Journal: Cellular & Molecular Biology Letters

Article Title: Impairment of α-tubulin and F-actin interactions of GJB3 induces aneuploidy in urothelial cells and promotes bladder cancer cell invasion

doi: 10.1186/s11658-024-00609-2

Figure Lengend Snippet: GJB3 controls ploidy in Y235T cells. A The presented bar graph illustrates the GJB3 mRNA amounts across various human tissues, with detailed information available in the Materials and Methods section. Urothelial cells (UC#1 and UC#2) were isolated from ureters from two separate patients who underwent nephrectomy at Ulm University. The mRNA levels were normalized to GAPDH . n = 3 independent experiments were performed. Error bars represent mean ± SEM. B The representative pictures display the HE, GJB3 and IgG staining in human ureter tissues (U#1 and U#2, respectively). C The representative Western blot result indicates GJB3 protein levels in Y235T cells with shGJB3. α-tubulin is used as a loading control. n = 3 independent experiments were performed. D The bar graphs depict the effectiveness of GJB3 knockdowns at the mRNA level in Y235T cells, with the measurements reference to the GAPDH mRNA level. n = 3 independent experiments were performed. Error bars represent mean ± SEM. E Representative pictures showing metaphase spreads of Y235T cells with shControl and shGJB3#2. Chromosomes are visualized by 4',6-diamidino-2-phenylindole (DAPI) staining. Control cells showing 46 chromosomes in most metaphase spreads. Exemplary pictures demonstrating the induction of aneuploidy in Y235T cells subsequent to GJB3 knockdown. The images show a metaphase spread of Y235T-shGJB3#2 cells with 51 chromosomes. F Chromosomes numbers of metaphase spreads from Y235T cells that were knockdown GJB3. n = numbers of (Each counting is indicated within the graph). Results are pooled from three independent sets of experiments. Mean ± SEM values are shown in the dot plot, and significance was determined by using Fisher’s exact test. G Representative pictures showing micronuclei of Y235T cells with shGJB3#1. Cell nuclei are stained with DAPI, and phalloidin Alexa Fluor 488 was used for F-actin visualization. White arrows indicate micronuclei. H Quantitation of cells with micronuclei upon knockdown of GJB3. Results from n = 3 separate series of experiments. The bar graph displays the mean ± SEM values, and the two-tailed Student's t-test was used to assess the significance. I Immunofluorescence results indicate the multinucleation of Y235T shGJB3#1 cell. Cell nuclei is visualized by DAPI, and F-actin is visualized by Alexa Fluor 488. J Quantitation of cells with multinucleation with knockdown of GJB3. Results from n = 3 independent sets of experiments. Mean ± SEM values are shown in the bar graph, and the significance was determined by two-tailed Student’s t -test. K Figures depict of mitotic abnormalities in metaphase and anaphase. DAPI (blue) indicates chromosomes, Cy5 (red) indicates α-tubulin, and Alexa Fluor 488 (green) labeling illustrates γ-tubulin. White arrows are used to indicate chromatid mislocation or multipolar centrosomes. L – M Quantitative evaluation of mitotic abnormalities. Results from n = 3 distinct experiments. The bar graph displays mean ± SEM data, and a two-tailed Student’s t -test was used to assess significance. Scale bars: 200 μm ( B main panels) 50 μm ( B insets) 20 μm ( E , G , I ) and 2 μm ( K ). Images are shot at total magnification of 100x ( B main panels), 630x ( B insets, E , G , I , K )

Article Snippet: The following primary antibodies were utilized: Anti-GJB3 rabbit antibody (1:2000 for Western blot (WB) and 1:200 for immunofluorescence (IF), ab236620, Abcam, Cambridge, UK); Anti-GJB3 mouse antibody (1:500 for WB and 1:200 for IHC on mouse samples; 1:400 for immunohistochemistry (IHC) on human samples, sc-81803, Santa Cruz, California, USA); Anti-Flag rabbit antibody (1:2000 for WB, F7425, Sigma-Aldrich, St. Louis, USA); Anti-α-tubulin mouse antibody (1:2000 for WB and 1:500 for IF, T5168, Sigma-Aldrich, St. Louis, USA); Anti-Cortactin mouse antibody (1:500 for IF, #H5, Santa Cruz, California, USA); Anti-γ-tubulin mouse antibody (1:2000 for WB and 1:500 for IF, T5192, Sigma-Aldrich, St. Louis, USA); Anti-β-actin mouse antibody (1:10,000 for WB, A1978, Sigma-Aldrich, St. Louis, USA).

Techniques: Isolation, Staining, Western Blot, Control, Knockdown, Quantitation Assay, Two Tailed Test, Immunofluorescence, Labeling

Journal: Cellular & Molecular Biology Letters

Article Title: Impairment of α-tubulin and F-actin interactions of GJB3 induces aneuploidy in urothelial cells and promotes bladder cancer cell invasion

doi: 10.1186/s11658-024-00609-2

Figure Lengend Snippet: GJB3 controls spindle orientation and microtubule dynamics. A Exemplary pictures illustrating the disorientation of Y235T-shGJB3#1 cells. The chromosomes are indicated by DAPI, γ-tubulin is visualized by Alexa Fluor 488, and α-tubulin is visualized by Cy5. B Quantitative assessment of the spindle pole displacement factor (SPDF) in Y235T cells. n = 256 (Y235T-shScr), 253 (Y235T-shGJB3#1), 263 (Y235T-shGJB3#2), C , Representative images showing reorientation of UMUC3 cells with ectopic GJB3. The chromosomes are indicated by DAPI, γ-tubulin is visualized by Alexa Fluor 488, and α-tubulin is visualized by Cy5. D Quantitative assessment of the spindle pole displacement factor (SPDF) in UMUC3 cells. n = 155 (UMUC3-EV), and 140 (UMUC3-GJB3). Experiments present combined data from three separate sets of independent experiments. The two-tailed Student’s t -test was used to evaluate significance, and the mean ± SEM data are displayed in the dot plot. To boost the proportion of prometaphase cells, cells were treated to dimerthylenastron for four hours prior to labeling. E Examples of images demonstrating microtubule growth in Y235T cells expressing shGJB3#2. F Rates of mitotic microtubule plus-end assembly in Y235T-shGJB3 cells. n = 60 cells are pooled from three independent sets of experiments. G Example of images demonstrating growth of microtubules in UMUC3-GJB3 cells. H Rates of mitotic microtubule plus-end assembly in UMUC3-GJB3 cells. n = 60 cells are combined from three separate sets of experiments. The two-tailed Student’s t -test was used to evaluate significance, and the mean ± SEM data are displayed in the dot plot. GJB3 interacts with α-tubulin. The deletion of GJB3 in UROtsa cells using the CRISPR-cas9 method was detailed in the main article. I Western blot displaying GJB3 protein levels in UROtsa cells with a control guide RNAs directed against green flourescent protein or two distinct gRNAs targeting GJB3 (gGJB3#1 and GJB3#2). α-tubulin serves as loading control. n = 3 separate experiments were conducted. J Exemplary pictures displaying GJB3 and α-tubulin colocalization in UROtsa cells during metaphase. GJB3 is visualized by Alexa Fluor 488 and α-tubulin is visualized by Cy5. Yellow signal indicates the overlap of GJB3 and α-tubulin. K Quantitation of GJB3 and α-tubulin colocalization in UROtsa cells by Pearson’s correlation coefficient. n = 49 (UROtsa-gControl), 58 (UROtsa-gGJB3#1), 53(UROtsa-gGJB3#2) are pooled from three to four independent experiments. L GJB3 protein level in UMUC3 cells with ectopic GJB3 was detected by Western blot. α-tubulin is used as a loading control. n = 3 independent experiments were performed. M Representative images displaying the colocalization of GJB3 and α-tubulin in UMUC3 cells during metaphase. GJB3 is visualized by Alexa Fluor 488 and α-tubulin is visualized by Cy5. Yellow signal indicates the overlap of GJB3 and α-tubulin. N Quantitation of GJB3 and α-tubulin colocalization in UMUC3 cells by Pearson’s correlation coefficient. n = 105 (UMUC3-EV), and 64 (UMUC3-GJB3) are pooled from three to four independent experiments. Mean ± SEM values are shown in the bar graph, and significance was determined by two-tailed Student’s t-test ( M , N ). O – P GJB3 bundle microtubule (MT) filament level was detected by Western blot. 5 × 10 11 MT/ml and 5–10 μm in length MTs were incubated with increasing concentrations of GJB3 (relative GJB3 amount is indicated by + or + +). Supernatant (S) and pellet (P) were subjected to 10% SDS-PAGE after high-speed centrifugation at 100,000 g . ( O ), Flag-GJB3, indicated by red arrowheads and ( P ), microtubules, indicated by red arrows, are visualized by specific antibodies. n = 3 independent experiments were performed. Scale bars: 5 μm ( A , C) and 1 μm ( E , G) and 2 μm ( J , M ). Images were captured at total magnification of 630x

Article Snippet: The following primary antibodies were utilized: Anti-GJB3 rabbit antibody (1:2000 for Western blot (WB) and 1:200 for immunofluorescence (IF), ab236620, Abcam, Cambridge, UK); Anti-GJB3 mouse antibody (1:500 for WB and 1:200 for IHC on mouse samples; 1:400 for immunohistochemistry (IHC) on human samples, sc-81803, Santa Cruz, California, USA); Anti-Flag rabbit antibody (1:2000 for WB, F7425, Sigma-Aldrich, St. Louis, USA); Anti-α-tubulin mouse antibody (1:2000 for WB and 1:500 for IF, T5168, Sigma-Aldrich, St. Louis, USA); Anti-Cortactin mouse antibody (1:500 for IF, #H5, Santa Cruz, California, USA); Anti-γ-tubulin mouse antibody (1:2000 for WB and 1:500 for IF, T5192, Sigma-Aldrich, St. Louis, USA); Anti-β-actin mouse antibody (1:10,000 for WB, A1978, Sigma-Aldrich, St. Louis, USA).

