• cBAF inhibition reduces chromatin accessibility mainly at RUNX1 binding sites and disrupts the RUNX1-driven oncogenic program in T-ALL.

  • cBAF regulates migration activity toward CXCL12 and cell-autonomous growth in T-ALL cells, thus representing a promising therapeutic target.

Abstract

Acute leukemia cells require bone marrow microenvironments, known as niches, which provide leukemic cells with niche factors that are essential for leukemic cell survival and/or proliferation. However, it remains unclear how the dynamics of the leukemic cell–niche interaction are regulated. Using a genome-wide CRISPR screen, we discovered that canonical BRG1/BRM-associated factor (cBAF), a variant of the switch/sucrose nonfermenting chromatin remodeling complex, regulates the migratory response of human T-cell acute lymphoblastic leukemia (T-ALL) cells to a niche factor CXCL12. Mechanistically, cBAF maintains chromatin accessibility and allows RUNX1 to bind to CXCR4 enhancer regions. cBAF inhibition evicts RUNX1 from the genome, resulting in CXCR4 downregulation and impaired migration activity. In addition, cBAF maintains chromatin accessibility preferentially at RUNX1 binding sites, ensuring RUNX1 binding at these sites, and is required for expression of RUNX1-regulated genes, such as CDK6; therefore, cBAF inhibition negatively impacts cell proliferation and profoundly induces apoptosis. This anticancer effect was also confirmed using T-ALL xenograft models, suggesting cBAF as a promising therapeutic target. Thus, we provide novel evidence that cBAF regulates the RUNX1-driven leukemic program and governs migration activity toward CXCL12 and cell-autonomous growth in human T-ALL.

1.
Leonard
JP
,
Martin
P
,
Roboz
GJ
.
Practical implications of the 2016 revision of the World Health Organization classification of lymphoid and myeloid neoplasms and acute leukemia
.
J Clin Oncol
.
2017
;
35
(
23
):
2708
-
2715
.
2.
Bassan
R
,
Bourquin
J-P
,
DeAngelo
DJ
,
Chiaretti
S
.
New approaches to the management of adult acute lymphoblastic leukemia
.
J Clin Oncol
.
2018
:
JCO2017773648
.
3.
Dombret
H
,
Gardin
C
.
An update of current treatments for adult acute myeloid leukemia
.
Blood
.
2016
;
127
(
1
):
53
-
61
.
4.
Pitt
LA
,
Tikhonova
AN
,
Hu
H
, et al
.
CXCL12-producing vascular endothelial niches control acute T cell leukemia maintenance
.
Cancer Cell
.
2015
;
27
(
6
):
755
-
768
.
5.
Ishikawa
F
,
Yoshida
S
,
Saito
Y
, et al
.
Chemotherapy-resistant human AML stem cells home to and engraft within the bone-marrow endosteal region
.
Nat Biotechnol
.
2007
;
25
(
11
):
1315
-
1321
.
6.
Jin
L
,
Hope
KJ
,
Zhai
Q
,
Smadja-Joffe
F
,
Dick
JE
.
Targeting of CD44 eradicates human acute myeloid leukemic stem cells
.
Nat Med
.
2006
;
12
(
10
):
1167
-
1174
.
7.
Morrison
SJ
,
Scadden
DT
.
The bone marrow niche for haematopoietic stem cells
.
Nature
.
2014
;
505
(
7483
):
327
-
334
.
8.
Pinho
S
,
Frenette
PS
.
Haematopoietic stem cell activity and interactions with the niche
.
Nat Rev Mol Cell Biol
.
2019
;
20
(
5
):
303
-
320
.
9.
Aoki
K
,
Kurashige
M
,
Ichii
M
, et al
.
Identification of CXCL12-abundant reticular cells in human adult bone marrow
.
Br J Haematol
.
2021
;
193
(
3
):
659
-
668
.
10.
Viñado
AC
,
Calvo
IA
,
Cenzano
I
, et al
.
The bone marrow niche regulates redox and energy balance in MLL::AF9 leukemia stem cells
.
Leukemia
.
2022
;
36
(
8
):
1969
-
1979
.
11.
Passaro
D
,
Irigoyen
M
,
Catherinet
C
, et al
.
CXCR4 is required for leukemia-initiating cell activity in T cell acute lymphoblastic leukemia
.
Cancer Cell
.
2015
;
27
(
6
):
769
-
779
.
12.
Tavor
S
,
Petit
I
,
Porozov
S
, et al
.
CXCR4 regulates migration and development of human acute myelogenous leukemia stem cells in transplanted NOD/SCID mice
.
Cancer Res
.
2004
;
64
(
8
):
2817
-
2824
.
13.
