• DNA POLθ–mediated DNA repair protects leukemia cells from the toxic effect of metabolically induced DNA damage.

  • DNA POLθ is a new therapeutic target to eradicate leukemia clones expressing oncogenic tyrosine kinases.

Leukemia cells accumulate DNA damage, but altered DNA repair mechanisms protect them from apoptosis. We showed here that formaldehyde generated by serine/1-carbon cycle metabolism contributed to the accumulation of toxic DNA-protein crosslinks (DPCs) in leukemia cells, especially in driver clones harboring oncogenic tyrosine kinases (OTKs: FLT3(internal tandem duplication [ITD]), JAK2(V617F), BCR-ABL1). To counteract this effect, OTKs enhanced the expression of DNA polymerase theta (POLθ) via ERK1/2 serine/threonine kinase-dependent inhibition of c-CBL E3 ligase-mediated ubiquitination of POLθ and its proteasomal degradation. Overexpression of POLθ in OTK-positive cells resulted in the efficient repair of DPC-containing DNA double-strand breaks by POLθ-mediated end-joining. The transforming activities of OTKs and other leukemia-inducing oncogenes, especially of those causing the inhibition of BRCA1/2-mediated homologous recombination with and without concomitant inhibition of DNA-PK–dependent nonhomologous end-joining, was abrogated in Polq−/− murine bone marrow cells. Genetic and pharmacological targeting of POLθ polymerase and helicase activities revealed that both activities are promising targets in leukemia cells. Moreover, OTK inhibitors or DPC-inducing drug etoposide enhanced the antileukemia effect of POLθ inhibitor in vitro and in vivo. In conclusion, we demonstrated that POLθ plays an essential role in protecting leukemia cells from metabolically induced toxic DNA lesions triggered by formaldehyde, and it can be targeted to achieve a therapeutic effect.

1.
Hanahan
D
,
Weinberg
RA
.
Hallmarks of cancer: the next generation
.
Cell
.
2011
;
144
(
5
):
646
-
674
.
2.
Inoue
S
,
Li
WY
,
Tseng
A
, et al
.
Mutant IDH1 downregulates ATM and alters DNA repair and sensitivity to DNA damage independent of TET2
.
Cancer Cell
.
2016
;
30
(
2
):
337
-
348
.
3.
Sulkowski
PL
,
Corso
CD
,
Robinson
ND
, et al
.
2-Hydroxyglutarate produced by neomorphic IDH mutations suppresses homologous recombination and induces PARP inhibitor sensitivity
.
Sci Transl Med
.
2017
;
9
(
375
):
eaal2463
.
4.
Nagy
K
,
Pollreisz
F
,
Takáts
Z
,
Vékey
K
.
Atmospheric pressure chemical ionization mass spectrometry of aldehydes in biological matrices
.
Rapid Commun Mass Spectrom
.
2004
;
18
(
20
):
2473
-
2478
.
5.
Luo
W
,
Li
H
,
Zhang
Y
,
Ang
CY
.
Determination of formaldehyde in blood plasma by high-performance liquid chromatography with fluorescence detection
.
J Chromatogr B Biomed Sci Appl
.
2001
;
753
:
253
-
257
.
6.
Heck
HD
,
Casanova-Schmitz
M
,
Dodd
PB
,
Schachter
EN
,
Witek
TJ
,
Tosun
T
.
Formaldehyde (CH2O) concentrations in the blood of humans and Fischer-344 rats exposed to CH2O under controlled conditions
.
Am Ind Hyg Assoc J
.
1985
;
46
(
1
):
1
-
3
.
7.
Thorndike
J
,
Beck
WS
.
Production of formaldehyde from N5-methyltetrahydrofolate by normal and leukemic leukocytes
.
Cancer Res
.
1977
;
37
(
4
):
1125
-
1132
.
8.
Anandarajan
V
,
Noguchi
C
,
Oleksak
J
,
Grothusen
G
,
Terlecky
D
,
Noguchi
E
.
Genetic investigation of formaldehyde-induced DNA damage response in Schizosaccharomyces pombe
.
Curr Genet
.
2020
;
66
(
3
):
593
-
605
.
9.
Langevin
F
,
Crossan
GP
,
Rosado
IV
,
Arends
MJ
,
Patel
KJ
.
