IL-6 underlies microenvironment immunosuppression and resistance to therapy in glioblastoma
Data files
Mar 02, 2026 version files 2.55 GB
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Fig4c_d_tumor.csv
3.84 KB
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Fig4e-g_Myeloid_AllDataframe_phenograph.csv
22.28 MB
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Fig4e-g_Myeloid_cluster_annotations.csv
411 B
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Fig4e-g_Tcells_AllDataframe_phenograph.csv
6.16 MB
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Fig4e-g_Tcells_cluster_annotations.csv
364 B
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Fig5d_GL261_APOA1_vs_GFP_20220103_GL261_APOA1_405_not(Beads).fcs.clustered.txt.scaffold
240.60 MB
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Fig5d_GL261_CCL4_vs_GFP_20220103_GL261_CCL4_387_not(Beads).fcs.clustered.txt.scaffold
237.01 MB
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Fig5d_GL261_IL-1B_vs_GFP_20220103_GL261_GFP_400_not(Beads).fcs.clustered.txt.scaffold
252.73 MB
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Fig5d_SB28_APOA1_vs_GFP_20220103_SB28_APOA1_105_not(Beads).fcs.clustered.txt.scaffold
200.98 MB
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Fig5d_SB28_CCL4_vs_GFP_20220103_SB28_CCL4_6_not(Beads).fcs.clustered.txt.scaffold
206.95 MB
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Fig5d_SB28_IL-1B_vs_GFP_20220103_SB28_GFP_13_not(Beads).fcs.clustered.txt.scaffold
201.42 MB
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Fig7c_Myeloid_T1_PlateA_D287_myeloid_export_for_scaffold_T1_aPD1.fcs.clustered.txt.scaffold
224.34 MB
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Fig7c_Myeloid_T2_PlateA_D347_myeloid_export_for_scaffold_T2_aPD1.fcs.clustered.txt.scaffold
341.28 MB
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Fig7c_Tcells_T1_PlateA_D287_T_cells_T1_aPD1.fcs.clustered.txt.scaffold
16.74 MB
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Fig7c_Tcells_T2_PlateA_D347_T_cells_T2_aPD1.fcs.clustered.txt.scaffold
21.34 MB
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Fig7d_Myeloid_AllDataframe_phenograph.csv
142.51 MB
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Fig7d_Myeloid_cluster_annotations.csv
369 B
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Fig7d_Tcells_AllDataframe_phenograph.csv
8.61 MB
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Fig7d_Tcells_cluster_annotations.csv
339 B
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Fig8b_GL261_20220103_GL261_GFP_400_not(Beads).fcs.clustered.txt.scaffold
211.30 MB
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Fig8b_SB28_20220103_SB28_GFP_13_not(Beads).fcs.clustered.txt.scaffold
170.24 MB
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Fig8c-e_Myeloid_AllDataframe_phenograph.csv
36.32 MB
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Fig8c-e_Myeloid_cluster_annotations.csv
476 B
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Fig8c-e_Tcells_AllDataframe_phenograph.csv
9.64 MB
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Fig8c-e_Tcells_cluster_annotations.csv
364 B
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README.md
11.98 KB
Abstract
The glioblastoma tumor immune microenvironment (TIME) is an immunosuppressive barrier to therapy that encumbers glioblastoma responses to immune checkpoint inhibition (ICI). Immunosuppressive cytokines, pro-tumor macrophages and myeloid cells, and exhausted T-cells are hallmarks of the glioblastoma TIME. Here we integrate spatial and single-cell analyses of patient-matched human glioblastoma samples before and after ICI with genetic, immunologic, single-cell, and therapeutic studies in preclinical models to show that interleukin-6 (IL-6) neutralization reprograms the glioblastoma TIME to sensitize mouse glioblastoma allografts to ICI and ICI plus radiotherapy. We find rare human glioblastomas that achieve clinical responses to ICI have lower pre-treatment IL-6 compared to glioblastomas that do not respond to ICI. We show that diverse immunostimulatory gene therapies suppress IL-6 in mouse glioblastoma allografts, and that IL-6 from multiple cell types the TIME reduces survival in preclinical models and in patients. IL-6 blockade with a neutralizing antibody sensitizes mouse glioblastoma allografts to ICI by increasing MHCII+ monocytes, CD103+ migratory dendritic cells (DCs), CD11b+ conventional DCs, and effector CD8+ T cells, and by decreasing immunosuppressive Tregs. To translate these findings to a therapeutically relevant combination treatment for patients, we show that IL-6 blockade plus ICI sensitizes mouse glioblastoma allografts to ablative radiotherapy.
