Single cell analysis defines the divergence between the innate lymphoid cell and lymphoid tissue inducer lineages. Mus musculus

The precise lineage relationships between innate lymphoid cells (ILC) and the lymphoid tissue inducer (LTi) are poorly understood. Using single-cell multiplex transcriptional analysis of 100 lymphoid genes and single-cell cultures of fetal liver precursor cells, we identified the common proximal precursor to these lineages and showed that its bifurcation was precisely marked by the differential induction of the transcription factors PLZF and TCF1. Acquisition of individual ILC1/2/3-specific effector programs was initiated later, at the common ILC precursor (ILCP) stage, by transient expression of mixed ILC1/2/3 transcriptional patterns whereas, in contrast, LTi development did not go through multilineage priming. These findings provide novel insights into divergent mechanisms of ILC and LTi lineage differentiation and establish a high-resolution map of their development. Overall design: We performed transcriptional analysis of single cells along the fetal pathway spanning the differentiation of the common lymphoid precursor into innate lymphoid cells (ILCs) and lymphoid tissue inducer (LTi) with the Biomark Fluidigm multiplex qRT-PCR system, using a panel of 100 lymphoid development factors including transcription factors, cytokine receptors and chemokine receptors. Data from 339 single precursor cells (Lin- IL7Rα+α4β7+), including 157 αLPs (PLZF-CXCR5-), 168 ILCPs (PLZF+), and 14 LTiPs (PLZF-CXCR5+) were compiled from two independent single-cell sorting experiments using pooled E15 fetal livers. After filtering by housekeeping gene expression, we considered the transcriptional profiles from 299 single cells for downstream analysis.