• T-bet acts as a tumor suppressor by enhancing interferon signaling and suppressing proliferation of malignant B cells.

  • T-bet expression in CLL cells is positively correlated with longer overall survival in patients with CLL.

Abstract

The T-box transcription factor T-bet is known as a master regulator of the T-cell response but its role in malignant B cells has not been sufficiently explored. Here, we conducted single-cell resolved multi-omics analyses of malignant B cells from patients with chronic lymphocytic leukemia (CLL) and studied a CLL mouse model with a genetic knockout of Tbx21. We found that T-bet acts as a tumor suppressor in malignant B cells by decreasing their proliferation rate. NF-κB activity, induced by inflammatory signals provided by the microenvironment, triggered T-bet expression, which affected promoter-proximal and distal chromatin coaccessibility and controlled a specific gene signature by mainly suppressing transcription. Gene set enrichment analysis identified a positive regulation of interferon signaling and negative control of proliferation by T-bet. In line, we showed that T-bet represses cell cycling and is associated with longer overall survival of patients with CLL. Our study uncovered a novel tumor suppressive role of T-bet in malignant B cells via its regulation of inflammatory processes and cell cycling, which has implications for the stratification and therapy of patients with CLL. Linking T-bet activity to inflammation explains the good prognostic role of genetic alterations in the inflammatory signaling pathways in CLL.

