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MYELOID NEOPLASIA
Division of Hematology/Oncology, Northwestern University, Chicago, IL; 2Division of Laboratory Genetics, Mayo Clinic, Rochester, MN; 3Leukemia Service,
Memorial Sloan-Kettering Cancer Center, New York, NY; 4Department of Oncology, Montefiore Medical Center, Bronx, NY; 5Division of Hematology/
Oncology/Bone Marrow Transplantation, Childrens Mercy Hospitals and Clinics, Kansas City, MO; 6Division of Hematology/Oncology, Childrens Hospital
of Michigan, Wayne State University, Detroit, MI; 7The Childrens Hospital of Philadelphia, Division of Hematology, University of Pennsylvania School
of Medicine, Philadelphia, PA; and 8Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
Acute megakaryoblastic leukemia (AMKL) is more frequently observed in Down syndrome (DS) patients, in whom it is often preceded by a transient myeloproliferative
disorder (TMD). The development of DS-TMD and DS-AMKL requires not only the
DNA methylation changes
presence of the trisomy 21 but also that of GATA1 mutations. Despite extensive studies
during the development of
DS-AMKL occur in sequential into the genetics of DS-AMKL, the importance of epigenetic deregulation in this disease
waves of opposing losses and has been unexplored. We performed DNA methylation profiling at different stages of
development of DS-AMKL and analyzed the dynamics of the epigenetic program. Early
gains of methylation.
genome-wide DNA methylation changes can be detected in trisomy 21 fetal liver
Each wave of DNA
mononuclear cells, prior to the acquisition of GATA1 mutations. These early changes
methylation abnormalities
are characterized by marked loss of DNA methylation at genes associated with detargets specific gene networks velopmental disorders, including those affecting the cardiovascular, neurological, and
that contribute to distinct
endocrine systems. This is followed by a second wave of changes detected in DS-TMD
biological features of the
and DS-AMKL, characterized by gains of methylation. This new wave of hypermethylation
disease.
targets a distinct set of genes involved in hematopoiesis and regulation of cell growth and
proliferation. These findings indicate that the final epigenetic landscape of DS-AMKL is
the result of sequential and opposing changes in DNA methylation occurring at specific times in the disease development. (Blood.
2013;122(14):e33-e43)
Key Points
Introduction
Acute megakaryoblastic leukemia (AMKL) is a rare form of acute
myeloid leukemia (AML), accounting for only 1% to 2% of all de
novo AMLs and as much as 10% of pediatric AML.1,2 Moreover, its
incidence is several-hundredfold higher in patients with Down syndrome (DS) than in children without DS.3 Four to 5% of DS fetuses
develop a preleukemic transient myeloproliferative disorder (DS-TMD),
diagnosed at the time of birth, that spontaneously resolves within a
few weeks in the majority of patients.4,5 Within the rst 4 years of
life, approximately 20% of DS cases that develop TMD in utero will
develop AMKL (DS-AMKL).6-9
DS-TMD and DS-AMKL invariably present with acquired mutations in the GATA1 gene that encodes a master regulator of erythromegakaryocytic development. These mutations arise in utero
and result in the expression of a short isoform of the GATA1 protein,
known as GATA1s.6,10 Oncogenic cooperation between GATA1
mutations and trisomy 21 is associated with the development of
DS-TMD and DS-AMKL. However, several observations in animal
models11-13 and in human specimens14-18 strongly suggest that
Submitted May 17, 2013; accepted August 15, 2013. Prepublished online as
Blood First Edition paper, August 26, 2013; DOI 10.1182/blood-2013-05503011.
The publication costs of this article were defrayed in part by page charge
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MALINGE et al
Methods
exponent of the right-tailed Fisher exact test used to estimate the likelihood that
the network-eligible molecules that are part of a network are found therein by
random chance alone.
Samples
Fetal liver mononuclear cells (MNC) with either a normal karyotype or
trisomy 21 were obtained from 2nd-trimester abortions. MNC cells were
isolated using a standard Ficoll separation method from a cohort of 7
DS-associated acute megakaryoblastic leukemias (DS-AMKL), 6 cases of
transient myeloproliferative disorder (DS-TMD), and 8 acute megakaryoblastic leukemias from adults without DS (nonDS-AMKL) received through
the Childrens Oncology Group and Eastern Cooperative Oncology Group
leukemia tissue banks. Supplemental Table 1 (found on the Blood Web site)
describes the patients characteristics. The diagnosis of megakaryoblastic
leukemia was established by morphology and conrmed by immunophenotyping. Institutional review board approval was obtained at Weill Cornell
Medical College, University of Pennsylvania, Childrens Hospital of Michigan,
and the University of Michigan. Eight specimens of human CD341 bone
marrow cells were provided by the Stem Cell and Xenograft Core Facility of
the University of Pennsylvania or purchased from AllCells (Emeryville,
CA). These studies were performed in accordance with the Declaration of
Helsinki protocols.
