Data from: Clathrin-independent endocytosis and retrograde transport in cancer cells tune immune synapse organization and CD8 T cell response
Data files
May 13, 2026 version files 267.73 KB
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README.md
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source_data_numerical_data.xlsx
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Abstract
Endophilin A3-mediated clathrin-independent endocytosis (EndoA3-mediated CIE) contributes to the internalization of immunoglobulin-like proteins, including key immune synapse components. Here, we identify ICAM1 as a novel EndoA3-dependent cargo, alongside ALCAM. We demonstrate that both proteins subsequently follow retromer-dependent retrograde transport to the trans-Golgi network (TGN) in cancer cells. From there, we propose that they undergo polarized redistribution to the plasma membrane, where they contribute to immune synapse formation between cancer cells and cytotoxic CD8 T cells. Disruption of EndoA3 or retromer components significantly affects the response of autologous cytotoxic CD8 T cells, as evidenced by reduced cytokine production and secretion, but increased lytic activity, while proliferation and later activation marker expression remain intact. This is accompanied by diminished ICAM1 density at the immune synapse, where we observe it arriving via polarized vesicular transport, indicating altered synapse organization. Indeed, cancer cells lacking EndoA3-mediated CIE or retromer form enlarged immune synapses that fail to sustain full T cell cytokine secretion, suggesting a compensatory attempt by T cells to overcome the defective synapse, while likely promoting more transient contacts that potentially favor serial killing. Together, these findings reveal that EndoA3-mediated CIE and retrograde transport act in concert in cancer cells to relocate immune synapse components via the Golgi, thereby fine-tuning the balance between cytotoxic T cell cytokine secretion and lytic activity. These insights contribute to a better understanding of the mechanisms governing immune synapse formation and organization, providing a necessary foundation for the long-term identification of new strategies to enhance T cell–mediated anti-tumor immunity.
Dataset DOI: 10.5061/dryad.bcc2fqzts
Description of the data and file structure
This dataset contains all numerical data used to generate figures, charts, and statistical analyses of the manuscript https://doi.org/10.7554/eLife.105821.3.
Files and variables
File: source_data_numerical_data.xlsx
Description: The data are provided in a single Excel file, organized by worksheet. Each worksheet corresponds to an individual figure or figure supplement of the manuscript https://doi.org/10.7554/eLife.105821.3, and includes the underlying numerical values used for the generation of graphs in each figure panel. For each panel, the numerical values are presented for each independent experiment (repeats are numbered #1, #2, #3, etc. in the Excel file).
| Worksheet | Panel | Description | Brief explanation & Units |
|---|---|---|---|
| Figure 1 | B | Numerical data used to generate the fluorescence intensity profile plot of Figure 1B. | TMR-Star and GalT-GFP-SNAP intensities (columns D and E, respectively; arbitrary units) along a profile line (column C; µm). From confocal images of GalT-GFP-SNAP and TMR-Star in HeLa cells stably expressing the Golgi-resident GFP-fused SNAP-tag construct (HeLa GalT-GFP-SNAP). |
| C | Numerical data for siCtrl, siVPS35 and siVPS26 conditions, used to generate the bar chart of Figure 1C. | Relative intensities of GalT-GFP-SNAP-anti-ALCAM western blot signals in siVPS35 (column D) and siVPS26A (column E) conditions, normalized to the negative control condition (siCtrl, column C, set to 1). Retrograde transport of ALCAM was performed using continuous BG-labeled anti-ALCAM antibody uptake for 4 h at 37°C in HeLa GalT-GFP-SNAP cells transfected for 72 h with siRNAs. | |
