEFs stained with catalase (peroxisomes).E) Representative images of Pex14 (peroxisomes) in DKO MEFs expressing either GFP (control) or GFP-tagged variant 4 of Miro1 (GFPv4).F) Bar graph comparing average peroxisomal area of Control, GFPMiro1 and GFPMiro2 overexpressing WT MEFs (n=60 cells per condition over three independent experiments). Data information: Calculation of statistical significance in F) was a one-way ANOVA with Newman-Keuls post-hoc. *, ** and *** denote p < 0.05, p < 0.01 and p < 0.001, respectively. Data are represented as mean ± SEM. Scale bar is 10 μm. Scale bar in zooms is 5 μm.G) Comparison of average area of individual peroxisomes between DKO MEFs expressing either GFP (control) or GFP-tagged variant 4 of Miro1 (GFPv4) (n=30 cells per condition over three independent experiments). Data information: Statistical test used in G) was a two-tailed Student's t test. *, ** and *** denote p < 0.05, p < 0.01 and p < 0.001, respectively. Data are represented as mean ± SEM. Scale bar is 10 μm. Scale bar in zooms is 5 μm.


Figure 6A ) Representative images of proximity - ligation assay ( PLA ) of Fis1 and Drp1 in WT and DKO MEFs . Scale bar is 10 μm . Red dots indicate interaction of Fis1 and Drp1 . Blue is DAPI . B ) Quantification of fluorescent dots from PLA of Fis1 and Drp1 in WT and DKO MEFs . Dotted line indicates the sum of the Fis1 and Drp1 single antibody controls ( n = 3 experiments ) . Data information : For B ) statistical significance was quantified by a two - tailed Student ' s t test . * , * * and * * * denote p < 0 . 05 , p < 0 . 01 and p < 0 . 001 , respectively . Data are represented as mean ± SEM . C ) Representative images of a Fis1 - Drp1 PLA in DKO MEFs expressing either GFP , GFPv1 ( GFP - tagged variant 1 of Miro1 ) or GFPv4 ( GFP - tagged variant 4 of Miro1 ) n = 30 cells per condition over three independent experiments ) . Scale bar is 10 μm . Red dots indicate interaction of Fis1 and Drp1 . Blue is DAPI . D ) Quantification of PLA fluorescent dots per cells between GFP , GFPv1 or GFPv4 transfected DKO MEFs ( n = 30 cells over three independent experiments ) . Data information : In D ) a one - way ANOVA with a Newman - Keuls post - hoc test was used to calculate statistical significance . * , * * and * * * denote p < 0 . 05 , p < 0 . 01 and p < 0 . 001 , respectively . Data are represented as mean ± SEM . E ) Western blot of Drp1 , Fis1 and actin from WT and DKO whole cell lysates . F ) Quantification of normalised band intensity of Drp1 and Fis1 in WT and DKO MEFs ( n = 3 ) . Data information F ) , statistical significance was quantified by a two - tailed Student ' s t test . G ) Zooms of endogenous Drp1 , mitochondria ( Mitotracker ) and peroxisomes ( PMP70 ) in WT and DKO MEFs . Scale bar is 5 μm . H ) Integrated density of Drp1 signal on Mitotracker - positive and PMP70 - negative structures in WT and DKO MEFs . I ) Integrated density of Drp1 signal on PMP70 - positive and Mitotracker - negative structures in WT and DKO MEFs . Data information G - I n = 42 cells per condition over three independent experiments . For , H ) statistical significance was quantified by a two - tailed Student ' s t test . * , * * and * * * denote p < 0 . 05 , p < 0 . 01 and p < 0 . 001 , respectively . Data are represented as mean ± SEM .

O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 6A) Representative images of proximity-ligation assay (PLA) of Fis1 and Drp1 in WT and DKO MEFs. Scale bar is 10 μm. Red dots indicate interaction of Fis1 and Drp1. Blue is DAPI. B) Quantification of fluorescent dots from PLA of Fis1 and Drp1 in WT and DKO MEFs. Dotted line indicates the sum of the Fis1 and Drp1 single antibody controls (n=3 experiments). Data information: For B) statistical significance was quantified by a two-tailed Student's t test. *, ** and *** denote p < 0.05, p < 0.01 and p < 0.001, respectively. Data are represented as mean ± SEM.C) Representative images of a Fis1-Drp1 PLA in DKO MEFs expressing either GFP, GFPv1 (GFP-tagged variant 1 of Miro1) or GFPv4 (GFP-tagged variant 4 of Miro1) n=30 cells per condition over three independent experiments). Scale bar is 10 μm. Red dots indicate interaction of Fis1 and Drp1. Blue is DAPI. D) Quantification of PLA fluorescent dots per cells between GFP, GFPv1 or GFPv4 transfected DKO MEFs (n=30 cells over three independent experiments). Data information: In D) a one-way ANOVA with a Newman-Keuls post-hoc test was used to calculate statistical significance. *, ** and *** denote p < 0.05, p < 0.01 and p < 0.001, respectively. Data are represented as mean ± SEM.E) Western blot of Drp1, Fis1 and actin from WT and DKO whole cell lysates. F) Quantification of normalised band intensity of Drp1 and Fis1 in WT and DKO MEFs (n=3). Data information F), statistical significance was quantified by a two-tailed Student's t test.G) Zooms of endogenous Drp1, mitochondria (Mitotracker) and peroxisomes (PMP70) in WT and DKO MEFs. Scale bar is 5 μm. H) Integrated density of Drp1 signal on Mitotracker-positive and PMP70-negative structures in WT and DKO MEFs. I) Integrated density of Drp1 signal on PMP70-positive and Mitotracker-negative structures in WT and DKO MEFs. Data information G-I n=42 cells per condition over three independent experiments. For , H) statistical significance was quantified by a two-tailed Student's t test. *, ** and *** denote p < 0.05, p < 0.01 and p < 0.001, respectively. Data are represented as mean ± SEM.


Figure 1 ( B - C ) Representative confocal images and their quantification of Gb3 accumulation within the lysosome , detected by fluorescent - conjugated Shiga toxin , from WT , CLN3 - KO and CLN7 - KO ARPE - 19 cells treated with PDMP or silenced for Gb3 synthase ( siGb3S ) ( * * * vs WT , ° ° ° vs DMSO ) . Data are presented as mean ± SD , ° ° ° / * * * : P ≤ 0 . 0001 , as determined by ANOVA ( n = 3 biological replicas in duplicate ) . Scale bars : 20 µm .

