Targeting Chromatin Regulators in Leukemia

1 PhD project offered in the IPP winter call 2022

Scientific Background

Acute myeloid leukemia (AML) originates from early hematopoietic progenitors characterized by a block of differentiation and clonal expansion. Epigenetic dysregulation has been identified as a standard feature of AML. Next-generation sequencing (NGS) efforts demonstrated that the majority of AML cases harbor recurrent mutations in epigenetic regulators. We described previously that the interaction between the histone methyltransferase MLL1 (MLL, KMT2A) and the adaptor protein menin (MEN1) is a dependency and provides a potential opportunity for the treatment of the most common AML subtype with a mutation in the NPM1 gene (Kühn et al. Cancer Discovery 2016). We demonstrated that menin-MLL1 interaction inhibitors reversed leukemogenic gene expression in NPM1 mutant leukemia, including the expression of self-renewal associated transcription factors MEIS1, PBX3, and to some degree also, HOX transcription factors. Also, we found that preclinical agents targeting the menin-MLL interaction had dramatic anti-leukemic activity in preclinical AML models. Promising clinical activity has been reported recently for two novel menin inhibitors currently being assessed in clinical phase-I trials on patients with relapsed and refractory AML.
An open question is how the menin-MLL1 complex modifies chromatin to control leukemogenic gene expression. Recent evidence suggests that the MLL1 SET domain harboring its H3K4 methyltransferase activity is not required for leukemic gene expression. Based on the hypothesis that menin and MLL1 drive leukemogenesis by recruiting other complex proteins to their target chromatin loci, we performed a high-definition CRISPR-domain scan of MEN1 and MLL1. We identified sequences within MEN1 and MLL1 that encode three binding sites for interacting chromatin regulatory proteins as novel dependencies. Currently, we are studying these interacting proteins in human and murine AML models and in primary AML patient samples and Patient-Derived Xenotransplantation (PDX) models of AML.

PhD Project: Epigenetic adaption drives non-genetic resistance to therapeutic chromatin complex targeting in leukemia

Menin-MLL inhibitors currently assessed in clinical phase I trials have shown very promising clinical activity and caused remissions in many heavily pretreated (relapsed or refractory) AML patients. However - as observed with other targeted epigenetic drugs before - most of these remissions were transient, and secondary resistance development occurred in almost all of these patients. 
In preliminary work for this project, we have developed human and murine models of menin-inhibitor-resistant AML cells. Of note, sequencing of the menin-inhibitor-resistant AML cells demonstrated no mutations in the drug binding sites. RNA sequencing of these cells demonstrated specific leukemic gene expression programs to be reactivated compared to their non-resistant counterparts exposed to menin inhibition. These results are consistent with a non-genetic adaptation as a mechanism of resistance.
This project aims to shed light on the fundamental question of what processes drive resistance to menin-inhibitors and, more generally, how non-genetic resistance develops in cancer cells exposed to targeted epigenetic drugs. These questions will be addressed by characterizing the phenotypic changes associated with resistance in detail. We will start by integrating the already available transcriptomic data with an assessment of histone marks, global menin- and MLL chromatin binding, as well as an assessment of chromatin state using cut & run as well as single-cell next-generation sequencing techniques. Potential co-dependencies on the above-described interacting proteins will be assessed using CRISPR-Cas9 deletion in murine and human AML models as well as primary AML patient material.
This project is most suitable for a Ph.D. student who aims to ask fundamental biological questions about how chromatin-based mechanisms drive oncogenic processes and would like to work on a translational topic that directly affects how patients with leukemia are being treated.

Publications relevant to this project

Shah V, Giotopoulos G, OsakiH, MeyerhöferM, MeduriE, SchubertB, YunH, HortonSJ, ´Agrawal-SinghS, HaehnelPS, BasheerF, LugoD, Kühn MWM, Guezguez B, TheobaldM, KindlerT, GallipoliP, PrinjhaRK, Huntly BJP, and Daniel Sasca. Acute resistance to BET inhibitors remodels compensatory transcriptional programs via p300 co-activation, preprint BioRxiv. 2022

Dzama MM, Steiner M, Rausch J, Sasca D, Schönfeld J, Kunz K, Taubert MC, McGeehan GM, Chen C, Mupo A, Hähnel PS, Theobald M, Kindler T, Koche RP, Vassiliou GS, Armstrong SA, and Kühn MWM. Synergistic Targeting of FLT3 Mutations in AML via Combined Menin-MLL and FLT3 Inhibition. Blood. 2020 Nov 19;136(21):2442-2456.

Kühn MWM, Song E, Feng Z, Sinha A, Chen CW, Deshpande AJ, Cusan M, Rahnamay Farnoud N, Mupo A, Grove C, Koche R, Bradner JE, de Stanchina E, McGeehan G, Vassiliou GS, Hoshii T, and Armstrong SA. Targeting Chromatin Regulators Inhibits Leukemogenic Gene Expression in NPM1 Mutant Leukemia. Cancer Discovery. 2016 Oct;6(10):1166-1181.

Review: Sasca D, Guezguez B, and Kühn MWM. Next generation epigenetic modulators to target myeloid neoplasms. Curr Opin Hematol. 2021 Sep 1;28(5):356-363.

Contact

Prof Dr Michael Kühn
University Medical Centre Mainz
Department of Hematology, Oncology, and Pneumology
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