dataset
posted on 2023-04-04, 00:44 authored by Hannah J. Uckelmann, Elena L. Haarer, Reina Takeda, Eric M. Wong, Charlie Hatton, Christian Marinaccio, Florian Perner, Masooma Rajput, Noa J.C. Antonissen, Yanhe Wen, Lu Yang, Lorenzo Brunetti, Chun-Wei Chen, Scott A. Armstrong Table S1. Read normalized ratios of ChIPseq signal of untreated versus dTAG-13 treated OCI-AML3-NPM1c-FKBP12 cells.Table S2. Summary of NPM1c and NPM1 Chromatin Binding Targets.Table S3. Patient info for patient derived xenograft (PDX) models used.Table S4. ChIPseq reads per kilobase (rpk) data summary of PDX samples with NPM1c-Ab and NPM1-Ab.Table S5. RNAseq differential expression data of OCI-AML3-NPM1c-FKBP12 treated with dTag-13 for 3 or 24 h and OCI-AML3 cells treated with Selinexor for 6 h.Table S6. SLAMseq differential expression data of OCI-AML3-NPM1c-FKBP12 cells treated with dTag-13 for 15, 30, 60, 120 or 180 minutes.Table S7. PROseq differentially transcribed genes in OCI-AML3-NPM1c-FKBP12 cells treated with dTag-13 for 30 or 60 minutes and OCI-AML3 cells treated with VTP-50469 for 48 hours.Table S8. CRISPR tiling screen with NPM1 WT specific guides (blue) and NPM1c specific guides (red).Table S9. ChIPseq rpk values for CRM1 and HA ChIPs in 293T cells.Table S10. RNAseq differential gene expression analysis in 293T cells after overexpression of NPM1c-HA compared to all other samples (MIG, NPM1wt-HA and AS1-HA).Table S11. Fold change in ChIPseq differential peak interval signal in OCI-AML3 cells treated with Selinexor (100 nM, 6 hours) or VTP-50469 (330 nM, 96 hours).Table S12. Oligos used in this study.Table S13. Antibodies used in this study.Table S14. Summary of total and mapped reads of ChIPseq samples.
Funding
National Institutes of Health (NIH)
History
ARTICLE ABSTRACT
The dysregulation of developmental and stem cell–associated genes is a common phenomenon during cancer development. Around half of patients with acute myeloid leukemia (AML) express high levels of HOXA cluster genes and MEIS1. Most of these AML cases harbor an NPM1 mutation (NPM1c), which encodes for an oncoprotein mislocalized from the nucleolus to the cytoplasm. How NPM1c expression in hematopoietic cells leads to its characteristic gene-expression pattern remains unclear. Here, we show that NPM1c directly binds to specific chromatin targets, which are co-occupied by the histone methyltransferase KMT2A (MLL1). Targeted degradation of NPM1c leads to a rapid decrease in gene expression and loss of RNA polymerase II, as well as activating histone modifications at its targets. We demonstrate that NPM1c directly regulates oncogenic gene expression in collaboration with the MLL1 complex and define the mechanism by which MLL1–Menin small-molecule inhibitors produce clinical responses in patients with NPM1-mutated AML.
We uncovered an important functional role of mutant NPM1 as a crucial direct driver of oncogenic gene expression in AML. NPM1c can bind to chromatin and cooperate with the MLL complex, providing the first functional insight into the mechanism of Menin–MLL inhibition in NPM1c leukemias.See related article by Wang et al., p. 724.This article is highlighted in the In This Issue feature, p. 517
