REPROcode: a single-cell platform to define transcription factors for immune cell reprogramming

Immunotherapy has revolutionized the treatment of cancer and there is enormous potential to extend the paradigm to other diseases. There is huge societal need for new strategies to harness the immune system to combat and prevent existing and emerging diseases. The generation of specific subsets of immune cells remains a major bottleneck to induce different types of immunity or tolerance required in each disease scenario. Rewiring cell identity by direct cellular reprogramming with overexpression of transcription factors (TFs) offers new strategies to generate immune cells, however only macrophages and conventional type 1 dendritic cells have been induced using this approach. Here we propose to identify TF codes to induce all immune cell types by direct reprogramming.
We will establish REPROcode, a novel approach that employs barcoded TFs coupled with single-cell transcriptional profiling to determine perturbations in cell identity and unveil TF combinations that instruct immune reprogramming. We will create a library of barcoded immune associated TFs and REPROcode: a single-cell platform to define transcription factors for immune cell reprogramming validate the use of the platform to identify TF combinations to program immune cell fates. We will then sequence thousands of induced immune cells and identify TF codes and their respective transcriptional programs. Using computational tools, we will analyse the data and integrate with gene expression profiles of natural immune cells. Finally, we will validate induced immune cell phenotype and function with in vitro and in vivo assays to explore their individual ability to elicit specific immune responses.
Collectively, this work will provide comprehensive insight into transcriptional regulatory networks underlying immune lineages and uncover key regulators underlying immune cell fate divergence. This project will open unprecedented applications of immune cells and their functions in cancer, chronic viral infections, autoimmunity, tissue repair, T-cell rejuvenation, immunosenescence and aging.