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Fractional killing arises from cell-to-cell variability in overcoming a caspase activity threshold

Jérémie Roux1,3, Marc Hafner1,3, Samuel Bandara1, Joshua J. Sims1, Hannah Hudson2, Diana Chai2, and Peter K. Sorger1
1 Department of Systems Biology, Harvard Medical School, Boston, MA; 2 Merrimack Pharmaceuticals, Cambridge, MA; 3 JR and MH contributed equally to this work.

Mol Syst Biol (2015) 11: 803.
doi:10.15252/msb.20145584 / PMID:25953765 / PMCID:PMC4461398

Overview

In the paper referenced above we identify a threshold in the rate and timing of initiator caspase activation that distinguishes cells that live after treatment with the death ligand TRAIL and its synthetic antibody mimics from those that die. By mapping this threshold we can predict fractional killing of cells exposed to natural and synthetic receptor agonists alone or in combination with sensitizing drugs such as bortezomib. A phenomenological model of the threshold also quantifies the contributions of two resistance genes (c-FLIP and Bcl-2), providing new insight into the control of cell fate by opposing pro-death and pro-survival proteins. The source data for the following analyses were originally published in the Roux et al. paper. Please cite this work when using any of the data or analyses presented here.

Treatment/dose lookup table

Here, we have produced figures containing single-cell trajectories for the FRET ratio (surviving cells in blue, dying in yellow) and the derivative of the FRET ratio (dFR/dt, equivalent to caspase-8 activity) as well as landscape plots (parameters τ and k computed from single-cell trajectories) for all of our experiments. Click on any dose entry in the following table to view the plots for the corresponding experiment. For more details on these plots, see the description of Figure 1 panels A, B and D in Roux et al.

  • The plots appear in pop-up windows. These windows can be moved around, and multiple windows may be opened at once to compare experiments.
  • The treatments in the table are split into sections based on which one of the three model parameters they perturb. To the right of each section is a schematic figure depicting how a change in the corresponding parameter would be reflected in the dFR/dt (caspase-8 activity) plot.
  • Where Bortezomib is used the concentration is always 100 nM; likewise ABT-263 is used at 10 μM.
  • Only one biological replicate is shown here for each experiment, but the data and trajectory/landscape figures for all replicates are available for download (see the bottom of this page).

Modulation of DISC activity (k)

Treatment Doses
TRAIL (ng/ml) 1 5 7.5 10 25 50 100 250 500
Mapatumumab (nM) 2.5 5 10 25 100 200
Apomab (nM) 25 50 100 200
Mapatumumab (nM) + anti-Fc 2.5 5 10 25 100 200
Apomab (nM) + anti-Fc 25 50 100 200
TRAIL (ng/ml) + FLIP-L overexpression 250 500
TRAIL (ng/ml) + FLIP-S overexpression 250 500

Modulation of activation timing (τ)

Treatment Doses
TRAIL (ng/ml) + Bortezomib 1 5 7.5 50 250 500
Mapatumumab (nM) + Bortezomib 10
Mapatumumab (nM) + Bortezomib + anti-Fc 10
Apomab (nM) + Bortezomib 25
Apomab (nM) + Bortezomib + anti-Fc 25
TRAIL (ng/ml) + Bortezomib + FLIP-L overexpression 250
TRAIL (ng/ml) + Bortezomib + FLIP-S overexpression 250

Modulation of the cellular apoptotic threshold (θ)

Treatment Doses
TRAIL (ng/ml) + ABT-263 1 25 50 250 500
TRAIL (ng/ml) + Bcl-2 overexpression 250 500
TRAIL (ng/ml) + ABT-263 + Bcl-2 overexpression 250
TRAIL (ng/ml) + Bcl-XL overexpression 25 50 250 500
TRAIL (ng/ml) + ABT-263 + Bcl-XL overexpression 250

Available data, signatures and software

Data and signatures All single-cell raw data, smoothed trajectories, and fitted parameters for each replicate for each treatment condition. Download (.zip)
Signatures Well-by-well summary of the fitted parameters for each replicate for each treatment condition (HMS Dataset #20232). Details Download (.tsv)
Data and signatures Population-based viability and C8 activity results for Apomab, Apomab + anti-Fc, and TRAIL treatments in multiple cell lines. Download (.zip)
Software The MATLAB code for the image processing routines developed for this project. Download (.zip)