EMBO/SourceData huggingface dataset:
Figure 1A. Experimental demonstration. A1. Illustration of the mapping principle between ChR2-expressed PV neurons (green) and regular pyramidal neuron (Pyr, orange). A2. Acute slices were obtained and recorded at ZT0 or ZT12. A3. Coronal brain atlas showing the primary visual cortex (Top left panel, modified from MBL mouse brain atlas). Yellow box highlights the region of experiment. Top right panel, the reference image taken with a 10x objective from a slice prepared from a PV:Ai32 mouse. The 0.45 mm2 shaded cubic area was divided into 15 x 15 grids for independent light stimulation. The white arrowhead indicates the position of the recording electrode. Bottom panel, representative raw traces of light-evoked IPSCs (LEIPSCs) recorded from one pyramidal neuron. A4. The spatial distribution of the LEIPSCs from the example in A3. A5. The heatmap of the LEIPSCs in A4.B. The average heatmaps at ZT0 and ZT12 after soma alignment. Soma position was indicated by the blue arrow head. C. Comparison of the cumulative distribution (Kolmogorov-Smirnov test [K-S test]; P = 0.002) and the mean (Inset. ZT0: 813.3 ± 53.13 pA; ZT12: 1306 ± 93.73 pA; P < 0.0001; Mann-Whitney U test) of the max LEIPSC amplitude between ZT0 and ZT12. D. Comparison of the cumulative distribution (K-S test, P = 0.0016) and the mean (Inset. ZT0: 10.44 ± 1.44 nA; ZT12: 18.87 ± 1.44 nA; P < 0.0001; Mann-Whitney U test) of the sum LEIPSC amplitude between ZT0 and ZT12. Data information: Sample sizes used in this figure: ZT0: 48 cells from 9 mice; ZT12: 51 cells from 9 mice. Error bars in all figures indicate standard error of mean (s.e.m). The level of significance was set at P < 0.05. *P < 0.05; **P < 0.01; ***P < 0.001; ****P<0.0001.E. The average heatmaps of LEIPSCs after pia aligned to the reference image in A3. Dark and light blue overlay traces on the side of the map depicted the marginal distribution of the sum LEIPSCs for ZT0 (Dark blue) and ZT12 (Light blue). F. Comparison of the cumulative distribution (K-S test, P = 0.0021) and the mean (Inset, ZT0: 0.067 ± 0.004 mm2; ZT12: 0.089 ± 0.0036 mm2; P = 0.0003; Mann-Whitney U test) inhibitory input size between ZT0 and ZT12. Data information: Sample sizes used in this figure: ZT0: 48 cells from 9 mice; ZT12: 51 cells from 9 mice. Error bars in all figures indicate standard error of mean (s.e.m). The level of significance was set at P < 0.05. *P < 0.05; **P < 0.01; ***P < 0.001; ****P<0.0001.
Figure 2A. mEPSC frequency was higher at ZT12 than ZT0. Top: example traces of mEPSC recordings. Bottom left: mEPSC frequency (ZT0: 12.17 ± 0.94Hz; ZT12: 17.03 ± 1.20Hz; P = 0.0036; Mann-Whitney U test). Bottom right: cumulative probability histogram of the inter-event intervals (K-S test, P < 0.0001). B. mIPSC frequency was lower at ZT12 than ZT0. Top: example traces. Bottom left: mIPSC frequency (ZT0: 19.15 ± 0.99Hz; ZT12: 15.19 ± 0.63Hz; P = 0.0042; Mann-Whitney U test). Bottom right: cumulative probability histogram of the inter-event intervals of mIPSCs (K-S test, P < 0.0001). C. mEPSC amplitude and kinetics did not differ between ZT0 and ZT12. Top: average traces of the well-isolated events. Bottom left: mEPSC amplitude (ZT0: 20.51 ± 0.78pA; ZT12: 21.26 ± 0.75pA; P = 0.34; Mann-Whitney U test). Bottom right: The distribution of mEPSC amplitude of all events (K-S test, P < 0.01). D. mIPSC amplitude and kinetics did not differ between ZT0 and ZT12. Top: average traces of the well-isolated mIPSCs. Bottom left: mIPSC amplitude (ZT0: 41.31 ± 1.91pA; ZT12: 44.39 ± 1.31pA; P = 0.35; Mann-Whitney U test). Bottom right: The cumulative distribution of mIPSC amplitudes (K-S test, P < 0.0001 Data information: Sample size is indicated as (mice, cells). Error bars in all figures indicate standard error of mean (s.e.m). The level of significance was set at P < 0.05. *P < 0.05; **P < 0.01.
