https://orcid.org/0000-0003-1324-6678
Key Points
Peripheral T-cell lymphomas have distinct DNMT3A mutation patterns and prognostic outcomes.
DNMT3A mutations are associated with an activated, cytotoxic phenotype in the PTCL-TBX21 subtype.
Abstract
Peripheral T-cell lymphomas (PTCLs) are heterogenous T-cell neoplasms often associated with epigenetic dysregulation. We investigated de novo DNA methyltransferase 3A (DNMT3A) mutations in common PTCL entities, including angioimmunoblastic T-cell lymphoma and novel molecular subtypes identified within PTCL–not otherwise specified (PTCL-NOS) designated as PTCL-GATA3 and PTCL-TBX21. DNMT3A-mutated PTCL-TBX21 cases showed inferior overall survival (OS), with DNMT3A-mutated residues skewed toward the methyltransferase domain and dimerization motif (S881–R887). Transcriptional profiling demonstrated significant enrichment of activated CD8+ T-cell cytotoxic gene signatures in the DNMT3A-mutant PTCL-TBX21 cases, which was further validated using immunohistochemistry. Genomewide methylation analysis of DNMT3A-mutant vs wild-type (WT) PTCL-TBX21 cases demonstrated hypomethylation in target genes regulating interferon-γ (IFN-γ), T-cell receptor signaling, and EOMES (eomesodermin), a master transcriptional regulator of cytotoxic effector cells. Similar findings were observed in a murine model of PTCL with Dnmt3a loss (in vivo) and further validated in vitro by ectopic expression of DNMT3A mutants (DNMT3A-R882, -Q886, and -V716, vs WT) in CD8+ T-cell line, resulting in T-cell activation and EOMES upregulation. Furthermore, stable, ectopic expression of the DNMT3A mutants in primary CD3+ T-cell cultures resulted in the preferential outgrowth of CD8+ T cells with DNMT3AR882H mutation. Single-cell RNA sequencing(RNA-seq) analysis of CD3+ T cells revealed differential CD8+ T-cell subset polarization, mirroring findings in DNMT3A-mutated PTCL-TBX21 and validating the cytotoxic and T-cell memory transcriptional programs associated with the DNMT3AR882H mutation. Our findings indicate that DNMT3A mutations define a cytotoxic subset in PTCL-TBX21 with prognostic significance and thus may further refine pathological heterogeneity in PTCL-NOS and suggest alternative treatment strategies for this subset.
REFERENCES
1.
Vose
JM
. Peripheral T-cell non-Hodgkin’s lymphoma
. Hematol Oncol Clin North Am.
2008
;22
(5
):997
-1005
.2.
Piccaluga
PP
, Tabanelli
V
, Pileri
SA
. Molecular genetics of peripheral T-cell lymphomas
. Int J Hematol.
2014
;99
(3
): 219
-226
.3.
Carson
KR
, Horwitz
SM
, Pinter-Brown
LC
, et al. A prospective cohort study of patients with peripheral T-cell lymphoma in the United States
. Cancer.
2017
;123
(7
):1174
-1183
.4.
Hsi
ED
, Horwitz
SM
, Carson
KR
, et al. Analysis of peripheral t-cell lymphoma diagnostic workup in the United States
. Clin Lymphoma Myeloma Leuk.
2017
;17
(4
):193
-200
.5.
Swerdlow
SH
, Campo
E
, Harris
NL
, eds et al. WHO Classification of tumours of haematopoietic and lymphoid tissues.
4th ed, revised. Lyon, France
: International Agency for Research on Cancer
; 2017
:2
6.
Agostinelli
C
, Piccaluga
PP
, Went
P
, et al. Peripheral T cell lymphoma, not otherwise specified: the stuff of genes, dreams and therapies
. J Clin Pathol.
2008
;61
(11
):1160
-1167
.7.
Pileri
SA
, Piccaluga
PP
. New molecular insights into peripheral T cell lymphomas
. J Clin Invest.
2012
;122
(10
):3448
-3455
.8.
Ballester
B
, Ramuz
O
, Gisselbrecht
C
, et al. Gene expression profiling identifies molecular subgroups among nodal peripheral T-cell lymphomas
. Oncogene.
2006
;25
(10
):1560
-1570
.9.
de Leval
L
, Rickman
DS
, Thielen
C
, et al. The gene expression profile of nodal peripheral T-cell lymphoma demonstrates a molecular link between angioimmunoblastic T-cell lymphoma (AITL) and follicular helper T (TFH) cells
. Blood.