DNA methylation by HELP
Genomic DNA was extracted using the Puregene kit from Qiagen (Valencia,
CA) or a standard phenol-chloroform isolation followed by ethanol precipitation. HELP (HpaII tiny fragment enrichment by ligation-mediated
polymerase chain reaction) representations were prepared from 100 ng of
DNA as previously described23,24 and hybridized onto a custom longoligonucleotide microarray designed to cover HpaII ampliable fragments (HAF) at gene promoter regions. HG19 array was manufactured by
Roche-NimbleGen, design ID: 100128_HG19_MKF_HELP_ChIP, covering 117 521 HAFs annotated to 29 606 unique RefSeq genes. MM9 array was
manufactured by Roche-NimbleGen, design ID: 100520_MM9_KF_Meth,
covering 119 260 HAFs annotated to 24 377 unique RefSeq genes. All samples
were processed and hybridized at the Weill Cornell Medical College
Epigenomics Core Facility. Labeling, hybridization, and scanning were
performed as previously described.25 Quality control and array normalization
were performed following our previously described methods,26 and any arrays
that did not pass our quality control were excluded from the analysis. In order to
correct for the introduction of hybridization batch effect, we subjected each
individual channel to batch correction using the ComBat algorithm,27 and the
adjusted channels were then used to calculate the nal HpaII:MspI ratio.
Microarray analysis
Supervised analysis for the different group comparisons was performed using
Bioconductor and the R 2.15 statistical software, and the genelter, stats, and
gplots packages. Pairwise comparisons were performed using Student t test,
followed by adjustment of the P value with the Benjamini-Hochberg approach
for multiple comparisons.28 Signicant differences were dened as those with
adjusted P value , .05 and an absolute difference in log2(HpaII/MspI) .2,
which corresponds to a minimal methylation difference of 30%.
Gene expression arrays
Normalized gene expression values for DS-AMKL, nonDS-AMKL, and
DS-TMD specimens were downloaded from the GEO repository from the
study by Bourquin et al29 (accession number GSE4119). Gene set enrichment analysis was performed using the Molecular Signatures Database
(MSigDB) c1 collection (positional).30
Network and pathway analysis
Network and pathway analysis using the Ingenuity Pathway Analysis software
(Ingenuity Systems, Redwood City, CA) was performed using the signatures
identied for the different comparisons and the Ingenuity Knowledge database
as a background reference. Network signicance was scored as the negative
Results
With the goal of studying epigenetic deregulation associated with
malignant transformation in the hematopoietic system of Down
syndrome patients, we performed genome-wide DNA methylation
analysis using the HELP assay23,24 on a custom high-density
oligonucleotide array designed to query to methylation status at
;200 000 distinct CpG sites (annotated to 29 606 RefSeq genes).
Given that the HELP assay uses as a reference an MspI-restricted
representation of the patients own genome, which serves as an
internal control for copy number and sequence variants,24,31 the
presence of a trisomic chromosome in some of the specimens in this
study is automatically controlled for and does not have an impact on
the ability of the assay to detect methylation differences, even within
chromosome 21. In order to evaluate epigenetic changes during the
different stages of disease development, the following samples were
collected: fetal liver (FL) MNC with normal karyotype (FL-MNC,
n 5 4), trisomy 21 FL MNC (Tri21 FL-MNC, n 5 4), MNC from
Down syndrome patients with either transient myeloproliferative
disorder (DS-TMD, n 5 6) or acute megakaryoblastic leukemia
(DS-AMKL, n 5 7), and MNC cells from patients with adult
nonDS-AMKL (n 5 8).
DS-AMKL is epigenetically distinct from nonDS-AMKL
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Figure 1. DS-AMKL and nonDS-AMKL are epigenetically distinct. (A) Heatmap representation of differentially methylated regions between normal CD341 cells
(NBM) and DS-AMKL blasts. Each row represents a
genomic region, and each column represents a sample.
(B) Volcano plot representing the comparison of DS-AMKL
blasts to normal CD341 cells. X-axis represents the
difference in DNA methylation between the 2 groups,
and the y-axis represents the statistical significance of
the differences. Red dots denote DMRs with absolute
log ratio difference .2 and FDR ,5%. (C) Heatmap
representation of differentially methylated regions between normal CD341 cells (NBM) and nonDS-AMKL
blasts. Each row represents a genomic region, and each
column represents a sample. (D) Volcano plot representing the comparison of nonDS-AMKL blasts to normal
CD341 cells. X-axis represents the difference in DNA
methylation between the 2 groups, and the y-axis
represents the statistical significance of the differences.