Figure 3B. Charges of sEPSCs recorded at light phase were higher compared to those at dark phase (ZT0: 4.21 ± 0.28 nC; ZT4: 7.05 ± 0.61 nC; ZT8: 7.74 ± 0.63 nC; ZT12: 7.81 ± 0.59 nC; ZT18: 5.25 ± 0.53 nC; One-way ANOVA, F(4,88) = 8.78, P <0.0001, Holm-Sidak post-hoc analysis). A copy of the 24-h sEPSCs was drawn with a dashed line to demonstrate the daily rhythm. C. Charges of sIPSCs oscillate during the light/dark cycle (ZT0: 45.73 ± 2.99 nC; ZT4: 28.85 ± 1.76 nC; ZT8: 28.25 ± 2.77 nC; ZT12: 28.04 ± 2.15 nC; ZT18: 43.37 ± 2.42 nC; One-way ANOVA, F(4,106) = 13.65, P <0.0001, Holm-Sidak post-hoc analysis). A copy of the 24-h sEPSCs was drawn with a dashed line to demonstrate the daily rhythm. Data information: Sample size is indicated as (mice, cells). Error bars in all figures indicate standard error of mean (s.e.m). The level of significance was set at P < 0.05. *P < 0.05; **P < 0.01; ***P < 0.001; ****P<0.0001.E. Dark exposure prevented the increase in sEPSCs that normally occurs at ZT12 (ZT12 as reported in B; Dark-ZT12: 5.46 ± 0.43 nC; P = 0.0082; Mann-Whitney U test). F. Dark exposure did not significantly affect the reduction of sIPSCs (ZT12 as reported in C; Dark-ZT12: 33.43 ± 1.74 nC; P = 0.07; Mann-Whitney U test). Data information: Sample size is indicated as (mice, cells). Error bars in all figures indicate standard error of mean (s.e.m). The level of significance was set at P < 0.05. *P < 0.05; **P < 0.01; ***P < 0.001; ****P<0.0001.H. Sleep deprivation further increased sEPSCs compared to ad lib sleep mice (ZT4 as reported in B; SD-ZT4: 11.22 ± 0.92 nC; P = 0.0013; Mann-Whitney U test). I. Sleep deprivation abolished the reduction of sIPSC (ZT4 as reported in C; SD-ZT4: 47.13 ± 3.39 nC; P < 0.0001; Mann-Whitney U test). Data information: Sample size is indicated as (mice, cells). Error bars in all figures indicate standard error of mean (s.e.m). The level of significance was set at P < 0.05. *P < 0.05; **P < 0.01; ***P < 0.001; ****P<0.0001.
