• EZH2 inhibition in B cells promotes AID-dependent chromosomal translocations in the presence of high AID activity or Ligase4 deficiency.

  • EZH2 inhibition depletes H3K27me3 and enhances H3K27ac, facilitating translocation formation by increasing transcriptional activity.

Abstract

The enhancer of zeste homolog 2 (EZH2) histone methyltransferase inhibitors tazemetostat and valemetostat recently have received approval for clinical use in follicular lymphoma and adult T-cell leukemia/lymphoma, respectively. In follicular lymphoma, the expression of activation-induced cytidine deaminase (AID) is responsible for increased mutational signatures and genomic instability. Because EZH2 inhibitors induce epigenetic and transcriptional changes in normal and lymphoma B cells, we studied whether these inhibitors could alter the pattern of AID-mediated chromosomal translocations. In this study, we showed that treatment with EZH2 inhibitors did not significantly change AID expression or AID-dependent chromosomal translocation frequency when used as monotherapy in either CH12F3 mouse B cells or MEC-1 human B cells. In contrast, when combined with phosphoinositide 3-kinase δ (PI3Kδ) inhibition, which enhances AID expression, EZH2 inhibition significantly increased the frequency of chromosomal translocations when compared with either EZH2 or PI3Kδ inhibition alone both in mouse CH12F3 cells and human MEC-1 cells. EZH2 inhibition also further enhanced translocation formation in mouse B cells that were DNA ligase IV (Ligase4) deficient. Mechanistically, EZH2 inhibition in B cells depletes the repressive histone modification H3 trimethylation at lysine 27 (H3K27me3) while concurrently enhancing the active histone modification H3 acetylation at lysine 27 (H3K27ac), thereby selectively increasing transcriptional activity and facilitating chromosomal translocation formation in the presence of high AID activity or Ligase4 deficiency. These findings highlight the impact of drugs that induce epigenetic changes to influence chromosomal translocations, and demonstrate the genetic safety of EZH2 inhibitors as monotherapy while highlighting the increased risk of genomic instability when used in cells prone to translocations, such as B cells with high AID levels or DNA repair deficiency.

1.
Bates
SE
.
Epigenetic therapies for cancer
.
N Engl J Med
.
2020
;
383
(
7
):
650
-
663
.
2.
Cao
R
,
Wang
L
,
Wang
H
, et al
.
Role of histone H3 lysine 27 methylation in Polycomb-group silencing
.
Science
.
2002
;
298
(
5595
):
1039
-
1043
.
3.
Cao
R
,
Zhang
Y
.
The functions of E(Z)/EZH2-mediated methylation of lysine 27 in histone H3
.
Curr Opin Genet Dev
.
2004
;
14
(
2
):
155
-
164
.
4.
Cai
Y
,
Zhang
Y
,
Loh
YP
, et al
.
H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions
.
Nat Commun
.
2021
;
12
(
1
):
719
.
5.
McCabe
MT
,
Ott
HM
,
Ganji
G
, et al
.
EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations
.
Nature
.
2012
;
492
(
7427
):
108
-
112
.
6.
Kim
KH
,
Roberts
CW
.
Targeting EZH2 in cancer
.
Nat Med
.
2016
;
22
(
2
):
128
-
134
.
7.
Duan
R
,
Du
W
,
Guo
W
.
EZH2: a novel target for cancer treatment
.
J Hematol Oncol
.
2020
;
13
(
1
):
104
.
8.
Lackraj
T
,
Goswami
R
,
Kridel
R
.
Pathogenesis of follicular lymphoma
.
Best Pract Res Clin Haematol
.
2018
;
31
(
1
):
2
-
14
.
9.
Italiano
A
,
Soria
JC
,
Toulmonde
M
, et al
.
Tazemetostat, an EZH2 inhibitor, in relapsed or refractory B-cell non-Hodgkin lymphoma and advanced solid tumours: a first-in-human, open-label, phase 1 study
.
Lancet Oncol
.