O O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 1(B-C) Representative confocal images and their quantification of Gb3 accumulation within the lysosome, detected by fluorescent-conjugated Shiga toxin, from WT, CLN3-KO and CLN7-KO ARPE-19 cells treated with PDMP or silenced for Gb3 synthase (siGb3S) (*** vs WT, °°° vs DMSO). Data are presented as mean ± SD, °°°/***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.


Figure 2 ( A - B ) Representative confocal images of Gb3 accumulation , revealed by STX staining , in brain sections from CLN7Δex2 mice at 3 and 7 . 5 months of age compared with CLN7 WT mice . Scale bars : 80 µm . ( E ) Lipidomic analysis of neurons isolated from CLN7 WT and CLN7Δex2 mouse forebrain . Data are presented as mean ± SD , * * : P ≤ 0 . 001 , * * * : P ≤ 0 . 0001 , as determined by ANOVA ( n = 3 biological replicas )

O O B-PANEL_START O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 2(A-B) Representative confocal images of Gb3 accumulation, revealed by STX staining, in brain sections from CLN7Δex2 mice at 3 and 7.5 months of age compared with CLN7 WT mice. Scale bars: 80 µm.(E) Lipidomic analysis of neurons isolated from CLN7 WT and CLN7Δex2 mouse forebrain. Data are presented as mean ± SD, **: P ≤ 0.001, ***: P ≤ 0.0001, as determined by ANOVA (n= 3 biological replicas)


Figure 3 ( A ) Representative confocal images and quantification of SCMAS staining within the lysosome of ARPE - 19 WT and CLN3 KO upon depletion of Gb3S ( siGb3S ) , LacCer ( siLCS ) , and GM3s ( siGM3S ) . ( * * * vs WT , ° ° ° vs CLN3 KO siSCR ) . Data are presented as mean ± SD , ° ° ° / * * * : P ≤ 0 . 0001 , as determined by ANOVA ( n = 3 biological replicas in duplicate ) . Scale bars : 20 µm . ( D ) Representative confocal images and quantification of STX staining within the lysosome of ARPE - 19 WT and CLN7 KO in DMSO or treated 48h with Tamoxifen . ( * * * vs WT , ° ° ° vs CLN3 KO DMSO ) . Data are presented as mean ± SD , ° ° ° / * * * : P ≤ 0 . 0001 , as determined by ANOVA ( n = 3 biological replicas in duplicate ) . Scale bars : 20 µm . ( E ) Representative confocal images and quantification of STX staining within the lysosome of NPCs WT and derived from CLN7Pa474 patient IPSCs in DMSO or treated with Tamoxifen for 48h . ( * * * vs WT , ° ° ° vs CLN7Pa474 DMSO ) . Data are presented as mean ± SD , ° ° ° / * * * : P ≤ 0 . 0001 , as determined by ANOVA ( n = 3 biological replicas in duplicate ) . Scale bars : 20 µm .

O O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 3(A) Representative confocal images and quantification of SCMAS staining within the lysosome of ARPE-19 WT and CLN3 KO upon depletion of Gb3S (siGb3S), LacCer (siLCS), and GM3s (siGM3S). (*** vs WT, °°° vs CLN3 KO siSCR). Data are presented as mean ± SD, °°°/***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.(D) Representative confocal images and quantification of STX staining within the lysosome of ARPE-19 WT and CLN7 KO in DMSO or treated 48h with Tamoxifen. (*** vs WT, °°° vs CLN3 KO DMSO). Data are presented as mean ± SD, °°°/***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.(E) Representative confocal images and quantification of STX staining within the lysosome of NPCs WT and derived from CLN7Pa474 patient IPSCs in DMSO or treated with Tamoxifen for 48h. (*** vs WT, °°° vs CLN7Pa474 DMSO). Data are presented as mean ± SD, °°°/***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.


Figure 4 ( A ) Representative confocal images and Quantification of STX within the lysosome in U2 - OS and HeLa cells after acute silencing of CLN3 ( siCLN3 ) in DMSO or treated 48h with Tamoxifen . ( * * * vs siSCR DMSO , ° ° ° vs siCLN3 DMSO ) . Data are presented as mean ± SD , ° ° ° / * * * : P ≤ 0 . 0001 , as determined by ANOVA ( n = 3 biological replicas in duplicate ) . Scale bars : 20 µm . ( B ) Representative confocal image and quantification of Gb3 in ARPE - 19 CLN3 KO cells silenced with siRNA against scramble sequence and TFEB ( siTFEB ) for 72h and treated for the last 48h with DMSO or Tamoxifen . Data are presented as mean ± SD , * * * : P ≤ 0 . 0001 , as determined by ANOVA ( n = 3 biological replicas in duplicate ) . Scale bars : 20 µm . ( C ) Representative confocal image and quantification of TFEB in U2 - OS cells silenced with siRNA against scramble sequence and CLN3 ( siCLN3 ) for 72h and treated for the last 48h with DMSO or Tamoxifen ( 5 µM and 10 µM ) . Data are presented as mean ± SD , * * * : P ≤ 0 . 0001 , as determined by ANOVA ( n = 3 biological replicas in duplicate ) . Scale bars : 20 µm .

O O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 4(A) Representative confocal images and Quantification of STX within the lysosome in U2-OS and HeLa cells after acute silencing of CLN3 (siCLN3) in DMSO or treated 48h with Tamoxifen. (*** vs siSCR DMSO, °°° vs siCLN3 DMSO). Data are presented as mean ± SD, °°°/***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.(B) Representative confocal image and quantification of Gb3 in ARPE-19 CLN3 KO cells silenced with siRNA against scramble sequence and TFEB (siTFEB) for 72h and treated for the last 48h with DMSO or Tamoxifen. Data are presented as mean ± SD, ***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.(C) Representative confocal image and quantification of TFEB in U2-OS cells silenced with siRNA against scramble sequence and CLN3 (siCLN3) for 72h and treated for the last 48h with DMSO or Tamoxifen (5 µM and 10 µM). Data are presented as mean ± SD, ***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.


Figure 5 ( C ) Representative confocal image and quantification of TFEB localization in HeLa TFEB - GFP transfected with RagC for 48h and treated for the last 3h with DMSO , Torin1 , Tamoxifen or Ospemifene . Ratios of nuclear to cytosolic TFEB localization in RagC non - expressing ( RagC - ) and RagC - expressing cells ( RagC + ) are presented as mean ± SD , * * * : P ≤ 0 . 0001 , as determined by ANOVA ( n = 3 biological replicas in duplicate ) . Scale bars : 20 µm . D ) Representative confocal images and quantification of STX in ARPE - 19 CLN3 KO cells transfected with empty vector or HA - RagC for 48h and treated for 48h with DMSO or Tamoxifen . STX average spot area presented as mean ± SD , * * * : P ≤ 0 . 0001 , as determined by ANOVA ( n = 3 biological replicas in duplicate ) . Scale bars : 20 µm .