Fancd2 counteracts the toxic effects of naturally produced aldehydes in mice
.
Nature
.
2011
;
475
(
7354
):
53
-
58
.
10.
Pontel
LB
,
Rosado
IV
,
Burgos-Barragan
G
, et al
.
Endogenous formaldehyde is a hematopoietic stem cell genotoxin and metabolic carcinogen
.
Mol Cell
.
2015
;
60
(
1
):
177
-
188
.
11.
Dingler
FA
,
Wang
M
,
Mu
A
, et al
.
Two aldehyde clearance systems are essential to prevent lethal formaldehyde accumulation in mice and humans
.
Mol Cell
.
2020
;
80
(
6
):
996
-
1012.e9
.
12.
Koptyra
M
,
Stoklosa
T
,
Hoser
G
, et al
.
Monoubiquitinated Fanconi anemia D2 (FANCD2-Ub) is required for BCR-ABL1 kinase-induced leukemogenesis
.
Leukemia
.
2011
;
25
(
8
):
1259
-
1267
.
13.
Ueda
F
,
Sumi
K
,
Tago
K
,
Kasahara
T
,
Funakoshi-Tago
M
.
Critical role of FANCC in JAK2 V617F mutant-induced resistance to DNA cross-linking drugs
.
Cell Signal
.
2013
;
25
(
11
):
2115
-
2124
.
14.
Stingele
J
,
Bellelli
R
,
Boulton
SJ
.
Mechanisms of DNA-protein crosslink repair
.
Nat Rev Mol Cell Biol
.
2017
;
18
(
9
):
563
-
573
.
15.
Chandramouly
G
,
Liao
S
,
Rusanov
T
, et al
.
Polθ promotes the repair of 5’-DNA-protein crosslinks by microhomology-mediated end-joining
.
Cell Rep
.
2021
;
34
(
10
):
108820
.
16.
Zahn
KE
,
Jensen
RB
.
Polymerase θ coordinates multiple intrinsic enzymatic activities during DNA repair
.
Genes
.
2021
;
12
(
9
):
1310
.
17.
Ramsden
DA
,
Carvajal-Garcia
J
,
Gupta
GP
.
Mechanism, cellular functions and cancer roles of polymerase-theta-mediated DNA end joining
.
Nat Rev Mol Cell Biol
.
2021
;
23
(
2
):
125
-
140
.
18.
Kent
T
,
Chandramouly
G
,
McDevitt
SM
,
Ozdemir
AY
,
Pomerantz
RT
.
Mechanism of microhomology-mediated end-joining promoted by human DNA polymerase theta
.
Nat Struct Mol Biol
.
2015
;
22
(
3
):
230
-
237
.
19.
Ceccaldi
R
,
Liu
JC
,
Amunugama
R
, et al
.
Homologous-recombination-deficient tumours are dependent on Poltheta-mediated repair
.
Nature
.
2015
;
18
(
7538
):
258
-
262
.
20.
Mateos-Gomez
PA
,
Gong
F
,
Nair
N
,
Miller
KM
,
Lazzerini-Denchi
E
,
Sfeir
A
.
Mammalian polymerase theta promotes alternative NHEJ and suppresses recombination
.
Nature
.
2015
;
518
(
7538
):
254
-
257
.
21.
Feng
W
,
Simpson
DA
,
Carvajal-Garcia
J
, et al
.
Genetic determinants of cellular addiction to DNA polymerase theta
.
Nat Commun
.
2019
;
10
(
1
):
4286
.
22.
Kumar
RJ
,
Chao
HX
,
Simpson
DA
, et al
.
Dual inhibition of DNA-PK and DNA polymerase theta overcomes radiation resistance induced by p53 deficiency
.
NAR Cancer
.
2020
;
2
(
4
):
zcaa038
.
23.
Shima
N
,
Munroe
RJ
,
Schimenti
JC
.
The mouse genomic instability mutation chaos1 is an allele of Polq that exhibits genetic interaction with Atm
.
Mol Cell Biol
.
2004
;
24
(
23
):
10381
-
10389
.
24.
Zatreanu
D
,
Robinson
HMR
,
Alkhatib
O
, et al
.
Polθ inhibitors elicit BRCA-gene synthetic lethality and target PARP inhibitor resistance
.