Techniques: Two Tailed Test, Labeling, Expressing, CRISPR, Western Blot, Control, Quantitation Assay, Incubation, SDS Page, Centrifugation

Journal: Cellular & Molecular Biology Letters

Article Title: Impairment of α-tubulin and F-actin interactions of GJB3 induces aneuploidy in urothelial cells and promotes bladder cancer cell invasion

doi: 10.1186/s11658-024-00609-2

Figure Lengend Snippet: GJB3 as tumor suppressors in bladder cancer. A–B ( A ) RT-qPCR was used to measure the GJB3 mRNA expression , and ( B ) Western blot was employed to ascertain protein amounts. The relative mRNA expression was quantified with respect to GAPDH . The qPCR shows results of n = 4 technical repeats. Error bars represent Mean ± SEM. α-tubulin serves as loading control in Western blot. n = 3 independent experiments were performed. C Comparison of GJB3 mRNA levels in the CNUH (GSE13507) cohort of NMIBC ( n = 103) and MIBC ( n = 62) human bladder tumors. Statistical differences were defined by two-way Fisher’s ANOVA test * = p ≤ 0.05. D The IHC images represent the GJB3 staining (red arrows) in human normal bladder and bladder cancer tissues. E Quantitation of GJB3-IHC staining scores in human normal bladder and bladder cancer groups. F The IHC images display Gjb3 staining (red arrows) in mouse normal bladder and bladder cancer tissues during BBN-induced BC progression. G Quantitation of Gjb3-IHC staining scores in normal bladder and bladder cancer tissues during the BBN-induced BC progression in mice. The expression of Gjb3 gradually diminished after the BBN treatment, in contrast to the control mice (black dots), which were given water (orange dots). The bar graph displays mean ± SEM data, and a two-tailed Student's t-test was used to assess significance. Scale bars: 200 μm ( D and F , main panels) and 50 μm ( D and F insets). Images were captured at total magnification of 100 × ( D and F main panels), and 630 × ( D and F insets)

Article Snippet: The following primary antibodies were utilized: Anti-GJB3 rabbit antibody (1:2000 for Western blot (WB) and 1:200 for immunofluorescence (IF), ab236620, Abcam, Cambridge, UK); Anti-GJB3 mouse antibody (1:500 for WB and 1:200 for IHC on mouse samples; 1:400 for immunohistochemistry (IHC) on human samples, sc-81803, Santa Cruz, California, USA); Anti-Flag rabbit antibody (1:2000 for WB, F7425, Sigma-Aldrich, St. Louis, USA); Anti-α-tubulin mouse antibody (1:2000 for WB and 1:500 for IF, T5168, Sigma-Aldrich, St. Louis, USA); Anti-Cortactin mouse antibody (1:500 for IF, #H5, Santa Cruz, California, USA); Anti-γ-tubulin mouse antibody (1:2000 for WB and 1:500 for IF, T5192, Sigma-Aldrich, St. Louis, USA); Anti-β-actin mouse antibody (1:10,000 for WB, A1978, Sigma-Aldrich, St. Louis, USA).

Techniques: Quantitative RT-PCR, Expressing, Western Blot, Control, Comparison, Staining, Quantitation Assay, Immunohistochemistry, Two Tailed Test

Journal: Cellular & Molecular Biology Letters

Article Title: Impairment of α-tubulin and F-actin interactions of GJB3 induces aneuploidy in urothelial cells and promotes bladder cancer cell invasion

doi: 10.1186/s11658-024-00609-2

Figure Lengend Snippet: GJB3 inhibits cells invasion and migration. A – B Western blots displaying the GJB3 protein quantity assessments in RT4 and in UMUC3 cells with experimental modifications. The loading control was provided by α-tubulin levels. The Western blots were repeated for three times. C Cell migratory capacity in RT4 cell line with shGJB3#1 was detected by Wound healing/scratch. The exemplary imaged were captured at 24 and 120 h. D Normalized cell free area was used to quantify the impact of GJB3 knockdown on RT4 cells by Wound healing assay. n = 3 distinct experiments. The bar graphs display mean ± SEM values, and a two-tailed Student's t-test was used to assess significance. E Cell migratory capacity in UMUC3 cell line with ectopic GJB3 was detected by Wound healing/scratch. The representative pictures captured at 12 and 24 h in case of UMUC3 cells. F Quantitation of normalized cell free area of UMUC3 cells with ectopic GJB3 performed by Wound healing assay n = 3 distinct experiments. The bar graphs display mean ± SEM values, and a two-tailed Student’s t -test was used to assess significance. G The invasion capacity of RT4 cell line with shGJB3#1 was detected by Boyden chamber. The exemplary images depict cell invasion through the Boyden chamber, stained at 144 h post-seeding. H Quantitation of invasive capacity of RT4 cells expressing the indicated shRNAs targeting GJB3. n = 3 distinct experiments. The bar graphs display mean ± SEM values, and a two-tailed Student’s t -test was used to assess significance. I The invasion capacity of UMUC3 cell line with ectopic of GJB3 was detected by Boyden chamber. The exemplary images depict cell invasion through the Boyden chamber, stained at 48 h post-seeding. J, Quantitation of invasive capacity of UMUC3 cells with ectopic GJB3 expression. n = 3 distinct experiments. The bar graphs display mean ± SEM values, and a two-tailed Student's t-test was used to assess significance. K Representative images of hematoxylin/eosin stainings showing the invasion capacity of RT4 cell line with shGJB3#2 by porcine bladder ex vivo organ culture method (the invasive capacity of BC cells in the ex vivo organ culture model was quantified as shown in Fig. S4). The cells were seeded on the surface of the de-epithelized porcine bladder for 21 days. L Quantitation graphs displaying the impact of GJB3 alteration on the invasive capacity of RT4 cells in ex vivo organ culture approach. n = 4 (RT4-shScr), n = 3 (RT4-shGJB3#1), n = 3 (RT4-shGJB3#2) M Representative images of hematoxylin/eosin stainings showing the invasion capacity of UMUC3 cell line with ectopic GJB3 by porcine bladder ex vivo organ culture approach. The cells were seeded on the surface of the de-epithelized porcine bladder for or 14 days. Insets: enlarged images of the areas shown by black boxes. Black arrows indicate the cells that have spread the farthest from the surface. n = 3 (UMUC3-EV), n = 4 (UMUC3-GJB3) independent experiments were performed. Mean ± SEM values are shown in the bar graph, and significance was determined by two-tailed Student’s t -test. Scale bars: 200 μm ( C , E , G , I , K main panels, M main panels) and 100 μm ( K insets, M insets). Images were captured at total magnification of 50 × ( C , E ), 100 × ( G , I , K main panels, M main panels), and 200 × ( K insets, M insets). O - V Morphological changes and actin-enriched protrusions in UMUC3, and RT4 cells with altered GJB3 expression. Cells with actin-enriched protrusions are marked with white arrows. O - P Brightfield microscopy images depict cells exhibiting a transition towards a round morphology ( O ) of UMUC3 cells with ectopic GJB3 expression. P RT4 cells with GJB3 knockdown demonstrate an elongated shape. Magnifications indicate 100 × or 400 × , respectively. The scale bars refer to 100 μm (left), and 50 µm (right). Q - T Quantification of round or elongated morphology on fixed cells. A cell with elongated or round morphology is identified by the ratio of longest and shortest diameter of the cell from images captured randomly at 630 × magnification using a Zeiss TCS SP5 confocal microscope. Scale bars: 20 μm. The ratio is calculated as the longest diameter of the cell dividing by the shortest diameter of the cell. The ratio is calculated as longest diameter dividing by shortest diameter. A cells with Ratio ≤ 2 is identified as round morphology, while ratio > 2 is elongated morphology. Q , R Immunofluorescence staining photos illustrate the round morphology shifting of ( Q ) UMUC3 cells with GJB3 overexpression compared to cells transfected with empty vector (EV). R RT4 cells with GJB3 knockdown display a transition towards an elongated morphology compared to cells transfected with shScramble (shScr). Cell nuclei are stained with DAPI, and F-actin is labeled with Phalloidin-AF488. S , T The bar graphs reveals percentages of cells with different morphology in total in each group, shown above in Q and R . The percentage was calculated as number of cells with elongated (or rounded) morphology divide cell numbers in total. The percentage values in different groups are marked above or in the bars. Black bars indicate percentages of cells with elongated morphology, and gray bars indicate the percentage of cells with rounded morphology. The statistical significance is calculated by using chi-square statistic. U , V The graphs show the fraction of cells with actin-enriched protrusions in response to GJB3 alterations ( U ) in RT4 or ( V ) in UMUC3 cells. For each picture, the percentage of cells with actin-enriched protrusions is calculated by the number of the cells with actin-enriched protrusions divided by total number of cells. (n) indicates the number of pictures taken in the group

Article Snippet: The following primary antibodies were utilized: Anti-GJB3 rabbit antibody (1:2000 for Western blot (WB) and 1:200 for immunofluorescence (IF), ab236620, Abcam, Cambridge, UK); Anti-GJB3 mouse antibody (1:500 for WB and 1:200 for IHC on mouse samples; 1:400 for immunohistochemistry (IHC) on human samples, sc-81803, Santa Cruz, California, USA); Anti-Flag rabbit antibody (1:2000 for WB, F7425, Sigma-Aldrich, St. Louis, USA); Anti-α-tubulin mouse antibody (1:2000 for WB and 1:500 for IF, T5168, Sigma-Aldrich, St. Louis, USA); Anti-Cortactin mouse antibody (1:500 for IF, #H5, Santa Cruz, California, USA); Anti-γ-tubulin mouse antibody (1:2000 for WB and 1:500 for IF, T5192, Sigma-Aldrich, St. Louis, USA); Anti-β-actin mouse antibody (1:10,000 for WB, A1978, Sigma-Aldrich, St. Louis, USA).