| D | Numerical data for siCtrl, siVPS35 and siVPS26 conditions, used to generate the bar chart of Figure 1D. | Relative intensities of GalT-GFP-SNAP-anti-ICAM1 western blot signals in siVPS35 (column D) and siVPS26A (column E) conditions, normalized to the negative control condition (siCtrl, column C, set to 1). Retrograde transport of ICAM1 was performed using continuous BG-labeled anti-ICAM1 antibody uptake for 4 h at 37°C in HeLa GalT-GFP-SNAP cells transfected for 72 h with siRNAs. | |
| E | Numerical data for siCtrl and siEndoA3 conditions, used to generate the bar chart of Figure 1E. | Relative intensities of GalT-GFP-SNAP-anti-ALCAM western blot signals in siEndoA3 condition (column D), normalized to the negative control condition (siCtrl, column C, set to 1). Retrograde transport of ALCAM was performed using continuous BG-labeled anti-ALCAM antibody uptake for 4 h at 37°C in HeLa GalT-GFP-SNAP cells transfected for 72 h with siRNAs. | |
| F | Numerical data for siCtrl and siEndoA3 conditions, used to generate the bar chart of Figure 1F. | Relative intensities of GalT-GFP-SNAP-anti-ICAM1 western blot signals in siEndoA3 condition (column D), normalized to the negative control condition (siCtrl, column C, set to 1). Retrograde transport of ALCAM was performed using continuous BG-labeled anti-ICAM1 antibody uptake for 4 h at 37°C in HeLa GalT-GFP-SNAP cells transfected for 72 h with siRNAs. | |
| Figure 2 | D | Numerical data for WT, empty plasmid (Φ) and EndoA3-expressing (EndoA3+) conditions, used to generate the graph of Figure 2D. Grey cells in the Excel file are empty, as each condition doesn't contain the same number of values. | Quantifications of anti-ALCAM antibody internalization from confocal images, expressed as fractions of WT condition (arbitrary units). Continuous uptake of anti-ALCAM antibody was performed for 15 min at 37°C in the following LB33-MEL cell lines: wild-type (WT, column C), stably transfected with empty plasmid (Φ, column D), or stably expressing EndoA3-GFP (LB33-MEL EndoA3+, column E). Internalized antibody was detected by immunofluorescence and imaged by confocal microscopy. |
| E | Numerical data for siCtrl and siEndoA3 conditions, used to generate the graph of Figure 2E. Grey cells in the Excel file are empty, as each condition doesn't contain the same number of values. | Quantifications of anti-ALCAM antibody internalization from confocal images, expressed as fractions of negative control siRNA (siCtrl) condition (arbitrary units). Continuous uptake of anti-ALCAM antibody was performed for 15 min at 37°C in LB33-MEL cells stably expressing EndoA3-GFP (LB33-MEL EndoA3+) transfected with siRNAs: negative control (siCtrl) or against EndoA3 (siEndoA3). Internalized antibody was detected by immunofluorescence and imaged by confocal microscopy. | |
| Figure 3 | B | Numerical data for siCtrl and siEndoA3 conditions, used to generate the graphs of Figure 3B (% IL-2 +, % TNFα +, % IFNγ +) | Quantifications of the fraction of cytokine producing CD8 T cells: IL-2, columns C-D; TNFα, columns G-H; IFNγ, columns K-L (units: %). CD8 T cells were stimulated by siCtrl or siEndoA3 treated LB33-MEL EndoA3+ cells. |
| C | Numerical data for siCtrl and siEndoA3 conditions, used to generate the graphs of Figure 3C (MFI of IL-2 +, TNFα + and IFNγ +) | Quantifications of the absolute amount of cytokines produced by CD8 T cells: IL-2, columns C-D; TNFα, columns G-H; IFNγ, columns K-L. Data are presented as median fluorescence intensity (MFI, arbitrary units). CD8 T cells were stimulated by siCtrl or siEndoA3 treated LB33-MEL EndoA3+ cells. | |
| E | Numerical data for siCtrl and siEndoA3 conditions, used to generate the bar chart of Figure 3E. | Quantification of IFNγ secretion (detected by ELISA) from CD8 T cells, cultured alone (T only, column G) or co-cultured for 20 h with the following LB33-MEL cell lines: wild-type LB33-MEL cells (WT, column C), LB33-MEL cells stably transfected with empty (Φ, column D) or EndoA3-GFP encoding plasmid (EndoA3+), treated with negative control siRNA (siCtrl, column E) or with EndoA3-targeting siRNA (siEndoA3, column F). Data are presented as fractions of WT siCtrl condition (set to 1, column C). | |
