DNMT3A
R882 mutations act as dominant negative alleles in vitro
1
and are associated with focal regions of DNA hypomethylation in primary acute myeloid
leukemia (AML) samples and non-leukemic hematopoietic cells
2
. In primary AML cells, this hypomethylation manifests both as methylation loss and
attenuated CpG island hypermethylation relative to normal hematopoietic stem/progenitor
cells. Although DNMT3A
R882 mutations have a clear effect on DNA methylation in AML cells, the functional
consequences of these changes are not yet clear. Future study of the downstream effects
of mutant DNMT3A-associated hypomethylation will require model systems to investigate
the genomic targets that are affected, and to understand whether these changes alter
gene regulation in ways that promote leukemogenesis. Examples of model systems include
genetically modified mice, patient-derived xenografts, and human cell lines containing
DNMT3A
R882 mutations. The methylation phenotypes of mice lacking Dnmt3a, or expressing mutant
Dnmt3a alleles, have been reported previously
3–6
, but much less is known about whether alterations in methylation caused by DNMT3A
R882 alleles are retained in either patient-derived xenografts or human AML cell lines,
and whether these models could therefore be used to accurately represent DNMT3A
R882-dependent methylation changes in AML cells.
To address this question, we performed whole-genome bisulfite sequencing (WGBS) using
DNA from OCI-AML3 cells, which is the only leukemia cell line currently known to have
a native DNMT3A
R882C mutation
7
. We also evaluated four xenografts derived from a primary AML sample containing the
DNMT3A
R882H mutation. The OCI-AML3 line was obtained from the DSMZ cell collection and cultured
via recommended conditions before DNA extraction at two independent passages for WGBS.
The presence of the DNMT3A
R882C allele in these cells was verified via targeted sequencing prior to methylation
analysis (Supplementary Figure S1), as were the recurrent NPM1 exon 12 insertion (NPMc)
and the NRAS
Q61L mutation. No functional mutations were identified in other recurrently mutated
AML genes with roles in epigenetic modification, such as IDH1, IDH2, ASXL1, EZH2,
or TET2. Two missense variants of unknown significance were present in TET1 (Supplementary
Table S2), which is not frequently mutated in AML samples. Importantly, we saw no
evidence for amplification of the wild-type DNMT3A allele in this cell line (data
not shown). We also extracted two replicate DNA samples from comparator AML cell lines
that are wild-type for DNMT3A, including Kasumi-1 and NB4, which have a t(8;21) translocation
(creating the RUNX1-RUNX1T1 fusion gene) and a t(15;17) translocation (resulting in
a PML-RARA fusion), respectively. Patient-derived AML xenografts were generated in
two independent humanized NSG mice (NSG-SGM3) from a primary AML sample with the DNMT3A
R882H mutation (along with NPM1 and FLT3-ITD mutations; AML 721214, described as AML88
in ref.
8
; Supplementary Table S1) via tail vein injection of 1 million cells. Mice were killed
at 16 weeks and flow cytometry analysis of bone marrow confirmed high human AML cell
engraftment (90% and 81% human CD45 chimerism in the marrow, respectively; Supplementary
Figure S2). Engrafted cells were subsequently transferred for two additional passages
in multiple mice, and DNA was isolated from unmanipulated, xenografted bone marrow
cells from both primary and tertiary passages in duplicate. WGBS libraries were prepared
from all samples (including the primary AML sample used for xenotransplantation) with
50ng of DNA using the Swift DNA methylation library prep kit and sequenced on Illumina
HiSeq X instruments to obtain 277 million to 1.5 billion paired 150 bp reads per sample,
which yielded a median of 4 to 50-fold coverage for at least 26 million CpGs in the
human reference genome for each sample (Supplementary Table S1).