Nat Commun
.
2021
;
12
(
1
):
3636
.
25.
Zhou
J
,
Gelot
C
,
Pantelidou
C
, et al
.
A first-in-class polymerase theta inhibitor selectively targets homologous-recombination-deficient tumors
.
Nat Cancer
.
2021
;
2
(
6
):
598
-
610
.
26.
Sullivan-Reed
K
,
Bolton-Gillespie
E
,
Dasgupta
Y
, et al
.
Simultaneous targeting of PARP1 and RAD52 triggers dual synthetic lethality in BRCA-deficient tumor cells
.
Cell Rep
.
2018
;
23
(
11
):
3127
-
3136
.
27.
Maifrede
S
,
Nieborowska-Skorska
M
,
Sullivan-Reed
K
, et al
.
Tyrosine kinase inhibitor-induced defects in DNA repair sensitize FLT3(ITD)-positive leukemia cells to PARP1 inhibitors
.
Blood
.
2018
;
132
(
1
):
67
-
77
.
28.
Nieborowska-Skorska
M
,
Maifrede
S
,
Dasgupta
Y
, et al
.
Ruxolitinib-induced defects in DNA repair cause sensitivity to PARP inhibitors in myeloproliferative neoplasms
.
Blood
.
2017
;
130
(
26
):
2848
-
2859
.
29.
Di Marcantonio
D
,
Martinez
E
,
Kanefsky
JS
, et al
.
ATF3 coordinates serine and nucleotide metabolism to drive cell cycle progression in acute myeloid leukemia
.
Mol Cell
.
2021
;
81
(
13
):
2752
-
2764.e6
.
30.
Nieborowska-Skorska
M
,
Wasik
MA
,
Slupianek
A
, et al
.
Signal transducer and activator of transcription (STAT)5 activation by BCR/ABL is dependent on intact Src homology (SH)3 and SH2 domains of BCR/ABL and is required for leukemogenesis
.
J Exp Med
.
1999
;
189
(
8
):
1229
-
1242
.
31.
Maifrede
S
,
Le
BV
,
Nieborowska-Skorska
M
, et al
.
TET2 and DNMT3A mutations exert divergent effects on DNA repair and sensitivity of leukemia cells to PARP inhibitors
.
Cancer Res
.
2021
;
81
(
19
):
5089
-
5101
.
32.
Nieborowska-Skorska
M
,
Kopinski
PK
,
Ray
R
, et al
.
Rac2-MRC-cIII-generated ROS cause genomic instability in chronic myeloid leukemia stem cells and primitive progenitors
.
Blood
.
2012
;
119
(
18
):
4253
-
4263
.
33.
Patel
JP
,
Gonen
M
,
Figueroa
ME
, et al
.
Prognostic relevance of integrated genetic profiling in acute myeloid leukemia
.
N Engl J Med
.
2012
;
366
(
12
):
1079
-
1089
.
34.
Nieborowska-Skorska
M
,
Sullivan
K
,
Dasgupta
Y
, et al
.
Gene expression and mutation-guided synthetic lethality eradicates proliferating and quiescent leukemia cells
.
J Clin Invest
.
2017
;
127
(
6
):
2392
-
2406
.
35.
Kumar
EA
,
Yuan
Z
,
Palermo
NY
, et al
.
Peptide truncation leads to a twist and an unusual increase in affinity for casitas B-lineage lymphoma tyrosine kinase binding domain
.
J Med Chem
.
2012
;
55
(
7
):
3583
-
3587
.
36.
Skorski
T
,
Bellacosa
A
,
Nieborowska-Skorska
M
, et al
.
Transformation of hematopoietic cells by BCR/ABL requires activation of a PI-3k/Akt-dependent pathway
.
EMBO J
.
1997
;
16
(
20
):
6151
-
6161
.
37.
Hu
Q
,
Klages-Mundt
N
,
Wang
R
, et al
.
The ARK assay is a sensitive and versatile method for the global detection of DNA-protein crosslinks
.
Cell Rep
.
2020
;
30
(
4
):
1235
-
1245.e4
.
38.
Truong
LN
,
Li
Y
,
Shi
LZ
, et al
.
Microhomology-mediated end joining and homologous recombination share the initial end resection step to repair DNA double-strand breaks in mammalian cells
.