Techniques: Migration, Western Blot, Control, Knockdown, Wound Healing Assay, Two Tailed Test, Quantitation Assay, Staining, Expressing, Ex Vivo, Organ Culture, Microscopy, Immunofluorescence, Over Expression, Transfection, Plasmid Preparation, Labeling

Journal: Cellular & Molecular Biology Letters

Article Title: Impairment of α-tubulin and F-actin interactions of GJB3 induces aneuploidy in urothelial cells and promotes bladder cancer cell invasion

doi: 10.1186/s11658-024-00609-2

Figure Lengend Snippet: GJB3 interactics with F-actin and influences invadopodia formation via actin dynamics. A Representative images demonstrating invadopodia formation of RT4 cells with shGJB3#2. B Quantitation of the invadopodia number was performed in RT4 cells. n = 959 (RT4-shScr), n = 718 (RT4-shGJB3#1), n = 481 (RT4-shGJB3#2). Cells are pooled from three independent sets of experiments. C, Representative pictures showing invadopodia formation of UMUC3 cells upon ectopic GJB3 expression. D Quantitation of the invadopodia number was performed in UMUC3 cells. n = 110 (UMUC3-EV), n = 137 (UMUC3-GJB3). Cells are pooled from three independent sets of experiments. F-actin is visualized by Alexa Fluor 488-phalloidin and Cortactin is visualized by Cy5, respectively. Yellow spots displaying cortactin and F-actin colocalization identify the invadopodia structures. The regions indicated by white boxes are magnified in the insets. The invadopodia are marked with white arrows. The dot plot displays the mean ± SEM data, and the two-tailed Student's t-test was used to assess significance. E Representative pictures indicate the gelatin degradation by RT4 cells upon GJB3 knockdown. F Gelatin degradation capacity of the cells was quantified by measuring the degradation area per RT4 cell. n = 2809 (RT4-shScr), n = 2447 (RT4-shGJB3#1), n = 3544 (RT4-shGJB3#2). G Representative pictures indicate the gelatin degradation by UMUC3-GJB3 cells. H Gelatin degradation capacity of the cells was quantified by measuring the degradation area per UMUC3 cell. n = 1048 (UMUC3-EV), and n = 1246 (UMUC3-GJB3) are pooled from three to four independent experiments. The dot plot displays the mean ± SEM data, and the two-tailed Student's t-test was used to assess significance. I The LifeAct–Ruby signal recovery duration in UMUC3 cells with or without GJB3 is depicted in representative images after LifeAct–Ruby signal bleaching. The white arrows indicate the areas of bleaching. J , The quantitation of bleaching recovery experiments with UMUC3 cells. n = 29 (UMUC3-EV), n = 31 (UMUC3-GJB3). Three different groups of separate experiments' cells are combined. The graphs' data points correspond to the mean ± SEM. P values were calculated using the two-tailed Student's t -test at t = 49 s. K Exemplary pictures displaying the colocalization of GJB3 with F-actin in control UROtsa cells. Insets: enlarged image of the areas shown by white box. L , Quantitation of GJB3 and F-actin colocalization in UROtsa by Pearson’s correlation coefficient. n = 161 (UROtsa-gControl), n = 206 (UROtsa-gGJB3#1), n = 276 (UROtsa-gGJB3#2). M Exemplary pictures displaying the GJB3/F-actin colocalization in UMUC3-GJB3 cells. Insets: enlarged image of the areas shown by white box. N Quantitation of GJB3 and F-actin colocalization in UMUC3 cells by Pearson’s correlation coefficient. n = 672 (UMUC3-EV), and n = 831 (UMUC3-GJB3) are combined from 3 separate experiments. The two-tailed Student's t-test was used to establish significance, and the bar graph displays mean ± SEM results. Alexa Fluor 647 illustrates the F-actin, and Alexa Fluor 488 illustrates GJB3. Yellow highlights denote GJB3 and F-actin overlap. Insets: enlarged images of the colocalized areas shown by white boxes. O , P GJB3 binds bundle actin filaments in a dose-dependent manner by Western blot. Actin (2.5 mg/ml) concentrations of GJB3 (relative GJB3 amount is indicated by + or + +). Supernatant (S) and pellet (P) were subjected to 10% SDS-PAGE after high-speed centrifugation at 100,000 g . Red arrowheads indicate the GJB3, and the red arrow indicates actin filaments visualized by western blot with specific antibodies. n = 3 independent experiments were performed. Scale bars: 10 μm ( A , C , E , G , K and M main panels), 1 μm ( A , C insets), 2 μm ( E , G , K and M insets) and 1 μm ( I ). Images were captured at total magnification of 630 × ( A , C , I , K , M ) and 400 × ( E , G )

Article Snippet: The following primary antibodies were utilized: Anti-GJB3 rabbit antibody (1:2000 for Western blot (WB) and 1:200 for immunofluorescence (IF), ab236620, Abcam, Cambridge, UK); Anti-GJB3 mouse antibody (1:500 for WB and 1:200 for IHC on mouse samples; 1:400 for immunohistochemistry (IHC) on human samples, sc-81803, Santa Cruz, California, USA); Anti-Flag rabbit antibody (1:2000 for WB, F7425, Sigma-Aldrich, St. Louis, USA); Anti-α-tubulin mouse antibody (1:2000 for WB and 1:500 for IF, T5168, Sigma-Aldrich, St. Louis, USA); Anti-Cortactin mouse antibody (1:500 for IF, #H5, Santa Cruz, California, USA); Anti-γ-tubulin mouse antibody (1:2000 for WB and 1:500 for IF, T5192, Sigma-Aldrich, St. Louis, USA); Anti-β-actin mouse antibody (1:10,000 for WB, A1978, Sigma-Aldrich, St. Louis, USA).

Techniques: Quantitation Assay, Expressing, Two Tailed Test, Knockdown, Control, Western Blot, SDS Page, Centrifugation

Journal: Nature Neuroscience

Article Title: Neuronal activity rapidly reprograms dendritic translation via eIF4G2:uORF binding

doi: 10.1038/s41593-024-01615-5

Figure Lengend Snippet: a , Immunofluorescence (IF) images of primary cortical neurons immunostained for glial fibrillary acidic protein (GFAP) and oligodendrocyte transcription factor 2 (OLIG2) simultaneously with PSD95 to show that the cultures are devoid of glial cells or oligodendrocytes, respectively. DAPI for nuclei; PSD95 for excitatory neurons. Magnification, ×40. Scale bars, 50 μm. b , TurboID-PSD95 was cloned without (top row) and with (bottom row) its 5′ and 3′ UTRs and lentivirally expressed in primary cortical neurons. White dashed boxes are zoomed in areas in black&white images. DAPI for nuclei; MAP2 for dendrites; Flag for each TurboID. % dendritically localized TurboID-PSD95 is quantified by co-localization with MAP2 signal in ImageJ. 3 different areas of images per replicate ( n = 3). Magnification, ×20. Scale bars, 50 μm. Significance was derived from biological replicates, showing the center line at mean. c , IF images of TurboID-PSD95-transduced neurons immunostained for DAPI (blue, for nuclei), PSD95 (red, for endogenous PSD95) and TurboID-PSD95 (cyan, detected by Flag). Magnification, ×60. Scale bar, 50 μm. d , IF images show the expression of a presynaptic marker, Synaptophysin (cyan), and TurboID-PSD95 (red, detected by Flag antibody) in primary cortical neurons transduced with TurboID-PSD95. DAPI (blue) marker for nuclei. Three zoomed in regions are marked by the white boxes. Magnification, ×60. Scale bar, 10 μm. e , IF images show TurboID expression and biotinylation in primary cortical neurons transduced with TurboID-PSD95 or Pan-TurboID after 30 minutes of biotin incubation. DAPI (blue, nuclei); MAP2 (green, dendrites); Flag (red, TurboID); and Streptavidin (cyan, biotinylated proteins). Magnification, ×20. Scale bars, 50 μm. f , Western blots stained for Flag and β-Actin from Pan-TurboID and TurboID-PSD95-transduced neurons in the absence (−) or presence (+) of exogenous biotin shown to indicate the relative expression levels of TurboID proteins. Quantifications of TurboID protein levels normalized to β-Actin are shown on the right ( n = 3); relative levels are not significant by two-tailed, paired Student’s t -test. g , Western blots stained for streptavidin signal in inputs (‘in’) and streptavidin pulldowns (‘pd’) from Pan-TurboID or TurboID-PSD95-transduced neurons in the absence (−) or presence (+) of exogenous biotin. h , Streptavidin pulldowns shown for dendritic (SHANK3, GKAP, NLGN1 and HOMER1) and negative control (GAPDH) proteins from TurboID-PSD95-transduced neurons in the absence (−) or presence (+) of exogenous biotin. Flag signal indicates self-biotinylation of each construct. Loaded on the gel are 10% (by volume) of input and 50% (by volume) of pulldowns. Percent isolated by TurboID-PSD95 in each condition is calculated by dividing the signal in the pulldown lane by that of the input lane, after each is adjusted to total, and quantifications are shown as bar graphs ( n = 3). P values: Flag = 0.58, SHANK3 = 0.0061, GKAP = 0.018, NLGN1 = 0.00052, HOMER1 = 0.021, GAPDH = 0.42. i , Streptavidin pulldowns shown for dendritic (BAIAP2 and DLGAP3) and nuclear (TBR1, H4 and H2AX) proteins from Pan-TurboID and TurboID-PSD95-transduced neurons in the presence (+) of exogenous biotin. Loaded on the gel are 10% (by volume) of input and 50% (by volume) of pulldowns. Percent isolated by each TurboID is calculated as in (h) ( n = 3). P values: BAIAP2 = 0.0052, DLGAP3 = 0.0035, TBR1 = 0.0063, H4 = 0.018, H2AX = 0.0037. j , Phosphorylation of EEF2, eIF2α, ERK1/2 and IRE1 and total levels of ATF4 and CHOP are shown in resting (rest), activated (DHPG, Dep) and stressed (Sodium arsenite (NaAsO 2 )) cells by using phospho-specific and total antibodies. The amount of phosphorylated or total protein is shown in the bar graphs, calculated by dividing the phosphorylated signal to total and β-Actin for the phosphorylated proteins and by dividing the total to β-Actin for ATF4 and CHOP ( n = 3). Significance was calculated with respect to rest. P values: P-EEF2 (DHPG = 0.0088, Dep = 0.0023, NaAsO 2 = 0.039), P-eIF2α (DHPG = 0.018, Dep = 0.0034, NaAsO 2 = 0.028), P-ERK1/2 (DHPG = 0.015, Dep = 0.0067, NaAsO 2 = 0.00084), P-IRE1 (DHPG = 0.06, Dep = 0.37, NaAsO 2 = 0.0027), ATF4 (DHPG = 0.038, Dep = 0.42, NaAsO 2 = 0.016), CHOP (DHPG = 0.044, Dep = 0.18, NaAsO 2 = 0.024). k , Quantitative PCR (qPCR) results shown for immediate early genes, Arc , Fos and Jun . The fold changes for each gene are calculated by first normalizing to the house-keeping gene β-Actin in each condition, then dividing the value of each condition by that of the resting state ( n = 3). l , Dendritic spine size in resting and KCl-depolarized neurons are measured using the Keyence microscope. Red squares are examples of spines that are counted ( n = 3, 12 spines from each biological replicate are counted as technical replicates). Significance was derived from the biological replicates using the two-tailed, unpaired Student’s t -test. Box plots show the min and max, with the center line at median. Magnification, ×100. Scale bars, 5 μm. m , Fluo-4-AM staining in resting, KCl-depolarized and DHPG-depolarized cells. Fluo4-AM was loaded in resting cells and measurements were taken at indicated time points after Fluo4-AM removal. In depolarized cells, the dye was loaded during silencing. After silencing, fluorescence was measured during stimulus at 10, 30 and 60-minute time points for the KCl treatment and at 10-minute for the DHPG-induced activation. Fluorescence was also measured 60 minutes after the stimulus removal (60′post KCl and 60′post DHPG). Circles represent data from 2 biological and 3 technical replicates. Below: Examples of Fluo4-AM fluorescence are shown in resting, 10-minute KCl-treated and 10-minute DHPG-treated neurons. Fluo4-AM loading (45 minutes) was performed during the last 45 minutes of the silencing step prior to stimulus addition for the KCl and DHPG treatment and simultaneously for the resting neurons. Imaging was performed 10 minutes after the stimulus was added. Scale bars, 50 μm. (b,f,h-k,m) Data are mean ± s.d. Significance was calculated using the two-tailed, paired Student’s t -test. P values: ns (not significant) >0.05; * <0.05; ** <0.01; *** <0.001; **** <0.0001. n indicates the number of biologically independent samples.