https://doi.org/10.5061/dryad.c59zw3rkm
Description of the data and file structure
Mass cytometry data for referenced manuscript
Files and variables
File: Fig4c_d_tumor.csv
Description: Input cell frequency data for PCA
Variables:
- filename: individual samples included in analysis, including GL261 mouse tumor GFP and untreated (unt) controls, SB28 GFP and untreated (unt) controls, and gbm human glioblastoma samples. Numbers following the sample designation indicate unique identifying mouse or human tumor sample number.
- B cells total: total B cell frequency
- CD4.conv: conventional CD4+ T cells frequency
- CD8: total CD8+ T cells frequency
- cDC1: conventional dendritic cells 1 frequency
- cDC2: conventional dendritic cells 2 frequency
- gd T: gamma delta T cells frequency
- Microglia: Microglia frequency
- mono/mac: monocytes and macrophages frequency
- Neutrophils: neutrophils frequency
- NKT: NK- T cells frequency
- pDCs: plasmacytoid dendritic cells frequency
- Tregs: CD4+ T regulatory cells frequency
File: Fig4e-g_Myeloid_AllDataframe_phenograph.csv
Description: Arcsinh transformed single-cell mass cytometry data for myeloid cells.
Variables:
- cell: identifier for each single cell analyzed
- filename: individual samples included in analysis, including GL261 mouse tumor GFP and untreated (unt) controls, SB28 GFP and untreated (unt) controls. Numbers following the sample designation indicate unique identifying mouse numbers.
- CD45 to MHCII: arcsinh-transformed marker intensity values for each marker
- phenograph: phenograph cluster assignment for each cell
- Ki67: arcsinh-transformed marker intensity values for Ki67
- UMAP1, UMAP2: UMAP coordinates for each cell
- Condition: combination of tumor model and treatment
- Timepoint: not applicable
- Treatment: GFP or untreated (unt)
- Tumor_model: GL261 or SB28 tumor models
- Mouse_number: unique mouse numbers from which the cells were derived
File: Fig4e-g_Myeloid_cluster_annotations.csv
Description: Cluster annotation data for numeric Phenograph clusters for myeloid cells
Variables:
- V1: cluster number
- annotations: myeloid cell cluster identity
File: Fig4e-g_Tcells_AllDataframe_phenograph.csv
Description: Arcsinh transformed single-cell mass cytometry data for T cells
Variables:
- cell: identifier for each single cell analyzed
- filename: individual samples included in analysis, including GL261 mouse tumor GFP and untreated (unt) controls, SB28 GFP and untreated (unt) controls. Numbers following the sample designation indicate unique identifying mouse numbers.
- CD45 to MHCII: arcsinh-transformed marker intensity values for each marker
- phenograph: phenograph cluster assignment for each cell
- Ki67: arcsinh-transformed marker intensity values for Ki67
- UMAP1, UMAP2: UMAP coordinates for each cell
- Condition: tumor model and treatment condition (GFP or unt) for each cell
- Timepoint: not applicable
- Mouse_number: unique mouse numbers from which the cells were derived
- percent_T_of_singlet: for the sample from which the cell was derived, percentage of total T cells out of singlets
File: Fig4e-g_Tcells_cluster_annotations.csv
Description: Arcsinh transformed single-cell mass cytometry data for myeloid cells
Variables:
- V1: cluster number
- annotations: T cell cluster identity
File: Fig5d_GL261_APOA1_vs_GFP_20220103_GL261_APOA1_405_not(Beads).fcs.clustered.txt.scaffold
Description: Scaffold file for GL261 APOA1 vs GFP
Variables: this file must be opened with the R scaffold package for visualization.
