REPROcode
Kurochkin I, Altman AR, Caiado I, Pértiga-Cabral D, Halitzki E, Minaeva M, Zimmermannová O, Henriques-Oliveira L, Klein D, Nair M, Oliveira D, Cajal LR, Knittel R, Feick C, Ringnér M, Martin M, Cirovic B, Pires CF, Rosa FF, Sitnicka E, Theis FJ, Pereira CF
2026 · Cell systems
Combinatorial barcoded TF screening in HEFs with 3′ scRNA-seq readout to discover immune reprogramming cocktails.
Abstract
From the original paper, Cell systems · PubMed
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.
Summary
Level-0 experimental perturbation-screen discovery: lentiviral barcoded TF pools in HEFs, FACS enrichment, and 3′ scRNA-seq with barcode capture rank combinatorial cocktails (PIB, TENE, and broader immune modules) via post-hoc demultiplexing, CellTypist/scTab annotation, and decision-tree/stepwise models, screening platform (not GRN dynamics); no forward inverse-design simulator.
Why this class
Level 0 because the method discovers candidate TF combinations from pooled functional screen outcomes rather than computing a post-intervention state or inverting a forward model. Representation family is signature / state-matching (atlas projection of reprogrammed cells). Cited in §3.1 of the review as a borderline experimental platform.