Figure 4B-E. Slices were obtained at ZT12 (B-C) or ZT0 (D-E) and pre-incubated with 50 µM CARB for more than 1h before recording mIPSCs in the presence of drug. Slices from the same animals were used as controls. CARB increased mIPSC frequency at ZT12 (CTL: 7.74 ± 0.55 Hz; CARB: 12.41 ± 1.03 Hz; P = 0.0001; Mann-Whitney U test), but not ZT0 (CTL:11.79 ± 1.00 Hz; CARB: 11.47 ± 1.60 Hz; P = 0.39; Mann-Whitney U test). mIPSC amplitude was unchanged at either time (C, ZT12: CTL: 40.94 ± 2.08 pA; CARB: 40.64 ± 1.66 pA; P = 0.99; E, ZT0: CTL: 34.73 ± 2.14 pA; CARB: 33.61 ± 2.39 pA; P = 0.85; Mann-Whitney U test). Data information: Sample size is indicated as (mice, cells). Error bars in all figures indicate standard error of mean (s.e.m). The level of significance was set at P < 0.05. *P < 0.05; **P < 0.01; ***P < 0.001.F-G. mIPSC frequency (F, CTL: 9.82± 0.74 Hz; Atr: 7.70 ± 0.57 Hz; P = 0.0009; Wilcoxon signed-rank test) and amplitude (G, CTL: 45.88 ± 2.87 pA; Atr: 43.64 ± 2.40 pA; P = 0.70; Wilcoxon signed-rank test) recorded at ZT0 with acute atropine (Atr) wash on. Data information: Sample size is indicated as (mice, cells). Error bars in all figures indicate standard error of mean (s.e.m). The level of significance was set at P < 0.05. *P < 0.05; **P < 0.01; ***P < 0.001.H-I. Effect of acute wash-on and wash-off of pirenzepine (Pir) on mIPSC frequency (H, CTL: 9.00 ± 1.24 Hz; Pir: 7.94 ± 1.07 Hz; Washout: 8.99 ± 1.14 Hz; One-way repeated measures ANOVA, F(2, 20) = 7.483, P = 0.0037; Holm-Sidak's multiple comparison test) and amplitude (I, CTL: 61.23 ± 3.72 pA; Pir: 58.85 ± 4.06 pA; Washout: 58.25 ± 4.20 pA; One-way repeated measures ANOVA, F(2, 20) = 3.197, P = 0.0624). Data information: Sample size is indicated as (mice, cells). Error bars in all figures indicate standard error of mean (s.e.m). The level of significance was set at P < 0.05. *P < 0.05; **P < 0.01; ***P < 0.001.J-K. Effect of pirenzepine or mecamylamine (MEC) on carbachol-induced elevation in mIPSC frequency at ZT12 (J, CARB: 10.02 ± 0.64 Hz; CARB+MEC: 10.95 ± 0.78 Hz; CARB+Pir: 7.75 ± 0.79 Hz; One-way ANOVA, F(2, 25) = 4.848, P = 0.0166; Holm-Sidak's multiple comparison test) and amplitude (K, CARB: 39.85 ± 2.60 pA; CARB+MEC: 42.17 ± 1.65 pA; CARB+Pir: 40.67 ± 4.34 pA; One-way ANOVA, F(2, 25) = 0.1501, P = 0.8614). Data information: Sample size is indicated as (mice, cells). Error bars in all figures indicate standard error of mean (s.e.m). The level of significance was set at P < 0.05. *P < 0.05; **P < 0.01; ***P < 0.001.
Figure 5A1. Diagram illustrating the in vivo two-photon imaging timeline. A2. GCaMP6s (green) was expressed in V1 of the PV:Ai9 mice (red: td-Tomato). Scale: 500 µm. A3. Schematics of the calcium imaging showing a mouse that was head-fixed and free running on an air-suspended arena during the imaging section. Locomotor activity was simultaneously monitored (bottom left) along with Ca2+ imaging (Top right. Scale: 100 µm). Example spontaneous ΔF/F0 traces (bottom right).B. Top panel, Example spontaneous ΔF/F0 traces from three PV neurons repetitively imaged at ZT0 and ZT12. Bottom panels, Heatmaps showing the spontaneous ΔF/F0 time-series traces of all PV neurons imaged at ZT0 and ZT12. The color code represents the magnitude of ΔF/F0(%). C. Cumulative probability distribution of the sum ΔF/F0 of all PV neurons imaged at ZT0 and ZT12 (K-S test; P = 0.02). Inset: the mean sum ΔF/F0 (ZT0: 401.6 ± 19.55; ZT12: 559.1 ± 35.29; P = 0.0002; Mann-Whitney U test). D. Left panel, diagram depicting repetitive imaging protocol. Right panel, mean activity of PV neurons indicated by Z score imaged at four timepoints. Data information: Sample size is indicated as (mice, cells). Error bars in all figures indicate standard error of mean (s.e.m). The level of significance was set at P < 0.05. *P < 0.05; **P < 0.01; ***P < 0.001.