Randhawa
S
,
Cho
BS
,
Ghosh
D
, et al
.
Effects of pharmacological and genetic disruption of CXCR4 chemokine receptor function in B-cell acute lymphoblastic leukaemia
.
Br J Haematol
.
2016
;
174
(
3
):
425
-
436
.
14.
Clapier
CR
,
Iwasa
J
,
Cairns
BR
,
Peterson
CL
.
Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes
.
Nat Rev Mol Cell Biol
.
2017
;
18
(
7
):
407
-
422
.
15.
Narlikar
GJ
,
Sundaramoorthy
R
,
Owen-Hughes
T
.
Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes
.
Cell
.
2013
;
154
(
3
):
490
-
503
.
16.
Hota
SK
,
Bruneau
BG
.
ATP-dependent chromatin remodeling during mammalian development
.
Development
.
2016
;
143
(
16
):
2882
-
2897
.
17.
Bayona-Feliu
A
,
Barroso
S
,
Muñoz
S
,
Aguilera
A
.
The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts
.
Nat Genet
.
2021
;
53
(
7
):
1050
-
1063
.
18.
Gatchalian
J
,
Liao
J
,
Maxwell
MB
,
Hargreaves
DC
.
Control of stimulus-dependent responses in macrophages by SWI/SNF chromatin remodeling complexes
.
Trends Immunol
.
2020
;
41
(
2
):
126
-
140
.
19.
Hohmann
AF
,
Martin
LJ
,
Minder
JL
, et al
.
Sensitivity and engineered resistance of myeloid leukemia cells to BRD9 inhibition
.
Nat Chem Biol
.
2016
;
12
(
9
):
672
-
679
.
20.
Shi
J
,
Whyte
WA
,
Zepeda-Mendoza
CJ
, et al
.
Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation
.
Genes Dev
.
2013
;
27
(
24
):
2648
-
2662
.
21.
Xiao
L
,
Parolia
A
,
Qiao
Y
, et al
.
Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer
.
Nature
.
2022
;
601
(
7893
):
434
-
439
.
22.
Koike-Yusa
H
,
Li
Y
,
Tan
E-P
,
Velasco-Herrera
MDC
,
Yusa
K
.
Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library
.
Nat Biotechnol
.
2014
;
32
(
3
):
267
-
273
.
23.
Tzelepis
K
,
Koike-Yusa
H
,
De Braekeleer
E
, et al
.
A CRISPR dropout screen identifies genetic vulnerabilities and therapeutic targets in acute myeloid leukemia
.
Cell Rep
.
2016
;
17
(
4
):
1193
-
1205
.
24.
Ong
SH
,
Li
Y
,
Koike-Yusa
H
,
Yusa
K
.
Optimised metrics for CRISPR-KO screens with second-generation gRNA libraries
.
Sci Rep
.
2017
;
7
(
1
):
7384
.
25.
Rago
F
,
Rodrigues
LU
,
Bonney
M
, et al
.
Exquisite sensitivity to dual BRG1/BRM ATPase inhibitors reveals broad SWI/SNF dependencies in acute myeloid leukemia
.
Mol Cancer Res
.
2022
;
20
(
3
):
361
-
372
.
26.
Hodges
HC
,
Stanton
BZ
,
Cermakova
K
, et al
.
Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers
.
Nat Struct Mol Biol
.
2018
;
25
(
1
):
61
-
72
.
27.
Mathur
R
,
Alver
BH
,
San Roman
AK
, et al
.
ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice
.
Nat Genet
.
2017
;
49
(
2
):
296
-
302
.
28.
Alver
BH
,
Kim
KH
,
Lu
P
, et al
.
The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers
.
Nat Commun
.
2017
;
8
:
14648
.
29.
Wang
X
,
Lee
RS
,
Alver
BH
, et al
.
SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation
.
Nat Genet
.
2017
;
49
(
2
):
289
-
295
.
30.
Nakayama
RT
,
Pulice
JL
,
Valencia
AM
, et al
.
SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters
.
Nat Genet
.
2017
;
49
(
11
):
1613
-
1623
.
31.
Barisic
D
,
Stadler
MB
,
Iurlaro
M
,
Schübeler
D
.
Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors
.
Nature
.
2019
;
569
(
7754
):
136
-
140
.
32.
Okuda
T
,
van Deursen
J
,
Hiebert
SW
,
Grosveld
G
,
Downing
JR
.
AML1, the target of multiple chromosomal translocations in human leukemia, is essential for normal fetal liver hematopoiesis
.
Cell
.
1996
;
84
(
2
):
321
-
330
.
33.
Ichikawa
M
,
Asai
T
,
Saito
T
, et al
.