Article Snippet: Puromycin (1:3,000, mouse, Kerafast, EQ0001, RRID: AB_2620162), Flag (1:3,000, mouse, Sigma-Aldrich, F1804, RRID: AB_262044), β-Actin antibody (1:2,500, mouse, Sigma-Aldrich, A1978, RRID: AB_476692), RPL10A (1:1,000, rabbit, Abcam, ab174318), MAP2 (1:2,500, guinea pig, Synaptic Systems, 188004, RRID: AB_2138181), GFAP (1:500, rabbit, Abcam, ab7260, RRID: AB_305808), OLIG2 (1:500, rabbit, Proteintech, 13999-1-AP, RRID: AB_2157541), PSD95 (1:500, mouse, Millipore, MABN68, RRID: AB_10807979), Synaptophysin (1:300, mouse, Abcam, ab8049, RRID: AB_2198854), SHANK3 (1:500, mouse, Novus, NBP1-47610, RRID: AB_10010567), GKAP (1:500, rabbit, Novus, NBP1-76911, RRID: AB_11017331), NLGN1 (1:200, mouse, Novus, NBP2-42192), HOMER1 (1:1,000, rabbit, Proteintech, 12433-1-AP, RRID: AB_2295573), GAPDH (1:5,000, mouse, Thermo Fisher Scientific, AM4300, RRID: AB_2536381), BAIAP2 (1:500, rabbit, Proteintech, 11087-2-AP, RRID: AB_2063075), DLGAP3 (1:500, rabbit, Proteintech, 55056-1-AP, RRID: AB_10858793), TBR1 (1:500, rabbit, Proteintech, 20932-1-AP, RRID: AB_10695502), H4 (1:1,000, mouse, Abcam, ab31830, RRID: AB_1209246), H2A.X (1:1,000, rabbit, Proteintech, 10856-1-AP, RRID: AB_2114985), EEF2 (1:1,000, rabbit, Cell Signaling Technology, 2332, RRID:AB_10693546), P-EEF2 (1:1,000, rabbit, Cell Signaling Technology, 2331, RRID: AB_10015204), eIF2α (1:1,000, rabbit, Cell Signaling Technology, 9722, RRID: AB_2230924), P-eIF2α (1:1,000, rabbit, Cell Signaling Technology, 3398, RRID: AB_2096481), p42/44 MAPK (1:1,000, rabbit, Cell Signaling Technology, 4695, RRID: AB_390779), P-p42/44 MAPK (1:1,000, rabbit, Cell Signaling Technology, 9101, RRID: AB_331646), P-IRE1 (1:500, rabbit, Novus, NB100-2323SS, RRID: AB_10145203), IRE1 (1:500, rabbit, Novus, NB100-2324SS, RRID: AB_10000972), CHOP (1:1,000, mouse, Cell Signaling, 2895T, RRID: AB_2089254), ATF4 (1:1,000, rabbit, Cell Signaling Technology, 11815S, RRID: AB_2616025), MPHOSPH (1:300, rabbit, Biorbyt, orb100446), KCNJ9 (1:300, rabbit, LSBio, LS-C352416), KCNJ9 (1:300, mouse, Antibodies Incorporated, 75-445, RRID: AB_2686912), eIF4G2 (1:1,000, rabbit, Cell Signaling Technology, RRID: AB_10622189 and rabbit, Cell Signaling Technology, RRID: AB_2261993), NSUN3 (1:250, rabbit, LSBio, LS-C163024), MTF1 (1:300, rabbit, Novus, NBP1-86380, RRID: AB_11011361), ZFP64 (1:300, rabbit, Proteintech, 17187-1-AP, RRID: AB_2218826) and KATNBL1 (1:250, rabbit, Proteintech, 24795-1-AP, RRID: AB_2879730).

Techniques: Immunofluorescence, Clone Assay, Derivative Assay, Expressing, Marker, Transduction, Incubation, Western Blot, Staining, Two Tailed Test, Negative Control, Construct, Isolation, Real-time Polymerase Chain Reaction, Microscopy, Fluorescence, Activation Assay, Imaging

Journal: Journal of cell science

Article Title: Carbonic anhydrase IX (CA9) modulates tumor-associated cell migration and invasion.

doi: 10.1242/jcs.072207

Figure Lengend Snippet: Fig. 1. The list of differentially expressed genes in C33A/CA9 and C33A/Mock cells. Differentially expressed genes were selected on the basis of fold-change in CA9-overexpressed (C33A/CA9) cells versus vector- transfected control (C33A/Mock) cells. Gene expressions were confirmed by RT-PCR and quantitative RT-PCR. The relative quantity for each molecule was normalized with GAPDH, which was used as an internal control. Each bar represents the mean (plus standard error) of four independent experiments. *P<0.05.

Article Snippet: Cell culture and stable transfection of C33A cells The human cervical cancer cell line C33A (ATCC number HTB-31) was stably transfected with either full-length human CA9 cDNA cloned into the pcDNA3 vector or empty vector control (Shin et al., 2008).

Techniques: Plasmid Preparation, Transfection, Control, Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR

Journal: Journal of cell science

Article Title: Carbonic anhydrase IX (CA9) modulates tumor-associated cell migration and invasion.

doi: 10.1242/jcs.072207

Figure Lengend Snippet: Fig. 2. Reorganization of actin cytoskeleton and alteration of focal adhesion induced by CA9 overexpression. (A)C33A/CA9 and C33A/Mock cells were incubated on glass slides pre-coated with BD Matrigel Matrix with the cultured medium for 24 hours. Actin filaments (green) of cytoskeleton, vinculin (red) of focal adhesion complex and nuclear DNA (blue) were stained with phalloidin conjugated with Alexa 488, anti-vinculin antibody labeled with Alexa 594 and DAPI, respectively. (B)HeLa cells were cultured under normoxic (20% O2) and hypoxic (0.1% O2) conditions and were stained in the same manner as in A. (C)Cells grown as described above were harvested and CA9 expression was confirmed using M75 monoclonal antibody. Expression and phosphorylation of paxillin was examined by immunoblotting, using the indicated antibodies (anti-paxillin, anti-pPaxillinY118). -actin was used as a loading control.

Article Snippet: Cell culture and stable transfection of C33A cells The human cervical cancer cell line C33A (ATCC number HTB-31) was stably transfected with either full-length human CA9 cDNA cloned into the pcDNA3 vector or empty vector control (Shin et al., 2008).

Techniques: Over Expression, Incubation, Cell Culture, Staining, Labeling, Expressing, Phospho-proteomics, Western Blot, Control

Journal: Journal of cell science

Article Title: Carbonic anhydrase IX (CA9) modulates tumor-associated cell migration and invasion.

doi: 10.1242/jcs.072207

Figure Lengend Snippet: Fig. 4. Rho-GTPase activity and changes in cytoskeletal structure and focal adhesion with CA9 overexpression. (A)The amount of GTP-bound Rho-GTPase was compared between two cells by GST-RBD pull-down assay. Band intensity of activated RhoA/B/C-GTPases was quantified by image software, Multi Gauge, V3.0 (FUJIFILM). (B)Changes in actin cytoskeleton and focal adhesions subsequent to blocking the Rho downstream with ROCK inhibitor (Y27632) were observed by immunofluorescence analysis. C33A/Mock and C33A/CA9 cells were plated as in Fig. 2A and treated with a final 10M Y27632 after 3 hours. Actin filaments, vinculins and nuclear DNA were stained as green, red and blue signal, respectively. (C)Total lysates from two cell line cultures treated with or without 10M Y27632 as described in B were used for immunoblotting for expression and phosphorylation of paxillin. -actin was used as a loading control.