Red dots denote DMRs with absolute log ratio difference
.2 and FDR ,5%. (E) Heatmap representation of
differentially methylated regions between nonDS-AMKL
and DS-AMKL blasts. Each row represents a genomic
region, and each column represents a patient sample.
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MALINGE et al
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and DS-AMKL blasts. Only 7 genes were found differentially expressed at an FDR ,5% and a minimum fold change of 2. These
ndings demonstrate that DS-TMD and DS-AMKL are virtually
identical, consistent with other reports that found relatively minor
differences in gene expression levels between TMD and DSAMKL.33,34 Moreover, although additional genetic lesions are
likely present at the DS-AMKL stage,14,15,35 they do not appear to
have a signicant impact on the transcriptional and epigenetic
programs of these cells.
DS-related hypomethylation on chromosome 21 is linked to
trisomic gene overexpression and affects the DS critical region
and nearby neighboring regions
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MALINGE et al
Molecules in network
Top functions
Score
56
neurological disease
45
44
32
embryonic development
30
30
embryonic development
28
transport
NPFF, P110, PAX4, PEMT, PEPCK, PRKCZ, Rab5, Ras, SRC, TBC1D3F,
THRA/B, NTRK1/2/3, USP17, USP17L2, VEGF, VN1R4
8
26
ACE, ACTA2, Akt, CD68, CD151, CD276, COL1, COL1A1/2, COL4, Cpla2, CSF2,
FGA/B/G, FMOD, ITGA5, ITGB5, KLK1/3/B1, LAG3, LAMA1/5, MAP2K1/2,
24
cardiovascular disease
23
Discussion
DS-AMKL development is associated with a series of wellcharacterized sequential genetic events.6 However, much less is
known about the epigenetic changes that occur during this process.
In the current study we report the rst genome-wide DNA methylation study of DS leukemogenesis. Taking advantage of the
multistep developmental process of DS-AMKL, we performed DNA
methylation proling at sequential stages of the disease. Our ndings
demonstrate that epigenetic deregulation in DS-AMKL leukemogenesis
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BLOOD, 3 OCTOBER 2013 x VOLUME 122, NUMBER 14
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Molecules in network
Top functions
ADCY, ADORA3, ADRB3, FOS/JUN, ATN1, CD9, CELSR1, CXCR7, DRD2, ESR1/
2, FPR3, GNAI1/2/3, GPR83, GPR101, HTR4, HTR5A, KCNA2, KCNA3,
Score
23
metabolism
KCNJ6, LTF, NCOR1/2, NGEF, NRL, NUPR1, PI3K, RAC1/2/3, RHOA-D, RXR,
S1PR3, VIPR1, VN1R4, ZFHX3
2
23
movement
23
21
15
15
CCDC82, CCL16, CRIPT, CSTF2T, DLG4, DNAH7, EPO, FAM107B, GLCE, GPX7,
HGS, HNF4A, ISOC1, LRRTM2, MCTS1, MIF4GD, MRPS7, MRPS23, MSRB2,
14
disease
function
12
response
12
12
methylation at a distinct set of target genes. Unlike hypomethylation associated with trisomy 21, which preferentially affected gene
networks associated with developmental disorders such as those seen
in DS, genes affected by aberrant hypermethylation in DS-TMD
blasts were specic to hematological development and regulation
of key cellular processes such as growth, proliferation, cell cycle
regulation, and cell death. How trisomy 21 may lead to hypomethylation while GATA1 mutations result in hypermethylation remains
unclear. These ndings, however, indicate that these 2 waves of
epigenetic reprogramming contribute to distinct aspects of DS
abnormalities (Figure 5). Additional experiments will be required
to functionally determine whether the predisposing role of the
additional chromosome 21 to leukemogenesis is mediated through
this trisomy 21driven hypomethylation, as well as to further dene
the precise nature of the epigenetic changes in sorted subpopulations
(hematopoietic stem cell and MEP) obtained from the different
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MALINGE et al
Figure 4. DNA hypomethylation is associated to overexpression of trisomic genes. (A) Visualization on the University of California at Santa Cruz (UCSC) genome
browser of DNA methylation changes detected by the HELP assay on 4 genes localized in neighboring regions of the DSCR. Each custom track represents the mean HELP
values measured for that group. Negative deflections below the zero line represent negative log ratios (methylated regions), and positive deflections above the zero line
represent positive log ratios (hypomethylated regions). Red arrows indicate HELP probesets with detectable differences in methylation between control samples (FL-MNC and
nonDS-AMKL) and DS-related samples (Tri21 FL-MNC, DS-AMKL, and DS-TMD). (B) Boxplots representing gene expression values for genes differentially methylated in
and around the DS critical region. P values are for t test comparisons between each of the 2 DS-related conditions vs the nonDS-AMKL values. (C) Gene set enrichment