We first performed comparisons of genome-wide DNA methylation levels between the AML
cell lines, data from normal human CD34+ cells, and primary AML samples with and without
DNMT3A
R882 mutations
2
. The primary AML samples demonstrated methylation patterns that were previously reported
to be associated with DNMT3A
R882 mutant AML samples, including lower methylation overall, and at CpG island-shores,
compared to normal CD34 + cells. We also detected attenuated hypermethylation at CpG
islands compared to AMLs with wild-type DNMT3A (Fig. 1a). In distinct contrast, CpGs
in all three AML cell lines were strikingly hypermethylated at CpG islands and island-shores
relative to the primary human cell samples (34–51% mean methylation in the cell lines
at CpG islands, vs. 17–19% in the AML samples), which is consistent with previous
studies of methylation in cancer cell lines compared to normal tissues
9–11
. Interestingly, the mean methylation of OCI-AML3 and NB4 cells across the entire
genome was dramatically lower than all other samples (68 and 64% for these two cell
lines, vs. 85% mean methylation for all other samples; see Fig. 1a). This difference
was manifest primarily as an increase in large “partially-methylated domains” (PMDs;
Supplementary Figure S3), a phenomenon that has been observed previously in some cell
lines regardless of DNMT3A mutation status, and that is associated with transcriptionally
inactive genomic regions
12
. The number of PMDs was similar between the OCI-AML3 and NB4 cell lines (Figure S3A
and S3B), indicating that these features in OCI-AML3 cells cannot be uniquely attributed
to the DNMT3A
R882 mutation. In contrast to all three cell lines, methylation levels in the patient-derived
xenografts from AMLs with DNMT3A
R882H closely resembled primary AML cells from the same tumor (and other AML samples
with DNMT3A
R882H mutations) in all genomic regions, including subtle hypomethylation at CpG island-shores,
and attenuated hypermethylation of CpG islands (Fig. 1a, blue points), as we described
previously
2
.
Fig. 1
DNMT3A
R882-associated methylation patterns in primary AML cells, patient-derived xenografts,
and AML cell lines.
a Genome-wide methylation statistics for all samples. Points show mean methylation
values for all CpGs, CpG islands, and CpGs in island-shores for each sample. Note
that the primary AML samples with DNMT3A
R882 mutations include four previously published samples
2
, and a fifth sample that was used to generate AML xenografts in four independent
mice. b Methylation patterns at 3898 DNMT3A-dependent differentially methylated regions
(DMRs) from primary AML samples, AML cell lines, and xenografts. Each heatmap shows
the mean methylation in 50 bp windows for a 6 kb window centered on a DMR locus (one
DMR per row), with methylation represented on a white (unmethylated) to red (methylated)
scale. c, d Example DMRs with either DNMT3A
R882-associated hypomethylation (c), or loci with DNMT3A-mediated hypermethylation
that is absent in AMLs with DNMT3A
R882 (d). The top tracks in each panel show mean methylation from normal CD34 cells
(N = 5), AML samples with and without DNMT3A
R882H/C (N = 4 each), and the bottom tracks show the mean methylation from OCI-AML3,
NB4, and Kasumi-1 cells (N = 2, each), and individual methylation levels for two AML
xenografts derived from AML sample 721214. All the methylation data in these panels
were smoothed
16
prior to plotting. Coordinates refer to human reference sequence build 37 (hg19)
We next used results from our previously published study of DNMT3A-dependent methylation
in AML to determine whether the 3,898 differentially methylated regions (DMRs) that
were hypomethylated in primary AML cells with DNMT3A
R882 were maintained in the OCI-AML3 cells and patient xenografts. The OCI-AML3 genome
was not hypomethylated at these loci, but in fact was hypermethylated relative to
both AMLs with DNMT3A
R882 and normal CD34 cells (Fig. 1b). Statistical analysis of these regions demonstrated
that 81% (3,183/3,898) of the DMRs were hypermethylated in OCI-AML3 cells compared
to normal CD34 cells (Supplementary Figure S4A), and 90% (3517/3898) were hypermethylated
compared to the primary DNMT3A
R882 AML samples (Supplementary Figure S4B); a similar number of DMRs were hypermethylated
in Kasumi-1 and NB4 cells (85 and 82% vs. CD34 cells; 91 and 95% vs. DNMT3A
R882 AML samples, respectively; Supplementary Figures S4C-F). We have shown that hypomethylation
in primary AML samples with DNMT3A
R882 reflects both methylation loss, and reduced CpG island hypermethylation relative
to normal CD34 cells
2
; a review of individual DMR loci from both of these categories demonstrates that
OCI-AML3 cells failed to recapitulate either of these phenotypes (Fig. 1c, d). We
performed the same analysis on the data from the primary AML sample with the DNMT3A
R882 mutation that was used for xenotransplantation, and the two passaged tumor cell
populations from this sample: all three were hypomethylated relative to the AML samples
that were wild-type for DNMT3A at most DMRs (e.g., > 73% of DMRs were statistically
hypomethylated relative to DNMT3A
WT AML samples, Supplementary Figures S4E-G). Xenotransplanted cells remained hypomethylated
at these loci following two additional passages through NSG-SGM3 mice (Supplementary
Figure S5), and the methylation relationships between samples with DNMT3A
R882 and normal CD34 cells were also preserved in all transplanted AML cells (Fig.