2007
;109
(11
):4952
-4963
.10.
Iqbal
J
, Weisenburger
DD
, Chowdhury
A
, et al; International Peripheral T-cell Lymphoma Project
. Natural killer cell lymphoma shares strikingly similar molecular features with a group of non-hepatosplenic γδ T-cell lymphoma and is highly sensitive to a novel aurora kinase A inhibitor in vitro
[published correction appears in Leukemia. 2011;25(8):1377]. Leukemia.
2011
;25
(2
): 348
-358
.11.
Iqbal
J
, Weisenburger
DD
, Greiner
TC
, et al; International Peripheral T-Cell Lymphoma Project
. Molecular signatures to improve diagnosis in peripheral T-cell lymphoma and prognostication in angioimmunoblastic T-cell lymphoma
. Blood.
2010
;115
(5
):1026
-1036
.12.
Iqbal
J
, Wright
G
, Wang
C
, et al; Lymphoma Leukemia Molecular Profiling Project and the International Peripheral T-cell Lymphoma Project
. Gene expression signatures delineate biological and prognostic subgroups in peripheral T-cell lymphoma
. Blood.
2014
;123
(19
):2915
-2923
.13.
Piccaluga
PP
, Agostinelli
C
, Califano
A
, et al. Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets
. J Clin Invest.
2007
;117
(3
):823
-834
.14.
Fujiwara
SI
, Yamashita
Y
, Nakamura
N
, et al. High-resolution analysis of chromosome copy number alterations in angioimmunoblastic T-cell lymphoma and peripheral T-cell lymphoma, unspecified, with single nucleotide polymorphism-typing microarrays
. Leukemia.
2008
;22
(10
):1891
-1898
.15.
Heavican
TB
, Bouska
A
, Yu
J
, et al. Genetic drivers of oncogenic pathways in molecular subgroups of peripheral T-cell lymphoma
. Blood.
2019
;133
(15
):1664
-1676
.16.
Watatani
Y
, Sato
Y
, Miyoshi
H
, et al. Molecular heterogeneity in peripheral T-cell lymphoma, not otherwise specified revealed by comprehensive genetic profiling
. Leukemia.
2019
;33
(12
):2867
-2883
.17.
Abate
F
, da Silva-Almeida
AC
, Zairis
S
, et al. Activating mutations and translocations in the guanine exchange factor VAV1 in peripheral T-cell lymphomas
. Proc Natl Acad Sci USA.
2017
;114
(4
):764
-769
.18.
Iqbal
J
, Amador
C
, McKeithan
TW
, Chan
WC
. Molecular and genomic landscape of peripheral T-cell lymphoma
. Cancer Treat Res.
2019
;176
:31
-68
.19.
Maura
F
, Agnelli
L
, Leongamornlert
D
, et al. Integration of transcriptional and mutational data simplifies the stratification of peripheral T-cell lymphoma
. Am J Hematol.
2019
;94
(6
):628
-634
.20.
Vallois
D
, Dobay
MP
, Morin
RD
, et al. Activating mutations in genes related to TCR signaling in angioimmunoblastic and other follicular helper T-cell-derived lymphomas
. Blood.
2016
;128
(11
):1490
-1502
.21.
Amador
C
, Greiner
TC
, Heavican
TB
, et al. Reproducing the molecular subclassification of peripheral T-cell lymphoma-NOS by immunohistochemistry
. Blood.
2019
;134
(24
):2159
-2170
.22.
Wang
T
, Feldman
AL
, Wada
DA
, et al. GATA-3 expression identifies a high-risk subset of PTCL, NOS with distinct molecular and clinical features
. Blood.
2014
;123
(19
):3007
-3015
.23.
Zhang
W
, Wang
Z
, Luo
Y
, Zhong
D
, Luo
Y
, Zhou
D
. GATA3 expression correlates with poor prognosis and tumor-associated macrophage infiltration in peripheral T cell lymphoma
. Oncotarget.
2016
;7
(40
): 65284
-65294
.24.
Lone
W
, Bouska
A
, Sharma
S
, et al. Genome-wide miRNA expression profiling of molecular subgroups of peripheral T-cell lymphoma
. Clin Cancer Res.
2021
;27
(21
):6039
-6053
.25.
Couronné
L
, Bastard
C
, Bernard
OA
. TET2 and DNMT3A mutations in human T-cell lymphoma
. N Engl J Med.
2012
;366
(1
): 95
-96
.26.
