Journal: bioRxiv

Article Title: Pharmacologically diverse antidepressant drugs disrupt the interaction of BDNF receptor TRKB and the endocytic adaptor AP-2

doi: 10.1101/591909

Figure Lengend Snippet: The colocalization (indicated by the arrows) of TRKB with (a-c) early (RAB5), (d-f) late (RAB7) and (g-i) recycling (RAB11) endosome markers was determined in the spines and neurites of cultured cortical neurons (14-16 DIV) treated with fluoxetine (1 μM/15 min) (n=16-37 spines or neurite shafts /group). *p<0.05 from ctrl group. Black crosses indicate mean ± SEM. The scale bars indicate 1 μm.

Article Snippet: The cells were stained with anti-TRKB antibody (1:500, #AF1494, R&D Systems) and anti-RAB5 antibody (1:500, #NB120-13253, Novus Biologicals), anti-RAB7 antibody (1:500, #D95F2, Cell Signaling), or anti-RAB11A antibody (5 μg/mL, #71-5300, Thermo Fisher Scientific) ON at 4°C under agitation.

Techniques: Cell Culture

Journal: The Journal of Biological Chemistry

Article Title: Rab5 nucleotide binding promotes oxidative metabolism to fuel hepatocellular carcinoma cell proliferation

doi: 10.1016/j.jbc.2026.111321

Figure Lengend Snippet: Rab5 is upregulated in HCC and associated with cancer hallmarks . A , volcano plot from TNMplot showing expression of known lipid droplet (LD)–associated proteins, including Rab5A/B/C, in HCC tumors versus adjacent normal tissues from n = 53 patients. B , representative immunohistochemistry images from a liver tissue microarray showing Rab5 staining in normal liver (n = 4) versus HCC specimens (n = 7). C , quantification of Rab5 immunohistochemistry scores from the tissue microarray (mean ± SD, ∗∗∗ p < 0.0002; Welch's t test). D , cancer hallmark gene set enrichment analysis based on the study by Menyhart et al . , showing Rab5-associated genes enriched in proliferation, invasion, and evading growth suppressors. E , Kaplan–Meier survival analysis from the TCGA–LIHC dataset stratified by Rab5 expression. High Rab5 expression correlates with poorer overall survival (log-rank test, p = 0.06). HCC, hepatocellular carcinoma; LIHC, Liver Hepatocellular Carcinoma Cohort; TCGA, The Cancer Genome Atlas.

Article Snippet: Antibodies against Rab5A (2143S), PLIN2 (95109), and EEA1 (2411S) were purchased from Cell Signaling Technology.

Techniques: Expressing, Immunohistochemistry, Microarray, Staining

Journal: Journal of Extracellular Vesicles

Article Title: Large-scale isolation and cytotoxicity of extracellular vesicles derived from activated human natural killer cells

doi: 10.1080/20013078.2017.1294368

Figure Lengend Snippet: Markers and TEM image of isolated aNK extracellular vesicles. (a) Western blot analysis of isolated EVs and their parental cells. Thirty μg protein were loaded in each lane and probed with antibodies to CD63 (GeneTex, GTX37555, 1:500), Rab5A (Aviva Systems Biology, ARP56563-P050), cytochrome C (Santa Cruz Biotech, sc-13560, 1:500), granulysin (Antibodies-online, Inc. ABON1107438, 1:500), CD56 (EMD Millipore, MAB2120Z, 1:500). For fibronectin, only 5 μg of protein was loaded (GeneTex, GTX72724, 1:1,000). The un-cropped images with size markers are shown in Figure S2. (b) Transmission electron microscopy of EVs. aNK EVs were isolated as described in . Aliquots of samples were subjected to TEM imaging as described in Materials and methods. A representative image is shown. Bar: 200 nm

Article Snippet: The blots were probed with antibodies to CD63 (GeneTex, GTX37555) ( )), or from BD Bioscience, H5C6 under non-reducing condition ( )), Rab5A (Aviva Systems Biology (San Diego, CA, USA), ARP56563-P050), cytochrome C (Santa Cruz Biotech, sc-13560, 1:500), fibronectin (GeneTex, GTX72724, 1:1,000), and granulysin (Antibodies-online, Inc., ABON1107438, 1:500).