File: Fig5d_GL261_IL-1B_vs_GFP_20220103_GL261_GFP_400_not(Beads).fcs.clustered.txt.scaffold
Description: Scaffold file for GL261 IL1B vs GFP
Variables: this file must be opened with the R scaffold package for visualization.
File: Fig5d_GL261_CCL4_vs_GFP_20220103_GL261_CCL4_387_not(Beads).fcs.clustered.txt.scaffold
Description: Scaffold file for GL261 CCL4 vs GFP
Variables: this file must be opened with the R scaffold package for visualization.
File: Fig5d_SB28_APOA1_vs_GFP_20220103_SB28_APOA1_105_not(Beads).fcs.clustered.txt.scaffold
Description: Scaffold file for SB28 APOA1 vs GFP
Variables: this file must be opened with the R scaffold package for visualization.
File: Fig5d_SB28_IL-1B_vs_GFP_20220103_SB28_GFP_13_not(Beads).fcs.clustered.txt.scaffold
Description: Scaffold file for SB28 IL1B vs GFP
Variables: this file must be opened with the R scaffold package for visualization.
File: Fig5d_SB28_CCL4_vs_GFP_20220103_SB28_CCL4_6_not(Beads).fcs.clustered.txt.scaffold
Description: Scaffold file for SB28 CCL4 vs GFP
Variables: this file must be opened with the R scaffold package for visualization.
File: Fig7c_Tcells_T1_PlateA_D287_T_cells_T1_aPD1.fcs.clustered.txt.scaffold
Description: Scaffold file for SB28 aPD-1/aIL-6 vs aPD-1 T cells for timepoint 1 (T1)
Variables: this file must be opened with the R scaffold package for visualization.
File: Fig7c_Tcells_T2_PlateA_D347_T_cells_T2_aPD1.fcs.clustered.txt.scaffold
Description: Scaffold file for SB28 aPD-1/aIL-6 vs aPD-1 T cells for timepoint 2 (T2)
Variables: this file must be opened with the R scaffold package for visualization.
File: Fig7c_Myeloid_T1_PlateA_D287_myeloid_export_for_scaffold_T1_aPD1.fcs.clustered.txt.scaffold
Description: Scaffold file for SB28 aPD-1/aIL-6 vs aPD-1 myeloid cells for timepoint 1 (T1)
Variables: this file must be opened with the R scaffold package for visualization.
File: Fig7c_Myeloid_T2_PlateA_D347_myeloid_export_for_scaffold_T2_aPD1.fcs.clustered.txt.scaffold
Description: Scaffold file for SB28 aPD-1/aIL-6 vs aPD-1 myeloid cells for timepoint 2 (T2)
Variables: this file must be opened with the R scaffold package for visualization.
File: Fig7d_Tcells_cluster_annotations.csv
Description: Cluster annotation data for numeric Phenograph clusters for T cells for SB28 T1 and T2 samples treated with Isotype, aIL6, aPD-1, or combination.
Variables:
- V1: cluster number
- annotations: cell cluster identity
File: Fig7d_Tcells_AllDataframe_phenograph.csv
Description: Arcsinh transformed single cell mass cytometry data for T cells for SB28 T1 and T2 samples treated with Isotype, aIL6, aPD-1, or combination.
Variables:
- cell: identifier for each single cell analyzed
- filename: individual samples included in analysis, including GL261 mouse tumor GFP and untreated (unt) controls, SB28 GFP and untreated (unt) controls. Numbers following the sample designation indicate unique identifying mouse numbers.
- CD45 to MHCII: arcsinh-transformed marker intensity values for each marker
- phenograph: phenograph cluster assignment for each cell
- Ki67: arcsinh-transformed marker intensity values for Ki67
- UMAP1, UMAP2: UMAP coordinates for each cell
- Condition: timepoint and treatment condition for each cell
- Timepoint: T1 timepoint 1 or T2 timepoint 2
- Treatment: Treatment condition
- Tumor_model: tumor model for the sample
- Mouse_number: unique mouse numbers from which the cells were derived
File: Fig7d_Myeloid_cluster_annotations.csv
Description: Cluster annotation data for numeric Phenograph clusters for myeloid cells for SB28 T1 and T2 samples treated with Isotype, aIL6, aPD-1, or combination.