1c, d, and Supplementary Figure S4).
Given the virtual absence of the focal, canonical hypomethylation phenotype in the
OCI-AML3 cell line, we performed additional experiments to assess the function of
DNMT3A
R882
in this cell line. We verified that the mutant and wild-type alleles of DNMT3A were
expressed equally in two replicate RNA-seq experiments (Supplementary Figure S6A).
Overall expression levels of both DNMT3A and DNMT3B (including active and inactive
isoforms) and other genes involved in DNA methylation were also similar between OCI-AML3
cells and a previously published set of 32 primary AML samples
2
, although expression of DNMT1 and BCAT1
13
were substantially higher in OCI-AML3 cells (Supplementary Figure S6B). Surprisingly,
the bulk in vitro methylation activity of OCI-AML3 cell lysates performed on an unmethylated
DNA substrate
1
was significantly higher than Kasumi-1 cell lines (Figure S6C), even though Kasumi-1
cells have significantly higher CpG methylation across the genome, suggesting that
de novo methylation in these cells is probably influenced by factors other than DNMT3A
R882.
Models of DNMT3A
R882 that accurately recapitulate the epigenetic phenotype of primary AML samples
with this mutation will be critical to understand its functional consequences, and
investigate targeted therapies. In this study, we found that DNMT3A
R882-associated hypomethylation was preserved in patient-derived AML xenografts with
DNMT3A
R882, which displayed the same global and focal hypomethylation phenotypes as primary
patient samples. The OCI-AML3 cell line, which harbors a DNMT3A
R882C allele, showed none of these patterns, and were in fact hypermethylated at many
of the DNMT3A-dependent loci. Although these cells have been used to represent AML
samples with DNMT3A
R882 mutations
5,14,15
, they are clearly not an appropriate model for understanding DNMT3A
R882-dependent methylation phenotypes in AML cells, or for making inferences about
specific genes or loci that may be dysregulated by DNMT3A
R882. We have proposed that CpG island hypermethylation may be a normal response to
abnormal proliferation in leukemic cells; these data suggest that the residual de
novo methylation activity present in OCI-AML3 cells is adequate to methylate these
DNMT3A-dependent regions during long periods of cell culture. It is also possible
that these cells never possessed the DNMT3A
R882 methylation signature, although previous analysis has shown that primary AML
samples with DNMT3A
R882 invariably display some level of focal hypomethylation at the loci examined here.
Moreover, the similarities between OCI-AML3 and other AML cells lines with different
initiating mutations suggests that the methylation patterns in these cells may be
related to properties that are associated with immortalization. Regardless, the methylation
patterns in OCI-AML3, cells are clearly very different from primary AML samples with
DNMT3A
R882 mutations, and therefore this cell line is not an appropriate model for understanding
genomic patterns of DNA methylation that are caused by the DNMT3A
R882 mutation.
Electronic supplementary material
Supplemental Figure Legends
Supplemental Figures
Supplemental Table S1
Supplemental Table S2