| F | Numerical data for siCtrl and siEndoA3 conditions, used to generate the graph of Figure 3F. | Quantification of CD8 T cell cytolytic efficiency against LB33-MEL EndoA3+ cells transfected with negative control siRNA (siCtrl, columns D-F) or siRNA against EndoA3 (siEndoA3, columns G-I) (units: %). CD8 T cell killing efficiency was determined by Chrome 51 release assay and is presented as percentage of lysed LB33-MEL EndoA3+ cells. Different T cell:Target cell ratios were tested (column C). | |
| G | Numerical data for siCtrl, siVPS35 and siVPS26 conditions, used to generate the bar chart of Figure 3G. | Quantification of IFNγ secretion (detected by ELISA) from CD8 T cells, cultured alone (T only, column F) or co-cultured for 20 h at 37°C with EndoA3+LB33 MEL cells transfected with siRNAs: negative control (siCtrl, column C), or against retromer subunits (siVPS35 or siVPS26A, columns D and E respectively). Data are presented as fractions of siCtrl condition (set to 1, column C). | |
| Figure 4 | C | Numerical values used to generate the track displacement plot in Figure 4C. | Tracking of ICAM1-positive carriers in stable HLA-A*68012–expressing HeLa cell transiently expressing ICAM1-mScarlet from spinning-disk confocal movies, in a cell region involved in an immune synapse with a CD8 T cell. Each individual track has a specific ID number (column B). For each track, the coordinates of the carrier are provided (X displacement and Y displacement, columns D and E respectively; units: µm) over time (Frames, column C; units: seconds). The first position of each track was arbitrarily set at (0,0) in XY position. |
| D | Numerical values used to generate the track displacement plot in Figure 4D. | Tracking of ICAM1-positive carriers in stable HLA-A*68012–expressing HeLa cell transiently expressing ICAM1-mScarlet from spinning-disk confocal movies, in a cell region that is not involved in an immune synapse. Each individual track has a specific ID number (column B). For each track, the coordinates of the carrier are provided (X displacement and Y displacement, columns D and E respectively; units: µm) over time (Frames, column C; units: seconds). The first position of each track was arbitrarily set at (0,0) in XY position. | |
| E | Numerical values used to generate the track displacement plot in Figure 4E. | Tracking of ICAM1-positive carriers in stable HLA-A*68012–expressing HeLa cell transiently expressing ICAM1-mScarlet from spinning-disk confocal movies, in a cell region that is not involved in an immune synapse. Each individual track has a specific ID number (column B). For each track, the coordinates of the carrier are provided (X displacement and Y displacement, columns D and E respectively; units: µm) over time (Frames, column C; units: seconds). The first position of each track was arbitrarily set at (0,0) in XY position. | |
| F | Numerical values used to generate the bar chart of Figure 4F. | Quantification of ICAM1-positive carrier track densities (units: number of tracks/µm2) in differents cellular regions. Tracking of ICAM1-positive carriers was performed in stable HLA-A*68012–expressing HeLa cell transiently expressing ICAM1-mScarlet imaged by spinning-disk confocal movies. Region 1 (column B) is involved in an immune synapse, while regions 2 and 3 (columns C and D) are not. | |
| G | Numerical values used to generate the plot of track proportion and direction in Figure 4G. Grey cells in the Excel file are empty, as each condition doesn't contain the same number of values. | Quantification of the proportion of ICAM1-positive carrier tracks in every direction (values expressed in angular degrees to an arbitrary direction) in differents cellular regions. Tracking of ICAM1-positive carriers was performed in stable HLA-A*68012–expressing HeLa cell transiently expressing ICAM1-mScarlet imaged by spinning-disk confocal movies. Region 1 (column B) is involved in an immune synapse, while regions 2 and 3 (columns C and D) are not. | |
| Figure 5 | B | Numerical data for siCtrl and siEndoA3 conditions, used to generate the graph of Figure 5B. Grey cells in the Excel file are empty, as each condition doesn't contain the same number of values. | Quantification of relative ICAM1 recruitment to the vicinity of CD8 T cell when an immune synapse-like conjugate is formed between a CD8 T cell and a stable HLA-A*68012-expressing HeLa cell transiently expressing ICAM1-mScarlet in suspension (arbitrary units). HLA-A*68012-expressing HeLa cells were transfected for 72 h with siRNAs: negative control (siCtrl, column C) or against EndoA3 (siEndoA3, column D). Quantified from confocal images. |
