Effect on gene expression of knock-out of Rosa or Kdm3b on wild-type or Idh2 R140Q hematopoetic stem and progenitor cells

Clonal hematopoiesis (CH) is a common premalignant state in the blood and confers an increased risk of blood cancers and all-cause mortality. Identification of therapeutic targets in CH has been hindered by the lack of an ex vivo platform amenable for studying primary hematopoietic stem and progenitor cells (HSPCs) with and without CH-associated mutations. Here, we utilize an ex vivo co-culture system of primary murine HSPCs with bone marrow endothelial cells to perform CRISPR/Cas9 screens and identify vulnerabilities specific to mutant versus wild-type HSPCs. Our data reveal that loss of the histone demethylase family members KDM3B and JMJD1C specifically reduces the fitness of IDH2- and TET2- mutant HSPCs, but not wild-type HSPCs, including in TET2-mutant human HSPCs and Tet2-mutant murine leukemia cells with cooperating disease alleles. KDM3B loss in mutant cells leads to decreased expression of critical cytokine receptors including MPL, rendering mutant HSPCs preferentially susceptible to inhibition of downstream JAK2 signaling. Our study provides a scalable platform to identify genetic dependencies in mutant HSPCs and reveals an atlas of dependencies in normal and CH-mutant HSPCs. This study nominates an epigenetic regulator and an epigenetically regulated receptor signaling pathway as genotype-specific therapeutic targets in a subset of CH and myeloid malignancies. Overall design: We co-cultured hematopoetic stem and progenitor cells from either wild-type or Idh2 R140Q mutant mice, infected them with lentivirus encoding sgRNAs against Rosa or Kdm3b, and co-cultured infected cells with bone marrow endothelial cells. Infected lineage negative cKIT positive cells were sorted after 7 days and used for RNA-sequencing.