2018
;
19
(
5
):
649
-
659
.
10.
Morschhauser
F
,
Tilly
H
,
Chaidos
A
, et al
.
Tazemetostat for patients with relapsed or refractory follicular lymphoma: an open-label, single-arm, multicentre, phase 2 trial
.
Lancet Oncol
.
2020
;
21
(
11
):
1433
-
1442
.
11.
Straining
R
,
Eighmy
W
.
Tazemetostat: EZH2 inhibitor
.
J Adv Pract Oncol
.
2022
;
13
(
2
):
158
-
163
.
12.
Isshiki
Y
,
Chen
X
,
Teater
M
, et al
.
EZH2 inhibition enhances T cell immunotherapies by inducing lymphoma immunogenicity and improving T cell function
.
Cancer Cell
.
2025
;
43
(
1
):
49
-
68.e9
.
13.
Izutsu
K
,
Makita
S
,
Nosaka
K
, et al
.
An open-label, single-arm phase 2 trial of valemetostat for relapsed or refractory adult T-cell leukemia/lymphoma
.
Blood
.
2023
;
141
(
10
):
1159
-
1168
.
14.
Keam
SJ
.
Valemetostat tosilate: first approval
.
Drugs
.
2022
;
82
(
16
):
1621
-
1627
.
15.
Yamagishi
M
,
Kuze
Y
,
Kobayashi
S
, et al
.
Mechanisms of action and resistance in histone methylation-targeted therapy
.
Nature
.
2024
;
627
(
8002
):
221
-
228
.
16.
Zinzani
PL
,
Izutsu
K
,
Mehta-Shah
N
, et al
.
Valemetostat for patients with relapsed or refractory peripheral T-cell lymphoma (VALENTINE-PTCL01): a multicentre, open-label, single-arm, phase 2 study
.
Lancet Oncol
.
2024
;
25
(
12
):
1602
-
1613
.
17.
Arribas
AJ
,
Napoli
S
,
Cascione
L
, et al
.
ERBB4-mediated signaling is a mediator of resistance to PI3K and BTK inhibitors in B-cell lymphoid neoplasms
.
Mol Cancer Ther
.
2023
;
23
(
3
):
368
-
380
.
18.
Arribas
AJ
,
Napoli
S
,
Cascione
L
, et al
.
Resistance to PI3Kδ inhibitors in marginal zone lymphoma can be reverted by targeting the IL-6/PDGFRA axis
.
Haematologica
.
2022
;
107
(
11
):
2685
-
2697
.
19.
Gopal
AK
,
Kahl
BS
,
de Vos
S
, et al
.
PI3Kδ inhibition by idelalisib in patients with relapsed indolent lymphoma
.
N Engl J Med
.
2014
;
370
(
11
):
1008
-
1018
.
20.
Flinn
IW
,
Kahl
BS
,
Leonard
JP
, et al
.
Idelalisib, a selective inhibitor of phosphatidylinositol 3-kinase-δ, as therapy for previously treated indolent non-Hodgkin lymphoma
.
Blood
.
2014
;
123
(
22
):
3406
-
3413
.
21.
Brown
JR
,
Byrd
JC
,
Coutre
SE
, et al
.
Idelalisib, an inhibitor of phosphatidylinositol 3-kinase p110δ, for relapsed/refractory chronic lymphocytic leukemia
.
Blood
.
2014
;
123
(
22
):
3390
-
3397
.
22.
O'Brien
S
,
Patel
M
,
Kahl
BS
, et al
.
Duvelisib, an oral dual PI3K-δ,γ inhibitor, shows clinical and pharmacodynamic activity in chronic lymphocytic leukemia and small lymphocytic lymphoma in a phase 1 study
.
Am J Hematol
.
2018
;
93
(
11
):
1318
-
1326
.
23.
Flinn
IW
,
Hillmen
P
,
Montillo
M
, et al
.
The phase 3 DUO trial: duvelisib vs ofatumumab in relapsed and refractory CLL/SLL
.
