Translational Epigenetics

Inhibitiors of the adaptor protein Menin are evolving as a novel class of drugs in acute leukemia with the potential to become the first targeted therapeutics that promise a causative treatment of MLL-fusion protein and NPM1c-driven leukemogenesis. Despite impressive clinical activity in early-phase clinical trials, disease persistence has been observed leading to resistance development in some patients. The question why leukemia cells are rapidly depleted and eventually eradicated in some cases, while cellular adaptation and persistence is observed in others remains elusive so far. In this project, we will characterize molecular signatures underlying disease persistence during Menin-inhibition and investigate how specific epigenetic regulators re-program leukemia cells towards a “persister-state”.

Understanding these molecular mechanisms will be critical for response monitoring and biomarker development to identify patient populations that can safely be treated with these well tolerated drugs over a longer period. Furthermore, the mechanistic understanding of persistence under chromatin targeted therapy will be essential for the development of rational combination therapy approaches.

Myeloid malignancies, including Acute Myeloid Leukemia (AML), Myeloproliferative Neoplasms (MPN) and Myelodysplastic Syndromes (MDS) are malignancies of the hematopoietic system and occur predominantly in the older population. Recent DNA-sequencing studies and lineage-tracing efforts have demonstrated that founding mutations of these diseases arise in hematopoietic stem cells early in live and undergo a lifelong process of clonal evolution. During aging of the hematopoietic system, intrinsic and environmental factors eventually lead to expansion of these clones and acquisition of additional mutational events promoting clonal evolution and disease development. The genes most frequently affected by age-related somatic variants in blood cells are coding for the DNA-methylation modifiers DNMT3A and TET2. Mutations in these enzymes lead to skewing in the distribution of methylcytosine and hydroxy-methylcytosine across the DNA and thereby impact stemness, lineage-identity and cytokine secretion by epigenetic re-programming. The exact molecular mechanisms that are critical for the cell-intrinsic competitive advantage of these mutant pre-leukemic cells remains poorly understood to date. Therefore, therapeutic interventions to prevent clonal evolution and ultimately blood cancer development have yet not been established.

Data from our group indicates, that cells harboring recurrent somatic mutations are selectively vulnerable to functional perturbation of MLL1, an evolutionary conserved histone methyltransferase. The question of how exactly these somatic mutations cause this dependency on a chromatin writer will be addressed in this project. To date, DNA methylation and chromatin biology are largely regarded as separate epigenetic regulatory principles. Our work aims to connect these epigenetic entities in the field of clonal evolution in hematopoiesis. Aside from the expected insights into basic biological principles, this work is of potential therapeutic relevance, since small molecule inhibitors targeting oncogenic MLL1 complexes have recently been developed and tested in early-phase clinical trials. Those molecules are highly selective, well tolerated and show promise for the treatment of patients with leukemia. In this project, we will test the ability of these novel compounds to selectively impair fitness of mutant clones and provide a proof of concept that targeting of premalignant clonal evolution is feasible. We hope that this work will be the basis for the development of therapeutic strategies that may help to prevent malignant transformation in patient at high risk in the future.

Clonal evolution and diversification is an important contributor to therapy-resistance and disease progression in MPN patients. A growing body of evidence indicates that both genetic and non-genetic factors such as aberrant chromatin states significantly contribute to intra-tumoral heterogeneity (ITH). While the importance of genetic and non-genetic ITH for disease pathogenesis and treatment response has been largely investigated in solid cancers, only few studies addressed this important topic in MPN patients. In this project, we will comprehensively characterize ITH and investigate how aberrant epigenetic regulation contributes to clonal diversification and disease progression in MPN. We hypothesize that specific chromatin modifiers, including the Menin-MLL1 complex as well as the histone demethylase LSD1, are critical for the establishment of pathogenic gene expression programs in clonal subpopulations of blood cells. Based on published and our preliminary data, we speculate that treatment with potent and selective inhibitors of these chromatin binding proteins can reverse the aberrant chromatin state and gene expression signatures in a genotype selective manner and target pathogenic clones in xenograft models of MPN. To this aim we will address three main research topics: i) reconstruction of lineage architecture and clonal heterogeneity in high-risk MPN, ii) definition of lineage-specific transcriptional signatures and chromatin accessibility patterns during disease progression in MPN, and iii) to assess the therapeutic efficacy of chromatin modifying therapies in xenograft models of high-risk MPN. A variety of highly innovative and modern technologies such as single-cell DNA genotyping, whole-genome and ATAC-sequencing will be coupled with respective in vitro and in vivo models in a combined forward/reverse translational manner.

For a full list of publications see https://scholar.google.de/citations?user=96SmlXwAAAAJ&hl=en&oi=ao.

Perner F., Stein E.M., Wenge D.V., Singh S., Kim J., Apazidis A., Rahnamoun H., Anand D., Marinaccio C., Hatton C., Wen Y., Stone R.M., Schaller D., Mowla S., Xiao W.,10, Gamlen H.A., Stonestrom A.J., Persaud S., Ener E., Cutler J.A., Doench J.G., McGeehan G.M., Volkamer A., Chodera J.D., Nowak R.P., Fischer E.S., Levine R.L.,  Armstrong S.A., Cai S.F. MEN1 mutations mediate clinical resistance to Menin inhibition. 2023. Nature. 615(7954):913-919. doi: 10.1038/s41586-023-05755-9.