Fukumoto
K
, Nguyen
TB
, Chiba
S
, Sakata-Yanagimoto
M
. Review of the biologic and clinical significance of genetic mutations in angioimmunoblastic T-cell lymphoma
. Cancer Sci.
2018
;109
(3
):490
-496
.27.
Wang
C
, McKeithan
TW
, Gong
Q
, et al. IDH2R172 mutations define a unique subgroup of patients with angioimmunoblastic T-cell lymphoma
. Blood.
2015
;126
(15
):1741
-1752
.28.
Palomero
T
, Couronné
L
, Khiabanian
H
, et al. Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas
. Nat Genet.
2014
;46
(2
):166
-170
.29.
Rohr
J
, Guo
S
, Huo
J
, et al. Recurrent activating mutations of CD28 in peripheral T-cell lymphomas
. Leukemia.
2016
;30
(5
):1062
-1070
.30.
Vaqué
JP
, Gómez-López
G
, Monsálvez
V
, et al. PLCG1 mutations in cutaneous T-cell lymphomas
. Blood.
2014
;123
(13
):2034
-2043
.31.
Cortes
JR
, Ambesi-Impiombato
A
, Couronné
L
, et al. RHOA G17V induces T follicular helper cell specification and promotes lymphomagenesis
. Cancer Cell.
2018
;33
(2
):259
-273.e7
.32.
Fujisawa
M
, Chiba
S
, Sakata-Yanagimoto
M
. Recent progress in the understanding of angioimmunoblastic T-cell lymphoma
. J Clin Exp Hematop.
2017
;57
(3
):109
-119
.33.
Ng
SY
, Brown
L
, Stevenson
K
, et al. RhoA G17V is sufficient to induce autoimmunity and promotes T-cell lymphomagenesis in mice
. Blood.
2018
;132
(9
):935
-947
.34.
Yue
X
, Lio
CJ
, Samaniego-Castruita
D
, Li
X
, Rao
A
. Loss of TET2 and TET3 in regulatory T cells unleashes effector function
. Nat Commun.
2019
;10
(1
):2011
.35.
Zhang
ZM
, Lu
R
, Wang
P
, et al. Structural basis for DNMT3A-mediated de novo DNA methylation
. Nature.
2018
;554
(7692
): 387
-391
.36.
Dukatz
M
, Holzer
K
, Choudalakis
M
, et al. H3K36me2/3 binding and DNA binding of the DNA methyltransferase DNMT3A PWWP domain both contribute to its chromatin interaction
. J Mol Biol.
2019
;431
(24
): 5063
-5074
.37.
Zhang
Y
, Jurkowska
R
, Soeroes
S
, et al. Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail
. Nucleic Acids Res.
2010
;38
(13
):4246
-4253
.38.
Ley
TJ
, Ding
L
, Walter
MJ
, et al. DNMT3A mutations in acute myeloid leukemia
. N Engl J Med.
2010
;363
(25
):2424
-2433
.39.
Gaidzik
VI
, Schlenk
RF
, Paschka
P
, et al. Clinical impact of DNMT3A mutations in younger adult patients with acute myeloid leukemia: results of the AML Study Group (AMLSG)
. Blood.
2013
;121
(23
):4769
-4777
.40.
Grossmann
V
, Haferlach
C
, Weissmann
S
, et al. The molecular profile of adult T-cell acute lymphoblastic leukemia: mutations in RUNX1 and DNMT3A are associated with poor prognosis in T-ALL
. Genes Chromosomes Cancer.
2013
;52
(4
):410
-422
.41.
Bond
J
, Touzart
A
, Leprêtre
S
, et al. DNMT3A mutation is associated with increased age and adverse outcome in adult T-cell acute lymphoblastic leukemia
. Haematologica.
2019
;104
(8
):1617
-1625
.42.
Brunetti
L
, Gundry
MC
, Goodell
MA
. DNMT3A in Leukemia
. Cold Spring Harb Perspect Med.
2017
;7
(2
):a030320
.43.
Yang
L
, Rau
R
, Goodell
MA
. DNMT3A in haematological malignancies
. Nat Rev Cancer.
2015
;15
(3
):152
-165
.44.
Stoeckius
M
, Zheng
S
, Houck-Loomis
B
, et al. Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single-cell genomics
. Genome Biol.
2018
;19
(1
):224
.45.
Dobay
MP
, Lemonnier
F
, Missiaglia
E
, et al. Integrative clinicopathological and molecular analyses of angioimmunoblastic T-cell lymphoma and other nodal lymphomas of follicular helper T-cell origin
. Haematologica.
2017
;102
(4
):e148
-e151
.46.
