MLL oncoprotein levels influence leukemia lineage identities

Derek H. Janssens, Melodie Duran, Dominik J. Otto, Weifang Wu, Yiling Xu, Danielle Kirkey, Charles G. Mullighan, Joanna S. Yi, Soheil Meshinchi, Jay F. Sarthy, Kami Ahmad () and Steven Henikoff ()
Additional contact information
Derek H. Janssens: Fred Hutchinson Cancer Center
Melodie Duran: Fred Hutchinson Cancer Center
Dominik J. Otto: Fred Hutchinson Cancer Center
Weifang Wu: Fred Hutchinson Cancer Center
Yiling Xu: Fred Hutchinson Cancer Center
Danielle Kirkey: Fred Hutchinson Cancer Center
Charles G. Mullighan: St. Jude Children’s Research Hospital
Joanna S. Yi: Baylor College of Medicine and Texas Children’s Hospital
Soheil Meshinchi: Fred Hutchinson Cancer Center
Jay F. Sarthy: Seattle Children’s Research Institute
Kami Ahmad: Fred Hutchinson Cancer Center
Steven Henikoff: Fred Hutchinson Cancer Center

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract Chromosomal translocations involving the mixed-lineage leukemia (MLL) locus generate potent oncogenic fusion proteins (oncoproteins) that disrupt regulation of developmental gene expression. By profiling the oncoprotein-target sites of 36 broadly representative MLL-rearranged leukemia samples, including three samples that underwent a lymphoid-to-myeloid lineage-switching event in response to therapy, we find the genomic enrichment of the oncoprotein is highly variable between samples and subject to dynamic regulation. At high levels of expression, the oncoproteins preferentially activate either an acute lymphoblastic leukemia (ALL) program, enriched for pro-B-cell genes, or an acute myeloid leukemia (AML) program, enriched for hematopoietic-stem-cell genes. The fusion-partner-specific-binding patterns over these gene sets are highly correlated with the prevalence of each mutation in ALL versus AML. In lineage-switching samples the oncoprotein levels are reduced and the oncoproteins preferentially activate granulocyte-monocyte progenitor (GMP) genes. In a sample that lineage switched during treatment with the menin inhibitor revumenib, the oncoprotein and menin are reduced to undetectable levels, but ENL, a transcriptional cofactor of the oncoprotein, persists on numerous oncoprotein-target loci, including genes in the GMP-like lineage-switching program. We propose MLL oncoproteins promote lineage-switching events through dynamic chromatin binding at lineage-specific target genes, and may support resistance to menin inhibitors through similar changes in chromatin occupancy.

Date: 2024
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DOI: 10.1038/s41467-024-53399-8

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