Soto-Feliciano Y.M.*, Sánchez-Rivera F.J.*, Perner F.*, Barrows D.W., Kastenhuber E.R., Ho Y.J., Carroll T., Xiong Y., Anand D., Soshnev A., Gates L., Beytagh M.C., Cheon D., Gu S., Liu X.S., Krivtsov A.V., Meneses M., de Stanchina E., Stone R.M., Armstrong S.A., Lowe S.W., and Allis C.D. A molecular switch between mammalian MLL complexes dictates response to Menin-MLL inhibition. 2023. Cancer Discovery, 13(1): p. 146-169.         * authors contributed equally

Perner F., Schnoeder T.M., Xiong Y., Jayavelu A.K., Mashamba N., Tubio Santamaria N., Huber N., Todorova K., Hatton C., Perner B., Eifert T., Murphy C., Hartmann M., Hoell J.I., Schröder N., Brandt S., Hochhaus A., Mertens P.R., Mann M., Armstrong S.A., Mandinova A., Heidel F.H. YBX1 mediates translation of oncogenic transcripts to control cell competition in AML. 2022. Leukemia; 36(2):426-437

Perner F., Gadrey J.Y., Xiong Y., Hatton C., Eschle B.K., Weiss A., Stauffer F., Gaul C., Tiedt R., Perry J.A., Armstrong S.A., & Krivtsov A.V. Novel Inhibitors of the Histone-Methyltransferase DOT1L Show Potent Antileukemic Activity in Patient-derived Xenografts. 2020. Blood. 136(17):1983-1988

Issa G.C., Aldoss I., DiPersio J., Cuglievan B., Stone R., Arellano M., Thirman M., Patel M.R., Dickens D.S., Shenoy S., Shukla N., Kantarjian H., Armstrong S.A., Perner F., Perry J.A., Rosen G., Bagley R.G., Meyers M.L., Ordentlich P., Gu Y., Kumar V., Smith S., McGeehan G.M., and Stein E.M. Clinical trial of the menin inhibitor revumenib for KMT2A-rearranged or NPM1-mutant leukemia. 2023. Nature. Mar;615(7954):920-924.

Tubío-Santamaría N., Jayavelu A.K., Schnoeder T.M., Eifert T., Hsu C.J., Perner F., Zhang Q., Wenge D.V., Hansen F.M., Kirkpatrick J.M., Jyotsana N., Lane S.W., von Eyss B., Deshpande A.J., Kühn M.W., Schwaller J., Cammann C., Seifert S., Ebstein F., Krüger E., Hochhaus A., Heuser M., Ori A., Mann M., Armstrong S.A., Heidel F.H. Immunoproteasome function maintains oncogenic gene expression in KMT2A-complex driven leukemia. 2023. Molecular Cancer. 22(1):196.

Uckelmann H.J., Haarer E.L., Takeda R., Wong E.M., Hatton C., Marinaccio C., Perner F., Rajput M., Antonissen N.J.C., Wen Y., Yang L., Brunetti L., Chen C.W. & Armstrong S.A.. Mutant NPM1 directly regulates oncogenic transcription in acute myeloid leukemia. 2023. Cancer Discovery, 13(3):746-765

Olsen S.N., Godfrey L., Healy J.P., Choi Y.A., Kai Y., Hatton C., Perner F., Haarer E.L., Nabet B., Yuan G.C. & Armstrong SA. MLL::AF9 degradation induces rapid changes in transcriptional elongation and subsequent loss of an active chromatin landscape. 2022. Molecular Cell, 82(6): p. 1140-1155 e11.

Aubrey B.A., Cutler B.J., Bourgeois W., Donovan K.A., Gu S., Hatton C., Perlee S., Perner F., Rahnamoun H., Theall A.C.P., Henrich J.A., Zhu Q., Nowak R.P., Kim Y.J., Parvin S., Cremer A., Olsen S.N., Eleuteri N.A., Pikman Y., McGeehan G.M., Stegmaier K., Letai A., Fischer E.S., Liu X.S., & Armstrong S.A., IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia. 2022. Nature Cancer, 3(5): p. 595-613.

Jayavelu, A.K.*, Schnoeder, T.M.*, Perner, F., Herzog, C., Meiler, A., Krishnamoorthy, G., Huber, N., Mohr, J., Edelmann-Stephan, B., Austin, R., Brandt, S., Palandri, F., Schroder, N., Isermann, B., Edlich, F., Sinha, A.U., Ungelenk, M., Hubner, C.A., Zeiser, R., Rahmig, S., Waskow, C., Coldham, I., Ernst, T., Hochhaus, A., Jilg, S., Jost, P. J., Mullally, A., Bullinger, L., Mertens, P.R., Lane, S.W., Mann, M., & Heidel, F.H. Splicing factor YBX1 mediates persistence of JAK2-mutated neoplasms. 2020. Nature, 588(7836), 157-163.