Frontier Nature: The most comprehensive map of acute myeloid leukemia to date was born, revealing a new pathogenesis

▎WuXi AppTec content team editor 

Acute myeloid leukemia (AML) is a common type of leukemia that can occur
in both children and adults.
This malignancy results from differentiation blockade and clonal proliferation of abnormal myeloblasts in the bone marrow, and its molecular features include mutations
in epigenetic modifiers, transcription factors, and kinases.
According to different molecular characteristics, AML can be subdivided into dozens of subtypes, and the biological characteristics of different subtypes vary
greatly.

Recently, Yue Feng, Chair Professor of Northwestern University School of Medicine, and Professor Zheng Hong of Pennsylvania State University collaborated to publish a paper in the top academic journal Nature, integrating samples from 25 AML patients and samples from 7 healthy donors, using transcriptome sequencing, epigenome sequencing, chromatin conformation capture (Hi-C), CRISPR and other technologies to systematically study and reveal the role of cis-regulatory elements, DNA methylation and 3D genome in AML for the first time
。

The research team noted that this work generated a genomic dataset of a total of 199 samples from primary AML patients, creating the most comprehensive AML atlas to date, providing an important resource
for leukemia research.

▲Schematic diagram of research process and method (Image source: Reference [1]).

Using chromatin conformational capture techniques, the researchers explored the extent to which mutations in AML drive changes in chromatin 3D structure, and found that A/B chromatin compartment-based grouping accurately reflected AML genetic subtypes, such as RUNX1 and CEBPA mutations
.
In addition, one group of samples contained KMT2B mutations, a classification
that had not previously been used as a major AML subtype.
Compared to healthy samples, 3.
2% of the genomes of primary AML patients changed from compartment A state to compartment B, and 2.
9% changed from compartment B state to zone
A.
These AML or AML subtype-specific A/B compartment switching regions can also be grouped by their gene mutation profile and contain known AML genes such as POUA2F1, FGF13, and BCL11
.

Further analysis also showed that recurrent and subtype-specific changes
in gene topological domains and chromatin rings also occurred in AML.

To explore the role of AML-specific chromatin rings in the pathogenesis of AML, the researchers performed RNA sequencing, ATAC sequencing, and CUT&Tag
for CTCF, H3K27ac, and H3K27me3 in the same AML samples.
With these methods, the researchers revealed widespread, recurring AML-specific promoter-enhancer (P-E) and promoter-silencing (P-S) rings
.

Approximately 200 AML-specific chromatin loops were found in each AML sample, showing a subtype-specific pattern containing many known AML proto-oncogenes (Image source: Reference [1]).

Subsequently, in the human AML cell line, the researchers verified the effect of
the inhibitory loop on its target gene through CRISPR deletion and interference experiments.
Taking the IKZF2 gene associated with poor prognosis as an example, the researchers performed 4C-seq and fluorescence in situ hybridization, and then used CRISPR deletion and interference to verify RTTN and IKZF2 P-S rings
.
Interference with the IKZF2 P-S ring resulted in a significant increase in target gene expression of more than 35-fold
.
The deletion of the RTTN P-S ring resulted in a 3-fold increase in gene expression while slowing the ability
of AML cells to proliferate and form clones.

Enhancer hijacking due to structural variation (SV) in the genome is an important driver of
tumorigenesis.
To detect enhancer hijacking events, the researchers predicted SV by abnormal Hi-C signals and used software developed in the same lab to predict SV-induced new chromatin rings, which were subsequently further identified
in AML samples.
Through CRISPR screening, the researchers demonstrated that hijacked enhancers play an important role
in AML cell growth.

Notably, this study also proposed the concept of silener hijacking for the first time, and demonstrated through CRISPR interference mediated at EXD1 and ALG10 gene loci that hijacked silencies have a down-regulating effect
on their target genes.

▲ Classification according to enhancer hijacking or silencing sub-hijacking and different types of SV, including deletions, inversions, and interchromosomal translocations (Image source: Reference [1]).

Finally, the team used genome-wide bisulfite sequencing of 20 AML and normal samples to reveal the delicate relationship
between DNA methylation, CTCF binding, and 3D genomic structure.
Treatment of AML cells with DNA hypomethylation drugs and triple knockdown of DNMT1, DNMT3A and DNMT3B to manipulate DNA methylation can restore 3D genomic structure and gene expression
.

The researchers concluded that the results shed light on new mechanisms of AML pathogenesis, highlighting the role of inhibitory rings and hijacked cis-elements in human disease, informing
the development of new therapies.
As a highly aggressive malignancy, AML remains a daunting challenge for clinical treatment, with a 5-year survival rate of only 27%
in adults.

。 It is expected that scientists' in-depth exploration of the basis of its pathogenesis will bring new treatment ideas
to AML patients and other cancer patients.

The common work of this work is Xu Jie and Dr.
Song Fan.

Huijue Lu, Mikoto Kobayashi and Dr.
Zhang Baozhen also made important contributions
.

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