Figure 6B. Heatmaps showing the spontaneous ΔF/F0 time-series traces of all PV neurons imaged at ZT4 and SD_ZT4. The color code represents the magnitude of ΔF/F0 (%). C. Cumulative probability distribution of the sum ΔF/F0 of all PV neurons imaged at ZT4 and SD_ZT4 (K-S test; P = 0.0001). Inset: the mean sum ΔF/F0 (ZT4: 322.4 ± 18.64; SD_ZT4: 424.0 ± 21.54; P = 0.0004; Mann-Whitney U test). Data information: Sample size is indicated as (mice, cells). Error bars in all figures indicate standard error of mean (s.e.m). The level of significance was set at P < 0.05. *P < 0.05; **P < 0.01; ***P < 0.001.D. Heatmaps showing the spontaneous ΔF/F0 time-series traces of all PV neurons imaged at SD_ZT4 and Dark_SD. The color code represents the magnitude of ΔF/F0(%). E. Cumulative probability distribution of the sum ΔF/F0 of all PV neurons imaged at SD_ZT4 and Dark_SD (K-S test; P = 0.015). Inset: the mean sum ΔF/F0 (SD_ZT4: 375.1 ± 20.19; Dark_SD: 293.8 ± 16.55; P = 0.0022; Mann-Whitney U test). Data information: Sample size is indicated as (mice, cells). Error bars in all figures indicate standard error of mean (s.e.m). The level of significance was set at P < 0.05. *P < 0.05; **P < 0.01; ***P < 0.001.
Figure 7A. Top panel, Example spontaneous ΔF/F0 traces from three putative pyramidal neurons repetitively imaged at ZT0 and ZT12. Bottom panels, Heatmaps showing the spontaneous ΔF/F0 time-series traces of all putative pyramidal neurons imaged at ZT0 and ZT12. B. The cumulative distribution of the sum ΔF/F0 of putative pyramidal neurons judged by skewness (K-S test; P < 0.0001). Inset: the means of sum ΔF/F0 (ZT0: 679.5 ± 38.22; ZT12: 485.8 ± 32.22; P < 0.0001; Mann-Whitney U test). C. Mean activity of putative pyramidal neurons indicated by Z score imaged at four timepoints. Data information: Sample size is indicated as (mice, cells). Error bars in all figures indicate standard error of mean (s.e.m). The level of significance was set at P < 0.05. *P < 0.05; **P < 0.01; ***P < 0.001; ****P<0.0001.D1. Schematic showing in vivo dLGN-evoked Ca2+ reponses in V1. D2. Immunofluorescent staining showing the GCaMP6s (green) and ChR2-mCherry (red) expression in V1 and dLGN respectively. The optical fiber track was also labeled. (Scale: 500 µm). D3. Response profile of an example neurons for dLGN stimulation during the light/dark cycle. Horizontal blue brief lines represent stimulus frequency.E-F. Top: color-coded calcium signals of all responsive neurons (% ΔF/F0). Bottom: The mean Ca2+ response waveform for individual mouse (dotted color lines) and all mice (thick black and gray lines). Trials were aligned to LED onset time (gray solid lines). Data information: Sample size is indicated as (mice, cells).G. The fraction of neurons responsive to dLGN stimulus in ZT0 and ZT12. Each gray line represents one imaging mouse. Black and white circles and error bars represent the mean and SEM (ZT0: 8.51 ± 1.86; ZT12: 5.96 ± 1.39; P = 0.015; Wilcoxon signed-rank test; n = 9 mice). H. The Response fidelity of each cell in ZT0 and ZT12. Black and white circles and error bars represent the mean and SEM (ZT0: 0.42 ± 0.022; ZT12: 0.31 ± 0.023; P < 0.0001; Wilcoxon signed-rank test; n = 195 cell). I. Comparison of peak evoked response of each cell in ZT0 and ZT12. Black and white circles and error bars represent the mean and SEM (ZT0: 81.01 ± 4.79; ZT12: 48.42 ± 3.82; P < 0.0001; Wilcoxon signed-rank test; n = 195 cell). Data information: Sample size is indicated as (mice, cells). Error bars in all figures indicate standard error of mean (s.e.m). The level of significance was set at *P < 0.05