Odejide
O
, Weigert
O
, Lane
AA
, et al. A targeted mutational landscape of angioimmunoblastic T-cell lymphoma
. Blood.
2014
;123
(9
):1293
-1296
.47.
Sakata-Yanagimoto
M
, Enami
T
, Yoshida
K
, et al. Somatic RHOA mutation in angioimmunoblastic T cell lymphoma
. Nat Genet.
2014
;46
(2
):171
-175
.48.
Holz-Schietinger
C
, Matje
DM
, Reich
NO
. Mutations in DNA methyltransferase (DNMT3A) observed in acute myeloid leukemia patients disrupt processive methylation
. J Biol Chem.
2012
;287
(37
):30941
-30951
.49.
Marcucci
G
, Metzeler
KH
, Schwind
S
, et al. Age-related prognostic impact of different types of DNMT3A mutations in adults with primary cytogenetically normal acute myeloid leukemia
. J Clin Oncol.
2012
;30
(7
):742
-750
.50.
Subramanian
A
, Kuehn
H
, Gould
J
, Tamayo
P
, Mesirov
JP
. GSEA-P: a desktop application for gene set enrichment analysis
. Bioinformatics.
2007
;23
(23
):3251
-3253
.51.
Chen
B
, Khodadoust
MS
, Liu
CL
, Newman
AM
, Alizadeh
AA
. Profiling tumor-infiltrating immune cells with CIBERSORT
. Methods Mol Biol.
2018
;1711
:243
-259
.52.
Aran
D
. Cell-type enrichment analysis of bulk transcriptomes using xCell
. Methods Mol Biol.
2020
;2120
:263
-276
.53.
Haney
SL
, Upchurch
GM
, Opavska
J
, et al. Loss of Dnmt3a induces CLL and PTCL with distinct methylomes and transcriptomes in mice
. Sci Rep.
2016
;6
(1
):34222
.54.
Haney
SL
, Upchurch
GM
, Opavska
J
, et al. Dnmt3a is a haploinsufficient tumor suppressor in CD8+ peripheral T-cell lymphoma
. PLoS Genet.
2016
;12
(9
):e1006334
.55.
An
J
, Fujiwara
H
, Suemori
K
, et al. Activation of T-cell receptor signaling in peripheral T-cell lymphoma cells plays an important role in the development of lymphoma-associated hemophagocytosis
. Int J Hematol.
2011
;93
(2
):176
-185
.56.
Dai
YJ
, Wang
YY
, Huang
JY
, et al. Conditional knockin of Dnmt3a R878H initiates acute myeloid leukemia with mTOR pathway involvement
. Proc Natl Acad Sci USA.
2017
;114
(20
):5237
-5242
.57.
Lu
R
, Wang
J
, Ren
Z
, et al. A model system for studying the DNMT3A hotspot mutation (DNMT3AR882) demonstrates a causal relationship between its dominant-negative effect and leukemogenesis
. Cancer Res.
2019
;79
(14
):3583
-3594
.58.
Jeong
M
, Park
HJ
, Celik
H
, et al. Loss of Dnmt3a immortalizes hematopoietic stem cells in vivo
. Cell Rep.
2018
;23
(1
):1
-10
.59.
Emperle
M
, Adam
S
, Kunert
S
, et al. Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns
. Nucleic Acids Res.
2019
;47
(21
):11355
-11367
.60.
Bera
R
, Chiu
MC
, Huang
YJ
, Huang
G
, Lee
YS
, Shih
LY
. DNMT3A mutants provide proliferating advantage with augmentation of self-renewal activity in the pathogenesis of AML in KMT2A-PTD-positive leukemic cells
. Oncogenesis.
2020
;9
(2
):7
.61.
Aran
D
, Looney
AP
, Liu
L
, et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage
. Nat Immunol.
2019
;20
(2
):163
-172
.62.
Iqbal
J
, Wilcox
R
, Naushad
H
, et al. Genomic signatures in T-cell lymphoma: how can these improve precision in diagnosis and inform prognosis?
Blood Rev.
2016
;30
(2
):89
-100
.63.
Ko
M
, Huang
Y
, Jankowska
AM
, et al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2
. Nature.
2010
;468
(7325
):839
-843
.64.
Bolouri
H
, Farrar
JE
, Triche
T
Jr, et al. The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions
[published corrections appear in Nat Med. 2018;24(4):526 and Nat Med. 2019;25(3):530].Nat Med.
2018
;24
(1
): 103
-112
.65.
