Transcription factor reorganization at chromatin secures myeloid progenitor cell survival in PU.1 downregulated leukemia [scRNAseq]

Transcription factors (TFs) orchestrating lineage-development also control genes required for cellular survival. One such TF is PU.1, which is essential for myeloid development. Mice with downregulated PU.1 levels develop fatal acute myeloid leukemia (AML). However, because PU.1 is required for expression of growth factor receptors and signaling molecules, it has been unclear how PU.1-downregulated progenitors survive long enough to acquire additional alterations promoting leukemic transformation. Combining a multi-omics approach with a functional genetic screen, we reveal herein that growth of PU.1-downregulated progenitors is secured by shifting survival control from cytokine-dependency towards overactivation of an autophagy-predominated stem cell program. This shift (for which we also find evidence in human AML) is linked to redirected binding of the PU.1 partner TF RUNX1 to chromatin sites previously not co-bound by PU.1. Hence, partner TF reallocation at chromatin can induce autophagy as a cell-autonomous failsafe mechanism to rescue cells from survival deficits caused by TF loss. Such growth-compensatory effects should be taken into account when considering TF as targets in cancer therapy. Overall design: FACS-sorted Lin-negative cKit-positive bone marrow cells (hematopoietic progenitors) were subjected to 10x Chromium v3 scRNA-seq. One 10x reaction was used per sample, in total we assayed 4 samples (2 from WT mice, 2 from UREd/d mice) so 2 vs 2 in terms of biological replicates, total about 20,000 cells. Cells from each replicate are from one mouse, no pooling was performed. Supplementary files contain both the raw- and normalized counts with column and row annotations for both the "unfiltered" data that went into downstream analysis in R as well as for the "filtered" one which is the data after all processing and filtering in the downstream analysis was applied.