Blood
.
2018
;
132
(
23
):
2446
-
2455
.
24.
Brach
D
,
Johnston-Blackwell
D
,
Drew
A
, et al
.
EZH2 inhibition by tazemetostat results in altered dependency on B-cell activation signaling in DLBCL
.
Mol Cancer Ther
.
2017
;
16
(
11
):
2586
-
2597
.
25.
An
R
,
Li
YQ
,
Lin
YL
,
Xu
F
,
Li
MM
,
Liu
Z
.
EZH1/2 as targets for cancer therapy
.
Cancer Gene Ther
.
2023
;
30
(
2
):
221
-
235
.
26.
Chiarle
R
.
Translocations in normal B cells and cancers: insights from new technical approaches
.
Adv Immunol
.
2013
;
117
:
39
-
71
.
27.
Mitelman
F
,
Johansson
B
,
Mertens
F
.
The impact of translocations and gene fusions on cancer causation
.
Nat Rev Cancer
.
2007
;
7
(
4
):
233
-
245
.
28.
Nussenzweig
A
,
Nussenzweig
MC
.
Origin of chromosomal translocations in lymphoid cancer
.
Cell
.
2010
;
141
(
1
):
27
-
38
.
29.
Gostissa
M
,
Alt
FW
,
Chiarle
R
.
Mechanisms that promote and suppress chromosomal translocations in lymphocytes
.
Annu Rev Immunol
.
2011
;
29
:
319
-
350
.
30.
Hardianti
MS
,
Tatsumi
E
,
Syampurnawati
M
, et al
.
Activation-induced cytidine deaminase expression in follicular lymphoma: association between AID expression and ongoing mutation in FL
.
Leukemia
.
2004
;
18
(
4
):
826
-
831
.
31.
Ye
X
,
Ren
W
,
Liu
D
, et al
.
Genome-wide mutational signatures revealed distinct developmental paths for human B cell lymphomas
.
J Exp Med
.
2021
;
218
(
2
):
e20200573
.
32.
Alt
FW
,
Zhang
Y
,
Meng
FL
,
Guo
C
,
Schwer
B
.
Mechanisms of programmed DNA lesions and genomic instability in the immune system
.
Cell
.
2013
;
152
(
3
):
417
-
429
.
33.
Chiarle
R
,
Zhang
Y
,
Frock
RL
, et al
.
Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells
.
Cell
.
2011
;
147
(
1
):
107
-
119
.
34.
Frock
RL
,
Hu
J
,
Meyers
RM
,
Ho
YJ
,
Kii
E
,
Alt
FW
.
Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases
.
Nat Biotechnol
.
2015
;
33
(
2
):
179
-
186
.
35.
Hu
J
,
Meyers
RM
,
Dong
J
,
Panchakshari
RA
,
Alt
FW
,
Frock
RL
.
Detecting DNA double-stranded breaks in mammalian genomes by linear amplification–mediated high-throughput genome-wide translocation sequencing
.
Nat Protoc
.
2016
;
11
(
5
):
853
-
871
.
36.
Meng
FL
,
Du
Z
,
Federation
A
, et al
.
Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability
.
Cell
.
2014
;
159
(
7
):
1538
-
1548
.
37.
Compagno
M
,
Wang
Q
,
Pighi
C
, et al
.
Phosphatidylinositol 3-kinase delta blockade increases genomic instability in B cells
.
Nature
.
2017
;
542
(
7642
):
489
-
493
.
38.
Qian
J
,
Wang
Q
,
Dose
M
, et al
.
B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity
.
Cell
.
2014
;
159
(
7
):
1524
-
1537
.
39.
Claringbould
A
,
Zaugg
JB
.
Enhancers in disease: molecular basis and emerging treatment strategies
.
Trends Mol Med
.
2021
;
27
(
11
):
1060
-
1073
.
40.
Gao
J
,
Tao
J
,
Liang
W
, et al
.
