EMBO/SourceData huggingface dataset:
Figure legend: "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,"
NCBI gene IDs:
"Axin2: 12006
Cre: 2777477
Ert2: 2099
Lgr5: 14160"
Figure legend: "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 &lt; 0.05; ** = p &lt; 0.01; *** = p &lt; 0.001; ns = not significant t-test for D"
NCBI gene IDs:
"Axin2: 12006
Cre: 2777477
Ert2: 2099
Lgr5: 14160"
Figure legend: "Lgr5fl/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 &lt; 0.05; ** = p &lt; 0.01; *** = p &lt; 0.001; ns = not significant t-test for E and F)."
NCBI gene IDs:
"Axin2: 12006
Gif: 14603
Cre: 2777477
Ert2: 2099
Itln1: 16429
Lgr4: 107515
Lgr5: 14160
Muc5ac: 17833
Muc6: 353328
Pgc: 109820
Tff2: 21785"
Figure legend: "Lgr4fl/fl/Axin2CreErt2 (Lgr4-/-) and control mice  were infected for 2 months with H. pylori. A Representative H&amp;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."
NCBI gene IDs:
"Axin2: 12006
Cre: 2777477
Ert2: 2099
Lgr4: 107515"
Figure legend: "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 &lt; 0.05; ** = p &lt; 0.01; *** = p &lt; 0.001; **** = p &lt; 0.0001; ns = not significant (one-way ANOVA + Tukey´s multiple comparison test for B"
NCBI gene IDs:
"Axin2: 12006
Cre: 2777477
Ert2: 2099
Lgr4: 107515"
Figure legend: "Lgr4fl/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 &lt; 0.05; ** = p &lt; 0.01; *** = p &lt; 0.001; **** = p &lt; 0.0001; ns = not significant (one-way ANOVA + Tukey´s multiple comparison test for C,"
NCBI gene IDs:
"Axin2: 12006
Cre: 2777477
Ert2: 2099
Lgr4: 107515"
Figure legend: "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 &lt; 0.05; ** = p &lt; 0.01; *** = p &lt; 0.001; **** = p &lt; 0.0001; ns = not significant t-test for D"
NCBI gene IDs:
"Axin2: 12006
Cre: 2777477
Ert2: 2099
Lgr4: 107515"
Figure legend: "Lgr4fl/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 &lt; 0.05; ** = p &lt; 0.01; *** = p &lt; 0.001; **** = p &lt; 0.0001; ns = not significant t-test for E and F)."
NCBI gene IDs:
"Axin2: 12006
Gif: 14603
Cre: 2777477
Ert2: 2099
Itln1: 16429
Lgr4: 107515
Lgr5: 14160
Muc5ac: 17833
Muc6: 353328
Pgc: 109820
Tff2: 21785"
Figure legend: "A, 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)."
NCBI gene IDs:
"Axin2: 12006
Cre: 2777477
Ert2: 2099
Lgr4: 107515"
Figure legend: "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 &lt; 0.05; ** = p &lt; 0.01; *** = p &lt; 0.001 (one-way ANOVA + Tukey´s multiple comparison test)."
NCBI gene IDs:
"Axin2: 12006
Lgr4: 107515
Sox9: 20682"
Figure legend: "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."
NCBI gene IDs:
"Lgr4: 107515"
Figure legend: "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."
NCBI gene IDs:
"Lgr4: 107515"
Figure legend: "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 &lt; 0.05; ** = p &lt; 0.01; *** = p &lt; 0.001 (one-way ANOVA + Tukey´s multiple comparison test)."
NCBI gene IDs:
"Lgr4: 107515"
Figure legend: "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."
NCBI gene IDs:
"Lgr4: 107515"
Figure legend: "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 &lt; 0.05; ** = p &lt; 0.01; *** = p &lt; 0.001 (one-way ANOVA + Tukey´s multiple comparison test)."
NCBI gene IDs:
"Ccl2: 20296
Cxcl1: 14825
Cxcl10: 15945
Cxcl2: 20310
Lgr4: 107515"
Figure legend: "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."
NCBI gene IDs:
"Lgr4: 107515"
Figure legend: "A 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."
NCBI gene IDs:
"Cre: 2777477
Ert2: 2099
Myh11: 17880
Rspo3: 72780
Rspondin3: 72780"
Figure legend: "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 &lt; 0.05; ** = p &lt; 0.01; ns = not significant (t-test for B"
NCBI gene IDs:
"Rspo3: 72780"
Figure legend: "C 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 &lt; 0.05; ** = p &lt; 0.01; ns = not significant (t-test for C and D"
NCBI gene IDs:
"Cxcl1: 14825
Cxcl2: 20310
Rspo3: 72780"
Figure legend: "E 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 &lt; 0.05; ** = p &lt; 0.01; ns = not significant one-way ANOVA + Tukey´s multiple comparison test for F, G and H)."
