High Density Domain-Focused CRISPR Screens Reveal Novel Epigenetic Regulators of HOX/MEIS Activation in Acute Myeloid Leukemia

Aberrant expression of stem-cell-associated genes is a common feature in acute myeloid leukemia (AML) and is linked to leukemic self-renewal and therapy resistance. Using AF10-rearranged leukemia as a prototypical example displaying a recurrent “stemness” network activated in AML, we screened for chromatin regulators that sustain aberrant activation of these networks. We deployed a CRISPR-Cas9 screen with a bespoke domain-focused library and identified several novel chromatin-modifying complexes as regulators of the TALE domain transcription factor MEIS1, a key leukemia stem cell (LSC)-associated gene. CRISPR droplet sequencing revealed that many of these MEIS1 regulators, controlled the transcription of several AML oncogenes. In particular, we identified a role for the Tudor-domain containing chromatin reader protein SGF29 in the transcription of key AML oncogenes. Furthermore, SGF29 deletion impaired leukemogenesis in models representative of multiple AML subtypes. Thus, our studies reveal a novel role for SGF29 as a non-oncogenic dependency in AML and identify the SGF29 Tudor domain as an attractive target for drug discovery. STATEMENT OF SIGNIFICANCE Screening for regulators of “stemness” genes using a bespoke epigenetics CRISPR library, we identify novel factors essential for transcription of key leukemia stem cell-associated oncogenes. We identify an important role for the SGF29 chromatin reader, and particularly its Tudor domain as a novel, attractive therapeutic target in AML.