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

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: Focused shRNA screen targeting a specific gene signature (see our manuscript for details) of about 340 genes plus killing (Psma1, Polr2b, Rpl30) and non-targeting (luciferase) controls in three cell lines: HoxWT, HoxURE (both immortalized hematopoietic progenitors from wildtype or UREd/d knockout mice) or B22 (in the manuscript called URE-AML, established from AML blasts of a UREd/d mouse with severe AML). shRNA library was transfected by lentivirus into the cell lines in three independent biological replicates, and either harvested 24h after transfection (input control) or once 10 cell divisions had happened ("final" library). Final vs input counts were used in MAGeCK to define "essential" genes that promote survival and proliferation.