Proc Natl Acad Sci U S A
.
2013
;
110
(
19
):
7720
-
7725
.
39.
O’Sullivan
J
,
Mersaoui
SY
,
Poirier
G
,
Masson
JY
.
Assessment of global DNA double-strand end resection using BrdU-DNA labeling coupled with cell cycle discrimination imaging
.
J Vis Exp
.
2021
(
170
).
40.
Slinker
BK
.
The statistics of synergism
.
J Mol Cell Cardiol
.
1998;30(4):723-731
.
41.
Blume-Jensen
P
,
Hunter
T
.
Oncogenic kinase signalling
.
Nature
.
2001
;
411
(
6835
):
355
-
365
.
42.
Scheijen
B
,
Griffin
JD
.
Tyrosine kinase oncogenes in normal hematopoiesis and hematological disease
.
Oncogene
.
2002
;
21
(
21
):
3314
-
3333
.
43.
Bjelosevic
S
,
Gruber
E
,
Newbold
A
, et al
.
Serine biosynthesis is a metabolic vulnerability in FLT3-ITD-driven acute myeloid leukemia
.
Cancer Discov
.
2021
;
11
(
6
):
1582
-
1599
.
44.
Stockard
B
,
Garrett
T
,
Guingab-Cagmat
J
,
Meshinchi
S
,
Lamba
J
.
Distinct metabolic features differentiating FLT3-ITD AML from FLT3-WT childhood acute myeloid leukemia
.
Sci Rep
.
2018
;
8
(
1
):
5534
.
45.
Burgos-Barragan
G
,
Wit
N
,
Meiser
J
, et al
.
Mammals divert endogenous genotoxic formaldehyde into one-carbon metabolism
.
Nature
.
2017
;
548
(
7669
):
549
-
554
.
46.
Ducker
GS
,
Ghergurovich
JM
,
Mainolfi
N
, et al
.
Human SHMT inhibitors reveal defective glycine import as a targetable metabolic vulnerability of diffuse large B-cell lymphoma
.
Proc Natl Acad Sci U S A
.
2017
;
114
(
43
):
11404
-
11409
.
47.
Hoang
VT
,
Buss
EC
,
Wang
W
, et al
.
The rarity of ALDH(+) cells is the key to separation of normal versus leukemia stem cells by ALDH activity in AML patients
.
Int J Cancer
.
2015
;
137
(
3
):
525
-
536
.
48.
Schuurhuis
GJ
,
Meel
MH
,
Wouters
F
, et al
.
Normal hematopoietic stem cells within the AML bone marrow have a distinct and higher ALDH activity level than co-existing leukemic stem cells
.
PLoS One
.
2013
;
8
(
11
):
e78897
.
49.
Skorski
T
.
Oncogenic tyrosine kinases and the DNA-damage response
.
Nat Rev Cancer
.
2002
;
2
(
5
):
351
-
360
.
50.
Sattler
M
,
Pride
YB
,
Quinnan
LR
, et al
.
Differential expression and signaling of CBL and CBL-B in BCR/ABL transformed cells
.
Oncogene
.
2002
;
21
(
9
):
1423
-
1433
.
51.
Oshikawa
G
,
Nagao
T
,
Wu
N
,
Kurosu
T
,
Miura
O
.
c-Cbl and Cbl-b ligases mediate17-allylaminodemethoxygeldanamycin-induced degradation of autophosphorylated Flt3 kinase with internal tandem duplication through the ubiquitin proteasome pathway
.
J Biol Chem
.
2011
;
286
(
35
):
30263
-
30273
.
52.
Huertas
P
,
Jackson
SP
.
Human CtIP mediates cell cycle control of DNA end resection and double strand break repair
.
J Biol Chem
.
2009
;
284
(
14
):
9558
-
9565
.
53.
Salles
D
,
Mencalha
AL
,
Ireno
IC
,
Wiesmuller
L
,
Abdelhay
E
.
BCR-ABL stimulates mutagenic homologous DNA double-strand break repair via the DNA-end-processing factor CtIP
.
Carcinogenesis
.
2011
;
32
(
1
):
27
-
34
.
54.
Hahnel
PS
,
Enders
B
,
Sasca
D
, et al
.
Targeting components of the alternative NHEJ pathway sensitizes KRAS mutant leukemic cells to chemotherapy
.