AML-1 is required for megakaryocytic maturation and lymphocytic differentiation, but not for maintenance of hematopoietic stem cells in adult hematopoiesis
.
Nat Med
.
2004
;
10
(
3
):
299
-
304
.
34.
Sanda
T
,
Lawton
LN
,
Barrasa
MI
, et al
.
Core transcriptional regulatory circuit controlled by the TAL1 complex in human T cell acute lymphoblastic leukemia
.
Cancer Cell
.
2012
;
22
(
2
):
209
-
221
.
35.
Choi
A
,
Illendula
A
,
Pulikkan
JA
, et al
.
RUNX1 is required for oncogenic Myb and Myc enhancer activity in T-cell acute lymphoblastic leukemia
.
Blood
.
2017
;
130
(
15
):
1722
-
1733
.
36.
Hollenhorst
PC
,
Chandler
KJ
,
Poulsen
RL
,
Johnson
WE
,
Speck
NA
,
Graves
BJ
.
DNA specificity determinants associate with distinct transcription factor functions
.
PLoS Genet
.
2009
;
5
(
12
):
e1000778
.
37.
Bal
E
,
Kumar
R
,
Hadigol
M
, et al
.
Super-enhancer hypermutation alters oncogene expression in B cell lymphoma
.
Nature
.
2022
;
607
(
7920
):
808
-
815
.
38.
Zhu
H
,
Uusküla-Reimand
L
,
Isaev
K
, et al
.
Candidate cancer driver mutations in distal regulatory elements and long-range chromatin interaction networks
.
Mol Cell
.
2020
;
77
(
6
):
1307
-
1321.e10
.
39.
Montefiori
LE
,
Bendig
S
,
Gu
Z
, et al
.
Enhancer hijacking drives oncogenic BCL11B expression in lineage-ambiguous stem cell leukemia
.
Cancer Discov
.
2021
;
11
(
11
):
2846
-
2867
.
40.
Iurlaro
M
,
Stadler
MB
,
Masoni
F
,
Jagani
Z
,
Galli
GG
,
Schübeler
D
.
Mammalian SWI/SNF continuously restores local accessibility to chromatin
.
Nat Genet
.
2021
;
53
(
3
):
279
-
287
.
41.
King
HW
,
Klose
RJ
.
The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells
.
Elife
.
2017
;
6
:
e22631
.
42.
Bakshi
R
,
Hassan
MQ
,
Pratap
J
, et al
.
The human SWI/SNF complex associates with RUNX1 to control transcription of hematopoietic target genes
.
J Cell Physiol
.
2010
;
225
(
2
):
569
-
576
.
43.
Seki
M
,
Kimura
S
,
Isobe
T
, et al
.
Recurrent SPI1 (PU.1) fusions in high-risk pediatric T cell acute lymphoblastic leukemia
.
Nat Genet
.
2017
;
49
(
8
):
1274
-
1281
.
44.
Della Gatta
G
,
Palomero
T
,
Perez-Garcia
A
, et al
.
Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL
.
Nat Med
.
2012
;
18
(
3
):
436
-
440
.
45.
Gutierrez
A
,
Kentsis
A
,
Sanda
T
, et al
.
The BCL11B tumor suppressor is mutated across the major molecular subtypes of T-cell acute lymphoblastic leukemia
.
Blood
.
2011
;
118
(
15
):
4169
-
4173
.
46.
Kadoch
C
,
Hargreaves
DC
,
Hodges
C
, et al
.
Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy
.
Nat Genet
.
2013
;
45
(
6
):
592
-
601
.
47.
Buscarlet
M
,
Krasteva
V
,
Ho
L
, et al
.
Essential role of BRG, the ATPase subunit of BAF chromatin remodeling complexes, in leukemia maintenance
.
Blood
.
2014
;
123
(
11
):
1720
-
1728
.
48.
Chambers
C
,
Cermakova
K
,
Chan
YS
, et al
.
SWI/SNF blockade disrupts PU.1-directed enhancer programs in normal hematopoietic cells and acute myeloid leukemia
.
Cancer Res
.
2023
;
83
(
7
):
983
-
996
.
49.
Guo
A
,
Huang
H
,
Zhu
Z
, et al
.
cBAF complex components and MYC cooperate early in CD8+ T cell fate
.
Nature
.
2022
;
607
(
7917
):
135
-
141
.
50.
Loo
C-S
,
Gatchalian
J
,
Liang
Y
, et al
.
A genome-wide CRISPR screen reveals a role for the non-canonical nucleosome-remodeling BAF complex in Foxp3 expression and regulatory T cell function
.
Immunity
.
2020
;
53
(
1
):
143
-
157.e8
.
You do not currently have access to this content.
Sign in via your Institution