NCBI gene IDs:
"Cre: 2777477
ERT2: 2099
Rosa26Sor: 14910
Myh11: 17880
Rspo3: 72780"
Figure legend: "I Immunofluorescence  labeling for p65 acetyl  K310 in infected Rspo3 KI and control mice. Insets show magnified images. Scale bars: 50 µm."
NCBI gene IDs:
"Rspo3: 72780"
Figure legend: "A 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 &lt; 0.01; *** = p &lt; 0.001; ns = not significant (one-way ANOVA + Tukey´s multiple comparison test)."
NCBI gene IDs:
"Lgr4: 107515
Lgr5: 14160"
Figure legend: "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 &lt; 0.05; ** = p &lt; 0.01; **** = p &lt; 0.0001 (one-way ANOVA + Tukey´s multiple comparison test for C and Genes without asterisks are not significantly altered."
NCBI gene IDs:
"Gif: 14603
Lgr5: 14160"
Figure legend: "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 &lt; 0.05; ** = p &lt; 0.01; **** = p &lt; 0.0001 ; t-test for E and F). Genes without asterisks are not significantly altered."
NCBI gene IDs:
"Ccl2: 20296
Cxcl1: 14825
Cxcl10: 15945
Cxcl2: 20310"
Figure legend: "A  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."
NCBI gene IDs:
"ctnnb1: 12387
NFKBIA: 18035"
Figure legend: "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 &lt; 0.05; ** = p &lt; 0.01; ns = not significant (t-test)."
NCBI gene IDs:
"Gif: 14603
Cxcl1: 14825
Cxcl2: 20310
Lgr4: 107515
Lgr5: 14160
Muc6: 353328
Pgc: 109820"
Figure legend: "A) Macrophages were transduced with non-specific scrambled shRNA (shNS), or TLR8 shRNA (shTLR8) and analyzed for TLR8 expression. Bottom, a representative blot is shown. Top, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4."
NCBI gene IDs:
"TLR8: 51311"
Figure legend: "(B) Macrophages transduced with shNS or shTLR8 from (A) were exposed to infectious HIV (+), AT-2-inactivated HIV (AT), or RNase/DNase I treated AT-2-inactivated HIV (R) or mock infected (-) for 24 h, harvested, lysed and analyzed for endogenous LC3B and SQSTM1 by Western blotting. Left, a representative blot is shown. Right, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4."
NCBI gene IDs:
"TLR8: 51311"
Figure legend: "(D) Macrophages were transduced with shNS or ATG13 shRNA (shATG13) and analyzed for ATG13 expression. Bottom, a representative blot is shown. Top, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4."
NCBI gene IDs:
"ATG13: 9776"
Figure legend: "(E) Macrophages transduced with shNS or shATG13 from (D) were exposed to infectious HIV, 5 μg/mL ssRNA40, 5 μg/mL ssRNA41, or 100 nmol/L sirolimus for 24 h, harvested, lysed and analyzed for endogenous LC3B and SQSTM1 by Western blotting. Left, a representative blot is shown. Right, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4."
NCBI gene IDs:
"ATG13: 9776"
Figure legend: "(E) Macrophages were transduced with non-specific scrambled shRNA (shNS), or TLR8 shRNA (shTLR8) and analyzed for TLR8 expression. Bottom, a representative blot is shown. Top, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4."
NCBI gene IDs:
"TLR8: 51311"
Figure legend: "(F) Macrophages transduced with shNS or shTLR8 from (E) were exposed to mock, infectious, AT-2-inactivated, or RNase/DNase I treated AT-2-inactivated purified HIV for 24 h. Cells were then harvested, lysed, fractionated for cytoplasmic and nuclear content, and analyzed for TFEB, ACTB and H3 histone by Western blotting. Top, a representative blot is shown. Bottom, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4."
NCBI gene IDs:
"TLR8: 51311"
Figure legend: "(A) Macrophages transduced with non-specific scrambled shRNA (shNS), or TFEB shRNA (shTFEB) were infected with HIV for 10 days. Cells were lysed and analyzed for TFEB and ACTB content by Western blotting. Left, a representative blot is shown. Right, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4."
NCBI gene IDs:
"TFEB: 7942"
Figure legend: "(C) Macrophages transduced with non-specific cDNA (Control), or TFEB cDNA (TFEB) then exposed to HIV. Cells were lysed and analyzed for TFEB and ACTB content by Western blotting. Bottom, a representative blot is shown. Top, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4."
NCBI gene IDs:
"TFEB: 7942"
Figure legend: "(A) qRT-PCR analysis of mRNA expression of autophagy (UVRAG and ATG9B) and lysosomal (MCOLN1) genes 24 h post-exposure to mock, infectious, or RNase/DNase I treated AT-2-inactivated purified HIV. Data are reported as mean ± s.e.m., n = 4."
