CRISPR Time-Delayed Safety Switch Models

This repository contains supplementary information for the paper:

Helen Scott, Dashan Sun, Jacob Beal, and Samira Kiani. "Simulation-Based Engineering of Time-Delayed Safety Switches for Safer Gene Therapies", to appear.

If you make use of any of the contents of this repository, please cite this paper.

Abstract

CRISPR-based gene editing is a powerful tool with great potential for applications in the treatment of many inherited and acquired diseases. The longer that CRISPR gene therapy is maintained within a patient, however, the higher the likelihood that it will result in problematic side effects such as off-target editing or immune response. One approach to mitigating these issues is to link the operation of the therapeutic system to a safety switch that autonomously disables its operation and removes the delivered therapeutics after some amount of time. We present here a simulation-based analysis of the potential for regulating the time-delay of such a safety switch using one or two transcriptional regulators and/or recombinases. Combinatorial circuit generation identifies 30 potential architectures for such circuits, which we evaluate in simulation with respect to tunability, sensitivity to parameter values, and sensitivity to cell-to-cell variation. This modeling predicts one of these circuit architectures to have the desired dynamics and robustness, which can be further tested and applied in the context of CRISPR therapeutics.

Contents of Repository

This repository contains:

• Python code that generates SBOL models each potential safety switch architecture
• Python code to export SBOL models into ODE equations in LaTeX and executable ODE simulation models in Matlab.
• Regression tests for validating the operation of the model generators.
• Simulation runners for experimentation with the models.
• Results and figures generated from these simulations.

Running the Code

How to Make a Circuit Model

The routines for building SBOL circuit components are in builders.py Import the module and run via a script like make_sbol_models.py

Generating LaTeX Equations

The routines for generating LaTeX from SBOL circuits are in latex_generation.py Import the module and run via a script like sbol_to_latex.py

Generating MATLAB Code

The routines for generating LaTeX from SBOL circuits are in matlab_generation.py Import the module and run via a script like sbol_to_matlab.py

Curve fitting

The function parameter_fitting.m is a Matlab function to fit an ODE model of a Cre-ON kill switch from to the data on said circuit from Chylinski et al. It uses the ODE in fit_Cre_on_Kill_Switch.m.