Figure 1Effects of DC and Beva treatment in 786-O orthoxenograft. Evaluation of tumor progression (average±SD) Box plots indicate median, Q1/Q3 and max/min value whiskers in Control (black), DC101 (red) and Beva (blue) treatment groups. 5-8 tumors/group were analyzed by Mann-Whitney test, and Mantel-Cox test for survival where *p < 0.05, **p < 0.01 and ***p < 0.001 and DC * p < 0.05 and Beva # p < 0.05 vs Control).Effects of DC and Beva treatment in 786-O orthoxenograft. Evaluation of (C) tumor weight at sacrifice, (D) vessel number, Box plots indicate median, Q1/Q3 and max/min value whiskers in Control (black), DC101 (red) and Beva (blue) treatment groups. 5-8 tumors/group were analyzed by Mann-Whitney test, and Mantel-Cox test for survival where *p < 0.05, **p < 0.01 and ***p < 0.001 and DC * p < 0.05 and Beva # p < 0.05 vs Control).Effects of DC and Beva treatment in 786-O orthoxenograft. Evaluation of percentage of necrotic area by histology, Box plots indicate median, Q1/Q3 and max/min value whiskers in Control (black), DC101 (red) and Beva (blue) treatment groups. 5-8 tumors/group were analyzed by Mann-Whitney test, and Mantel-Cox test for survival where *p < 0.05, **p < 0.01 and ***p < 0.001 and DC * p < 0.05 and Beva # p < 0.05 vs Control).Effects of DC and Beva treatment in 786-O orthoxenograft. Evaluation of survival by Kaplan Meier plot in control and treated animals. Box plots indicate median, Q1/Q3 and max/min value whiskers in Control (black), DC101 (red) and Beva (blue) treatment groups. 5-8 tumors/group were analyzed by Mann-Whitney test, and Mantel-Cox test for survival where *p < 0.05, **p < 0.01 and ***p < 0.001 and DC * p < 0.05 and Beva # p < 0.05 vs Control).G) Representative invasive front profile of 786-O control and short-term DC and Beva treated tumors in vimentin stained sections (4X). Front (red line) and rear (white line) edges of tumor protrusion into kidney determine the depth of invasion (green arrow) perpendicularly connecting red and white lines. Box plot shows the quantification of invasion indicating median, Q1/Q3 and max/min value whiskers of fold-invasion (∆ invasion) in treated vs control tumors (7 samples/group; *p < 0.05 by Mann-Whitney test).H) Evaluation of lung micrometastases in survival experiments. Incidence (pie chart, *p < 0.05 by Chi-square) and proportion of mice with 0, 1, 2 or > 3 metastases (mets) per lungs (*p < 0.05 by Mann-Whitney test) are shown.
Figure 2Overall mass architecture of paired human specimens and Ren-PDOX tumors observed by HE staining (20X). TNM staging and Fuhrman grade (F) of implanted tumors are reported. For Ren-PDOXs, lung micrometastases in HE and vimentin stained sections are shown (40X).Human to mouse stroma substitution. CD34/CD31 staining for respectively human (h) and mouse (m) blood vessels in original human specimens and paired Ren13 and 28-PDOX are shown (20X). Ren-PDOX OT referred to tumor generated from first implantation of human specimen in mice. Insets show human and mouse kidney as positive/negative controls of staining (20X).Frequency histogram of SNV and/or indels found in Ren-PDOX by high-throughput sequencing in Ren13, Ren28, Ren36, Ren86 (targeted-NGS analysis by Haloplex) and Ren50-PDOX (WES). Only non-synonymous/stop gain SNVs and frameshift indels novel or with MAF<0.01 are included.
