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Dryad

Multidimensional control of therapeutic human cell function with synthetic gene circuits

Cite this dataset

Khalil, Ahmad et al. (2022). Multidimensional control of therapeutic human cell function with synthetic gene circuits [Dataset]. Dryad. https://doi.org/10.5061/dryad.s7h44j19v

Abstract

Synthetic gene circuits that precisely control human cell function could expand the capabilities of gene and cell-based therapies. However, platforms for developing circuits in primary human cells that drive robust functional changes in vivo and have compositions suitable for clinical use are lacking. Here, we develop synthetic transcriptional regulators that are compact and based largely on human-derived proteins (synZiFTRs). As a proof of principle, we engineer gene switches and circuits that allow precise, user-defined control over therapeutically-relevant genes in primary T cells using orthogonal, FDA-approved small molecule inducers. Our circuits can instruct T cells to sequentially activate multiple cellular programs, such as proliferation and anti-tumor activity, to drive synergistic therapeutic responses. This platform should accelerate development and clinical translation of synthetic gene circuits in diverse human cell types and contexts.

Methods

These data were generated to support the development and characterization of a mammalian gene circuit engineering platform based on synthetic transcriptional regulators that are compact and based largely on human-derived proteins (synZiFTRs). In the published work, we applied the platform to engineer gene switches and circuits that allow precise, user-defined control over therapeutically-relevant genes in primary T cells using orthogonal, FDA-approved small molecule drugs. Our circuits can instruct T cells to sequentially activate multiple cellular programs, such as proliferation and anti-tumor activity, to drive cellular responses both in vitro and in vivo.

Our datasets, comprised of numerous experimental and computational techniques, support the 5 major figures in our manuscript: 

  1. The clinically-driven design of compact, humanized, synthetic gene regulators (synZiFTRs) for mammalian cell engineering.
  2. SynZiFTR gene switches that allow precise, user-defined control over gene expression in human cells using clinically-approved small molecules.
  3. A synZiFTR gene circuit for drug-regulated, post-delivery control over CAR expression and T-cell killing in vivo.
  4. A synZiFTR gene circuit for drug-regulated, on-demand immune cell proliferation.
  5. SynZiFTR gene circuits used to enact sequential control of immune cell function to drive synergistic in vivo responses.

The final processed dataset for generating all figures, including supplemental figures, is compiled in a .xlsx file, named “Dataset_Li-Israni”, which is organized by Fig#/ Supplemental Fig#. 

In addition, processed datasets for each figure are included in .xlsx files, named “Fig#_arranged_processed”, along with relevant raw dataset files. The raw datasets require Flowjo software to open. 

Please refer to the README file for a more detailed description of the data and file structure.

Usage notes

Please refer to the README file.

Funding

National Institute of Biomedical Imaging and Bioengineering, Award: R01EB029483

Office of the Director, Award: DP1OD006862

National Science Foundation, Award: MCB-1713855

National Science Foundation, Award: DGE-1247312

Defense Advanced Research Projects Agency, Award: D16AP00142

Office of the Director, Award: DP2AI131083

United States Department of Defense, Award: N00014-20-1-2825