Techniques: Isolation, Western Blot, Transmission Assay, Electron Microscopy, Imaging

Journal: iScience

Article Title: Centrosomal P4.1-associated protein is a novel regulator of ESCRT pathway function during endosome maturation

doi: 10.1016/j.isci.2026.114659

Figure Lengend Snippet: CPAP depletion does not affect Rab5 recruitment to the endosomes and ligand-bound EGFR-positive endosomes HeLa cells expressing control or CPAP shRNA were treated with AF555-EGF ligand for the indicated time points, stained, and subjected to 4-color imaging by confocal microscopy. Images representing the detection of Rab5 and EEA1 (A), Rab5 and CD63 (B), and Rab5 (along with AF555-EGF) (C) are shown. Left (A–C): maximum intensity-projection images of confocal Z stacks. Right (A–C): single Z-plane of images. Bottom left graph in (C): co-localization (yellow) was quantified by determining the percentages of EGF-positive (red) puncta containing Rab5 (green) puncta in representative single Z-planes of each cell and quantified from multiple cells across at least three experiments. Bottom right graph in (C): relative integrated fluorescence intensity values of Rab5 staining quantified in representative single Z-planes of each cell and quantified from multiple cells across at least three experiments. Scale bars: 10 μm. p values were not statistically significant. Zoomed images correspond to the dashed inset boxes of the indicated images. Note: (B) and (C) present data from the same experiments where 4-color imaging was done and convey information on two different aspects based on three markers at a time. Since the visuals of the same cell can help with more reliable interpretation of the data, images of the same cell were used, where possible, for (B) and (C) with the same or different pseudo-color. Hence, duplication of some sub-images among (B) and (C) is intentional.

Article Snippet: Rab5 antibody , Proteintech , 20228-1-AP.

Techniques: Expressing, Control, shRNA, Staining, Imaging, Confocal Microscopy, Fluorescence

Journal: iScience

Article Title: Centrosomal P4.1-associated protein is a novel regulator of ESCRT pathway function during endosome maturation

doi: 10.1016/j.isci.2026.114659

Figure Lengend Snippet: CPAP depletion disrupts Rab5-to-Rab7 conversion (A) HeLa cells expressing control or CPAP shRNA were treated with untagged EGF for 60 min, stained for Rab5 and Rab7, and imaged by Airyscan super-resolution microscopy. Left: maximum intensity-projection images of Z stacks; middle: single Z-plane of images; right: co-localization (yellow) was quantified by determining the percentages of Rab5-positive (green) puncta containing Rab7 (red) puncta in representative single Z-planes of each cell and quantified from multiple cells across at least three experiments. (B) HeLa cells expressing control or CPAP shRNA were transfected with GFP-Rab5 and mCherry-Rab7 constructs, treated with untagged EGF for 60 min, and imaged by Airyscan super-resolution microscopy. Left: maximum intensity-projection images of Z stacks; middle: single Z-plane of images; right: co-localization (yellow) was quantified by determining the percentages of GFP-Rab5-positive (green) puncta containing mCherry-Rab7 (red) puncta in representative single Z-planes of each cell and quantified from multiple cells across at least three experiments. The object-based co-localization macro tool FIJI was employed. (C) HeLa cells stably expressing control or CPAP-shRNA were transfected with control vector (GFP), GFP-Rab7 (WT; wild-type) or GFP-Rab7 (DN; dominant negative) vector constructs, treated with AF555-EGF ligand for 60 min, and stained for CD63 to mark MVBs/late endosomes, and imaged by confocal microscopy to determine AF555-EGF and CD63 co-localization. Left top row: GFP expression in control and Rab7 construct-expressing cells; left bottom rows: representative single Z-plane of images showing ligand-bound EGFR-CD63 co-localization; right: co-localization (yellow) was quantified by determining the percentages of EGF-positive (red) puncta containing CD63 (green) puncta in representative single Z-planes of each cell and quantified from multiple cells across at least three experiments. Zoomed images correspond to the dashed inset boxes of the indicated images. Scale bars: 10 μm. p values: ∗∗∗∗<0.0001 by unpaired nonparametric Mann-Whitney test.

