DOI: 10.5061/dryad.hmgqnk9qg
title: A bacterial effector manipulates host lysosomal protease activity-dependent plasticity in cell death modalities to facilitate infection

description: 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.
description: # **A bacterial effector manipulates host lysosomal protease
 activity-dependent plasticity in cell death modalities to facilitate
 infection**
 [https://doi.org/10.5061/dryad.hmgqnk9qg](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](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](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.