analysis using positional gene sets MSigDB collections (c1) showing significant enrichment for genes localized in 21q22 band in DS-AMKL samples from a publicly available
DS-AMKL microarray dataset.29
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Another interesting nding is that a specic region of the chromosome 21 around the DSCR remains hypomethylated during the
whole process of DS-leukemogenesis, whereas from the TMD stage
onward, additional changes in methylation are dominated by hypermethylation. This region has been specically associated to DSAMKL development using human specimens with segmental
trisomy 21,38 gene expression proling29,49 and animal models.13
We correlated this hypomethylation to the overexpression of genes
contained in this region including DYRK1A, which has been shown
to cooperate with Gata1s and MPL W515L expression to promote
DS-AMKL in vivo.13 Notably, only a small fraction of the
chromosome 21 genes were upregulated in the DS-AMKL and DSTMD specimens in relation to nonDS-AMKL, indicating that upregulation of these genes is not simply the result of the increased
copy number due to the trisomy. Taken together, these observations
strongly suggest that the observed epigenetic memory of hypomethylated DSCR genes is submitted to a selective pressure required
for DS-leukemogenesis.
In summary, our study shows that the genetic changes linked to
the specic stages in DS-AMKL are associated with distinct sets of
changes in DNA patterning. Whether the epigenetic pattern changes
contribute to disease or simply reect the underlying genetic lesions
remains to be determined. In support of a pathogenic role of the
aberrant gene methylation, it is notable that the earlier changes
associated with hypomethylation tended to affect developmental
pathways comprising Down syndrome. The later acquired changes
in methylation in cell cycle control pathways also support the idea
that the changes in DNA methylation are a cause and not an effect
of disease. The mechanisms through which these epigenetic changes
become established are yet to be identied and require careful consideration of the genes in the critical region of chromosome 21 as well
as pathways downstream of GATA1, because GATA1 target genes
were not among the hypermethylated sites in TMD and DS-AMKL.
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MALINGE et al
Acknowledgments
The authors thank the Weill Cornell Medical Center Epigenetics
Core Facility for performing the HELP microarrays and Jason
Berman, Soheil Meshinchi, Todd Alonzo, and Sommer Castro and
the Childrens Oncology Group for their assistance with DS-AMKL
specimens. This articles contents are solely the responsibility
of the authors and does not necessarily represent the ofcial
views of the National Cancer Institute.
M.E.F. is supported in part by a Special Fellow Award from the
Leukemia and Lymphoma Society. S.M. was supported by a
Leukemia and Lymphoma Society Special Fellowship (no. 511010). This work was supported in part by grants from the National
Cancer Institute (NCI) (CA101774) and the Samuel Waxman
Cancer Research Foundation. J.W.T. is supported by an R01 grant
from the NCI (CA120772). This work was partially funded by grant
K08 HL093290 from the National Heart, Lung, and Blood Institute
(NHLBI) (to S.T.C.) and The American Society of Hematology (to
S.T.C.). This study was coordinated by the Eastern Cooperative
Oncology Group (Robert L. Comis, Chair) and supported in part by
Public Health Service Grants CA23318, CA66636, CA21115,
CA17145, CA13650, CA15488, and CA14958 from the NCI,
National Institutes of Health, and the Department of Health and
Authorship
Contribution: J.C. and M.E.F. conceived and designed the study;
S.M., T.C., L.C.D., and M.E.F. performed experiments; T.C., L.C.D.,
and M.E.F. analyzed the data; S.M. and J.C. critically revised the data;
S.C., R.P.K., M.S.T., E.P., M.J.W., A.G., and J.W.T. contributed key
resources and specimens; M.E.F., S.M., and J.C. wrote the manuscript; and T.C., S.C., M.J.W., R.P.K., E.P., M.S.T., A.G., and J.W.T.
revised and approved the manuscript.
Conict-of-interest disclosure: The authors declare no competing nancial interests.
Correspondence: Maria E. Figueroa, Department of Pathology,
University of Michigan, 109 Zina Pitcher Place, 2019 BSRB, Ann
Arbor, MI 48109-2200; e-mail: margue@med.umich.edu; or John
D. Crispino, Northwestern University Feinberg School of Medicine,
Division of Hematology and Oncology, 303 E Superior St, Lurie
Research Building 5-113, Chicago, IL 60611; e-mail: j-crispino@
northwestern.edu.
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