Article Snippet: Cell culture and stable transfection of C33A cells The human cervical cancer cell line C33A (ATCC number HTB-31) was stably transfected with either full-length human CA9 cDNA cloned into the pcDNA3 vector or empty vector control (Shin et al., 2008).

Techniques: Activity Assay, Over Expression, Pull Down Assay, Software, Blocking Assay, Immunofluorescence, Staining, Western Blot, Expressing, Phospho-proteomics, Control

Journal: Journal of cell science

Article Title: Carbonic anhydrase IX (CA9) modulates tumor-associated cell migration and invasion.

doi: 10.1242/jcs.072207

Figure Lengend Snippet: Fig. 3. Increased invasive and metastatic ability with CA9 overexpression. (A)C33A/CA9 and C33A/Mock cells were suspended as single cells and were cultured in Matrigel for two weeks. Images of the spheroid colonies were acquired using a light microscope (100 magnification). (B,C)Migratory and invasive ability of two cell lines were examined using Transwell chambers with or without Matrigel coating. The cells migrating through the filters were enumerated and the relative ratio of migrating C33A/CA9 cells to migrating C33A/Mock cells was determined. Each illustration shows the typical image and each bar represents the mean (plus standard error) of six independent experiments (*, P<0.05 compared with C33A/Mock cells).

Article Snippet: Cell culture and stable transfection of C33A cells The human cervical cancer cell line C33A (ATCC number HTB-31) was stably transfected with either full-length human CA9 cDNA cloned into the pcDNA3 vector or empty vector control (Shin et al., 2008).

Techniques: Over Expression, Cell Culture, Light Microscopy

Journal: Journal of cell science

Article Title: Carbonic anhydrase IX (CA9) modulates tumor-associated cell migration and invasion.

doi: 10.1242/jcs.072207

Figure Lengend Snippet: Fig. 5. Migratory and invasive potential improved with Rho-GTPase inactivation in C33A/CA9 cells. (A)C33A/Mock and C33A/CA9 cells were cultured in Matrigel for 8 days, as in Fig. 3A and were treated with final 10 M Y27632 at this time to start cells clumping. Y27632 inhibitor was treated two more times and the cells were observed using a light microscope (100 magnification). (B,C)Migrating and invading ability of the cells were examined as in Fig. 3B and 3C. Cells were seeded onto respective Transwell chambers and were treated with 10 M Y27632 3 hours after seeding. Each figure illustrates the typical image obtained and each bar represents the mean (plus standard error) of six independent experiments.

Article Snippet: Cell culture and stable transfection of C33A cells The human cervical cancer cell line C33A (ATCC number HTB-31) was stably transfected with either full-length human CA9 cDNA cloned into the pcDNA3 vector or empty vector control (Shin et al., 2008).

Techniques: Cell Culture, Light Microscopy

Journal: Journal of cell science

Article Title: Carbonic anhydrase IX (CA9) modulates tumor-associated cell migration and invasion.

doi: 10.1242/jcs.072207

Figure Lengend Snippet: Fig. 6. The role of Rho-GTPase signaling in the EMT process. (A)The expression and localization of E-cadherin and vimentin were examined by immunofluorescence analysis. Prepared under the same conditions as in Fig. 4B, the cells were stained for E-cadherin (red) and vimentin (green) with Alexa-594- and Alexa-488-labeled secondary antibodies, respectively. (B)Thirty micrograms of the membranous and cytoplasmic fraction of proteins obtained from the cells were loaded and the expression of E-cadherin was analyzed by western blotting. PMCA4 (plasma membrane calcium ATPase 4) and - tubulin were used as controls for membranous and cytoplasmic proteins, respectively. (C)Expression of epithelial markers (E-cadherin and -catenin) and mesenchymal markers (vimentin and N- cadherin) were examined by western blot in both C33A/Mock and C33A/CA9 cells, with or without Y27632 treatment. -actin was used as a loading control. Band intensity from western blot images was quantified by Multi Gauge V3.0 (FUJIFILM). Each bar represents the mean (plus standard error).

Article Snippet: Cell culture and stable transfection of C33A cells The human cervical cancer cell line C33A (ATCC number HTB-31) was stably transfected with either full-length human CA9 cDNA cloned into the pcDNA3 vector or empty vector control (Shin et al., 2008).

Techniques: Expressing, Immunofluorescence, Staining, Labeling, Western Blot, Clinical Proteomics, Membrane, Control

Journal: Journal of cell science

Article Title: Carbonic anhydrase IX (CA9) modulates tumor-associated cell migration and invasion.

doi: 10.1242/jcs.072207

Figure Lengend Snippet: Fig. 7. Rho signaling is crucial to form the migratory phenotypes. The role of Rho signaling was validated using two types of siRNAs against RhoA at a concentration of 25 nM. A double-stranded non- specific siRNA was used as a negative control (CNT). (A)Block efficiency of si-Rho and quantitative changes of EMT markers were analyzed by western blot. -actin was used as a loading control. (B)An invasion assay using Transwell chambers with Matrigel coating was repeated six times. The cells migrating through the filters were enumerated and the relative ratio of invasive cells was normalized by the number of migrating C33A/Mock-CNT cells. Illustrations show the typical images and the bars represent the mean (plus standard error).

Article Snippet: Cell culture and stable transfection of C33A cells The human cervical cancer cell line C33A (ATCC number HTB-31) was stably transfected with either full-length human CA9 cDNA cloned into the pcDNA3 vector or empty vector control (Shin et al., 2008).

Techniques: Concentration Assay, Negative Control, Blocking Assay, Western Blot, Control, Invasion Assay

Journal: Journal of cell science

Article Title: Carbonic anhydrase IX (CA9) modulates tumor-associated cell migration and invasion.

doi: 10.1242/jcs.072207

Figure Lengend Snippet: Fig. 8. The effect of CA9 on migration and invasion is validated by siRNAs against CA9. (A)Block efficiency of si-CA9 was validated by western blot. A double-stranded non-specific siRNA was used as a negative control (CNT). C33A/CA9 cells were transfected with 150 nM siRNA against CA9 for 24 hours and then were transferred onto Matrigel-coated dishes. After incubation for 24 hours, total cell lysates were analyzed for small GTPases such as Rho, RAC, CDC42 and paxillin using a pull-down assay and western blot analysis. Band intensity from western blot images was quantified by Multi Gauge V3.0. (B,C)At 24 hours post- transfection, the cells were prepared for migration and invasion assays as in Fig. 5B and C. (D)Cells were prepared as in Fig. 8A and were analyzed for EMT markers by western blot analysis. After silencing of CA9 expression, epithelial markers increased in expression, whereas mesenchymal markers decreased in C33A/CA9 cells. Each bar represents the mean (plus standard error).

Article Snippet: Cell culture and stable transfection of C33A cells The human cervical cancer cell line C33A (ATCC number HTB-31) was stably transfected with either full-length human CA9 cDNA cloned into the pcDNA3 vector or empty vector control (Shin et al., 2008).

Techniques: Migration, Blocking Assay, Western Blot, Negative Control, Transfection, Incubation, Pull Down Assay, Expressing

Journal: International Journal of Molecular Medicine

Article Title: Tanshinone IIA confers protection against myocardial ischemia/reperfusion injury by inhibiting ferroptosis and apoptosis via VDAC1

doi: 10.3892/ijmm.2023.5312

Figure Lengend Snippet: TSN alleviates ferroptosis of A/R-induced H9c2 cardiomyocytes via downregulation of VDAC1. (A) Cell Counting Kit-8 detection of viability in A/R-induced cells following TSN or Fer-1 pretreatment. (B) LDH, (C) MDA, (D) total iron, (E) GSH, GSSG, GSH/GSSG and (F) ROS were determined by quantitative kits in A/R-induced cells following TSN or Fer-1 treatment (magnification, ×200; scale bar, 50 μ m). (G) Expression of (H) ferroptosis-related proteins and VDAC1 were detected by western blot analysis in A/R-induced cells following TSN or Fer-1 pretreatment. Data are expressed as the mean ± SD (n=3). *** P<0.05. TSN, Tanshinone IIA; A/R, Anoxia/reoxygenation; VDAC1, Voltage-dependent anion channel 1; Fer-1, ferrostatin-1; LDH, lactate dehydrogenase; MDA, malondialdehyde; GSH, Glutathione; GSSG, Glutathione disulfide; ROS, reactive oxygen species; PTGS2, Prostaglandin endoperoxide synthase 2; GPX, Glutathione peroxidase 4.

Article Snippet: An equal amount of total protein (40 μ g/lane) in each sample was separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis, transferred to polyvinylidene fluoride membranes and blocked with 5% non-fat dry milk in Tris-buffered saline with 0.1% Tween-20 buffer at room temperature for 2 h. Subsequently, membranes were incubated with primary antibodies against PTGS2 (ProteinTech Group, Inc.; cat. no. #12375-1-AP; 1:1,000), VDAC1 (ProteinTech Group, Inc.; cat. no. #55259-1-AP; 1:1,000), GPX4 (ZENBIO; cat. no. #381958; 1:1,000), Bcl-2 (ZENBIO; cat. no. #250412; 1:1,000), Bax (ZENBIO; cat. no. #380709; 1:1,000) and β-actin (ProteinTech Group, Inc.; cat. no. #20536-1-AP; 1:1,000) at 4°C overnight in a shaker.

Techniques: Cell Counting, Expressing, Western Blot

Journal: International Journal of Molecular Medicine

Article Title: Tanshinone IIA confers protection against myocardial ischemia/reperfusion injury by inhibiting ferroptosis and apoptosis via VDAC1

doi: 10.3892/ijmm.2023.5312

Figure Lengend Snippet: TSN binds to VDAC1. (A) Chemical structure of TSN. (B) Molecular structure of VDAC1. (C) 3D and (D) 2D diagram of the interaction between TSN and VDAC1. TSN, Tanshinone IIA; VDAC1, Voltage-dependent anion channel 1.