| D | Numerical data for siCtrl and siEndoA3 conditions, used to generate the graph of Figure 5D. Grey cells in the Excel file are empty, as each condition doesn't contain the same number of values. | Quantifications of the sizes of immune synapse-like conjugates formed between CD8 T cells and stable EndoA3-GFP-expressing LB33-MEL cells transfected with siRNAs: negative control (siCtrl, column C) or against EndoA3 (siEndoA3, column D) (units: µm). Quantified from confocal images. | |
| F | Numerical data for siCtrl and siVPS26 conditions, used to generate the graph of Figure 5F. Grey cells in the Excel file are empty, as each condition doesn't contain the same number of values. | Quantifications of the sizes of immune synapse-like conjugates formed between CD8 T cells and stable EndoA3-GFP-expressing LB33-MEL cells transfected with siRNAs: negative control (siCtrl, column C) or against VPS26 (siVPS26A, column D) (units: µm). Quantified from confocal images. | |
| Figure 1—figure supplement 1 | A | Numerical data used to generate the fluorescence intensity profile plot of Figure 1—figure supplement 1 A. | TMR-Star and GalT-GFP-SNAP intensities (columns D and E, respectively; arbitrary units) along a profile line (column C; µm). From confocal images of GalT-GFP-SNAP and TMR-Star in LB33-MEL cells stably expressing the Golgi-resident GFP-fused SNAP-tag construct (LB33-MEL GalT-GFP-SNAP). |
| B | Numerical data used to generate the fluorescence intensity profile plot of Figure 1—figure supplement 1 B. | TGN46 and GalT-GFP-SNAP intensities (columns D and E, respectively; arbitrary units) along a profile line (column C; µm). From confocal images of GalT-GFP-SNAP and immunolabeled TGN46 in LB33-MEL cells stably expressing the Golgi-resident GFP-fused SNAP-tag construct (LB33-MEL GalT-GFP-SNAP). | |
| C | Numerical data for siCtrl, siVPS35 and siVPS26 conditions, used to generate the bar charts of Figure 1—figure supplement 1 C. | Quantifications of VPS26 (columns C-E) and VPS35 (columns G-I) relative band intensities from western blots on HeLa GalT-GFP-SNAP cells treated with siRNAs: negative control (siCtrl, columns C and G), against VPS35 (siVPS35, columns D and H) or against VPS26 (siVPS26A, columns E and I). Intensities were normalized to the negative control condition (siCtrl, column C and G, set to 1). | |
| D | Numerical data for siCtrl, siVPS35 and siVPS26 conditions, used to generate the bar chart of Figure 1—figure supplement 1 D. | Relative intensities of GalT-GFP-SNAP-anti-ICAM1 western blot signals in siVPS35 (column D) and siVPS26A (column E) conditions, normalized to the negative control condition (siCtrl, column C, set to 1). Retrograde transport of ICAM1 was performed using continuous BG-labeled anti-ICAM1 antibody uptake for 4 h at 37°C in LB33-MEL GalT-GFP-SNAP cells transfected for 72 h with siRNAs. | |
| E | Numerical data for siCtrl, siVPS35 and siVPS26 conditions, used to generate the bar charts of Figure 1—figure supplement 1 E. | Quantifications of VPS26 (columns C-E) and VPS35 (columns G-I) relative band intensities from western blots on LB33-MEL GalT-GFP-SNAP cells treated with siRNAs: negative control (siCtrl, columns C and G), against VPS35 (siVPS35, columns D and H) or against VPS26 (siVPS26A, columns E and I). Intensities were normalized to the negative control condition (siCtrl, column C and G, set to 1). | |
| F | Numerical data for siCtrl and siRab6 conditions, used to generate the bar chart of Figure 1—figure supplement 1 F. | Relative intensities of GalT-GFP-SNAP-anti-ALCAM western blot signals in siRab6 condition (column D), normalized to the negative control condition (siCtrl, column C, set to 1). Retrograde transport of ALCAM was performed using continuous BG-labeled anti-ALCAM antibody uptake for 4 h at 37°C in HeLa GalT-GFP-SNAP cells transfected for 72 h with siRNAs. | |