O O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 5(C) Representative confocal image and quantification of TFEB localization in HeLa TFEB-GFP transfected with RagC for 48h and treated for the last 3h with DMSO, Torin1, Tamoxifen or Ospemifene. Ratios of nuclear to cytosolic TFEB localization in RagC non-expressing (RagC-) and RagC-expressing cells (RagC+) are presented as mean ± SD, ***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.D) Representative confocal images and quantification of STX in ARPE-19 CLN3 KO cells transfected with empty vector or HA-RagC for 48h and treated for 48h with DMSO or Tamoxifen. STX average spot area presented as mean ± SD, ***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.


Figure 6Representative confocal images of STX in the Cortex , Hippocampus , and Cerebellum brain section derived from 7 . 5 months - old mouse WT or CLN7Δex2 injected with vehicle or Tamoxifen ( Tamox ) . Quantification of confocal images , the plot shows the quantification of the STX average spot area normalized for the number of Hoechst positive cells . ( * * * vs WT , ° ° ° / ° ° vs CLN7Δex2 Vehicle ) . Data are presented as mean ± SD , * * / oo : P ≤ 0 . 001 , * * * / ooo : P ≤ 0 . 0001 , as determined by ANOVA ( N ≥ 3 biological replicas ) . Scale bars : 60 µm .

Figure 6Representative confocal images of STX in the Cortex, Hippocampus, and Cerebellum brain section derived from 7.5 months-old mouse WT or CLN7Δex2 injected with vehicle or Tamoxifen (Tamox). Quantification of confocal images, the plot shows the quantification of the STX average spot area normalized for the number of Hoechst positive cells. (*** vs WT, °°°/°° vs CLN7Δex2 Vehicle). Data are presented as mean ± SD, **/oo: P ≤ 0.001, ***/ooo: P ≤ 0.0001, as determined by ANOVA (N≥3 biological replicas). Scale bars: 60 µm.


Figure 7Representative confocal images of SCMAS in the Cortex , Hippocampus , and Cerebellum brain section derived from mouse WT or CLN7Δex2 injected with vehicle or Tamoxifen . Quantification of confocal images , the plot shows the quantification of the SCMAS average spot area normalized for the number of Hoechst positive cells . ( * * * vs WT , ° ° ° vs CLN7Δex2 Vehicle ) . Data are presented as mean ± SD , * * * : P ≤ 0 . 0001 , as determined by ANOVA ( N ≥ 3 biological ) . Scale bars : 60 µm .

O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 7Representative confocal images of SCMAS in the Cortex, Hippocampus, and Cerebellum brain section derived from mouse WT or CLN7Δex2 injected with vehicle or Tamoxifen. Quantification of confocal images, the plot shows the quantification of the SCMAS average spot area normalized for the number of Hoechst positive cells. (*** vs WT, °°° vs CLN7Δex2 Vehicle). Data are presented as mean ± SD, ***: P ≤ 0.0001, as determined by ANOVA (N≥3 biological). Scale bars: 60 µm.


Figure 8 ( A - B ) Representative confocal images and quantification of IBA - 1 in the Cortex , Hippocampus , and Cerebellum brain section derived from WT or CLN7Δex2 mice injected with the vehicle or Tamoxifen . ( * * * / * * / * vs WT , ° ° ° / ° ° / ° vs CLN7Δex2 Vehicle ) . Data are presented as mean ± SD , * / o : P ≤ 0 . 01 , * * / oo : P ≤ 0 . 001 , * * * : P ≤ 0 . 0001 , as determined by ANOVA ( N ≥ 3 biological replicas ) . Scale bars : 50 µm . ( D ) Representative Images of hindlimb clasping test in mouse WT or CLN7Δex2 injected with vehicle or Tamoxifen .

O O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O

Figure 8(A-B) Representative confocal images and quantification of IBA-1 in the Cortex, Hippocampus, and Cerebellum brain section derived from WT or CLN7Δex2 mice injected with the vehicle or Tamoxifen. (***/**/* vs WT, °°°/°°/° vs CLN7Δex2 Vehicle). Data are presented as mean ± SD, */o: P ≤ 0.01, **/oo: P ≤ 0.001, ***: P ≤ 0.0001, as determined by ANOVA (N≥3 biological replicas). Scale bars: 50 µm.(D) Representative Images of hindlimb clasping test in mouse WT or CLN7Δex2 injected with vehicle or Tamoxifen.


Figure 1Lgr5fl / fl / Axin2CreErt2 ( Lgr5 - / - ) and control mice were infected for 2 months with H . pylori . A Representative H & E staining from antral glands ( upper row ) . The dotted line marks the gland base cell area , which expands upon infection in Lgr5 - / - and control mice . Immunofluorescence labeling for GSII and Ki67 ( middle row ) and GIF and Muc5ac ( lower row ) of antral epithelium from Lgr5 - / - and control mice uninfected and after 2 months of infection . Scale bars : 50 µm . Lgr5fl / fl / Axin2CreErt2 ( Lgr5 - / - ) and control mice were infected for 2 months with H . pylori . B Quantification of antral gland height in Lgr5 - / - compared to control mice . Uninfected control ( n = 5 ) versus uninfected Lgr5 - / - ( n = 4 ) versus infected control ( n = 4 ) versus infected Lgr5 - / - ( n = 4 ) . Data information : B , data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; * * * = p < 0 . 001 ; ns = not significant ( one - way ANOVA + Tukey ´ s multiple comparison test for B , Lgr5fl / fl / Axin2CreErt2 ( Lgr5 - / - ) and control mice were infected for 2 months with H . pylori . C Quantifications of GSII + area ( n = 4 - 5 biological replicates per group , n = 10 glands per mouse ) , Ki67 as percentage of total DAPI - stained cells ( n = 3 - 4 biological replicates per group , n = 20 glands per mouse ) , GIF + area ( n = 4 - 5 biological replicates per group , n = 10 glands per mouse ) , Muc5ac + area ( n = 4 - 5 biological replicates per group , n = 10 glands per mouse ) . Data information : For ( one - way ANOVA + Tukey ´ s multiple comparison test for C , Lgr5fl / fl / Axin2CreErt2 ( Lgr5 - / - ) and control mice were infected for 2 months with H . pylori . D H . pylori CFUs in Lgr5 - / - ( n = 5 ) and control mice ( n = 5 ) . Data information : For D , data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; * * * = p < 0 . 001 ; ns = not significant t - test for DLgr5fl / fl / Axin2CreErt2 ( Lgr5 - / - ) and control mice were infected for 2 months with H . pylori . E qPCR expression levels of Lgr4 , Lgr5 , Axin2 , gland base cell markers ( Gif , Pgc , Tff2 , Muc6 ) , pit cell marker Muc5ac , and Itln1 in uninfected Lgr5 - / - ( n = 6 - 10 ) and control mice ( n = 4 - 10 ) . F qPCR expression levels of Lgr4 , Lgr5 , gland base cell markers ( Gif , Pgc , Muc6 ) , and Itln1 in Lgr5 - / - ( n = 5 ) and control mice ( n = 5 ) after 2 months of infection . Data information : For E and F , data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; * * * = p < 0 . 001 ; ns = not significant t - test for E and F ) .