Article Snippet: An equal amount of total protein (40 μ g/lane) in each sample was separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis, transferred to polyvinylidene fluoride membranes and blocked with 5% non-fat dry milk in Tris-buffered saline with 0.1% Tween-20 buffer at room temperature for 2 h. Subsequently, membranes were incubated with primary antibodies against PTGS2 (ProteinTech Group, Inc.; cat. no. #12375-1-AP; 1:1,000), VDAC1 (ProteinTech Group, Inc.; cat. no. #55259-1-AP; 1:1,000), GPX4 (ZENBIO; cat. no. #381958; 1:1,000), Bcl-2 (ZENBIO; cat. no. #250412; 1:1,000), Bax (ZENBIO; cat. no. #380709; 1:1,000) and β-actin (ProteinTech Group, Inc.; cat. no. #20536-1-AP; 1:1,000) at 4°C overnight in a shaker.

Techniques:

Journal: International Journal of Molecular Medicine

Article Title: Tanshinone IIA confers protection against myocardial ischemia/reperfusion injury by inhibiting ferroptosis and apoptosis via VDAC1

doi: 10.3892/ijmm.2023.5312

Figure Lengend Snippet: TSN inhibits ferroptosis of A/R-induced H9c2 cardiomyocytes by downregulating VDAC1. (A) Cell Counting Kit-8 detection of viability in A/R-induced cells after TSN, pAd/VDAC1 and pAd/NC pretreatment. (B) LDH, (C) MDA, (D) total iron, (E) GSH, GSSG, GSH/GSSG and (F) ROS were determined by quantitative kits in A/R-induced cells following TSN, pAd/VDAC1 and pAd/NC treatment (magnification, x200; scale bar, 50 μ m). (G) Expression of (H) ferroptosis-associated proteins and VDAC1 were detected by western blot analysis in A/R-induced cells after TSN, pAd/VDAC1 and pAd/NC pretreatment. Data are expressed as the mean ± SD (n=3). *** P<0.05. TSN, tanshinone IIA; A/R, anoxia/reoxygenation; VDAC1, voltage-dependent anion channel 1; NC, negative control; LDH, lactate dehydrogenase; MDA, malondialdehyde; GSH, Glutathione; GSSG, Glutathione disulfide; ROS, reactive oxygen species; PTGS2, Prostaglandin endoperoxide synthase 2; GPX4, Glutathione peroxidase 4.

Article Snippet: An equal amount of total protein (40 μ g/lane) in each sample was separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis, transferred to polyvinylidene fluoride membranes and blocked with 5% non-fat dry milk in Tris-buffered saline with 0.1% Tween-20 buffer at room temperature for 2 h. Subsequently, membranes were incubated with primary antibodies against PTGS2 (ProteinTech Group, Inc.; cat. no. #12375-1-AP; 1:1,000), VDAC1 (ProteinTech Group, Inc.; cat. no. #55259-1-AP; 1:1,000), GPX4 (ZENBIO; cat. no. #381958; 1:1,000), Bcl-2 (ZENBIO; cat. no. #250412; 1:1,000), Bax (ZENBIO; cat. no. #380709; 1:1,000) and β-actin (ProteinTech Group, Inc.; cat. no. #20536-1-AP; 1:1,000) at 4°C overnight in a shaker.

Techniques: Cell Counting, Expressing, Western Blot, Negative Control

Journal: International Journal of Molecular Medicine

Article Title: Tanshinone IIA confers protection against myocardial ischemia/reperfusion injury by inhibiting ferroptosis and apoptosis via VDAC1

doi: 10.3892/ijmm.2023.5312

Figure Lengend Snippet: TSN improves mitochondrial function and integrity in H9c2 cardiomyocytes exposed to A/R by downregulating VDAC1. (A) Fluorescent probe BBcellProbe M61 indicating mPTP opening was detected by flow cytometry with the FL1-A: B525-FITC channel. (B) mPTP flow cytometry. (C) Flameng score and (D) transmission electron microscopy of H9c2 cells (magnification, ×8,000; scale bar, 2 μ m). Data are expressed as the mean ± SD (n=3). *** P<0.05. TSN, tanshinone IIA; A/R, Anoxia/reoxygenation; VDAC1, Voltage-dependent anion channel 1; mPTP, Mitochondrial permeability transition pore; NC, negative control.

Article Snippet: An equal amount of total protein (40 μ g/lane) in each sample was separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis, transferred to polyvinylidene fluoride membranes and blocked with 5% non-fat dry milk in Tris-buffered saline with 0.1% Tween-20 buffer at room temperature for 2 h. Subsequently, membranes were incubated with primary antibodies against PTGS2 (ProteinTech Group, Inc.; cat. no. #12375-1-AP; 1:1,000), VDAC1 (ProteinTech Group, Inc.; cat. no. #55259-1-AP; 1:1,000), GPX4 (ZENBIO; cat. no. #381958; 1:1,000), Bcl-2 (ZENBIO; cat. no. #250412; 1:1,000), Bax (ZENBIO; cat. no. #380709; 1:1,000) and β-actin (ProteinTech Group, Inc.; cat. no. #20536-1-AP; 1:1,000) at 4°C overnight in a shaker.

Techniques: Flow Cytometry, Transmission Assay, Electron Microscopy, Permeability, Negative Control

Journal: International Journal of Molecular Medicine

Article Title: Tanshinone IIA confers protection against myocardial ischemia/reperfusion injury by inhibiting ferroptosis and apoptosis via VDAC1

doi: 10.3892/ijmm.2023.5312

Figure Lengend Snippet: TSN inhibits apoptosis of A/R-induced H9c2 cardiomyocytes by downregulating VDAC1. (A) Expression of (B) apoptosis-associated proteins was detected by western blot analysis in A/R-induced cells following TSN, pAd/VDAC1 and pAd/NC pretreatment. (C) Caspase-3 activity was measured using a Caspase-3 kit in A/R-induced cells after TSN, pAd/VDAC1 and pAd/NC treatment. (D) MMP and (E) apoptosis were detected by flow cytometry. (F) MMP levels detected by JC-1 in H9c2 cells indicated by the red/green fluorescence ratio. (G) Apoptotic rate measured by Annexin V-FITC/PI flow cytometry. Data are expressed as the mean ± SD (n=3). *** P<0.05. TSN, Tanshinone IIA; A/R, Anoxia/reoxygenation; VDAC1, Voltage-dependent anion channel 1; NC, negative control; MMP, mitochondrial membrane potential.

Article Snippet: An equal amount of total protein (40 μ g/lane) in each sample was separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis, transferred to polyvinylidene fluoride membranes and blocked with 5% non-fat dry milk in Tris-buffered saline with 0.1% Tween-20 buffer at room temperature for 2 h. Subsequently, membranes were incubated with primary antibodies against PTGS2 (ProteinTech Group, Inc.; cat. no. #12375-1-AP; 1:1,000), VDAC1 (ProteinTech Group, Inc.; cat. no. #55259-1-AP; 1:1,000), GPX4 (ZENBIO; cat. no. #381958; 1:1,000), Bcl-2 (ZENBIO; cat. no. #250412; 1:1,000), Bax (ZENBIO; cat. no. #380709; 1:1,000) and β-actin (ProteinTech Group, Inc.; cat. no. #20536-1-AP; 1:1,000) at 4°C overnight in a shaker.

Techniques: Expressing, Western Blot, Activity Assay, Flow Cytometry, Fluorescence, Negative Control, Membrane

Journal: International Journal of Molecular Medicine

Article Title: Tanshinone IIA confers protection against myocardial ischemia/reperfusion injury by inhibiting ferroptosis and apoptosis via VDAC1

doi: 10.3892/ijmm.2023.5312

Figure Lengend Snippet: Potential mechanism of TSN in myocardial ischemia/reperfusion injury. TSN pretreatment upregulates the expression of VDAC1, thereby decreasing the accumulation of ROS and iron and abnormal lipid metabolism, maintaining mitochondrial function and protecting the myocardium against anoxia/reoxygenation-induced ferroptosis and apoptosis. TSN, tanshinone IIA; VDAC1, Voltage-dependent anion channel 1; ROS, reactive oxygen species; MDA, malondialdehyde; GSH, Glutathione; GSSG, Glutathione disulfide; LDH, lactate dehydrogenase; MMP, Mitochondrial membrane potential.

Article Snippet: An equal amount of total protein (40 μ g/lane) in each sample was separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis, transferred to polyvinylidene fluoride membranes and blocked with 5% non-fat dry milk in Tris-buffered saline with 0.1% Tween-20 buffer at room temperature for 2 h. Subsequently, membranes were incubated with primary antibodies against PTGS2 (ProteinTech Group, Inc.; cat. no. #12375-1-AP; 1:1,000), VDAC1 (ProteinTech Group, Inc.; cat. no. #55259-1-AP; 1:1,000), GPX4 (ZENBIO; cat. no. #381958; 1:1,000), Bcl-2 (ZENBIO; cat. no. #250412; 1:1,000), Bax (ZENBIO; cat. no. #380709; 1:1,000) and β-actin (ProteinTech Group, Inc.; cat. no. #20536-1-AP; 1:1,000) at 4°C overnight in a shaker.

