A bacterial effector manipulates host lysosomal protease activity-dependent plasticity in cell death modalities to facilitate infection
Data files
Feb 06, 2025 version files 39.89 KB
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README.md
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Source_Data_Figure_1B.csv
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Source_Data_Figure_1C.csv
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Source_Data_Figure_1D.csv
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Source_Data_Figure_1E.csv
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Source_Data_Figure_1F.csv
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Source_Data_Figure_1G.csv
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Source_Data_Figure_1H.csv
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Source_Data_Figure_1J.csv
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Source_Data_Figure_3A.csv
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Source_Data_Figure_5E.csv
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Source_Data_Figure_5G.csv
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Source_Data_Figure_5I.csv
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Source_Data_Figure_5J.csv
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Source_Data_Figure_6A.csv
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Source_Data_Figure_6B.csv
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Source_Data_Figure_6C.csv
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Source_Data_Figure_6D.csv
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Source_Data_Figure_6E.csv
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Abstract
Crosstalk between cell death programs confers appropriate host anti-infection immune responses, but how pathogens co-opt host molecular switches of cell death pathways to reprogram cell death modalities for facilitating infection remains largely unclear. Here, we identify mammalian cell entry 3C (Mce3C) as a pathogenic cell death regulator secreted by Mycobacterium tuberculosis (Mtb), which causes tuberculosis featuring lung inflammation and necrosis. Mce3C binds host cathepsin B (CTSB), a non-caspase protease acting as a lysosome-derived molecular determinant of cell death modalities, to inhibit its protease activity towards BH3-interacting domain death agonist (BID) and receptor-interacting protein kinase 1 (RIPK1), thereby preventing the production of pro-apoptotic truncated BID (tBID) while maintaining the abundance of pro-necroptotic RIPK1. Disrupting the Mce3C-CTSB interaction promotes host apoptosis while suppressing necroptosis with attenuated Mtb survival and mitigated lung immunopathology in mice. Thus, pathogens manipulate host lysosomal protease activity-dependent plasticity between cell death pathways to promote infection and pathogenicity.
https://doi.org/10.5061/dryad.hmgqnk9qg
This dataset is the source data of the main figures in the paper titled “A bacterial effector manipulates host lysosomal protease activity-dependent plasticity in cell death modalities to facilitate infection”, which is expected to be published in PNAS (Proceedings of the National Academy of Sciences) (https://doi.org/10.1073/pnas.2406715122).
All other source images (including unprocessed immunoblots, immunofluorescence staining, H&E staining, etc.), source movies, as well as source data underlying the supplementary figures of the aforementioned paper, can be obtained from figshare (https://doi.org/10.6084/m9.figshare.28327367).
If this dataset is used for a publication, please cite that paper.
Description of the data
Variable list in csv first row
- Infection: This is for clarification of the indicated bacterial strains used for cell infection experiments.
- Replicate (1, 2, 3, … ): The observed values of each experiment replication.
- Mean: The mean value of all replicates (e.g., “Replicate 1, 2, 3, …”).
- S.E.M: The standard error of the mean.
- Measurement: This is for clarification of the testing objects.
- Time (h) or Time (d): The time points post treatment of cells or mice. h, hour; d, day.
- Celltype: This refers to the cell types used in the experiments (e.g., wild type or gene knockout cell lines).
- Treatment: This is for clarification of the drugs used for cell** **treatment.
Abbreviations in our datasets
- Del.: Gene knockout, such as Del. Mce3C meaning knockout the Mce3C gene.
- null: The value was not observed or calculated in our experiment.
Dataset files and description
File: Source Data Figure 1B.csv
- Description: Utilized for plotting the intensity of annexin V in U937 cells during Mycobacterium bovis bacillus Calmette-Guérin (BCG) infection.
- Variable lists: Infection, Replicate 1, Replicate 2, Replicate 3, Mean, S.E.M., Measurement.
File: Source Data Figure 1C.csv
- Description: Utilized for plotting the intensity of Propidium Iodide (PI) in U937 cells during Mycobacterium bovis BCG infection.
- Variable lists: Infection, Replicate 1, Replicate 2, Replicate 3, Mean, S.E.M., Measurement.
File: Source Data Figure 1D.csv
- Description: Utilized for plotting the caspase-3/7 activation in U937 cells during Mycobacteria tuberculosis (Mtb) infection.
- Variable lists: Infection, Replicate 1, Replicate 2, Replicate 3, Replicate 4, Mean, S.E.M., Measurement.