NCBI gene IDs:
"ATG9B: 285973
MCOLN1: 57192
UVRAG: 7405"
Figure legend: "(B) Macrophages were transduced with non-specific scrambled shRNA (shNS), or TLR8 shRNA (shTLR8) and analyzed for TLR8 expression. Bottom, a representative blot is shown. Top, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4."
NCBI gene IDs:
"TLR8: 51311"
Figure legend: "(C) Macrophages from (B) were exposed to mock, infectious, or RNase/DNase I treated AT-2-inactivated purified HIV for 24 h. Cells were harvested and qRT-PCR for UVRAG, ATG9B, MCOLN1 was performed. Data were normalized to the shNS mock infected control for each gene. Bar charts are reported as mean ± s.e.m., n = 4."
NCBI gene IDs:
"ATG9B: 285973
MCOLN1: 57192
UVRAG: 7405"
Figure legend: "(A) Macrophages transduced with non-specific scrambled shRNA (shNS), or BECN1 shRNA (shBECN1) were infected with HIV for 10 days. Cells were lysed and analyzed for BECN1 and ACTB content by Western blotting. Left, a representative blot is shown. Right, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4."
NCBI gene IDs:
"BECN1: 8678"
Figure legend: "(A) Macrophages were infected with HIVNL(AD8) or HIVNL(AD8)ΔNef. At 1, 3, 5, 7, and 10 days post-infection cells were harvested, lysed and analyzed for endogenous LC3B, SQSTM1, and ACTB by Western blotting. Left, representative blots are shown. Right, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4."
NCBI gene IDs:
"Nef: 156110"
Figure legend: "(B) Macrophages were infected with HIVNL(AD8) or HIVNL(AD8)ΔNef. At 1, 3, 5, 7, and 10 days post-infection cells were harvested, lysed, fractionated for cytoplasmic and nuclear content, and analyzed for TFEB, ACTB and H3 histone by Western blotting. Left, representative blots are shown. Right, densitometric analysis of immunoblots from independent donors presented as means ± s.e.m., n = 4."
NCBI gene IDs:
"Nef: 156110"
Figure legend: "WB in Tg-APP total brain lysates on 4-12% NuPAGE SDS gel (Invitrogen) show total Abl (top blot) T412 Abl (2nd blot), soluble parkin level (3rd blot), and LC3 (4th blot) relative to MAP-2 (N = 9)."
NCBI gene IDs:
"APP: 351"
Figure legend: "Quantitative ELISA showing soluble (STEN extract) and insoluble (4 M urea extract) mouseparkin in Tg-APP (N = 9). Parkin−/−brains were used as a specificity control."
NCBI gene IDs:
"APP: 351
Parkin: 50873"
Figure legend: "In situ proximity ligation assay (PLA) shows endogenous parkin-Beclin-1 complexes in (G) WT C57BL/6mice (N = 5) and (H) parkin−/− as control.PLA in Tg-APPmice IP injected once daily for 3 weeks with (I) DMSO (J) 5 mg/kg Bosutinib and (K) 10 mg/kg Nilotinib (N = 5)."
NCBI gene IDs:
"APP: 351
parkin: 50873"
Figure legend: "Graph represents human Aβ1-42ELISA in rat B35 neuroblastoma cells transfected with human cDNA Aβ1-42 (or LacZ) or Beclin-1 shRNA for 24 hr, and then treated with 1 μM Bosutinib for an additional 24 hr (N = 12). *Significantly different to control or as indicated, Mean ± SEM, ANOVA with NeumannKeuls multiple comparison."
NCBI gene IDs:
"Aβ: 351
Beclin-1: 8678"
Figure legend: "Staining of 20 μm brain sections shows plaque formation with 6E10 antibody and DAB in the brain in different (A,B) Tg-APP + DMSO and (C) thioflavin-S staining in Tg-APP treated with DMSO (N = 7). (D,E) Tg-APP treated with 5 mg/kg Bosutinib for 3-weeks and (F) thioflavin-s staining."
NCBI gene IDs:
"APP: 351"
Figure legend: "Staining of 20 μm thick brain sections shows (G) parkin, (H) Aβ1-42 and (I) merged figure in cortex of Tg-APPmice after 3 weeks of DMSO treatment, and (J) parkin, (K) Aβ1-42 and (L) merged figure in cortex of Tg-APPmice after 3 weeks of 5 mg/kg Bosutinib treatment. (M) Parkin, (N) Aβ1-42 and (O) merged figure in hippocampus of Tg-APPmice after 3 weeks of DMSO treatment, and (P) parkin, (Q) Aβ1-42 and (R) merged figure in cortex of Tg-APPmice after 3 weeks of Bosutinib treatment (N = 7)."
