Chromatin Regulatory Complexes in benign and malignant hematopoiesis

1 PhD project offered in the IPP summer call 2021

Scientific Background

Acute myeloid leukemia (AML) is a disease originating from early hematopoietic progenitors that are characterized by a block of differentiation and clonal expansion. Epigenetic dysregulation has been identified as a common feature of AML. Next generation sequencing efforts demonstrated that the majority of AML cases harbor recurrent mutations in epigenetic regulators. We described 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. Drugs inhibiting the menin-MLL1 interaction had dramatic anti-leukemic activity in preclinical AML models and in a first clinical trial. We also 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. An open question is how the menin-MLL1 complex specifically modifies chromatin to control leukemogenic gene expression as 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 specific sequences within MEN1 and MLL1 that encode three binding sites for interacting chromatin regulatory proteins as novel dependencies.

PhD project: Chromatin regulators control self-renewal associated gene expression in leukemia and ageing hematopoiesis

We now plan to study the function of these chromatin regulatory proteins in leukemia and ageing hematopoietic stem cells as they share the expression of specific self-renewal associated genes that are believed to be controlled by the menin-MLL1 complex.

Candidates will work with human and murine AML models as well as murine HSCs from an ageing murine hematopoiesis model to characterize the effects of CRISPR-Cas9 based genetic deletion and pharmacologic manipulation of these chromatin regulators. They will assess chromatin binding and potential co-localization with menin and MLL1. Also, they will define transcriptional as well as binding targets to understand how these proteins control self-renewal associated gene expression.

The successful candidate will have a strong background in Molecular Biology and an interest in chromatin-related techniques such as chromatin immunoprecipitation or next-generation sequencing. We also welcome applicants with experience in working with murine hematopoiesis or leukemia models.

Publications relevant to the project

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 (2020) Synergistic Targeting of FLT3 Mutations in AML via Combined Menin-MLL and FLT3 Inhibition. Blood, 136(21):2442-2456 Link

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 (2016) Targeting Chromatin Regulators Inhibits Leukemogenic Gene Expression in NPM1 Mutant Leukemia. Cancer Discovery, 6(10):1166-1181 Link

Kühn MWM, Hadler MJ, Daigle SR, Koche RP, Krivtsov AV, Olhava EJ, Caligiuri MA, Huang G, Bradner JE, Pollock RM, Armstrong SA (2015) MLL-PTD leukemia cells are sensitive to small molecule DOT1L inhibition. Haematologica, 100(5):e190-3 Link

Dolnik A, Engelmann JC, Scharfenberger-Schmeer M, Mauch J, Kelkenberg-Schade S, Haldemann B, Fries T, Krönke J, Kühn MWM, Paschka P, Kayser, Wolf S, Gaidzik VI, Schlenk RF, Rücker FG, Döhner H, Lottaz C, Döhner K, and Bullinger L (2012) Commonly altered genomic regions in acute myeloid leukemia are enriched for somatic mutations involved in chromatin-remodeling and splicing. Blood, 120(18):e83-92 Link

 

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Dr Michael Kühn

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