Article Snippet: Rab5 antibody , Proteintech , 20228-1-AP.

Techniques: Expressing, Control, shRNA, Staining, Super-Resolution Microscopy, Transfection, Construct, Stable Transfection, Plasmid Preparation, Dominant Negative Mutation, Confocal Microscopy, MANN-WHITNEY

Journal: iScience

Article Title: Centrosomal P4.1-associated protein is a novel regulator of ESCRT pathway function during endosome maturation

doi: 10.1016/j.isci.2026.114659

Figure Lengend Snippet: Rab5-to-Rab7 conversion and EGFR trafficking to late endosomes are restored in CPAP-depleted cells upon HRS, but not TSG101, overexpression (A) Schematic of the experimental strategy using control and CPAP-specific siRNA-treated HeLa cells with and without GFP-HRS or GFP-TSG101 expression. (B and C) Control and CPAP-specific siRNA-treated HeLa cells were subjected to mock or GFP-HRS or GFP-TSG101 vector transfection for 24 h, treated with untagged EGF for 60 min, and stained for Rab5 and Rab7 (B) or treated with AF555-EGF for 30 min and stained for Rab7 (C) and imaged by Lightning super resolution microscopy. Left: representative single Z-plane of images showing localization of Rab7 on Rab5-positive puncta (B) and AF555-EGF on Rab7-positive puncta (C) in cells with and without GFP-HRS or GFP-TSG101 expression. Right: co-localization (yellow) was quantified by determining the percentages of Rab5-positive (green) puncta containing Rab7-positive (red) puncta in (B) and EGF-positive (red) puncta containing Rab7 (green, pseudo-color) in (C) in representative single Z-planes of each cell and quantified from multiple cells across at least three experiments. Zoomed images correspond to the dashed inset boxes of the indicated images. Scale bars: 10 μm. p values: ∗<0.05, ∗∗ <0.01, ∗∗∗∗<0.0001 by unpaired nonparametric Mann-Whitney test.

Article Snippet: Rab5 antibody , Proteintech , 20228-1-AP.

Techniques: Over Expression, Control, Expressing, Plasmid Preparation, Transfection, Staining, Super-Resolution Microscopy, MANN-WHITNEY

Journal: iScience

Article Title: Centrosomal P4.1-associated protein is a novel regulator of ESCRT pathway function during endosome maturation

doi: 10.1016/j.isci.2026.114659

Figure Lengend Snippet: Rab5-to-Rab7 conversion and EGFR trafficking to MVB are restored in CPAP- and HRS-depleted cells upon exogenous CPAP expression (A) Schematic of the experimental strategy using control and CPAP- and HRS-specific siRNA-treated HeLa cells with and without siRNA-resistant GFP-CPAP expression. (B) Airyscan super-resolution microscopy images showing cells stained for Rab5 and Rab7 at 60 min time point. Left: representative single Z-plane of images showing localization of Rab5- and Rab7-positive puncta in cells with and without GFP expression. Right: co-localization (yellow) was quantified by determining the percentages of Rab5-positive (green) puncta containing Rab7-positive (red) puncta in representative single Z-planes of each cell and quantified from multiple cells across at least three experiments. (C) Confocal microscopy images showing cells stained for CD63 and AF555-EGF at 60 min time point. Left: representative single Z-plane of images showing localization of CD63 − and EGF-positive puncta in cells with and without GFP expression. Right: co-localization (yellow) was quantified by determining the percentages of EGF-positive (red) puncta containing CD63-positive (green) puncta in representative single Z-planes of each cell and quantified from multiple cells across at least three experiments. The object-based co-localization macro tool FIJI was employed for (B) and (C). Zoomed images correspond to the dashed inset boxes of the indicated images. Scale bars: 10 μm. p values: ∗∗∗<0.001, ∗∗∗∗<0.0001 by unpaired nonparametric Mann-Whitney test.