Identification and characterization of phosphodiesterases that specifically degrade 3'3'-cyclic GMP-AMP
.
Cell Res
.
2015
;
25
(
5
):
539
-
550
.
41.
Deng
MJ
,
Tao
J
,
E
C
, et al
.
Novel mechanism for cyclic dinucleotide degradation revealed by structural studies of vibrio phosphodiesterase V-cGAP3
.
J Mol Biol
.
2018
;
430
(
24
):
5080
-
5093
.
42.
Tao
J
,
Wang
Q
,
Mendez-Dorantes
C
,
Burns
KH
,
Chiarle
R
.
Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites
.
Nat Commun
.
2022
;
13
(
1
):
3685
.
43.
Zhang
X
,
Zhang
Y
,
Ba
Z
,
Kyritsis
N
,
Casellas
R
,
Alt
FW
.
Fundamental roles of chromatin loop extrusion in antibody class switching
.
Nature
.
2019
;
575
(
7782
):
385
-
389
.
44.
Huang
X
,
Yan
J
,
Zhang
M
, et al
.
Targeting epigenetic crosstalk as a therapeutic strategy for EZH2-aberrant solid tumors
.
Cell
.
2018
;
175
(
1
):
186
-
199.e19
.
45.
Nakamura
M
,
Kondo
S
,
Sugai
M
,
Nazarea
M
,
Imamura
S
,
Honjo
T
.
High frequency class switching of an IgM+ B lymphoma clone CH12F3 to IgA+ cells
.
Int Immunol
.
1996
;
8
(
2
):
193
-
201
.
46.
Han
L
,
Yu
K
.
Altered kinetics of nonhomologous end joining and class switch recombination in ligase IV-deficient B cells
.
J Exp Med
.
2008
;
205
(
12
):
2745
-
2753
.
47.
Xie
X
,
Gan
T
,
Rao
B
, et al
.
C-terminal deletion-induced condensation sequesters AID from IgH targets in immunodeficiency
.
Embo j
.
2022
;
41
(
11
):
e109324
.
48.
Hu
J
,
Zhang
Y
,
Zhao
L
, et al
.
Chromosomal loop domains direct the recombination of antigen receptor genes
.
Cell
.
2015
;
163
(
4
):
947
-
959
.
49.
Masani
S
,
Han
L
,
Meek
K
,
Yu
K
.
Redundant function of DNA ligase 1 and 3 in alternative end-joining during immunoglobulin class switch recombination
.
Proc Natl Acad Sci U S A
.
2016
;
113
(
5
):
1261
-
1266
.
50.
Yan
CT
,
Boboila
C
,
Souza
EK
, et al
.
IgH class switching and translocations use a robust non-classical end-joining pathway
.
Nature
.
2007
;
449
(
7161
):
478
-
482
.
51.
Panchakshari
RA
,
Zhang
X
,
Kumar
V
, et al
.
DNA double-strand break response factors influence end-joining features of IgH class switch and general translocation junctions
.
Proc Natl Acad Sci U S A
.
2018
;
115
(
4
):
762
-
767
.
52.
Kaya-Okur
HS
,
Wu
SJ
,
Codomo
CA
, et al
.
CUT&Tag for efficient epigenomic profiling of small samples and single cells
.
Nat Commun
.
2019
;
10
(
1
):
1930
.
53.
Qiao
Q
,
Wang
L
,
Meng
FL
,
Hwang
JK
,
Alt
FW
,
Wu
H
.
AID recognizes structured DNA for class switch recombination
.
Mol Cell
.
2017
;
67
(
3
):
361
-
373.e4
.
54.
Pucella
JN
,
Chaudhuri
J
.
AID invited to the G4 summit
.
Mol Cell
.
2017
;
67
(
3
):
355
-
357
.
55.
Ribeiro de Almeida
C
,
Dhir
S
,
Dhir
A
, et al
.
RNA helicase DDX1 converts RNA G-quadruplex structures into R-loops to promote IgH class switch recombination
.
Mol Cell
.