| G | Numerical data for siCtrl and siRab6 conditions, used to generate the bar chart of Figure 1—figure supplement 1 G. | Quantifications of Rab6 relative band intensities from western blots on HeLa GalT-GFP-SNAP cells treated with siRNAs: negative control (siCtrl, column C), or against Rab6 (siRab6, column D). Intensities were normalized to the negative control condition (siCtrl, column C, set to 1). | |
| H | Numerical data for siCtrl and siEndoA3 conditions, used to generate the bar chart of Figure 1—figure supplement 1 H. | Quantifications of EndoA3 relative band intensities from western blots on HeLa GalT-GFP-SNAP cells treated with siRNAs: negative control (siCtrl, column C), or against EndoA3 (siEndoA3, column D). Intensities were normalized to the negative control condition (siCtrl, column C, set to 1). | |
| I | Numerical data for GFP+ and EndoA3+ conditions, used to generate the bar chart of Figure 1—figure supplement 1 I. | Relative intensities of GalT-GFP-SNAP-anti-ALCAM western blot signals in LB33-MEL cells expressing GFP alone (column C) or EndoA3-GFP (column D). Retrograde transport of ALCAM was performed using continuous BG-labeled anti-ALCAM antibody uptake for 4 h at 37°C in LB33-MEL GalT-GFP-SNAP cells transfected with plasmids allowing transient expression of GFP alone (GFP+, column C) or EndoA3-GFP (EndoA3+, column D). GFP alone (GFP+) condition was used as reference for normalization. | |
| Figure 2—figure supplement 2 | C | Numerical data for siCtrl and siEndoA3 conditions, used to generate the bar chart of Figure 2—figure supplement 2 C. | Quantifications of EndoA3 relative band intensities from western blots on LB33-MEL EndoA3+ cells (expressing EndoA3-GFP) treated with siRNAs: negative control (siCtrl, column C), or against EndoA3 (siEndoA3, column D). Intensities were normalized to the negative control condition (siCtrl, column C, set to 100%). |
| Figure 3—figure supplement 1 | A | Numerical data for siCtrl and siEndoA3 conditions, used to generate the graph of Figure 3—figure supplement 1 A. | Flow cytometry analysis of LB33-MEL cells stably expressing EndoA3-GFP (LB33-MEL EndoA3+) transfected with siRNAs: negative control (siCtrl, column C) or against EndoA3 (siEndoA3, column D). Quantification is based on GFP signal and presented as normalized MFI (mean fluorescence intensity) of GFP relative to siCtrl condition. |
| B | Numerical data for siCtrl and siEndoA3 conditions, used to generate the graph of Figure 3—figure supplement 1 B. Grey cells in the Excel file are empty, as each condition doesn't contain the same number of values. | Quantification of surface area of LB33-MEL EndoA3+ cells transfected with siRNAs: negative control (siCtrl, column C) or against EndoA3 (siEndoA3, column D) (units: µm2 per cell). | |
| C | Numerical data for siCtrl and siEndoA3 conditions, used to generate the graph of Figure 3—figure supplement 1 C. Grey cells in the Excel file are empty, as each condition doesn't contain the same number of values. | Quantification of aspect ratio of LB33-MEL EndoA3+ cells transfected with siRNAs: negative control (siCtrl, column C) or against EndoA3 (siEndoA3, column D). The aspect ratio is the ratio of major axis to minor axis of a fitted ellipse to each cell, and is always ≥1. An aspect ratio of 1 is a perfect circle and higher values indicate elongation. | |
| D | Numerical data for siCtrl and siEndoA3 conditions, used to generate the graph of Figure 3—figure supplement 1 D. Grey cells in the Excel file are empty, as each condition doesn't contain the same number of values. | Quantification of roundness of LB33-MEL EndoA3+ cells transfected with siRNAs: negative control (siCtrl, column C) or against EndoA3 (siEndoA3, column D) (artibtrary units). The roundness is a relative value comprised between 0 and 1. A value of 1 indicates a perfect circle. As the value approaches 0, the shape is increasingly elongated or irregular. | |
| E | Numerical data for siCtrl and siEndoA3 conditions, used to generate the bar chart of Figure 3—figure supplement 1 E. | Quantification of surface ICAM1 levels on LB33-MEL EndoA3+ cells transfected with siRNAs: negative control (siCtrl, column C) or against EndoA3 (siEndoA3, column D). Quantified by flow cytometry analysis and presented as normalized MFI of ICAM1 signal in siCtrl condition. | |