Variables:
- V1: cluster number
- annotations: cell cluster identity
File: Fig7d_Myeloid_AllDataframe_phenograph.csv
Description: Arcsinh transformed single cell mass cytometry data for myeloid cells for SB28 T1 and T2 samples treated with Isotype, aIL6, aPD-1, or combination.
Variables:
- first column: identifier for each single cell analyzed
- filename: individual samples included in analysis, including GL261 mouse tumor GFP and untreated (unt) controls, SB28 GFP and untreated (unt) controls. Numbers following the sample designation indicate unique identifying mouse numbers.
- CD45 to MHCII: arcsinh-transformed marker intensity values for each marker
- phenograph: phenograph cluster assignment for each cell
- Ki67: arcsinh-transformed marker intensity values for Ki67
- UMAP1, UMAP2: UMAP coordinates for each cell
- Condition: timepoint and treatment condition for each cell
- Timepoint: T1 timepoint 1 or T2 timepoint 2
- Treatment: Treatment condition
- Tumor_model: tumor model for the sample
- Mouse_number: unique mouse numbers from which the cells were derived
File: Fig8b_SB28_20220103_SB28_GFP_13_not(Beads).fcs.clustered.txt.scaffold
Description: Scaffold file for SB28 RT vs. control
Variables: this file must be opened with the R scaffold package for visualization.
File: Fig8b_GL261_20220103_GL261_GFP_400_not(Beads).fcs.clustered.txt.scaffold
Description: Scaffold file for GL261 RT vs control
Variables: this file must be opened with the R scaffold package for visualization.
File: Fig8c-e_Tcells_cluster_annotations.csv
Description: Annotation data for numeric phenograph clusters for T cells, GL261, and SB28 control vs RT
Variables:
- V1: cluster number
- annotations: cell cluster identity
File: Fig8c-e_Tcells_AllDataframe_phenograph.csv
Description: arcsinh transformed single cell mass cytometry data for T cells, GL261, and SB28 control vs RT
Variables:
- Cells: identifier for each single cell analyzed
- filename: individual samples included in analysis, including GL261 mouse tumor GFP and untreated (unt) controls, SB28 GFP and untreated (unt) controls. Numbers following the sample designation indicate unique identifying mouse numbers.
- CD45 to MHCII: arcsinh-transformed marker intensity values for each marker
- phenograph: phenograph cluster assignment for each cell
- Ki67: arcsinh-transformed marker intensity values for Ki67
- UMAP1, UMAP2: UMAP coordinates for each cell
- Condition: timepoint and treatment condition for each cell
- Timepoint: not applicable
- Treatment: Treatment condition
- Tumor_model: tumor model for the sample
- Mouse_number: unique mouse numbers from which the cells were derived
- Condition2: collated treatment condition annotation for control vs RT
File: Fig8c-e_Myeloid_cluster_annotations.csv
Description: Annotation data for numeric phenograph clusters for myeloid cells, GL261 and SB28 control vs RT
Variables:
- V1: cluster number
- annotations: cell cluster identity
File: Fig8c-e_Myeloid_AllDataframe_phenograph.csv
Description: arcsinh transformed single cell mass cytometry data for myeloid cells, GL261 and SB28 control vs RT
Variables:
- Cells: identifier for each single cell analyzed
- filename: individual samples included in analysis, including GL261 mouse tumor GFP and untreated (unt) controls, SB28 GFP and untreated (unt) controls. Numbers following the sample designation indicate unique identifying mouse numbers.
- CD45 to MHCII: arcsinh-transformed marker intensity values for each marker
- phenograph: phenograph cluster assignment for each cell
- Ki67: arcsinh-transformed marker intensity values for Ki67
- UMAP1, UMAP2: UMAP coordinates for each cell
- Condition: timepoint and treatment condition for each cell
- Timepoint: not applicable
- Treatment: Treatment condition
- Tumor_model: tumor model for the sample
- Mouse_number: unique mouse numbers from which the cells were derived
- Condition2: collated treatment condition annotation for control vs RT
Code/software
For viewing scaffold files, an installation of Statistical Scaffold in R is required: https://github.com/SpitzerLab/statisticalScaffold
Access information
Other publicly accessible locations of the data:
- None
