-Author name in bold denotes the presenting author
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Clinically Relevant Abstract denotes an abstract that is clinically relevant.

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836 Epigenetic Classification of Acute Myeloid Leukemia Revealed By Genome-Wide Chromatin Profiling

Program: Oral and Poster Abstracts
Type: Oral
Session: 617. Acute Myeloid Leukemias: Biomarkers, Molecular Markers and Minimal Residual Disease in Diagnosis and Prognosis: Deciphering Risk by Genetic and Epigenetic Features
Hematology Disease Topics & Pathways:
Acute Myeloid Malignancies, AML, genomics, Diseases, Biological Processes, Myeloid Malignancies
Monday, December 11, 2023: 3:00 PM

Yotaro Ochi, MD, PhD1*, Yasuhito Nannya, MD, PhD1,2, Markus Liew-Littorin3*, Senji Kasahara, MD, PhD4*, Nobuhiro Hiramoto, MD5*, Nobuhiro Kanemura, MD, PhD6, Nobuo Sezaki7*, Maki Sakurada8*, Makoto Iwasaki, MD, PhD9*, Junya Kanda, MD, PhD10*, Yasunori Ueda, MD, PhD11, Satoshi Yoshihara, MD, PhD12, Albin Osterroos, MD13*, Masanori Motomura1*, Masahiro Marshall Nakagawa, MD, PhD1, Ryunosuke Saiki1*, Akinori Yoda, PhD1*, Rurika Okuda, MSc, BS1*, Yuichi Shiraishi14*, Takayuki Ishikawa, MD15, Satoru Miyano14,16*, Akifumi Takaori-Kondo, MD, PhD8, Soren Lehmann, MD, PhD13,17* and Seishi Ogawa18,19,20

1Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
2Division of Hematopoietic Disease Control, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
3Division of Hematology, Department of Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
4Department of Hematology, Gifu Municipal Hospital, Gifu, Japan
5Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Japan
6Department of Hematology and Infectious Disease, Gifu University Hospital, Gifu, Japan
7Department of Hematology, Chugoku Central Hospital, Hiroshima, Japan
8Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
9Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Nara, NAR, Japan
10Department of Hematology / Oncology, Kyoto University Graduate School of Medicine, Kyoto, Japan
11Department of Hematology/Oncology, Transfusion and Hemapheresis Center, Kurashiki Central Hospital, Kurashiki, Japan
12Department of Respiratory Medicine and Hematology, Hyogo Medical University, Nishinomiya, Japan
13Department of Medical Sciences, Hematology, Uppsala University, Uppsala, Sweden
14Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
15Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
16Department of Integrated Analytics, M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
17Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
18Center for Hematology and Regenerative Medicine, Department of Medicine (MedH), Karolinska Institutet, Huddinge, Sweden
19Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
20Department of Pathology and Tumor Biology, Kyoto University Graduate School of Medicine, Sakyoku, KYO, Japan


Acute myeloid leukemia (AML) is a clinically and molecularly heterogeneous disease and is predominantly defined by genetic abnormalities and morphology. However, many lines of evidence suggest the role of epigenetic alterations in the pathogenesis and the classification of AML, whereas no large-scale comprehensive analyses of both genetic and epigenetic alterations in AML have been reported.


We enrolled a total of 1,564 primary AML cases (524 from Japanese and 1,040 from Swedish cohorts), whose diagnostic samples were subjected to ATAC sequencing together with targeted capture sequencing using an in-house gene panel including 331 known AML driver genes and an additional 1,158–1,317 probes for copy number detection. We also performed RNA (N=1,398) and H3K27ac-targeted ChIP sequencing (N=80). Normal bone marrow samples from 25 donors as well as 15 remission samples were analyzed by ATAC-seq as a control.


ATAC-seq revealed approximately 300,000 reproducible peaks in primary AML. Most peaks were found in gene-distal regions, and explained a large variance across samples. Among all peaks, 72% were not detected in control samples and thus, specific to AML. Analysis of the correlations between ATAC-seq accessibility and gene expression revealed a subset of regulatory elements that regulate nearby gene expression; each peak was linked to a median of 1 gene (0–31), while each gene was associated with a median of 11 peaks (0­­–110). We next estimated the cellular composition of the bulk AML samples by deconvolution analysis using ATAC-seq data. The predominance of hematopoietic stem cell (HSC), monocyte, and erythroid signatures was associated with French-American-British (FAB) subtypes of minimal differentiation/without maturation subtypes (M0/M1), myelomonocytic/monoblastic/monocytic subtypes (M4/M5), and erythroid subtype (M6), respectively, suggesting bulk ATAC-seq of AML samples reflected the differentiation potential of leukemic cells.

