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Acute Myeloid Leukemia 3D Genome Analysis Uncovers Subtype-Specific Changes

NEW YORK – Changes in three-dimensional (3D) chromatin structure and related methylation alterations may provide subtype-specific clues for understanding and treating acute myeloid leukemia (AML), new research suggests.

"In this study, we also sought to delineate the relationship between DNA methylation and the 3D genome structure and whether a [hypomethylating agent (HMA)] can restore normal chromatin organization and gene regulation in AML cells," the authors, led by co-senior and co-corresponding authors Feng Yue, a researcher at Northwestern University, and Hong Zheng of the Penn State Cancer Institute, wrote in Nature on Wednesday.

Using whole-genome sequencing, in situ Hi-C-based chromosome interaction analysis, ATAC-seq chromatin accessibility profiling, RNA sequencing, "cleavage under targets and tagmentation" (CUT&Tag) profiling of histone marks, and other approaches, the researchers profiled chromatin organization compartments, topologically associating domains (TAD), and chromatin loop features in the context of other genomic alterations in more than two dozen AML cases, comparing the results to those from four hematopoietic stem cell progenitor cell samples and three peripheral blood mononuclear cells (PBMC) collected from cancer-free individuals.

The team's analyses highlighted chromatin organizational features that differed from one genetic subtype of AML to the next, along with recurrent chromatin loops showing specific enhancer or silencer activity on promoters in the diverse myeloid tissue malignancies — results backed up by subsequent CRISPR-based gene editing or CRISPR-interference experiments and additional AML analyses.

"Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening," the authors reported, "whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression."

To better understand the connections between 3D genome and chromatin structures, CTCF transcription factor binding, and DNA methylation patterns, the team turned to whole-genome bisulfite sequencing to profile 18 AML samples and two samples representing normal PBMCs as well as to perform CUT&Tag-based CTCF profiling in 10 AML samples. There, enhanced methylation appeared to correspond with reduced CTCF binding, TAD boundary shifts, and other chromatin changes.

On the other hand, the AML-related genome organization and expression effects appeared to be somewhat reversed in the presence of hypomethylating agents such as 5-azacytidine or decitabine or in cells with lower-than-usual levels of genes coding for DNA methyltransferase enzymes.

"These results suggest that treatment with an HMA may achieve therapeutic efficacy, at least in part, through restoration of normal chromatin architecture," the authors noted, adding that "combining HMA therapy with other agents that complement the restoration of normal genome architecture might increase the therapeutic responses and inform new mechanism-based therapeutic approaches to improve treatment outcomes in AML and other cancers."