Weinberg
DN
, Papillon-Cavanagh
S
, Chen
H
, et al. The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape
. Nature.
2019
;573
(7773
):281
-286
.66.
Russler-Germain
DA
, Spencer
DH
, Young
MA
, et al. The R882H DNMT3A mutation associated with AML dominantly inhibits wild-type DNMT3A by blocking its ability to form active tetramers
. Cancer Cell.
2014
; 25
(4
):442
-454
.67.
Lemonnier
F
, Safar
V
, Beldi-Ferchiou
A
, et al. Integrative analysis of a phase 2 trial combining lenalidomide with CHOP in angioimmunoblastic T-cell lymphoma
. Blood Adv.
2021
;5
(2
):539
-548
.68.
Tse
E
, Kwong
Y-L
. How I treat NK/T-cell lymphomas
. Blood.
2013
;121
(25
):4997
-5005
.69.
Tse
E
, Au-Yeung
R
, Kwong
YL
. Recent advances in the diagnosis and treatment of natural killer/T-cell lymphomas
. Expert Rev Hematol.
2019
;12
(11
):927
-935
.70.
Tse
E
, Kwong
Y-L
. The diagnosis and management of NK/T-cell lymphomas
. J Hematol Oncol.
2017
;10
(1
):85
.71.
Metzeler
KH
, Walker
A
, Geyer
S
, et al. DNMT3A mutations and response to the hypomethylating agent decitabine in acute myeloid leukemia
. Leukemia.
2012
;26
(5
):1106
-1107
.72.
Cedena
MT
, Rapado
I
, Santos-Lozano
A
, et al. Mutations in the DNA methylation pathway and number of driver mutations predict response to azacitidine in myelodysplastic syndromes
. Oncotarget.
2017
;8
(63
):106948
-106961
.73.
Coombs
CC
, Sallman
DA
, Devlin
SM
, et al. Mutational correlates of response to hypomethylating agent therapy in acute myeloid leukemia
. Haematologica.
2016
;101
(11
):e457
-e460
.74.
Thol
F
, Damm
F
, Lüdeking
A
, et al. Incidence and prognostic influence of DNMT3A mutations in acute myeloid leukemia
. J Clin Oncol.
2011
;29
(21
): 2889
-2896
.75.
Celik
H
, Kramer
A
, Challen
GA
. DNA methylation in normal and malignant hematopoiesis
. Int J Hematol.
2016
;103
(6
):617
-626
.76.
Ehrentraut
S
, Nagel
S
, Pommerenke
C
, et al. Peripheral T-cell lymphoma cell line T8ML-1 highlights conspicuous targeting of PVRL2 by t(14;19)(q11.2;q13.3)
. Haematologica.
2017
;102
(9
):e356
-e359
.77.
Lu
R
, Wang
P
, Parton
T
, et al. Epigenetic perturbations by Arg882-mutated DNMT3A potentiate aberrant stem cell gene-expression program and acute leukemia development
. Cancer Cell.
2016
;30
(1
):92
-107
.78.
Jones
B
, Chen
J
. Inhibition of IFN-gamma transcription by site-specific methylation during T helper cell development
. EMBO J.
2006
;25
(11
):2443
-2452
.79.
Pham
D
, Yu
Q
, Walline
CC
, Muthukrishnan
R
, Blum
JS
, Kaplan
MH
. Opposing roles of STAT4 and Dnmt3a in Th1 gene regulation
. J Immunol.
2013
;191
(2
):902
-911
.80.
Thomas
RM
, Gamper
CJ
, Ladle
BH
, Powell
JD
, Wells
AD
. De novo DNA methylation is required to restrict T-helper lineage plasticity
. J Biol Chem.
2012
;287
(27
):22900
-22909
.81.
Ladle
BH
, Li
KP
, Phillips
MJ
, et al. De novo DNA methylation by DNA methyltransferase 3a controls early effector CD8+ T-cell fate decisions following activation
. Proc Natl Acad Sci USA.
2016
;113
(38
):10631
-10636
.82.
Youngblood
B
, Hale
JS
, Kissick
HT
, et al. Effector CD8 T cells dedifferentiate into long-lived memory cells
. Nature.
2017
; 552
(7685
):404
-409
.83.
Petiti
L
, Pace
L
. The persistence of stemness
. Nat Immunol.
2020
;21
(5
):492
-494
.84.
Yagi
M
, Kabata
M
, Tanaka
A
, et al. Identification of distinct loci for de novo DNA methylation by DNMT3A and DNMT3B during mammalian development
. Nat Commun.
2020
;11
(1
):3199
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