Blood
.
2014
;
123
(
15
):
2355
-
2366
.
55.
Fan
J
,
Li
L
,
Small
D
,
Rassool
F
.
Cells expressing FLT3/ITD mutations exhibit elevated repair errors generated through alternative NHEJ pathways: implications for genomic instability and therapy
.
Blood
.
2010
;
116
(
24
):
5298
-
5305
.
56.
Sallmyr
A
,
Tomkinson
AE
,
Rassool
FV
.
Up-regulation of WRN and DNA ligase IIIalpha in chronic myeloid leukemia: consequences for the repair of DNA double-strand breaks
.
Blood
.
2008
;
112
(
4
):
1413
-
1423
.
57.
Slupianek
A
,
Poplawski
T
,
Jozwiakowski
SK
, et al
.
BCR/ABL stimulates WRN to promote survival and genomic instability
.
Cancer Res
.
2011
;
71
(
3
):
842
-
851
.
58.
Tobin
LA
,
Robert
C
,
Rapoport
AP
, et al
.
Targeting abnormal DNA double-strand break repair in tyrosine kinase inhibitor-resistant chronic myeloid leukemias
.
Oncogene
.
2013
;
32
(
14
):
1784
-
1793
.
59.
Carvajal-Garcia
J
,
Cho
JE
,
Carvajal-Garcia
P
, et al
.
Mechanistic basis for microhomology identification and genome scarring by polymerase theta
.
Proc Natl Acad Sci U S A
.
2020
;
117
(
15
):
8476
-
8485
.
60.
van Schendel
R
,
van Heteren
J
,
Welten
R
,
Tijsterman
M
.
Genomic scars generated by polymerase theta reveal the versatile mechanism of alternative end-joining
.
PLoS Genet
.
2016
;
12
(
10
):
e1006368
.
61.
Podszywalow-Bartnicka
P
,
Wolczyk
M
,
Kusio-Kobialka
M
, et al
.
Downregulation of BRCA1 protein in BCR-ABL1 leukemia cells depends on stress-triggered TIAR-mediated suppression of translation
.
Cell Cycle
.
2014
;
13
(
23
):
3727
-
3741
.
62.
Esposito
MT
,
Zhao
L
,
Fung
TK
, et al
.
Synthetic lethal targeting of oncogenic transcription factors in acute leukemia by PARP inhibitors
.
Nat Med
.
2015
;
21
(
12
):
1481
-
1490
.
63.
Fröhling
S
,
Scholl
C
,
Levine
RL
, et al
.
Identification of driver and passenger mutations of FLT3 by high-throughput DNA sequence analysis and functional assessment of candidate alleles
.
Cancer Cell
.
2007
;
12
(
6
):
501
-
513
.
64.
Slupianek
A
,
Hoser
G
,
Majsterek
I
, et al
.
Fusion tyrosine kinases induce drug resistance by stimulation of homology-dependent recombination repair, prolongation of G(2)/M phase, and protection from apoptosis
.
Mol Cell Biol
.
2002
;
22
(
12
):
4189
-
4201
.
65.
Wang
J
,
Kong
G
,
Liu
Y
, et al
.
Nras(G12D/+) promotes leukemogenesis by aberrantly regulating hematopoietic stem cell functions
.
Blood
.
2013
;
121
(
26
):
5203
-
5207
.
66.
Stoklosa
T
,
Poplawski
T
,
Koptyra
M
, et al
.
BCR/ABL inhibits mismatch repair to protect from apoptosis and induce point mutations
.
Cancer Res
.
2008
;
68
(
8
):
2576
-
2580
.
67.
Canitrot
Y
,
Falinski
R
,
Louat
T
, et al
.
p210 BCR/ABL kinase regulates nucleotide excision repair (NER) and resistance to UV radiation
.
Blood
.
2003
;
102
(
7
):
2632
-
2637
.
68.
Slupianek
A
,
Schmutte
C
,
Tombline
G
, et al
.
BCR/ABL regulates mammalian RecA homologs, resulting in drug resistance
.
Mol Cell
.
2001
;
8
(
4
):
795
-
806
.
69.
Nakamura
J
,
Nakamura
M
.
DNA-protein crosslink formation by endogenous aldehydes and AP sites
.
DNA Repair
.