O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 1Lgr5fl/fl/Axin2CreErt2 (Lgr5-/-) and control mice were infected for 2 months with H. pylori. A Representative H&E staining from antral glands (upper row). The dotted line marks the gland base cell area, which expands upon infection in Lgr5-/- and control mice. Immunofluorescence labeling for GSII and Ki67 (middle row) and GIF and Muc5ac (lower row) of antral epithelium from Lgr5-/- and control mice uninfected and after 2 months of infection. Scale bars: 50 µm.Lgr5fl/fl/Axin2CreErt2 (Lgr5-/-) and control mice were infected for 2 months with H. pylori. B Quantification of antral gland height in Lgr5-/- compared to control mice. Uninfected control (n = 5) versus uninfected Lgr5-/- (n = 4) versus infected control (n = 4) versus infected Lgr5-/- (n = 4). Data information: B, data are mean + SD. * = p < 0.05; ** = p < 0.01; *** = p < 0.001; ns = not significant (one-way ANOVA + Tukey´s multiple comparison test for B,Lgr5fl/fl/Axin2CreErt2 (Lgr5-/-) and control mice were infected for 2 months with H. pylori. C Quantifications of GSII+ area (n = 4-5 biological replicates per group, n = 10 glands per mouse), Ki67 as percentage of total DAPI-stained cells (n = 3-4 biological replicates per group, n = 20 glands per mouse), GIF+ area (n = 4-5 biological replicates per group, n = 10 glands per mouse), Muc5ac+ area (n = 4-5 biological replicates per group, n = 10 glands per mouse). Data information: For (one-way ANOVA + Tukey´s multiple comparison test for C,Lgr5fl/fl/Axin2CreErt2 (Lgr5-/-) and control mice were infected for 2 months with H. pylori. D H. pylori CFUs in Lgr5-/- (n = 5) and control mice (n = 5). Data information: For D, data are mean + SD. * = p < 0.05; ** = p < 0.01; *** = p < 0.001; ns = not significant t-test for DLgr5fl/fl/Axin2CreErt2 (Lgr5-/-) and control mice were infected for 2 months with H. pylori. E qPCR expression levels of Lgr4, Lgr5, Axin2, gland base cell markers (Gif, Pgc, Tff2, Muc6), pit cell marker Muc5ac, and Itln1 in uninfected Lgr5-/- (n = 6-10) and control mice (n = 4-10). F qPCR expression levels of Lgr4, Lgr5, gland base cell markers (Gif, Pgc, Muc6), and Itln1 in Lgr5-/- (n = 5) and control mice (n = 5) after 2 months of infection. Data information: For E and F, data are mean + SD. * = p < 0.05; ** = p < 0.01; *** = p < 0.001; ns = not significant t-test for E and F).


Figure 2Lgr4fl / fl / Axin2CreErt2 ( Lgr4 - / - ) and control mice were infected for 2 months with H . pylori . A Representative H & E staining from antral glands ( upper row ) . The dotted line marks the gland base cell area , which does not expand in infected Lgr4 - / - but does expand in the corresponding control mice . Immunofluorescence labeling for GSII and Ki67 ( middle row ) and GIF and Muc5ac ( bottom row ) of antral epithelium from Lgr4 - / - and control mice uninfected and after 2 months of infection . Scale bars : 50 µm . Lgr4fl / fl / Axin2CreErt2 ( Lgr4 - / - ) and control mice were infected for 2 months with H . pylori . B Quantification of antral gland height in Lgr4 - / - compared to control mice . Uninfected control ( n = 2 ) versus uninfected Lgr4 - / - ( n = 4 ) versus infected control ( n = 4 ) versus infected Lgr4 - / - ( n = 4 ) . Data information : For B , , data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; * * * = p < 0 . 001 ; * * * * = p < 0 . 0001 ; ns = not significant ( one - way ANOVA + Tukey ´ s multiple comparison test for BLgr4fl / fl / Axin2CreErt2 ( Lgr4 - / - ) and control mice were infected for 2 months with H . pylori . C Quantifications of GSII + area ( n = 2 - 4 biological replicates per group , n = 10 glands per mouse ) , Ki67 as percentage of total DAPI - stained cells ( n = 2 - 4 biological replicates per group , n = 20 glands per mouse ) , GIF + area ( n = 2 - 4 biological replicates per group , n = 10 glands per mouse ) , Muc5ac + area ( n = 4 - 5 biological replicates per group , n = 10 glands per mouse ) . Data information : For C , data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; * * * = p < 0 . 001 ; * * * * = p < 0 . 0001 ; ns = not significant ( one - way ANOVA + Tukey ´ s multiple comparison test for C , Lgr4fl / fl / Axin2CreErt2 ( Lgr4 - / - ) and control mice were infected for 2 months with H . pylori . D H . pylori CFUs show higher colonization in Lgr4 - / - ( n = 5 ) compared to control mice ( n = 4 ) . Data information : For D , , data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; * * * = p < 0 . 001 ; * * * * = p < 0 . 0001 ; ns = not significant t - test for DLgr4fl / fl / Axin2CreErt2 ( Lgr4 - / - ) and control mice were infected for 2 months with H . pylori . E qPCR expression levels of Lgr4 , Lgr5 , Axin2 , gland base cell markers ( Gif , Pgc , Tff2 , Muc6 ) , pit cell marker Muc5ac , and Itln1 in uninfected Lgr4 - / - ( n = 4 - 10 ) and control mice ( n = 4 - 6 ) . F qPCR expression levels of Lgr4 , Lgr5 , gland base cell markers ( Gif , Pgc , Muc6 ) , and Itln1 in Lgr4 - / - ( n = 5 ) and control mice ( n = 5 ) after 2 months of infection . Data information : For E and F , data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; * * * = p < 0 . 001 ; * * * * = p < 0 . 0001 ; ns = not significant t - test for E and F ) .