Article Snippet: Rab5 antibody , Proteintech , 20228-1-AP.

Techniques: Expressing, Control, Super-Resolution Microscopy, Staining, Confocal Microscopy, MANN-WHITNEY

Journal: bioRxiv

Article Title: IFITM proteins promote SARS-CoV-2 infection and are targets for virus inhibition

doi: 10.1101/2020.08.18.255935

Figure Lengend Snippet: a , PLA between SARS-CoV-2 Spike and ACE2 in Calu-3 depleted of IFITM1, IFITM2 or IFITM3 and infected with genuine SARS-CoV-2. Lines represent means of n=2 (a) n=3 (b) (60-100 cells) ±SEM. b , PLA between Spike and ACE2 in Calu-3 cells depleted of IFITM2 and infected with SARS-CoV-2 virus on ice for 2 h and then incubated for 15 min at 37°C. Lines represent means of n=3 (200-300 cells) ±SEM. c , PLA assay between Spike and RAB5A in Calu-3 cells infected as in c . Lines represent means of n=2 (130-200 cells) ±SEM. DAPI (blue), nuclei. PLA signal (yellow). Scale bar, 20 µm. d , Quantification of ACE2-Spike and Spike-RAB5 alpha proximity upon SARS-CoV-2 infection.

Article Snippet: For staining following antibodies were used: IFITM1 (α-IFITM1 Cell Signaling 13126 S), IFITM2 (α-IFITM2 Abcam 236735), IFITM3 (α-IFITM3 Cell Signaling 59212S), SARS Spike CoV-2 (SARS-CoV / SARS-CoV-2 (COVID-19) spike antibody [1A9], GTX-GTX632604), Rab5 alpha (Rab5 (RAB5A) Goat Polyclonal Antibody Origene AB0009-200) and ACE2 (Rabbit polyclonal anti-ACE2 Abcam, ab166755).

Techniques: Infection, Virus, Incubation

Journal: Oncology reports

Article Title: miR-101 inhibits autophagy and enhances cisplatin-induced apoptosis in hepatocellular carcinoma cells.

doi: 10.3892/or.2013.2338

Figure Lengend Snippet: Figure 2. miR-101 targets STMN1, RAB5A, ATG4D and mTOR. (A) Four target gene (STMN1, RAB5A, ATG4D and mTOR) plasmids containing matching or mutant sequences of each gene were constructed. (B) miR-101 significantly reduced the activity of the STMN1, RAB5A, ATG4D and mTOR 3'-UTR luciferase plasmids, while plasmids containing mutant sequences were not significantly affected (*P<0.05). (C) miR-101-mimic significantly reduced STMN1, RAB5A, ATG4D and mTOR mRNA levels, whereas miR-101-inhibitor elevated the mRNA levels of these four genes (*P<0.05). (D) Western blotting showed that miR-101 downregulated the expression levels of STMN1, RAB5A, ATG4D and mTOR protein.

Article Snippet: The primary antibodies used were: microtubuleassociated protein light chain 3 (LC3) and RAB5A rabbit polyclonal antibodies (Novus Biologicals, Littleton, CO, USA), STMN1 and mTOR antibodies (Cell Signaling Technology, Danvers, MA, USA).

Techniques: Mutagenesis, Construct, Activity Assay, Luciferase, Western Blot, Expressing