2018
;
70
(
4
):
650
-
662.e8
.
56.
Wang
Y
,
Zhang
S
,
Yang
X
, et al
.
Mesoscale DNA feature in antibody-coding sequence facilitates somatic hypermutation
.
Cell
.
2023
;
186
(
10
):
2193
-
2207.e19
.
57.
Dai
P
,
Tan
Y
,
Luo
Y
, et al
.
Transcription-coupled AID deamination damage depends on ELOF1-associated RNA polymerase II
.
Mol Cell
.
2025
;
85
(
7
):
1280
-
1295.e9
.
58.
Wu
L
,
Yadavalli
AD
,
Senigl
F
, et al
.
Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination
.
Mol Cell
.
2025
;
85
(
7
):
1296
-
1310.e7
.
59.
Hao
Q
,
Zhan
C
,
Lian
C
, et al
.
DNA repair mechanisms that promote insertion-deletion events during immunoglobulin gene diversification
.
Sci Immunol
.
2023
;
8
(
81
):
eade1167
.
60.
Proudman
D
,
Nellesen
D
,
Gupta
D
,
Adib
D
,
Yang
J
,
Mamlouk
K
.
A matching-adjusted indirect comparison of single-arm trials in patients with relapsed or refractory follicular lymphoma who received at least two prior systemic treatments: tazemetostat was associated with a lower risk for safety outcomes versus the PI3-kinase inhibitors idelalisib, duvelisib, copanlisib, and umbralisib
.
Adv Ther
.
2022
;
39
(
4
):
1678
-
1696
.
61.
Altmann
T
,
Gennery
AR
.
DNA ligase IV syndrome; a review
.
Orphanet J Rare Dis
.
2016
;
11
(
1
):
137
.
62.
Sun
B
,
Chen
Q
,
Wang
Y
, et al
.
LIG4 syndrome: clinical and molecular characterization in a Chinese cohort
.
Orphanet J Rare Dis
.
2020
;
15
:
131
.
63.
Kaminski
AM
,
Tumbale
PP
,
Schellenberg
MJ
, et al
.
Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis
.
Nat Commun
.
2018
;
9
(
1
):
2642
.
64.
Ben-Omran
TI
,
Cerosaletti
K
,
Concannon
P
,
Weitzman
S
,
Nezarati
MM
.
A patient with mutations in DNA ligase IV: clinical features and overlap with Nijmegen breakage syndrome
.
Am J Med Genet A
.
2005
;
137A
(
3
):
283
-
287
.
65.
Enders
A
,
Fisch
P
,
Schwarz
K
, et al
.
A severe form of human combined immunodeficiency due to mutations in DNA ligase IV
.
J Immunol
.
2006
;
176
(
8
):
5060
-
5068
.
66.
Toita
N
,
Hatano
N
,
Ono
S
, et al
.
Epstein-Barr virus-associated B-cell lymphoma in a patient with DNA ligase IV (LIG4) syndrome
.
Am J Med Genet A
.
2007
;
143A
(
7
):
742
-
745
.
67.
Sharapova
SO
,
Chang
EY
,
Guryanova
IE
, et al
.
Next generation sequencing revealed DNA ligase IV deficiency in a “developmentally normal” patient with massive brain Epstein-Barr virus-positive diffuse large B-cell lymphoma
.
Clin Immunol
.
2016
;
163
:
108
-
110
.
68.
Bacon
CM
,
Wilkinson
SJ
,
Spickett
GP
, et al
.
Epstein-Barr virus-independent diffuse large B-cell lymphoma in DNA ligase 4 deficiency
.
J Allergy Clin Immunol
.
2013
;
131
:
1237
-
1239.e1
.
69.
Mareckova
A
,
Malcikova
J
,
Tom
N
, et al
.
ATM and TP53 mutations show mutual exclusivity but distinct clinical impact in mantle cell lymphoma patients
.
Leuk Lymphoma
.
2019
;
60
(
6
):
1420
-
1428
.
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