Reversing Epigenetic Drug Resistance towards MLL-Menin Inhibitors in Acute Myeloid Leukemia

• Applicant: Dr. Daniela Wenge
• Subject Area: Hematology, Oncology
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 511811315

Despite current treatment advances, acute leukemias with MLL-gene rearrangements that lead to fusion proteins and thus cause an increased potential of self-renewal and a block in hematopoietic differentiation, still represent a poor prognostic subgroup. These leukemias are associated with high expression levels of the transcription factor HOXA9 and its cofactor MEIS1. HOXA9 exerts its function through so-called enhancers that lead to its increased expression.Professor Armstrong’s laboratory and others have recently developed targeted therapies directed against members of the MLL-fusion protein complex such as the adapter protein Menin. Inhibitors of the MLL-Menin interaction (in the following referred to as Menin-inhibitors) disrupt Menin from chromatin, which leads to potent activity against leukemia. Early clinical trials investigating orally available Menin-inhibitors in relapsed/ refractory acute leukemias are ongoing (NCT04067336 and NCT04065399). The response rates are promising, but several relapses after initial remission under Menin-inhibition have been documented. To date, the underlying resistance mechanisms remain poorly understood.In this research project, we plan to investigate which enhancers are being regulated by HOXA9 and MEIS1 and mediate resistance towards Menin-inhibitors in MLL-rearranged acute myeloid leukemia. Using CUT&RUN-, ChIP- and ATAC-sequencing, we will define chromatin state changes in Menin-inhibitor sensitive and resistant cells and integrate these data with changes in gene expression levels investigated by RNA sequencing. Furthermore, a CRISPR-Cas9 screen performed in Professor Armstrong’s laboratory has revealed the histone acetyl transferase KAT6A as a potential mediator of resistance towards Menin-inhibition. In vitro studies of combined Menin- and KAT6A-inhibition could re-sensitize Menin-inhibitor resistant MLL-rearranged leukemia cells towards Menin-inhibitor treatment.We will evaluate the potential of this epigenetic combination therapy to reverse Menin-inhibitor resistance in MLL-rearranged acute myeloid leukemia in different cell lines and mouse models of patient-derived xenografts. RNA sequencing will be performed to unravel differences in gene expression under the therapy with both the Menin- and KAT6A-inhibitor as compared to the monotherapy with the Menin-inhibitor. The analysis will also focus on the differences in gene expression at defined HOXA9 and MEIS1 target genes. Thus, we aim to decipher which functionally relevant transcriptional networks controlled by the MLL-fusion oncogene are primarily affected by the drug combination.Our overall goal is to develop novel strategies to overcome the therapeutic limitations of Menin-inhibitors in acute leukemia that are currently being faced in the clinical setting.

• DFG Programme: WBP Fellowship
• International Connection: USA
• Host: Professor Dr. Scott A. Armstrong, Ph.D.