Techniques: Expressing, Membrane

Journal: Cell Communication and Signaling : CCS

Article Title: Src family kinases interfere with dimerization of STAT5A through a phosphotyrosine-SH2 domain interaction

doi: 10.1186/s12964-014-0081-7

Figure Lengend Snippet: The SH2 domain of STAT5A is required for efficient binding to Src kinases. (A) Domain structure of fluorescently labeled STAT5A-eYFP. (B) Subcellular localization of STAT5A-eYFP in the absence or presence of Epo. HeLa T-REx HA-EpoR cells stably transfected with STAT5A-eYFP were stimulated with 1 U/ml Epo for 30 min and the localization of STAT5A-eYFP was analyzed by confocal microscopy. Scale bars: 20 μm. (C) Subcellular localization of STAT5A-eYFP (upper panel), STAT5A R618Q -eYFP (middle panel) and STAT3-eYFP (lower panel) was investigated in the presence of vSrc-dsRed. HeLa T-REx vSrc-dsRed cells were treated with 5 ng/ml doxycycline and transfected with the indicated constructs and the distribution of fluorescently labeled fusion proteins was analyzed after 24 h by confocal microscopy. Scale bars: 20 μm. (D) Quantification of the relative subcellular distribution of eYFP-labeled STAT3 and STAT5A constructs in HeLa T-REx HA-EpoR cells stably expressing STAT5A-eYFP (B) and HeLa T-REx vSrc-dsRed cells transfected with STAT5A-eYFP, STAT5A R618Q -eYFP or STAT3-eYFP (C) . The expression of the HA-EpoR and vSrc-dsRed was induced with 5 ng/ml doxycycline for 24 hours. Mean fluorescence intensities (MFI) of the cytoplasm and nucleus were determined using the Zen 2012 software and changes in the ratio between the compartments were plotted. The data shown are means ± SD of n = 30 cells and were statistically evaluated by Student’s t -test. ***p < 0.0005. n.s. = not significant. (E + F) HeLa T-REx FRT cells were co-transfected with plasmids coding for STAT5A-eYFP or STAT5A R618Q -eYFP and vSrc-dsRed or Hck-dsRed. Fluorescently labeled STAT5 was immunoprecipitated from cell lysates using a GFP antibody and analyzed by immunoblotting for the presence of vSrc-dsRed or Hck-dsRed 24 h after transfection. The expression and phosphorylation of STAT5A and vSrc/Hck proteins was analyzed in the whole cellular lysates (WCL) using antibodies against pY 416 -Src, Src, Hck, pY 694/699 -STAT5A/B and GFP.

Article Snippet: Anti-pY 694/699 -STAT5A/B (#9351), anti-pY 416 -Src (#2101), anti-pY 412 -Abl (#2865), anti-Hsp70 (#4872, Cell Signaling, Beverly, USA), anti-STAT5A (clone #5073, rabbit polyclonal antiserum was kindly provided by Richard Moriggl, Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, Austria), anti-GFP (600-103-215, Rockland, Gilbertsville, USA), anti-FLAG (F3165), anti-α-tubulin (T5168, Sigma, St. Louis, USA), anti-GAPDH (sc-32233), anti-Abl (sc-131), anti-Hck (sc-72), anti-cSrc (sc-19, Santa Cruz Biotechnology, Santa Cruz, USA), anti-vSrc (MABS193, Millipore, Billerica, MA, USA) and anti-HA (MMS-101R, Covance, Princeton, New Jersey, USA) antibodies were used for immunoblotting.

Techniques: Binding Assay, Labeling, Stable Transfection, Transfection, Confocal Microscopy, Construct, Expressing, Fluorescence, Software, Immunoprecipitation, Western Blot

Journal: Cell Communication and Signaling : CCS

Article Title: Src family kinases interfere with dimerization of STAT5A through a phosphotyrosine-SH2 domain interaction

doi: 10.1186/s12964-014-0081-7

Figure Lengend Snippet: STAT5A binds to the phosphorylated activation loop of SFK. (A) Domain structure of vSrc-dsRed. Selected amino acids are highlighted. A multiple sequence alignment of the activation loop of SFK is shown. Autophosphorylation site is highlighted (red). (*) conserved amino acids, (:) similar properties . Bold characters highlight peptide sequence used for precipitation. (B + C) HeLa T-REx FRT cells stably expressing STAT5A-eYFP were transfected with the indicated vSrc-dsRed variants. Phosphorylation was analyzed 24 h after transfection using antibodies against pY 416 -Src, Src, pY 694/699 -STAT5A/B and STAT5A. CTRL = untransfected cells. (D) Quantification of relative subcellular distribution of STAT5A in HeLa T-REx FRT stably expressing STAT5A-eYFP and the indicated vSrc-dsRed mutants. Mean fluorescence intensity (MFI) of eYFP-fluorescence in the cytoplasm and nucleus were determined using the Zen 2012 software and changes in the ratio between the compartments were plotted. Data show means ± SD of n = 10 cells and were statistically evaluated by Student’s t -test. ***p < 0.0005, **p < 0.005, *p < 0.05, n.s. = not significant. (E) HeLa T-REx FRT cells stably expressing STAT5A-eYFP were transfected with vSrc K295N -dsRed or vSrc Y416F -dsRed. Subcellular distribution of STAT5A-eYFP was analyzed 24 h after transfection by confocal microscopy. Scale bars: 20 μm. (F + G) HeLa T-REx FRT cells were co-transfected with plasmids coding for vSrc-dsRed (Hck-dsRed), vSrc K295N -dsRed (Hck K269N -dsRed) or vSrc Y416F -dsRed (Hck Y390F -dsRed) and STAT5A-eYFP. STAT5-eYFP was immunoprecipitated from cell lysates using a GFP antibody and analyzed by immunoblotting for the presence of vSrc-dsRed (Hck-dsRed) 24 h after transfection. Expression and phosphorylation of STAT5A and vSrc proteins was analyzed in the WCL using antibodies against pY 416 -Src, Src, Hck, pY 694/699 -STAT5A/B and GFP. (s) short exposure, (l) long exposure. (H) HeLa T-REx FRT cells expressing STAT5A-eYFP or STAT5A R618Q -eYFP were lysed and incubated with a Src-peptide containing tyrosine- or phosphotyrosine 416. Precipitates and WCL were analyzed by immunoblotting using a GFP-specific antibody.

Article Snippet: Anti-pY 694/699 -STAT5A/B (#9351), anti-pY 416 -Src (#2101), anti-pY 412 -Abl (#2865), anti-Hsp70 (#4872, Cell Signaling, Beverly, USA), anti-STAT5A (clone #5073, rabbit polyclonal antiserum was kindly provided by Richard Moriggl, Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, Austria), anti-GFP (600-103-215, Rockland, Gilbertsville, USA), anti-FLAG (F3165), anti-α-tubulin (T5168, Sigma, St. Louis, USA), anti-GAPDH (sc-32233), anti-Abl (sc-131), anti-Hck (sc-72), anti-cSrc (sc-19, Santa Cruz Biotechnology, Santa Cruz, USA), anti-vSrc (MABS193, Millipore, Billerica, MA, USA) and anti-HA (MMS-101R, Covance, Princeton, New Jersey, USA) antibodies were used for immunoblotting.

Techniques: Activation Assay, Sequencing, Stable Transfection, Expressing, Transfection, Fluorescence, Software, Confocal Microscopy, Immunoprecipitation, Western Blot, Incubation

Journal: Cell Communication and Signaling : CCS

Article Title: Src family kinases interfere with dimerization of STAT5A through a phosphotyrosine-SH2 domain interaction

doi: 10.1186/s12964-014-0081-7

Figure Lengend Snippet: SFK-mediated cytoplasmic localization of STAT5A is dominant over BCR-ABL induced nuclear accumulation. (A) HeLa T-REx BCR-ABL cells were transiently transfected with STAT5A-eYFP and either treated with 5 ng/ml doxycycline for 24 h to induce BCR-ABL expression (lower panel) or left untreated (upper panel). Fixation was performed with methanol. Fixed cells were stained for BCR-ABL using a cABL-specific primary antibody and a secondary antibody conjugated to Alexa Fluor-405. The subcellular distribution of STAT5A-eYFP was analyzed by confocal microscopy. Scale bars: 20 μm. (B) The subcellular distribution of STAT5A-eYFP was investigated in the presence of vSrc-dsRed (upper panel), vSrc K295N -dsRed (middle panel) or vSrc Y416F -dsRed (lower panel) in HeLa T-REx BCR-ABL cells that were treated with 5 ng/ml doxycycline for 24 h. Fixation was performed with methanol. Fixed cells were stained for BCR-ABL using an Abl-specific primary antibody and a secondary antibody conjugated to Alexa Fluor-405. Scale bars: 20 μm. (C) HeLa T-REx BCR-ABL cells were co-transfected with vSrc-dsRed, or the respective kinase activity affecting mutants vSrc K295N -dsRed or vSrc Y416F -dsRed and STAT5A-eYFP. The cells were either treated with 5 ng/ml doxycycline for 24 h (lanes 1–3) to induce the expression of BCR-ABL or left untreated (lane 4). Protein expression and phosphorylation in the cellular extracts was investigated by immunoblotting with antibodies against pY 412 -cABL, cABL, pY 694/699 -STAT5A/B, STAT5A, pY 416 -Src and Src. α-Tubulin served as a loading control.

Article Snippet: Anti-pY 694/699 -STAT5A/B (#9351), anti-pY 416 -Src (#2101), anti-pY 412 -Abl (#2865), anti-Hsp70 (#4872, Cell Signaling, Beverly, USA), anti-STAT5A (clone #5073, rabbit polyclonal antiserum was kindly provided by Richard Moriggl, Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, Austria), anti-GFP (600-103-215, Rockland, Gilbertsville, USA), anti-FLAG (F3165), anti-α-tubulin (T5168, Sigma, St. Louis, USA), anti-GAPDH (sc-32233), anti-Abl (sc-131), anti-Hck (sc-72), anti-cSrc (sc-19, Santa Cruz Biotechnology, Santa Cruz, USA), anti-vSrc (MABS193, Millipore, Billerica, MA, USA) and anti-HA (MMS-101R, Covance, Princeton, New Jersey, USA) antibodies were used for immunoblotting.