O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 2Lgr4fl/fl/Axin2CreErt2 (Lgr4-/-) and control mice were infected for 2 months with H. pylori. A Representative H&E staining from antral glands (upper row). The dotted line marks the gland base cell area, which does not expand in infected Lgr4-/- but does expand in the corresponding control mice. Immunofluorescence labeling for GSII and Ki67 (middle row) and GIF and Muc5ac (bottom row) of antral epithelium from Lgr4-/- and control mice uninfected and after 2 months of infection. Scale bars: 50 µm.Lgr4fl/fl/Axin2CreErt2 (Lgr4-/-) and control mice were infected for 2 months with H. pylori. B Quantification of antral gland height in Lgr4-/- compared to control mice. Uninfected control (n = 2) versus uninfected Lgr4-/- (n = 4) versus infected control (n = 4) versus infected Lgr4-/- (n = 4). Data information: For B, , data are mean + SD. * = p < 0.05; ** = p < 0.01; *** = p < 0.001; **** = p < 0.0001; ns = not significant (one-way ANOVA + Tukey´s multiple comparison test for BLgr4fl/fl/Axin2CreErt2 (Lgr4-/-) and control mice were infected for 2 months with H. pylori. C Quantifications of GSII+ area (n = 2-4 biological replicates per group, n = 10 glands per mouse), Ki67 as percentage of total DAPI-stained cells (n = 2-4 biological replicates per group, n = 20 glands per mouse), GIF+ area (n = 2-4 biological replicates per group, n = 10 glands per mouse), Muc5ac+ area (n = 4-5 biological replicates per group, n = 10 glands per mouse). Data information: For C, data are mean + SD. * = p < 0.05; ** = p < 0.01; *** = p < 0.001; **** = p < 0.0001; ns = not significant (one-way ANOVA + Tukey´s multiple comparison test for C,Lgr4fl/fl/Axin2CreErt2 (Lgr4-/-) and control mice were infected for 2 months with H. pylori. D H. pylori CFUs show higher colonization in Lgr4-/- (n = 5) compared to control mice (n = 4). Data information: For D, , data are mean + SD. * = p < 0.05; ** = p < 0.01; *** = p < 0.001; **** = p < 0.0001; ns = not significant t-test for DLgr4fl/fl/Axin2CreErt2 (Lgr4-/-) and control mice were infected for 2 months with H. pylori. E qPCR expression levels of Lgr4, Lgr5, Axin2, gland base cell markers (Gif, Pgc, Tff2, Muc6), pit cell marker Muc5ac, and Itln1 in uninfected Lgr4-/- (n = 4-10) and control mice (n = 4-6). F qPCR expression levels of Lgr4, Lgr5, gland base cell markers (Gif, Pgc, Muc6), and Itln1 in Lgr4-/- (n = 5) and control mice (n = 5) after 2 months of infection. Data information: For E and F, data are mean + SD. * = p < 0.05; ** = p < 0.01; *** = p < 0.001; **** = p < 0.0001; ns = not significant t-test for E and F).


Figure 3A , B GSEA comparing microarray data from 2 - month infected Lgr4fl / fl / Axin2CreErt2 ( Lgr4 - / - ) mice with publicly available data demonstrating downregulation of antral stem cell signature ( A ) and beta - catenin targets ( B ) . C qPCR expression levels for beta catenin targets Axin2 and Sox9 in uninfected and infected Lgr4 - / - and control mice ( n = 2 - 9 ) . Data information : For C , data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; * * * = p < 0 . 001 ( one - way ANOVA + Tukey ´ s multiple comparison test ) . D GSEA comparing microarray data from 2 - month infected Lgr4 - / - mice with publicly available data demonstrating downregulation of the TNF - α signaling via NF - κB . E Immunofluorescence labeling for p65 , Ki67 and GSII in the mouse antrum tissue from uninfected and infected Lgr4 - / - and control mice . Insets show magnified images . Scale bars : 50 µm . F Quantification of p65 + area as percentage of total DAPI - stained cells of uninfected and infected Lgr4 - / - and control mice ( n = 4 biological replicates per group , n = 20 glands per mouse ) . Data information : For data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; * * * = p < 0 . 001 ( one - way ANOVA + Tukey ´ s multiple comparison test ) . G Immunofluorescence co - localization of p65 acetyl K310 ( activated form of NF - κB ) in the mouse antrum tissue of infected Lgr4 - / - and in control mice . Insets show magnified images . Scale bars : 50µm . Data information : For G images represent findings that were reproduced at least twice in the laboratory in independent biological replicates . H qPCR expression levels of Cxcl1 , Cxcl2 , Cxcl10 , Ccl2 in uninfected and infected Lgr4 - / - mice ( n = 4 - 5 ) and control mice ( n = 2 - 5 ) . Data information : For H , data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; * * * = p < 0 . 001 ( one - way ANOVA + Tukey ´ s multiple comparison test ) . I Immunofluorescence labeling for Cxcl1 in the mouse antrum tissue in infected Lgr4 - / - and in control mice . Scale bars : 50 µm . Data information : For I images represent findings that were reproduced at least twice in the laboratory in independent biological replicates .

O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O 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-PANEL_START O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 3A, B GSEA comparing microarray data from 2-month infected Lgr4fl/fl/Axin2CreErt2 (Lgr4-/-) mice with publicly available data demonstrating downregulation of antral stem cell signature (A) and beta-catenin targets (B).C qPCR expression levels for beta catenin targets Axin2 and Sox9 in uninfected and infected Lgr4-/- and control mice (n = 2-9). Data information: For C, data are mean + SD. * = p < 0.05; ** = p < 0.01; *** = p < 0.001 (one-way ANOVA + Tukey´s multiple comparison test).D GSEA comparing microarray data from 2-month infected Lgr4-/- mice with publicly available data demonstrating downregulation of the TNF-α signaling via NF-κB.E Immunofluorescence labeling for p65, Ki67 and GSII in the mouse antrum tissue from uninfected and infected Lgr4-/- and control mice. Insets show magnified images. Scale bars: 50 µm.F Quantification of p65+ area as percentage of total DAPI-stained cells of uninfected and infected Lgr4-/- and control mice (n = 4 biological replicates per group, n = 20 glands per mouse). Data information: For data are mean + SD. * = p < 0.05; ** = p < 0.01; *** = p < 0.001 (one-way ANOVA + Tukey´s multiple comparison test).G Immunofluorescence co-localization of p65 acetyl K310 (activated form of NF-κB) in the mouse antrum tissue of infected Lgr4-/- and in control mice. Insets show magnified images. Scale bars: 50µm. Data information: For G images represent findings that were reproduced at least twice in the laboratory in independent biological replicates.H qPCR expression levels of Cxcl1, Cxcl2, Cxcl10, Ccl2 in uninfected and infected Lgr4-/- mice (n = 4-5) and control mice (n = 2-5). Data information: For H, data are mean + SD. * = p < 0.05; ** = p < 0.01; *** = p < 0.001 (one-way ANOVA + Tukey´s multiple comparison test).I Immunofluorescence labeling for Cxcl1 in the mouse antrum tissue in infected Lgr4-/- and in control mice. Scale bars: 50 µm. Data information: For I images represent findings that were reproduced at least twice in the laboratory in independent biological replicates.