The ATAC-based clustering identified 11 distinct epigenetic subgroups, including three well-known genetic classes defined by gene fusions, such as PML::RARA, RUNX1::RUNX1T1, and CBFB::MYH11. By contrast, some genetic classes defined by a single mutation, such as NPM1 or CEBPA mutation, were further classified into multiple distinct epigenetic subgroups. For example, the NPM1-mutated subtype was separated into four subgroups based on the varying degrees of ATAC signatures associated with HSC and monocytes. Each subgroup of NPM1-mutated AML showed different clinical characteristics such as white blood cell counts, age, and prognosis, and co-mutation pattern in FLT3, DNMT3A, and IDH1/IDH2 mutations. Gene ontology analysis revealed that the subgroup of NPM1-mutated AML with high HSC signature showed upregulated TGF-β signaling, while one with monocytic signature showed upregulated TNF-α signaling and interferon-γ response.

Next, we evaluated transcription factor (TF) binding sites in a genome-wide manner, using TF motifs and foot printing in upregulated ATAC-peaks in each subgroup and revealed distinct profiles of activated TFs in each epigenetic subgroup of NPM1-mutated AML. In the subgroup characterized by high HSC signature, HSC-related TFs that belong to MECOM, HOX, and RUNX families, were more active. By contrast, other TFs, such as IRF, CEBP, and JUN/FOS families, were more enriched in the subgroup showing high monocyte signature.

By developing a prediction model for these subgroups of NPM1-mutated AML based on the gene expression profile, we reproduced these subgroups and validated clinical and molecular features in an external Beat AML cohort. Utilizing ex vivo drug sensitivity dataset in the Beat AML, we identified candidate drugs showing subgroup-specific effectiveness such as panobinostat for NPM1-mutated AML with monocytic differentiation.

Finally, ChIP-seq analysis identified a number of super-enhancers in the vicinity of leukemia-related TFs and oncogenes.


Through comprehensive profiling of chromatin accessibility and gene mutations/expression in a large cohort of AML patients, we demonstrate the epigenetic heterogeneity and identify novel AML subgroups that had unique epigenetic and clinical features. Our findings highlight the role of epigenetic alterations in AML pathogenesis and impact on molecular classification of AML.

Disclosures: Ochi: Kyowa Kirin Co.,Ltd.: Honoraria; Nippon Shinyaku Co., Ltd.: Honoraria, Research Funding. Nannya: Daiichi Sankyo Company Limited: Research Funding; Amelieff Corporation: Speakers Bureau; Otsuka Pharmaceutical Co., Ltd: Speakers Bureau. Kanda: Amgen: Ended employment in the past 24 months, Honoraria; Janssen Pharmaceutical K.K.: Honoraria; Novartis Pharma K.K.: Honoraria; Sanofi K.K.: Honoraria; AbbVie Pharma: Honoraria; Megakaryon Co.: Honoraria; Eisai Co.: Research Funding. Takaori-Kondo: Bristol Myers Squibb: Honoraria; Janssen Pharmaceutical K.K: Honoraria; Otsuka Pharmaceutical: Honoraria, Other: Subsidies ; Megakaryon: Honoraria; Ono Pharmaceutical: Research Funding; COGNANO: Research Funding; DKS Co. Ltd.: Research Funding; Pharma Essentia Japan: Research Funding; Takeda Pharmaceutical: Other: Subsidies; Kyowa Kirin: Other: Subsidies ; Chugai Pharmaceutical: Other; Eisai: Other; Ohara Pharmaceutical: Other; Kinshikouraininjin: Other; AbbVie: Other; Shionogi Pharma: Other; ASAHI KASEI PHARMA: Other; Nippon Shinyaku Co., Ltd.: Honoraria, Other: Subsidies.

*signifies non-member of ASH