Techniques: Transfection, Expressing, Staining, Confocal Microscopy, Activity Assay, Western Blot

Journal: Cell Communication and Signaling : CCS

Article Title: Src family kinases interfere with dimerization of STAT5A through a phosphotyrosine-SH2 domain interaction

doi: 10.1186/s12964-014-0081-7

Figure Lengend Snippet: Binding of STAT5A to Src kinases interferes with dimerization. (A) HeLa T-REx HA-EpoR cells stably expressing STAT5A-eYFP were transfected with STAT5A-FLAG. The cells were treated with 5 ng/ml doxyxcyline for 24 h to induce the expression of the HA-tagged EpoR and stimulated with 5 U/ml Epo for 30 minutes or left untreated. HeLa T-REx vSrc-dsRed cells stably expressing STAT5A-eYFP were transfected with STAT5A-FLAG. The expression of vSrc-dsRed was induced for 8 h with 5 ng/ml doxycycline or the cells were left untreated. STAT5A-eYFP was immunoprecipitated from cell lysates using a GFP antibody and analyzed by immunoblotting for the presence of STAT5A-FLAG. The expression and phosphorylation of STAT5A-eYFP and STAT5A-FLAG was analyzed in the WCL using antibodies against pY 694/699 -STAT5A/B, GFP and the FLAG-tag. (B) HeLa T-REx HA-EpoR cells stably expressing STAT5A-eYFP were treated with 5 ng/ml doxyxcyline for 24 h to induce the expression of the human EpoR and stimulated with 5 U/ml Epo for 30 minutes or left untreated. HeLa T-REx vSrc-dsRed cells stably expressing STAT5A-eYFP or a STAT5A S710F -eYFP were treated with 5 ng/ml doxyxcline for 8 h or the cells were left untreated. Cellular extracts were prepared under native conditions and STAT5A-eYFP dimers were separated from monomers by blue native PAGE electrophoresis (NP). STAT5A-eYFP dimer complexes were measured by the detection of the eYFP fluorescence. The cellular extracts were subjected to immunoblotting using antibodies against pY 694/699 -STAT5A/B, STAT5A, Src and the HA-tag of the EpoR. (C) Confocal microscopy analysis of HeLa T-REx FRT cells co-expressing vSrc-dsRed together with STAT5A S710F -eYFP (upper panel), a serine phosphorylation mimicking mutant STAT5A S710D -eYFP (middle panel) or a serine phosphorylation deficient mutant STAT5A S710A -eYFP (lower panel). Methanol fixation was performed 24 h after transfection. Scale bars: 20 μm.

Article Snippet: Anti-pY 694/699 -STAT5A/B (#9351), anti-pY 416 -Src (#2101), anti-pY 412 -Abl (#2865), anti-Hsp70 (#4872, Cell Signaling, Beverly, USA), anti-STAT5A (clone #5073, rabbit polyclonal antiserum was kindly provided by Richard Moriggl, Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, Austria), anti-GFP (600-103-215, Rockland, Gilbertsville, USA), anti-FLAG (F3165), anti-α-tubulin (T5168, Sigma, St. Louis, USA), anti-GAPDH (sc-32233), anti-Abl (sc-131), anti-Hck (sc-72), anti-cSrc (sc-19, Santa Cruz Biotechnology, Santa Cruz, USA), anti-vSrc (MABS193, Millipore, Billerica, MA, USA) and anti-HA (MMS-101R, Covance, Princeton, New Jersey, USA) antibodies were used for immunoblotting.

Techniques: Binding Assay, Stable Transfection, Expressing, Transfection, Immunoprecipitation, Western Blot, FLAG-tag, Blue Native PAGE, Electrophoresis, Fluorescence, Confocal Microscopy, Mutagenesis

Journal: Cell Communication and Signaling : CCS

Article Title: Src family kinases interfere with dimerization of STAT5A through a phosphotyrosine-SH2 domain interaction

doi: 10.1186/s12964-014-0081-7

Figure Lengend Snippet: Activated SFK interfere with dimerization and nuclear translocation of pSTAT5A in BCR-ABL expressing cells. Left scheme: Classical activation of the JAK2-STAT5A signaling pathway downstream of the EpoR. Right scheme: BCR-ABL directly phosphorylates STAT5A Y694 resulting in STAT5A dimerization, nuclear accumulation and finally target gene expression . In the presence of BCR-ABL, a predominantly cytoplasmic localization of pSTAT5A is achieved (i) upon binding to the scaffolding adaptor Gab2 resulting in pro-survival signaling through PI3K/Akt activation and (ii) through binding of the STAT5A SH2 domain to the phosphorylated activation loop of SFK, a mechanism that interferes with STAT5A dimerization and subsequent nuclear accumulation. Constitutively active STAT5A S710F escapes the SFK-mediated cytoplasmic retention. Flashes indicate phosphorylation events.

Article Snippet: Anti-pY 694/699 -STAT5A/B (#9351), anti-pY 416 -Src (#2101), anti-pY 412 -Abl (#2865), anti-Hsp70 (#4872, Cell Signaling, Beverly, USA), anti-STAT5A (clone #5073, rabbit polyclonal antiserum was kindly provided by Richard Moriggl, Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, Austria), anti-GFP (600-103-215, Rockland, Gilbertsville, USA), anti-FLAG (F3165), anti-α-tubulin (T5168, Sigma, St. Louis, USA), anti-GAPDH (sc-32233), anti-Abl (sc-131), anti-Hck (sc-72), anti-cSrc (sc-19, Santa Cruz Biotechnology, Santa Cruz, USA), anti-vSrc (MABS193, Millipore, Billerica, MA, USA) and anti-HA (MMS-101R, Covance, Princeton, New Jersey, USA) antibodies were used for immunoblotting.

Techniques: Translocation Assay, Expressing, Activation Assay, Binding Assay, Scaffolding

Journal: The Journal of Cell Biology

Article Title: Mechanism of Stx17 recruitment to autophagosomes via IRGM and mammalian Atg8 proteins

doi: 10.1083/jcb.201708039

Figure Lengend Snippet: IRGM recruits Stx17 to autophagosomal membranes. (A) Left: Effects of IRGM knockdown on Stx17-LC3 colocalization. HeLa cells were knocked down for IRGM and transfected with GFP-Stx17. Bars: (main images) 5 µm; (insets) 1 µm. Right: Colocalization (Pearson’s correlation coefficient) between LC3 and GFP-Stx17 analyzed by confocal microscopy. The Western blot indicates IRGM knockdown in cells used for microscopy. (B) CoIP analysis of IRGM overexpression effects on interactions between FLAG-Stx17 and endogenous LC3 in 293T cells. TrueBlot secondary antibody was used to avoid IgG bands. Data indicate means ± SEM of ratios between LC3-II and LC3-I intensities in FLAG-Stx17 IPs normalized to LC3-II/LC3-I ratios in cells/input. (C) Effects of IRGM knockdown on distribution of Stx17 in 25k pellets (schematic shows sequential differential centrifugation as in ). P, pellet; S, supernatant. Right: Intensities of Stx17 normalized to Sec22b in 25k fractions. Data indicate means ± SEM of relative intensities. (D) Differential fractionation (schematic) and immunoblotting analysis showing effects of IRGM knockdown on relocalization of Stx17 from membranes pelleted at 100,000 g to 100K supernatant containing cytosol from cell extracts (293T cells). The blot below the schematic shows a comparison of Stx17 levels in total cell lysates from control and IRGM siRNA–treated cells. The graph shows quantifications of Stx17 levels normalized to actin in 100K supernatant. Data indicate means ± SEM of relative intensities. **, P < 0.01 ( n = 3) t test.

Article Snippet: In some instances, rabbit TrueBlot anti–rabbit IgG HRP (18-8816-33; Rockland), which preferentially recognizes unreduced IgG, was used as a secondary antibody to avoid the 55-kD heavy chain and 23-kD light chain IgG bands.

Techniques: Knockdown, Transfection, Confocal Microscopy, Western Blot, Microscopy, Over Expression, Centrifugation, Fractionation, Comparison, Control

Journal: The Journal of Cell Biology

Article Title: Mechanism of Stx17 recruitment to autophagosomes via IRGM and mammalian Atg8 proteins

doi: 10.1083/jcb.201708039

Figure Lengend Snippet: IRGM relationship with R-SNARE and HOPS complexes participating in autophagosome–lysosome fusion. (A) CoIP analysis between endogenous VAMP8 and IRGM in 293T cells. (B) 293T cells were knocked down for IRGM, and endogenous VAMP8 and Stx17 interactions were analyzed by coIP. Right: Quantifications of Stx17 IP/input ratio in VAMP8 IPs. (C) CoIP analysis of FLAG-IRGM and GFP-VAMP8 interactions upon induction of autophagy with pp242 in 293T cells; pp242 activity was monitored by pP70S6K phosphorylation (bottom). Right: FLAG-IRGM intensities normalized to GFP-VAMP8 in GFP-VAMP8 IPs. Data indicate means ± SEM of normalized intensities. **, P < 0.01 ( n = 3) t test. (D) CoIP analysis of pp242 effect on interactions between FLAG-IRGM and GFP-VAMP8 in 293T cells. In IP blots, GFP-VAMP8 and GFP sections were cropped to avoid IgG bands. (E and F) CoIP analysis of GFP-IRGM and HOPS subunits (endogenous VPS39 and VPS33A) in 293T cells. In E, IP blots for GFP-VAMP8 and GFP sections were cropped to avoid IgG bands. In F, TrueBlot secondary antibody was used to avoid IgG bands. (G) Analysis GFP-IRGM IPs for presence of VPS8 (CORVET subunit) in 293T cells. (H) Analyses of effects of VPS33A knockdown on interactions between GFP-LC3B and endogenous Stx17. Data indicate means ± SEM of intensity ratios (normalization to GFP-LC3B in IP). *, P < 0.01 ( n = 3) t test. WB, Western blot.

Article Snippet: In some instances, rabbit TrueBlot anti–rabbit IgG HRP (18-8816-33; Rockland), which preferentially recognizes unreduced IgG, was used as a secondary antibody to avoid the 55-kD heavy chain and 23-kD light chain IgG bands.

Techniques: Activity Assay, Phospho-proteomics, Knockdown, Western Blot