Figure 4A Immunofluorescence labeling for p65 and E - cadherin in the mouse antrum tissue of 2 weeks infected B6 - Myh11CreErt2 / Rspondin3fl / fl ( Rspo3 - / - ) and control mice . Arrows in infected control mice indicate nuclear p65 that is not observed in Rspo3 - / - mice . Scale bars : 50 µm . B Quantification of p65 + area as percentage of total DAPI - stained cells of infected Rspo3 - / - and control mice ( n = 3 biological replicates per group , n = 20 glands per mouse ) . Data information : For B , data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; ns = not significant ( t - test for BC qPCR expression level of Cxcl1 and Cxcl2 in 2 - week infected Rspo3 - / - mice ( n = 3 ) versus infected control mice ( n = 4 ) . D qPCR expression level of Cxcl1 and Cxcl2 in 2 - month infected Rspo3 - / - mice ( n = 5 ) versus infected control mice ( n = 6 ) . Data information : For C , D , data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; ns = not significant ( t - test for C and DE Myh11CreERT2 / Rosa26Sor6 ( CAG - Rspo3 ) ( Rspo3 KI ) mice were infected for 6 weeks with H . pylori . Immunofluorescence labeling for p65 , GSII and KI67 in uninfected and infected Rspo3 KI and control mice . Scale bars : 50 µm . F Quantification of p65 + area as percentage of total DAPI - stained cells of uninfected and infected Rspo3 KI and control mice ( n = 2 - 3 biological replicates per group , n = 20 glands per mouse ) . G Quantification of GSII + area of uninfected and infected Rspo3 KI and control mice ( n = 2 - 3 biological replicates per group , n = 20 glands per mouse ) . H Quantification of Ki67 as percentage of total DAPI - stained cells of uninfected and infected Rspo3 KI and control mice ( n = 2 - 3 biological replicates per group , n = 20 glands per mouse ) . Data information : For , F , G and H data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; ns = not significant one - way ANOVA + Tukey ´ s multiple comparison test for F , G and H ) . I Immunofluorescence labeling for p65 acetyl K310 in infected Rspo3 KI and control mice . Insets show magnified images . Scale bars : 50 µm .

O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 4A Immunofluorescence labeling for p65 and E-cadherin in the mouse antrum tissue of 2 weeks infected B6-Myh11CreErt2/Rspondin3fl/fl (Rspo3-/-) and control mice. Arrows in infected control mice indicate nuclear p65 that is not observed in Rspo3-/- mice. Scale bars: 50 µm.B Quantification of p65+ area as percentage of total DAPI-stained cells of infected Rspo3-/- and control mice (n = 3 biological replicates per group, n = 20 glands per mouse). Data information: For B, data are mean + SD. * = p < 0.05; ** = p < 0.01; ns = not significant (t-test for BC qPCR expression level of Cxcl1 and Cxcl2 in 2-week infected Rspo3-/- mice (n = 3) versus infected control mice (n = 4). D qPCR expression level of Cxcl1 and Cxcl2 in 2-month infected Rspo3-/- mice (n = 5) versus infected control mice (n = 6). Data information: For C, D, data are mean + SD. * = p < 0.05; ** = p < 0.01; ns = not significant (t-test for C and DE Myh11CreERT2/Rosa26Sor6(CAG-Rspo3) (Rspo3 KI) mice were infected for 6 weeks with H. pylori. Immunofluorescence labeling for p65, GSII and KI67 in uninfected and infected Rspo3 KI and control mice. Scale bars: 50 µm. F Quantification of p65+ area as percentage of total DAPI-stained cells of uninfected and infected Rspo3 KI and control mice (n = 2-3 biological replicates per group, n = 20 glands per mouse). G Quantification of GSII+ area of uninfected and infected Rspo3 KI and control mice (n = 2-3 biological replicates per group, n = 20 glands per mouse). H Quantification of Ki67 as percentage of total DAPI-stained cells of uninfected and infected Rspo3 KI and control mice (n = 2-3 biological replicates per group, n = 20 glands per mouse). Data information: For , F, G and H data are mean + SD. * = p < 0.05; ** = p < 0.01; ns = not significant one-way ANOVA + Tukey´s multiple comparison test for F, G and H).I Immunofluorescence labeling for p65 acetyl K310 in infected Rspo3 KI and control mice. Insets show magnified images. Scale bars: 50 µm.


Figure 5A Immunofluorescence labelling for MPO in uninfected and 2 - month infected Lgr4 - / - and control mice ( top panel ) and 2 - month infected Lgr5 - / - and control mice ( bottom panel ) . Asterisks indicate nonspecific staining . Scale bars : 50 µm . B Quantification of MPO + cells in uninfected and 2 - month infected Lgr4 - / - and control mice ( n = 2 biological replicates per group , n = 5 - 10 FOVs per mouse ) ( left panel ) and 2 - month infected Lgr5 - / - and control mice ( n = 2 biological replicates per group , n = 6 - 8 FOVs per mouse ) ( right panel ) . Data information : For B data are mean + SD . * * = p < 0 . 01 ; * * * = p < 0 . 001 ; ns = not significant ( one - way ANOVA + Tukey ´ s multiple comparison test ) .

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Figure 5A Immunofluorescence labelling for MPO in uninfected and 2-month infected Lgr4-/- and control mice (top panel) and 2-month infected Lgr5-/- and control mice (bottom panel). Asterisks indicate nonspecific staining. Scale bars: 50 µm. B Quantification of MPO+ cells in uninfected and 2-month infected Lgr4-/- and control mice (n = 2 biological replicates per group, n = 5-10 FOVs per mouse) (left panel) and 2-month infected Lgr5-/- and control mice (n = 2 biological replicates per group, n = 6-8 FOVs per mouse) (right panel). Data information: For B data are mean + SD. ** = p < 0.01; *** = p < 0.001; ns = not significant (one-way ANOVA + Tukey´s multiple comparison test).