| F | Numerical data for siCtrl and siEndoA3 conditions, used to generate the bar chart of Figure 3—figure supplement 1 F. | Quantification of surface ALCAM levels on LB33-MEL EndoA3+ cells transfected with siRNAs: negative control (siCtrl, column C) or against EndoA3 (siEndoA3, column D). Quantified by flow cytometry analysis and presented as normalized MFI of ALCAM signal in siCtrl condition. | |
| G | Numerical data for siCtrl and siEndoA3 conditions, used to generate the graph of Figure 3—figure supplement 1 G. | Quantification of the surface levels of the T cell activation marker PD-1 after 4 days of stimulation by LB33-MEL EndoA3+ cells transfected with either control siRNAs (siCtrl, column C), or siRNAs against EndoA3 (siEndoA3, column D). Quantified by flow cytometry analysis and presented as absolute MFI (arbitrary units). | |
| H | Numerical data for siCtrl and siEndoA3 conditions, used to generate the graph of Figure 3—figure supplement 1 H. | Quantification of the surface levels of the T cell activation marker CD137 after 4 days of stimulation by LB33-MEL EndoA3+ cells transfected with either control siRNAs (siCtrl, column C), or siRNAs against EndoA3 (siEndoA3, column D). Quantified by flow cytometry analysis and presented as absolute MFI (arbitrary units). | |
| I | Numerical data for siCtrl and siEndoA3 conditions, used to generate the graph of Figure 3—figure supplement 1 I. | Quantification of the surface levels of the T cell activation marker TIM-3 after 4 days of stimulation by LB33-MEL EndoA3+ cells transfected with either control siRNAs (siCtrl, column C), or siRNAs against EndoA3 (siEndoA3, column D). Quantified by flow cytometry analysis and presented as absolute MFI (arbitrary units). | |
| J | Numerical data for siCtrl and siEndoA3 conditions, used to generate the graph of Figure 3—figure supplement 1 J. | Quantification of CD8 T cell proliferation after 4 days of stimulation by LB33-MEL EndoA3+ cells transfected with either control siRNAs (siCtrl, column C) or siRNAs against EndoA3 (siEndoA3, column D). Quantified by flow cytometry analysis and presented as proliferation index. | |
| K | Numerical data for siCtrl and siEndoA3 conditions, used to generate the graph of Figure 3—figure supplement 1 K. | Quantification of CD8 T cell degranulation percentage after a 10 min stimulation by LB33-MEL EndoA3+ cells transfected with either control siRNAs (siCtrl, column C) or siRNAs against EndoA3 (siEndoA3, column D). Quantified by flow cytometry analysis as the percentage of CD107a-positive cells. | |
| Figure 4—figure supplement 1 | A | Numerical data for 'No MUM3' and 'With MUM3', WT or HLA+ conditions, used to generate the bar chart of Figure 4—figure supplement 1 A. | Quantification of IFNγ secretion (detected by ELISA) from anti-MUM-3 CD8 T cells, co-cultured for 20 h with wild-type HeLa cells (WT, columns C and E) or stable HLA-A*68012-expressing HeLa cells (HLA+, columns D and F), with or without the presence of 300 ng/mL MUM-3 antigenic peptide (columns C-D or E-F, respectively). Data show absolute concentration of secreted IFNγ (units: pg/mL). |
| C | Numerical data used to generate the fluorescence intensity profile plot of Figure 4—figure supplement 1 C. | CD45 and ICAM1-mScarlet intensities (columns D and E, respectively; arbitrary units) along a profile line (column C; µm). From an Airyscan image of an immune synapse-like conjugate formed between a CD8 T cell (immunolabeled for CD45) and an adherent stable HLA-A*68012-expressing HeLa cell transiently expressing ICAM1-mScarlet. | |
| Figure 5—figure supplement 1 | A | Numerical data used to generate the fluorescence intensity profile plot of Figure 5—figure supplement 1 A. | CD45 and ICAM1-mScarlet intensities (columns D and E, respectively; arbitrary units) along a profile line (column C; µm). From an Airyscan image of an immune synapse-like conjugate formed between a CD8 T cell (immunolabeled for CD45) and a stable HLA-A*68012-expressing HeLa cell in suspension transiently expressing ICAM1-mScarlet. |
