Abstract PR001: Mutant NPM1 hijacks transcriptional hub to maintain pathogenic gene programs and block differentiation in acute myeloid leukemia

Abstract

Abstract Nucleophosmin (NPM1) is a ubiquitously expressed nucleolar protein with a wide range of functions including ribosome biogenesis, mRNA processing, and maintenance of genomic stability. In acute myeloid leukemia (AML), the terminal exon of NPM1 is often mutated (~30% of adult AMLs), changing the nucleolar localization signal into a nuclear export signal, which results in a shift of the protein to the cytoplasm (NPM1c). AMLs carrying this mutation have an aberrant expression of the HOXA genes, whose overexpression leads to leukemogenic transformation. The gene regulatory role of NPM1c has long been an enigma. Recently, it was shown that depletion or re-localization of the NPM1c protein into the nucleus [PG1] causes downregulation of the HOXA genes, leading to the speculation that NPM1c modulates transcription of HOXA genes. Here, we found NPM1c binds to chromatin and is located genome-wide at gene promoters and colocalized at active regions marked by H3K27ac in NPM1c leukemia cell lines and primary leukemia blasts. NPM1c clearly binds to known leukemia-driving genes - posterior HOXA, HOXB, and MEIS1/PBX3 genes as well as novel targets -IRX5 and NKX2-3. After PROTAC degradation of NPM1c, we observed a significant RNA polymerase II elongation defect genome-wide. The dramatic elongation defect is caused by the loss of the Super Elongation Complex (SEC) chromatin binding. Further tests suggest that loss of NPM1c leads to disruption of RNA polymerase II condensates as well as other direct transcriptional regulators of HOX genes - Menin and AFF4 through IDR interactions. We found that pulse PROTAC degradation of NPM1c leads to sustained differentiation with the loss of histone acetylation at NPM1c target loci. Further, NPM1c maintains the active chromatin state of target genes by antagonizing HDAC activity. Additionally, we found that NPM1c’s activation of the leukemia driving genes depends on the pre-established active chromatin state in the transformed hematopoietic stem and progenitor cells. NPM1c alone is not sufficient to activate these leukemia driving genes with heterochromatin marks accumulated. We also found that NPM1c binds to genomic regions that have been pre-bound by its export partner, XPO1. The XPO1 inhibitors Selinexor and Eltanexor can displace NPM1c from chromatin. The combination of clinical-grade XPO1 inhibitor eltanexor and Menin inhibitor MI-3454 displayed a strong synergy in inducing differentiation and reducing leukemia driving gene expression in the NPM1 mutated leukemia cell lines and PDX model, which promises to be an effective combination therapy for NPM1c leukemia patients. Citation Format: Xue Qing Wang, Dandan Fan, Yiman Liu, Qinyu Han, Jolanta Grembecka, Tomasz Cierpicki, Jianzhong Su, Shasha Chong, Liling Wan, Xiaotian Zhang. Mutant NPM1 hijacks transcriptional hub to maintain pathogenic gene programs and block differentiation in acute myeloid leukemia. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr PR001.