Targeting nucleoporin 214 selectively eliminates leukemia stem cells by inducing ferroptosis [CUT&Tag 6]

Leukemia stem cells (LSCs) give rise to mature leukemia blasts and are the major cause of therapy resistance and relapse in acute myeloid leukemia (AML). We propose a novel strategy to eliminate heterogeneous LSCs but spare hematopoietic stem cells (HSCs) by targeting essential genes that are highly expressed in LSCs than that in HSCs. Nucleoporin 214 (NUP214) is determined as a dose-dependently essential gene (DDEG) in LSCs. Homozygous deletion of Nup214 eliminates LSCs and HSCs; however, Nup214 haploinsufficiency impairs LSC maintenance but spares HSCs by selectively inducing ferroptosis of LSCs. Mechanistically, NUP214 locates to chromatin and interacted with Sub1 to inhibit the transcription of heme oxygenase-1 (Hmox1) and arachidonate 15-lipoxygenase (Alox15), thus protecting LSCs against lipid peroxidation. We screened and identified a small molecule 0449-b as a molecular glue that links NUP214 and an NEDD8 E3 ligase, Rbx2, to induce neddylation and degradation of NUP214. 0449-b shows efficacy in selective eradication of LSCs but has a negligible effect on normal hematopoietic stem and progenitor cells. These biological and chemical findings provide a valuable strategy to eliminate LSCs by targeting DDEGs. Overall design: HSCs (CD48-CD150+LSK) from Nup214fl/+ mice and LSCs (Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven Nup214fl/+ mice were sorted, followed by Sub1-CUT&Tag-seq