Figure 3Effects of DC and Beva treatments on Ren13, Ren86, Ren28 and Ren50-PDOX. Evaluation of tumor progression average and SD in control (black) compared to DC (red, *p < 0.05) and Beva (blue, # p < 0.05) treatments from 5-13 animals per tumor and treatment group by Mann Whitney test. Effects of DC and Beva treatments on Ren13, Ren86, Ren28 and Ren50-PDOX. Quantification of tumor weight in control and treated tumors from 4-5 samples/tumor/treatment group by Mann Whitney test. Box plots indicate median, Q1/Q3 and max/min value whiskers.  Effects of DC and Beva treatments on Ren13, Ren86, Ren28 and Ren50-PDOX. Quantification of vessel number in control and treated tumors from 4-5 samples/tumor/treatment group by Mann Whitney test. Box plots indicate median, Q1/Q3 and max/min value whiskers.  Effects of DC and Beva treatments on Ren13, Ren86, Ren28 and Ren50-PDOX. Quantification of tumor necrosis in control and treated tumors from 4-5 samples/tumor/treatment group by Mann Whitney test. Box plots indicate median, Q1/Q3 and max/min value whiskers.  Effects of DC and Beva treatments on Ren13, Ren86, Ren28 and Ren50-PDOX. Evaluation of overall survival comparing Control (black), DC101 (red) and Beva (blue) treated mice from 4-13 mice/tumor/treatment group by Mantel-Cox test where *p < 0.05, **p < 0.01 and ***p < 0.001.
Figure 4Effects of DC and Beva treatment on Ren13, Ren86, Ren28 and Ren50-PDOX on capsular invasion Incidence of Capsular invasion (stripes) in each model and treatment. 5-8 animals per model and treatment group were analyzed by Chi-square test where *p < 0.05, **p < 0.01. C) Effects of DC and Beva treatment on Ren13, Ren86, Ren28 and Ren50-PDOX on tumor front of invasion Representative images of Vimentin staining (4X), as described in Figure 1, and box plot quantification of fold-invasion (∆ invasion) of treated vs control tumors indicating median, Q1/Q3 and max/min value whiskers. 6-12 animals per model and treatment group were analyzed by Mann-Whitney test where *p < 0.05, **p < 0.01. D) Effects of sunitinib treatment on Ren13BM and Ren28 on capsular invasion and tumor front invasion. Bar graphs show incidence of capsular invasion (stripes) in control and sunitinib treated tumors. 3-9 animals per model and treatment group were analyzed by Chi-square test where *p < 0.05, **p < 0.01. Box plots represent median, Q1/Q3 and max/min value whiskers of fold-invasion (∆ invasion) of sunitinib-treated vs control tumors. 5-8 animals per model and treatment group were analyzed by Mann-Whitney test. *p < 0.05, **p < 0.01.
Figure 5Evaluation of lung micrometastases using HE and vimentin-stained lung sections upon antiangiogenic therapies in Ren13BM Representative images of lung metastasis in Ren13BM upon antiangiogenic therapies. Evaluation of lung micrometastases using HE and vimentin-stained lung sections upon antiangiogenic therapies in Ren13BM and Ren28. proportion of mice with 0, 1, 2 or > 3 metastases (mets) per lungs (*p < 0.05 by Mann-Whitney test) are shown.
Figure 6Tumor specific (human) enriched gene sets in Ren13 and Ren50 Ren-PDOX tumors, after GSEA analysis from RNAseq data. Gene sets most significantly enriched in Ren13 or Ren50 are indicated in the table (left), including their normalized enrichment score (NES), p-value and false discovery rate (FDR q-value). Heatmaps illustrate expression levels of the genes responsible for the enrichment of KRAS signaling up and down in Ren13 and Ren50, respectively (right).Validation of candidate gene expression in unique series of 39 RCC patients (GSE29609), where microvascular invasion (MVI) and renal vein involvement (RV) are specifically annotated. Progressive invasion relates to the three progressive degrees of invasion toward the vena cava in this series: 1st, no invasion; 2nd, microvascular invasion; and 3rd, renal vein involvement. The gene expression is shown for each variable and condition in box plots representing median, Q1/Q3 and max/min value whiskers, *p < 0.05 **p < 0.01 by Mann-Whitney test.