NCBI gene IDs:
"APP: 351"
Figure legend: "(S) Graphs represent quantification of amyloidplaques in Tg-APP with and without Bosutinib."
NCBI gene IDs:
"APP: 351"
Figure legend: "WB in Tg-APP total brain lysates on 4-12% NuPAGE SDS gel (Invitrogen) showing (T) levels of BACE1 (1st blot), ADAM-10 (2nd blot) and presinilin-1 (3rd blot) relative to actin"
NCBI gene IDs:
"APP: 351"
Figure legend: "WB in Tg-APP total brain lysates on 4-12% NuPAGE SDS gel (Invitrogen) showing (U) total APP (top blot), CTFs (2nd blot) and phospho-tyrosine (3rd blot) relative to actin (N = 9)."
NCBI gene IDs:
"APP: 351"
Figure legend: "Graphs represent ELISA of human Aβ1-42 in (A) brain levels and (B) bloodAβ1-42 levels in 8-month old Tg-APPmice injected I.P. every other day for 6 weeks with Bosutinib or Nilotinib (N = 10)."
NCBI gene IDs:
"APP: 351"
Figure legend: "ELISA of human soluble and insoluble brain (C) Aβ1-42 and (D) Aβ1-40 levels in 8-month old Tg-APPmice injected IP daily for 3 weeks with 5 mg/kg Bosutinib (N = 9)."
NCBI gene IDs:
"APP: 351"
Figure legend: "ELISA of (E) mouse p-Tau levels in 8-month old Tg-APP mice injected IP daily for 3 weeks with 5 mg/kg Bosutinib (N = 9)."
NCBI gene IDs:
"APP: 351"
Figure legend: "WB in Tg-APP total brain lysates on 4-12% NuPAGE SDS gel (Invitrogen) show total Tau (1st blot), serine 396 p-Tau (2nd blot), threonine 231 (AT180, 3rd blot) and serine 199 p-Tau (AT8, 4th blot) relative to actin (N = 7)."
NCBI gene IDs:
"APP: 351"
Figure legend: "WB on 4-12% NuPAGE SDS gel of total brain lysates in 1 year old wild type and parkin−/−mice treated with 5 mg/kg Bosutinib for 3 weeks on 4-12% NuPAGE SDS gel (Invitrogen) showing parkin (1st blot)total Abl (2nd blot), T412 Abl (3rd blot), Beclin-1 (4th blot) and LC3 (5th blot) relative to actin (N = 7)."
NCBI gene IDs:
"parkin: 50873"
Figure legend: "Staining of 20μm brain sections shows plaque formation with 6E10 antibody and DAB 6 weeks post-injection with (G) lentiviralAβ1-42 + 3 weeks DMSO treatment and (H) IP injection with 5 mg/kg Bosutinib 3 weeks post-lentiviral expression (3 weeks treatment) clears plaques in WT mice (N = 7).(I) Lentiviral Aβ1-42 + DMSO and (J) IP injection with 5 mg/kg Bosutinib 3 weeks post-lentiviral expression (3 weeks treatment) in parkin−/−mice (N = 7)."
NCBI gene IDs:
"parkin: 50873"
Figure legend: "Graphs represent ELISA (N = 5) in autophagic vacuoles (AVs) in the brain of 4 and 8 months old Tg-APPmice treated with 10 mg/kg Nilotinib or 5 mg/kg Bosutinib (N = 5) for 3 weeks showing (A)humanAβ1-42 (Insert is WB analysis of AVs showing LC3-B in AV10 and AV20 (1st blot) and LAMP2a in Lys (2nd blot) fraction) and (B)Aβ1-40,(C) p-Tau and (D) parkin."
NCBI gene IDs:
"APP: 351"
Figure legend: "ELISA in autophagic vacuoles of 1 year old WT and parkin−/−mice (N = 5) injected with lentiviralAβ1-42 for 3 weeks and treated with 10 mg/kg Nilotinib and 5 mg/kg Bosutinib for 3 additional weeks showing (E) humanAβ1-42 and (F) p-Tau levels."
NCBI gene IDs:
"parkin: 50873"
Figure legend: "(A) Represents results of Morris water maze test in lentiviralAβ1-42-injected ± Bosutinib WT (N = 12) and parkin−/− (N = 10) mice, and (B) heat maps for each group.Graphs represent total number of entry into platform area and distance travelled."
NCBI gene IDs:
"Aβ: 351
parkin: 50873"
Figure legend: "Represents results of Morris water maze test in Tg-APP ± Bosutinib (N = 12) mice.Graphs represent total number of entry into platform area and distance travelled."
NCBI gene IDs:
"APP: 351"
Figure legend: "(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."
NCBI gene IDs:
"Gb3 synthase: 53947
Gb3S: 53947
CLN3: 1201
CLN7: 256471"