Figure 6Antrum organoids from wildtype mice were grown in full medium ( FM ) for 2 - 3 days , followed by respective medium conditions for 3 - 5 days ( FM , - Rspo , - Rspo / - Wnt , + BMP2 ) . 0 . 5 µM ADP heptose or 10 ng / ml TNF - α was added for 2 h to all organoid conditions prior to analysis . A Bright - field images of organoids in respective conditions before treatment with ADP heptose or TNF - α . Scale bars : 200 µm . Antrum organoids from wildtype mice were grown in full medium ( FM ) for 2 - 3 days , followed by respective medium conditions for 3 - 5 days ( FM , - Rspo , - Rspo / - Wnt , + BMP2 ) . 0 . 5 µM ADP heptose or 10 ng / ml TNF - α was added for 2 h to all organoid conditions prior to analysis . B Immunofluorescence labeling for GSII and Muc5ac of organoids in respective conditions before treatment with ADP heptose or TNF - α . Scale bars : 50 µm . Antrum organoids from wildtype mice were grown in full medium ( FM ) for 2 - 3 days , followed by respective medium conditions for 3 - 5 days ( FM , - Rspo , - Rspo / - Wnt , + BMP2 ) . C qPCR expression level of Lgr5 in untreated organoids in respective medium conditions ( n = 4 - 5 biological replicates ) . D qPCR expression level of Gif in untreated organoids in respective medium conditions ( n = 4 - 5 biological replicates ) . Data information : For C , D , data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; * * * * = p < 0 . 0001 ( one - way ANOVA + Tukey ´ s multiple comparison test for C and Genes without asterisks are not significantly altered . Antrum organoids from wildtype mice were grown in full medium ( FM ) for 2 - 3 days , followed by respective medium conditions for 3 - 5 days ( FM , - Rspo , - Rspo / - Wnt , + BMP2 ) . 0 . 5 µM ADP heptose or 10 ng / ml TNF - α was added for 2 h to all organoid conditions prior to analysis . E qPCR expression level of Cxcl1 , Cxcl2 , Cxcl10 , Ccl2 in organoids after treatment with ADP heptose compared to untreated controls within the respective medium conditions ( n = 6 biological replicates per condition ) . F qPCR expression level of Cxcl1 , Cxcl2 , Cxcl10 , Ccl2 in organoids after treatment with TNF - α compared to untreated controls within the respective medium conditions ( n = 2 - 3 biological replicates per condition ) . Data information : For E and F data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; * * * * = p < 0 . 0001 ; t - test for E and F ) . Genes without asterisks are not significantly altered .

O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 6Antrum organoids from wildtype mice were grown in full medium (FM) for 2-3 days, followed by respective medium conditions for 3-5 days (FM, -Rspo, -Rspo/-Wnt, +BMP2). 0.5 µM ADP heptose or 10 ng/ml TNF-α was added for 2 h to all organoid conditions prior to analysis. A Bright-field images of organoids in respective conditions before treatment with ADP heptose or TNF-α. Scale bars: 200 µm.Antrum organoids from wildtype mice were grown in full medium (FM) for 2-3 days, followed by respective medium conditions for 3-5 days (FM, -Rspo, -Rspo/-Wnt, +BMP2). 0.5 µM ADP heptose or 10 ng/ml TNF-α was added for 2 h to all organoid conditions prior to analysis. B Immunofluorescence labeling for GSII and Muc5ac of organoids in respective conditions before treatment with ADP heptose or TNF-α. Scale bars: 50 µm.Antrum organoids from wildtype mice were grown in full medium (FM) for 2-3 days, followed by respective medium conditions for 3-5 days (FM, -Rspo, -Rspo/-Wnt, +BMP2). C qPCR expression level of Lgr5 in untreated organoids in respective medium conditions (n = 4-5 biological replicates). D qPCR expression level of Gif in untreated organoids in respective medium conditions (n = 4-5 biological replicates). Data information: For C, D, data are mean + SD. * = p < 0.05; ** = p < 0.01; **** = p < 0.0001 (one-way ANOVA + Tukey´s multiple comparison test for C and Genes without asterisks are not significantly altered.Antrum organoids from wildtype mice were grown in full medium (FM) for 2-3 days, followed by respective medium conditions for 3-5 days (FM, -Rspo, -Rspo/-Wnt, +BMP2). 0.5 µM ADP heptose or 10 ng/ml TNF-α was added for 2 h to all organoid conditions prior to analysis. E qPCR expression level of Cxcl1, Cxcl2, Cxcl10, Ccl2 in organoids after treatment with ADP heptose compared to untreated controls within the respective medium conditions (n = 6 biological replicates per condition). F qPCR expression level of Cxcl1, Cxcl2, Cxcl10, Ccl2 in organoids after treatment with TNF-α compared to untreated controls within the respective medium conditions (n = 2-3 biological replicates per condition). Data information: For E and F data are mean + SD. * = p < 0.05; ** = p < 0.01; **** = p < 0.0001 ; t-test for E and F). Genes without asterisks are not significantly altered.


Figure 7Antrum organoids from wildtype mice were grown in full medium ( FM ) for 2 - 3 days , followed by respective medium conditions for 3 - 5 days ( FM , - Rspo , - Rspo / - Wnt , + BMP2 ) . 0 . 5 µM ADP heptose was added for 2 h to all organoid conditions prior to analysis . A Electrophoretic mobility shift assay ( EMSA ) and SDS - PAGE western blot from whole cell protein ( WCL ) lysates from gastric organoids untreated or treated with ADP heptose , and maintained either in FM in medium without Rspo , without Wnt and Rspo , or + BMP2 . Representative images from n = 3 biological replicates . B Quantification of EMSA based on n = 3 biological replicates using ImageJ with normalization to loading ( ɑ - Tubulin ) . Data information : For B data are mean + SD . Significance is calculated by one - way ANOVA , F = 9 . 21 . C EMSA supershift from FM + ADP heptose organoids with the antibodies indicated . Blue arrow indicates NF - κB binding . Red arrow points to gel expected locations of supershifts from antibodies against p65 , cRel , or RelB . Grey arrow points to supershift location on the gel from antibodies against p52 or p50 . IgG lane serves as a negative control .

O B-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 7Antrum organoids from wildtype mice were grown in full medium (FM) for 2-3 days, followed by respective medium conditions for 3-5 days (FM, -Rspo, -Rspo/-Wnt, +BMP2). 0.5 µM ADP heptose was added for 2 h to all organoid conditions prior to analysis. A Electrophoretic mobility shift assay (EMSA) and SDS-PAGE western blot from whole cell protein (WCL) lysates from gastric organoids untreated or treated with ADP heptose, and maintained either in FM in medium without Rspo, without Wnt and Rspo, or +BMP2. Representative images from n = 3 biological replicates. B Quantification of EMSA based on n = 3 biological replicates using ImageJ with normalization to loading (ɑ-Tubulin). Data information: For B data are mean + SD. Significance is calculated by one-way ANOVA, F = 9.21.C EMSA supershift from FM + ADP heptose organoids with the antibodies indicated. Blue arrow indicates NF-κB binding. Red arrow points to gel expected locations of supershifts from antibodies against p65, cRel, or RelB. Grey arrow points to supershift location on the gel from antibodies against p52 or p50. IgG lane serves as a negative control.