File: Source Data Figure 1E.csv
- Description: Utilized for plotting the number of PI-positive U937 cells during Mtb infection.
- Variable lists: Infection, Replicate 1, Replicate 2, Replicate 3, Replicate 4, Mean, S.E.M., Measurement.
File: Source Data Figure 1F.csv
- Description: Utilized for plotting bacterial colony-forming unit (CFU) in 0-48 hours during Mtb infection.
- Variable lists: Infection, Replicate 1, Replicate 2, Replicate 3, Replicate 4, Mean, S.E.M., Measurement.
File: Source Data Figure 1G.csv
- Description: Utilized for plotting in vitro growth kinetics of Mtb strains.
- Variable lists: Time (d), Replicate 1, Replicate 2, Replicate 3, Replicate 4, Mean, S.E.M., Infection, Measurement.
File: Source Data Figure 1H.csv
- Description: Utilized for plotting bacterial CFU in mice per lung during Mtb infection.
- Variable lists: Time (d), Replicate 1, Replicate 2, Replicate 3, Replicate 4, Replicate 5, Mean, S.E.M., Infection, Measurement.
File: Source Data Figure 1J.csv
- Description: Utilized for plotting inflammatory infiltration area in mice per lung during Mtb infection.
- Variable lists: Measurement, Time (d), Replicate 1, Replicate 2, Replicate 3, Replicate 4, Replicate 5, Mean, S.E.M., Infection.
File: Source Data Figure 3A.csv
- Description: Utilized for plotting the gene enrichment result. Row 2-28 are the gene-enriched items (pathways) in our paper.
- Variable list:
- Term: The enriched items.
- Overlap: The overlapped genes with all mouse genes.
- Adjusted P-value: enriched adjusted P-value.
- -Log10 (P-value): -log10 (Adjusted P-value).
- Genes: All enriched genes in our experiment.
File: Source Data Figure 5E.csv
- Description: Utilized for plotting CTSB enzyme activity in vitro.
- Variable list: Treatment, Replicate 1, Replicate 2, Replicate 3, Replicate 4, Mean, S.E.M., Measurement.
File: Source Data Figure 5G.csv
- Description: Utilized for plotting bacterial CFU in WT or CTSB gene knockout cells during Mtb infection.
- Variable list: Celltype, Infection, Replicate 1, Replicate 2, Replicate 3, Replicate 4, Mean, S.E.M., Measurement.
File: Source Data Figure 5I.csv
- Description: Utilized for plotting cleaved caspase-3-positive cells in mouse lungs during Mtb infection.
- Variable list: Infection, Replicate 1, Replicate 2, Replicate 3, Replicate 4, Replicate 5, Mean, S.E.M., Measurement.
File: Source Data Figure 5J.csv
- Description: Utilized for plotting p-MLKL-positive cells in mouse lungs during Mtb infection.
- Variable list: Infection, Replicate 1, Replicate 2, Replicate 3, Replicate 4, Replicate 5, Mean, S.E.M., Measurement.
File: Source Data Figure 6A.csv
- Description: Utilized for plotting bacterial CFU per lung in C57BL/6 mice during Mtb infection.
- Variable list: Time (d), Replicate 1, Replicate 2, Replicate 3, Replicate 4, Replicate 5, Mean, S.E.M., Measurement, Infection.
File: Source Data Figure 6B.csv
- Description: Utilized for plotting bacterial CFU per lung in C3HeB/FeJ mice during Mtb infection.
- Variable list: Time (d), Replicate 1, Replicate 2, Replicate 3, Replicate 4, Replicate 5, Mean, S.E.M., Measurement, Infection.
File: Source Data Figure 6C.csv
- Description: Utilized for plotting inflammatory infiltration area in C57BL/6 mice lung during Mtb infection.
- Variable list: Measurement, Time (d), Replicate 1, Replicate 2, Replicate 3, Replicate 4, Replicate 5, Mean, S.E.M., Infection.
File: Source Data Figure 6D.csv
- Description: Utilized for plotting inflammatory infiltration area in C3HeB/FeJ mice lung during Mtb infection.
- Variable list: Measurement, Time (d), Replicate 1, Replicate 2, Replicate 3, Replicate 4, Replicate 5, Mean, S.E.M., Infection.
File: Source Data Figure 6E.csv
- Description: Utilized for plotting survival curve in mice during Mtb infection.
- Variable list: Time (d), Replicate, Infection.
Usage
All of the csv files could be opened by Microsoft Excel and can be imported into GraphPad software for analysis.
