Blockade of IKK signaling induces RIPK1-independent apoptosis in human macrophages
Data files
Jul 30, 2024 version files 1.86 MB
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Caspase-Glo.xlsx
48.99 KB
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CellTiter-Glo.xlsx
50.82 KB
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ELISA_IL-18_THP-1.xlsx
22.57 KB
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ELISA_TNF_hMDM_Infection.xlsx
45.44 KB
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ELISA_TNF_THP-1.xlsx
33.69 KB
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LDH_BMDM_Infection.xlsx
23.58 KB
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LDH_hMDM_Infection.xlsx
84.42 KB
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LDH_hMDM_Stim.xlsx
137.74 KB
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LDH_THP-1_Stim.xlsx
318.65 KB
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PI_Uptake_hMDM.xlsx
1.09 MB
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README.md
3.21 KB
Abstract
Regulated cell death in response to microbial infection plays an important role in immune defense and is triggered by pathogen disruption of essential cellular pathways. Gram-negative bacterial pathogens in the Yersinia genus disrupt NF-κB signaling via translocated effectors injected by a type III secretion system, thereby preventing induction of cytokine production and antimicrobial defense. In murine models of infection, Yersinia blockade of NF-κB signaling triggers cell-extrinsic apoptosis through Receptor Interacting Serine-Threonine Protein Kinase 1 (RIPK1) and caspase-8, which is required for bacterial clearance and host survival. Unexpectedly, we find that human macrophages undergo apoptosis independently of RIPK1 in response to Yersinia or chemical blockade of IKKβ. Instead, IKK blockade led to decreased cFLIP expression, and overexpression of cFLIP contributed to protection from IKK blockade-induced apoptosis in human macrophages. We found that IKK blockade also induces RIPK1 kinase activity-independent apoptosis in human T cells and human pancreatic cells. Altogether, our data indicate that, in contrast to murine cells, blockade of IKK activity in human cells triggers a distinct apoptosis pathway that is independently of RIPK1 kinase activity. These findings have implications for the contribution of RIPK1 to cell death in human cells and the efficacy of RIPK1 inhibition in human diseases.
We have submitted our raw data for the luminescent Caspase-Glo 3/7 Assay Kit by Promega (Caspase-Glo.xlsx), luminescent cell viability CellTiter-Glo 2.0 Assay Kit by Promega (CellTiter-Glo.xlsx), colorimetric ELISA Assay Kit by R&D Systems for the human cytokine TNFa (ELISA_TNF_hMDM_Infection.xlsx , ELISA_TNF_THP-1.xlsx) and for the human cytokine IL-18 (ELISA_IL-18_THP-1.xlsx), colorimetric LDH Cytotoxicity Detection Kit by Sigma (LDH_BMDM_Infection.xlsx, LDH_hMDM_Infection.xlsx, LDH_hMDM_Stim.xlsx, LDH_THP-1_Stim.xlsx), and fluorescent Propidium iodide (PI) uptake cytotoxicity assay (PI_Uptake_hMDM).
Apart from the PI Uptake data file (PI_Uptake_hMDM), each file is made up of an excel sheet with multiple tabs, starting with summarized compiled data (Summary), followed by data from individual experiments, labeled by date (YYYY/MM/DD). The PI Uptake data file (PI_Uptake_hMDM) does not contain a summary tab, but it does contain a guide tab with a key for abbreviations, followed by data from individual experiments, labeled by date (YYYY/MM/DD).
Description of the data and file structure
We have enclosed datasets for multiple assays, as described above.
Cell types are as follows: human monocyte-derived macrophages (hMDMs: each unique healthy donor is indicated as ND###, and each donor is highlighted in the corresponding color of the colored dot displayed in the manuscript figure graphs), THP-1 cells (various genotypes), PANC-1 cells, and Jurkat T cells.
Please disregard any other highlighting or colors, as they were used for personal reference.
The various genotypes for THP-1 cells are as follows: WT THP-1 (wild-type cells), RIPK1-/- Clone 1 (CRISPR-mediated knockout, single-cell clone, labeled as clone 2B8), RIPK1-/- Clone 2 (labeled as clone 2F11), CFLAR-/- Clone 1 (labeled as 1B4) , CFLAR-/- Clone 2 (labeled as 2C3), plenti-CFLAR (CFLAR-overexpressing cells, bulk population, also abbreviated as pCFLAR), plenti-mCherry (mCherry-overexpressing WT control cells), FADD-/- Clone 1 (labeled as 1B7), FADD-/- Clone 3 (labeled as 1C10), and TRADD-/- (bulk population). We also utilized siRNA-mediated silencing of the gene BID (siBid) in WT THP-1 cells.
Inhibitor, stimulation, and infection labels and abbreviations are as follows:
- UT = Untreated, UI or Mock = Uninfected, TX = Triton, L = LPS, LI = LPS+IKKi, LIN = LPS+IKKi+Nec-1, LZ = LPS+ZVAD, LZN = LPS+ZVAD+Nec-1
- T = TNF, TI = TNF+IKKi, TIN = TNF+IKKi+Nec-1, TSm = TNF+Smac Mimetic (LCL161), TSmN = TNF+Smac Mimetic + Nec-1
- Chx = Cycloheximide, Apt-1 = Apostatin-1 TRADD inhibitor
For ELISA assays: cytokine concentration values were calculated from the detected values through nonlinear transformation and interpolated using GraphPad Prism. ND indicates that the values were not detected, due to falling outside of the standard curve.
Sharing/Access information
Refer to manuscript for further details and methods, which is available on bioRxiv: https://www.biorxiv.org/content/10.1101/2023.06.20.545781v1
- Nataraj, Neha M.; Herrmann, Beatrice; Shin, Sunny; Brodsky, Igor E. (2023), Blockade of IKK signaling induces RIPK1-independent apoptosis in human cells, [], Posted-content, https://doi.org/10.1101/2023.06.20.545781
- Nataraj, Neha M.; Sillas, Reyna Garcia; Herrmann, Beatrice I. et al. (2024). Blockade of IKK signaling induces RIPK1-independent apoptosis in human macrophages. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1012469