Figure 8A Bright - field images of antrum organoids from 129 ; 129P2 - ctnnb1tm ( NFKBIAΔN ) 1Rsu ( ΔN ) mice and control mice , passage 0 , day 6 . Scale bars : 500 µm . B , C qPCR expression levels of Lgr4 , Lgr5 , Gif , Pgc , Muc6 ( B ) and Cxcl1 , Cxcl2 ( C ) of organoids ( n = 3 biological replicates ) . Data information : For B , C , data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; ns = not significant ( t - test ) . D Representative H & E staining and immunofluorescence labeling for GSII , Ki67 and MUC5AC in uninfected ΔN and control mice . Scale bars : 50 µm . E Quantification of GSII and Ki67 as percentage of total DAPI - stained cells in ΔN and control mice ( n = 5 biological replicates per group , n = 20 glands per mouse ) . Data information : For E data are mean + SD . * = p < 0 . 05 ; * * = p < 0 . 01 ; ns = not significant ( t - test ) .

O B-PANEL_START O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 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-PANEL_START O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

Figure 8A Bright-field images of antrum organoids from 129;129P2-ctnnb1tm(NFKBIAΔN)1Rsu (ΔN) mice and control mice, passage 0, day 6. Scale bars: 500 µm.B, C qPCR expression levels of Lgr4, Lgr5, Gif, Pgc, Muc6 (B) and Cxcl1, Cxcl2 (C) of organoids (n = 3 biological replicates). Data information: For B, C, data are mean + SD. * = p < 0.05; ** = p < 0.01; ns = not significant (t-test).D Representative H&E staining and immunofluorescence labeling for GSII, Ki67 and MUC5AC in uninfected ΔN and control mice. Scale bars: 50 µm. E Quantification of GSII and Ki67 as percentage of total DAPI-stained cells in ΔN and control mice (n = 5 biological replicates per group, n = 20 glands per mouse). Data information: For E data are mean + SD. * = p < 0.05; ** = p < 0.01; ns = not significant (t-test).


Figure 1B . Subcellular fractionation and Western blots of 293T cells with ectopically expressed GASZ , NRF1 , MVH , or MitoPLD . C . Localization of GFP fused with wild - type or mutant MLS of GASZ in HeLa cells . Mitochondrial localization was monitored by MitoTracker ( Red ) staining . Scale bars : 15 m .

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Figure 1B. Subcellular fractionation and Western blots of 293T cells with ectopically expressed GASZ, NRF1, MVH, or MitoPLD.C. Localization of GFP fused with wild-type or mutant MLS of GASZ in HeLa cells. Mitochondrial localization was monitored by MitoTracker (Red) staining. Scale bars: 15 m.


Figure 2A . IHF of GASZ and Cytochrome C ( Cyt C ) of testical sections from mice at day 7 postnatal , or MILI and MVH of gonad sections from wild - type embryos or embryos with MLS deletion at 16 . 5 dpc . Scale bars : 5 m . B . Western blots of GASZ expression of testes at day 5 postnatal . C . Gross morphology of testes from adult mice at 3 months postnatal with mutated MLS compared to their wild - type littermates . D . Histological studies of testis sections from wild - type mice or mice with MLS deletion at different time points after birth . Scale bars : 50 m . E . EM of testis sections from wild - type neonatal mice or mice with MLS mutation . Red arrows point to IMC among mitochondria . F . Expression of transposable elements analyzed by real - time RT - PCR on testes from wild - type mice or mice with mutated MLS at various time points after birth . Data were shown as mean ( of expression from three biological replicates ) ± one s . e . m . n = 3 for each genotype . * * : p < 0 . 01 . * : p < 0 . 05 .

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Figure 2A. IHF of GASZ and Cytochrome C (Cyt C) of testical sections from mice at day 7 postnatal, or MILI and MVH of gonad sections from wild-type embryos or embryos with MLS deletion at 16.5 dpc. Scale bars: 5 m.B. Western blots of GASZ expression of testes at day 5 postnatal.C. Gross morphology of testes from adult mice at 3 months postnatal with mutated MLS compared to their wild-type littermates.D. Histological studies of testis sections from wild-type mice or mice with MLS deletion at different time points after birth. Scale bars: 50 m.E. EM of testis sections from wild-type neonatal mice or mice with MLS mutation. Red arrows point to IMC among mitochondria.F. Expression of transposable elements analyzed by real-time RT-PCR on testes from wild-type mice or mice with mutated MLS at various time points after birth. Data were shown as mean (of expression from three biological replicates) ± one s.e.m. n=3 for each genotype. **: p<0.01. *: p<0.05.


Figure 3B . 293T cells with ectopically expressed proteins were extracted for soluble and membrane bound fraction and examined by Western blots . C . Mitochondrial fraction from 293T cells ectopically expressing GASZ , MitoPLD , AIFM1 , or SIRT3 were treated in the presence or absence of Triton X - 100 and / or Proteinase K , and examined by Western blots . D . GST pull - down assay of GST - tagged GASZ with FLAG - GASZ produced from 293T cells . E . Co - IP assays of FLAG or GFP - tagged GASZ in 293T cells . Antibodies for Co - IP ( IP ) or Western blots ( WB ) were listed on the left . F . BiFC assays in which YFP was detected by flow cytometry in control 293T cells , or 293T cells co - expressed with GASZ fused with N - or C - terminal half of YFP . Ctrl : empty vector control . G . Co - IP assays of GFP - GASZ with various FLAG - tagged wild - type GASZ or its deletion mutants in 293T

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Figure 3B. 293T cells with ectopically expressed proteins were extracted for soluble and membrane bound fraction and examined by Western blots.C. Mitochondrial fraction from 293T cells ectopically expressing GASZ, MitoPLD, AIFM1, or SIRT3 were treated in the presence or absence of Triton X-100 and/or Proteinase K, and examined by Western blots.D. GST pull-down assay of GST-tagged GASZ with FLAG-GASZ produced from 293T cells.E. Co-IP assays of FLAG or GFP-tagged GASZ in 293T cells. Antibodies for Co-IP (IP) or Western blots (WB) were listed on the left.F. BiFC assays in which YFP was detected by flow cytometry in control 293T cells, or 293T cells co-expressed with GASZ fused with N- or C-terminal half of YFP. Ctrl: empty vector control.G. Co-IP assays of GFP-GASZ with various FLAG-tagged wild-type GASZ or its deletion mutants in 293T cells