Publications
A combinatorial transcription factor screening platform for immune cell reprogramming
January 14, 2026 / 17
Cell Systems
Ilia Kurochkin, Abigail R. Altman, Inês Caiado, Diogo Pértiga-Cabral, Evelyn Halitzki, Mariia Minaeva, Olga Zimmermannová, Luís Henriques-Oliveira, Dominik Klein, Malavika Nair, Daniel Oliveira, Laura Rabanal Cajal, Ramin Knittel, Cora Feick, Markus Ringnér, Marcel Martin, Branko Cirovic, Cristiana F. Pires, Fabio F. Rosa, Ewa Sitnicka, Fabian J. Theis, Carlos-Filipe Pereira
Highlights
- REPROcode enables combinatorial single-cell screens of immune TFs
- Identifies TF stoichiometry, regulators of cDC1 cell state, and reprogramming fidelity
- Reveals dominant TFs that map hierarchical transcriptional networks for immune lineages
- Uncovers TF combinations for reprogramming to DC, monocyte, macrophage, and NK identities
Summary
Direct reprogramming of immune cells holds promise for immunotherapy but is constrained by limited knowledge of transcription factor (TF) networks. Here, we developed REPROcode, a combinatorial single-cell screening platform to identify TF combinations for immune cell reprogramming. We first validated REPROcode by inducing type-1 conventional dendritic cells (cDC1s) with multiplexed sets of 9, 22, and 42 factors. With cDC1-enriched TFs, REPROcode enabled identification of optimal TF stoichiometry, fidelity enhancers, and regulators of cDC1 states. We then constructed an arrayed lentiviral library of 408 barcoded immune TFs to explore broader reprogramming capacity. Screening 48 TFs enriched in dendritic cell subsets yielded myeloid and lymphoid phenotypes and enabled the construction of a TF hierarchy map to guide immune reprogramming. Finally, we validated REPROcode’s discovery power by inducing natural killer (NK)-like cells. This study deepens our understanding of immune transcriptional control and provides a versatile toolbox for engineering immune cells to advance immunotherapy.
Cover design credit: Lilith Lawrence.
Mapping the tulip field of immune cell identity – About the Cover
The artwork depicts a field of blooming tulips symbolizing the diversity of the immune system, with each flower representing a transcription factor and its stem rooted in unique combinations that define specific immune cell fates. Through combinatorial transcription factor screening, Kurochkin et al. map the landscape of immune identity, cultivating a framework for directing immune cell reprogramming. Illustration by Lilith Lawrence.
