Clonal multi-omics reveals Bcor as a negative regulator of emergency dendritic cell development

• DOI: 10.1016/j.immuni.2021.03.012
• Publication Date: 2021-04-16T09:51:24Z
• Authors: Luyi Tian; Sara Tomei; Jaring Schreuder; Tom S. Weber; Daniela Amann-Zal...; Dawn S. Lin; Jessica Tran; Cindy Audiger; Mathew Chu; Andrew Jarratt; Tracy Willson; Adrienne Hilton; Ee Shan Pang; Timothy Patton; Madison Kelly; Shian Su; Quentin Gouil; Peter Diakumis; Melanie Bahlo; Toby Sargeant; Lev M. Kats; Philip D. Hodgkin; Meredith O’Keeffe; Ashley P. Ng; Matthew E. Ritchie; Shalin H. Naik
• Keywords: Male; 0301 basic medicine; Stem Cells; Gene Expression; Membrane Proteins; Cell Differentiation; Dendritic Cells; Cell Line; Mice, Inbred C57BL; Repressor Proteins; 03 medical and health sciences; HEK293 Cells; Proto-Oncogene Proteins; Animals; Humans; Cell Lineage; Female

Despite advances in single-cell multi-omics, a single stem or progenitor cell can only be tested once. We developed clonal multi-omics, in which daughters of a clone act as surrogates of the founder, thereby allowing multiple independent assays per clone. With SIS-seq, clonal siblings in parallel "sister" assays are examined either for gene expression by RNA sequencing (RNA-seq) or for fate in culture. We identified, and then validated using CRISPR, genes that controlled fate bias for different dendritic cell (DC) subtypes. This included Bcor as a suppressor of plasmacytoid DC (pDC) and conventional DC type 2 (cDC2) numbers during Flt3 ligand-mediated emergency DC development. We then developed SIS-skew to examine development of wild-type and Bcor-deficient siblings of the same clone in parallel. We found Bcor restricted clonal expansion, especially for cDC2s, and suppressed clonal fate potential, especially for pDCs. Therefore, SIS-seq and SIS-skew can reveal the molecular and cellular mechanisms governing clonal fate.