Figure 7 Representative images of ALDH1A3 expression on pro-invasive (Ren13 and Ren86) and non-pro-invasive (Ren28 and Ren50) tumors. Confirmation of ALDH1A3 mRNA levels of gene expression in pro-invasive (Ren13 and Ren86) and non-pro-invasive (Ren28 and Ren50) tumors. Average ± SD of 4-6 independent replicates per group were analyzed by Mann-Whitney test *p < 0.05 **p < 0.01.Association of pre-treatment ALDH1A3 protein levels by IHC on a series of Ren-PDOX models treated with sunitinib. (C) Representation of ALDH1A3 expression on pro-invasive and non-pro-invasive Ren-PDOX after suntinib treatment (**p < 0.01 by Chi-Square test). D) Association of pre-treatment ALDH1A3 protein levels by IHC on a series of Ren-PDOX models treated with sunitinib. (D) Correlation of pre-treatment ALDH1A3 protein levels by IHC with increased tumor invasion found after sunitinib treatment. n=7, Spearman's non-parametric correlation, p=0.0095. F) Representation of ALDH1A3 score (0=absent, 1=low, 2=high expression) on pre-treatment samples of pro-aggressive and non-pro-aggressive ccRCC patients described above. n=15, Chi-square test for independence p=0.015, and Chi-square test for trend p=0.030 (*).
Figure 1(A) Quantification of the amount of LC3‐II protein in mouse Rab‐knockdown cells. Representative blots are shown in supplementary Fig S1C online. Error bars represent the means and s.e.m. of three independent experiments.(B) Quantification of the amount of p62 protein in candidates Rab‐knockdown cells. Representative blots are shown in supplementary Fig S1D online. Error bars represent the means and s.e.m. of three independent experiments.(C,D) Control and Rab12‐knockdown MEFs were cultured under N or S conditions, fixed and then immunostained with the antibodies indicated. Representative images are shown in supplementary Fig S2 online. The mean numbers of LC3‐positive (C) or Atg16L1‐positive (D) dots per cell are shown. Error bars represent the means and s.e.m. of representative data (n≥80) from three independent experiments.(E) MEFs that had been transfected with the control siRNA or Rab12 siRNA were cultured as in (C,D), and their lysates were analysed by immunoblotting with the antibodies indicated.(F) Quantification of (E).(G) Control and Rab12‐knockdown MEFs were cultured under N or S conditions in the absence or presence of 100 μM bafilomycin A1 for 1 h. Cell lysates were analysed by immunoblotting with the antibodies indicated, and the intensity of the LC3‐II band was quantified. The normalized amount (arbitrary units) of LC3‐II in lanes 1, 2, 3, 4, 5 and 6 is 1.0, 2.3, 4.3, 0.9, 1.6 and 3.8, respectively.(H) MEFs transiently expressing mStr‐Rab12 were cultured under starved conditions and immunostained with the antibodies indicated. Scale bar, 20 μm. MEFs, mouse embryonic fibroblasts; N, nutrient‐rich; S, starved; siRNA, short interfering RNA. *P0.05; **P0.01; ***P0.005.
Figure 2(A) Control and Rab12‐knockdown MEFs were cultured under nutrient‐rich or starved conditions, fixed and then immunostained with the antibodies indicated. Scale bar, 20 μm.(B) Control and Rab12‐knockdown MEFs were cultured as in (A), and their lysates were analysed by immunoblotting with the antibodies indicated.(C) Lysates of MEFs that had been transfected with control or Rab12 siRNA were analysed by immunoblotting with the antibodies indicated.(D,E) Quantification of the phospho‐S6K levels and phospho‐Akt levels shown in (C). MEFs, mouse embryonic fibroblasts; N, nutrient‐rich; S, starved; siRNA, short interfering RNA. *P0.05; **P0.01.