2020
;
88
:
102806
.
70.
Shen
X
,
Wang
R
,
Kim
MJ
, et al
.
A surge of DNA damage links transcriptional reprogramming and hematopoietic deficit in fanconi anemia
.
Mol Cell
.
2020
;
80
(
6
):
1013
-
1024.e6
.
71.
Boila
LD
,
Chatterjee
SS
,
Banerjee
D
,
Sengupta
A
.
KDM6 and KDM4 histone lysine demethylases emerge as molecular therapeutic targets in human acute myeloid leukemia
.
Exp Hematol
.
2018
;
58
:
44
-
51.e7
.
72.
Niebel
D
,
Kirfel
J
,
Janzen
V
,
Höller
T
,
Majores
M
,
Gütgemann
I
.
Lysine-specific demethylase 1 (LSD1) in hematopoietic and lymphoid neoplasms
.
Blood
.
2014
;
124
(
1
):
151
-
152
.
73.
Shi
Y
,
Lan
F
,
Matson
C
, et al
.
Histone demethylation mediated by the nuclear amine oxidase homolog LSD1
.
Cell
.
2004
;
119
(
7
):
941
-
953
.
74.
Tsukada
Y
,
Fang
J
,
Erdjument-Bromage
H
, et al
.
Histone demethylation by a family of JmjC domain-containing proteins
.
Nature
.
2006
;
439
(
7078
):
811
-
816
.
75.
Bao
J
,
Gur
G
,
Yarden
Y
.
Src promotes destruction of c-Cbl: implications for oncogenic synergy between Src and growth factor receptors
.
Proc Natl Acad Sci U S A
.
2003
;
100
(
5
):
2438
-
2443
.
76.
Vanson
S
,
Li
Y
,
Wood
RD
,
Doublié
S
.
Probing the structure and function of polymerase θ helicase-like domain
.
DNA Repair
.
2022
;
116
:
103358
.
77.
Zahn
KE
,
Jensen
RB
,
Wood
RD
,
Doublié
S
.
Human DNA polymerase θ harbors DNA end-trimming activity critical for DNA repair
.
Mol Cell
.
2021
;
81
(
7
):
1534
-
1547.e4
.
78.
Chen
E
,
Ahn
JS
,
Massie
CE
, et al
.
JAK2V617F promotes replication fork stalling with disease-restricted impairment of the intra-S checkpoint response
.
Proc Natl Acad Sci U S A
.
2014
;
111
(
42
):
15190
-
15195
.
79.
Brambati
A
,
Barry
RM
,
Sfeir
A
.
DNA polymerase theta (Polθ) - an error-prone polymerase necessary for genome stability
.
Curr Opin Genet Dev
.
2020
;
60
:
119
-
126
.
80.
Goullet de Rugy
T
,
Bashkurov
M
,
Datti
A
, et al
.
Excess Polθ functions in response to replicative stress in homologous recombination-proficient cancer cells
.
Biol Open
.
2016
;
5
(
10
):
1485
-
1492
.
81.
Ley
TJ
,
Miller
C
,
Ding
L
, et al
.
Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia
.
N Engl J Med
.
2013
;
368
(
22
):
2059
-
2074
.
82.
Maifrede
S
,
Martin
K
,
Podszywalow-Bartnicka
P
, et al
.
IGH/MYC translocation associates with BRCA2 deficiency and synthetic lethality to PARP1 inhibitors
.
Mol Cancer Res
.
2017
;
15
(
8
):
967
-
972
.
83.
Huang
D
,
Kraus
WL
.
The expanding universe of PARP1-mediated molecular and therapeutic mechanisms
.
Mol Cell
.
2022
;
82
(
12
):
2315
-
2334
.
84.
Drzewiecka
M
,
Barszczewska-Pietraszek
G
,
Czarny
P
,
Skorski
T
,
Śliwiński
T
.
Synthetic lethality targeting Polθ
.
Genes
.
2022
;
13
(
6
):
1101
.
85.
Feldman
T
,
Bercovich
A
,
Moskovitz
Y
, et al
.
Recurrent deletions in clonal hematopoiesis are driven by microhomology-mediated end joining
.
Nat Commun
.
2021
;
12
(
1
):
2455
.
You do not currently have access to this content.
Sign in via your Institution