1.
Szabo
SJ
,
Kim
ST
,
Costa
GL
,
Zhang
X
,
Fathman
CG
,
Glimcher
LH
.
A novel transcription factor, T-bet, directs Th1 lineage commitment
.
Cell
.
2000
;
100
(
6
):
655
-
669
.
2.
Sullivan
BM
,
Juedes
A
,
Szabo
SJ
,
von Herrath
M
,
Glimcher
LH
.
Antigen-driven effector CD8 T cell function regulated by T-bet
.
Proc Natl Acad Sci U S A
.
2003
;
100
(
26
):
15818
-
15823
.
3.
Townsend
MJ
,
Weinmann
AS
,
Matsuda
JL
, et al
.
T-bet regulates the terminal maturation and homeostasis of NK and Valpha14i NKT cells
.
Immunity
.
2004
;
20
(
4
):
477
-
494
.
4.
Hao
Y
,
O'Neill
P
,
Naradikian
MS
,
Scholz
JL
,
Cancro
MP
.
A B-cell subset uniquely responsive to innate stimuli accumulates in aged mice
.
Blood
.
2011
;
118
(
5
):
1294
-
1304
.
5.
Rubtsov
AV
,
Rubtsova
K
,
Fischer
A
, et al
.
Toll-like receptor 7 (TLR7)-driven accumulation of a novel CD11c(+) B-cell population is important for the development of autoimmunity
.
Blood
.
2011
;
118
(
5
):
1305
-
1315
.
6.
Cancro
MP
.
Age-associated B cells
.
Annu Rev Immunol
.
2020
;
38
(
1
):
315
-
340
.
7.
Ratliff
M
,
Alter
S
,
Frasca
D
,
Blomberg
BB
,
Riley
RL
.
In senescence, age-associated B cells secrete TNFalpha and inhibit survival of B-cell precursors
.
Aging Cell
.
2013
;
12
(
2
):
303
-
311
.
8.
Keller
B
,
Strohmeier
V
,
Harder
I
, et al
.
The expansion of human T-bet(high)CD21(low) B cells is T cell dependent
.
Sci Immunol
.
2021
;
6
(
64
):
eabh0891
.
9.
Barnett
BE
,
Staupe
RP
,
Odorizzi
PM
, et al
.
Cutting edge: B cell-intrinsic T-bet expression is required to control chronic viral infection
.
J Immunol
.
2016
;
197
(
4
):
1017
-
1022
.
10.
Rubtsova
K
,
Rubtsov
AV
,
van Dyk
LF
,
Kappler
JW
,
Marrack
P
.
T-box transcription factor T-bet, a key player in a unique type of B-cell activation essential for effective viral clearance
.
Proc Natl Acad Sci U S A
.
2013
;
110
(
34
):
E3216
-
E3224
.
11.
Moir
S
,
Malaspina
A
,
Ogwaro
KM
, et al
.
HIV-1 induces phenotypic and functional perturbations of B cells in chronically infected individuals
.
Proc Natl Acad Sci U S A
.
2001
;
98
(
18
):
10362
-
10367
.
12.
Warnatz
K
,
Wehr
C
,
Drager
R
, et al
.
Expansion of CD19(hi)CD21(lo/neg) B cells in common variable immunodeficiency (CVID) patients with autoimmune cytopenia
.
Immunobiology
.
2002
;
206
(
5
):
502
-
513
.
13.
Nellore
A
,
Zumaquero
E
,
Scharer
CD
, et al
.
A transcriptionally distinct subset of influenza-specific effector memory B cells predicts long-lived antibody responses to vaccination in humans
.
Immunity
.
2023
;
56
(
4
):
847
-
863.e8
.
14.
Peng
SL
,
Szabo
SJ
,
Glimcher
LH
.
T-bet regulates IgG class switching and pathogenic autoantibody production
.
Proc Natl Acad Sci U S A
.
2002
;
99
(
8
):
5545
-
5550
.
15.
Rubtsova
K
,
Rubtsov
AV
,
Thurman
JM
,
Mennona
JM
,
Kappler
JW
,
Marrack
P
.
B cells expressing the transcription factor T-bet drive lupus-like autoimmunity
.
J Clin Invest
.
2017
;
127
(
4
):
1392
-
1404
.
16.
Abram
CL
,
Roberge
GL
,
Hu
Y
,
Lowell
CA
.
Comparative analysis of the efficiency and specificity of myeloid-Cre deleting strains using ROSA-EYFP reporter mice
.
J Immunol Methods
.
2014
;
408
:
89
-
100
.
17.
Liu
Y
,
Zhou
S
,
Qian
J
, et al
.
T-bet(+)CD11c(+) B cells are critical for antichromatin immunoglobulin G production in the development of lupus
.
Arthritis Res Ther
.
2017
;
19
(
1
):
225
.
18.
Wang
S
,
Wang
J
,
Kumar
V
, et al
.
IL-21 drives expansion and plasma cell differentiation of autoreactive CD11c(hi)T-bet(+) B cells in SLE
.
Nat Commun
.
2018
;
9
(
1
):
1758
.
19.
Hagglof
T
,
Vanz
C
,
Kumagai
A
, et al
.
T-bet(+) B cells accumulate in adipose tissue and exacerbate metabolic disorder during obesity
.
Cell Metab
.
2022
;
34
(
8
):
1121
-
1136.e6
.
20.
Frasca
D
,
Diaz
A
,
Romero
M
,
Vazquez
T
,
Blomberg
BB
.
Obesity induces pro-inflammatory B cells and impairs B cell function in old mice
.
Mech Ageing Dev
.
2017
;
162
:
91
-
99
.
21.
Frasca
D
,
Romero
M
,
Garcia
D
,
Diaz
A
,
Blomberg
BB
.
Obesity accelerates age-associated defects in human B cells through a metabolic reprogramming induced by the fatty acid palmitate
.
Front Aging
.
2021
;
2
:
828697
.
22.
Malle
L
,
Patel
RS
,
Martin-Fernandez
M
, et al
.
Autoimmunity in down's syndrome via cytokines, CD4 T cells and CD11c(+) B cells
.
Nature
.
2023
;
615
(
7951
):
305
-
314
.
23.
Naradikian
MS
,
Myles
A
,
Beiting
DP
, et al
.
Cutting edge: IL-4, IL-21, and IFN-gamma interact to govern T-bet and CD11c expression in TLR-activated B cells
.
J Immunol
.
2016
;
197
(
4
):
1023
-
1028
.
24.
Myles
A
,
Gearhart
PJ
,
Cancro
MP
.
Signals that drive T-bet expression in B cells
.
Cell Immunol
.
2017
;
321
:
3
-
7
.
25.
Russell Knode
LM
,
Naradikian
MS
,
Myles
A
, et al
.
Age-associated B cells express a diverse repertoire of V(H) and Vkappa genes with somatic hypermutation
.
J Immunol
.
2017
;
198
(
5
):
1921
-
1927
.
26.
Yang
R
,
Avery
DT
,
Jackson
KJL
, et al
.
Human T-bet governs the generation of a distinct subset of CD11c(high)CD21(low) B cells
.
Sci Immunol
.
2022
;
7
(
73
):
eabq3277
.
27.
Stone
SL
,
Peel
JN
,
Scharer
CD
, et al
.
T-bet transcription factor promotes antibody-secreting cell differentiation by limiting the inflammatory effects of IFN-gamma on B cells
.
Immunity
.
2019
;
50
(
5
):
1172
-
1187.e7
.
28.
Dorfman
DM
,
Hwang
ES
,
Shahsafaei
A
,
Glimcher
LH
.
T-bet, a T-cell-associated transcription factor, is expressed in a subset of B-cell lymphoproliferative disorders
.
Am J Clin Pathol
.
2004
;
122
(
2
):
292
-
297
.
29.
Johrens
K
,
Stein
H
,
Anagnostopoulos
I
.
T-bet transcription factor detection facilitates the diagnosis of minimal hairy cell leukemia infiltrates in bone marrow trephines
.
Am J Surg Pathol
.
2007
;
31
(
8
):
1181
-
1185
.
30.
Chakraborty
S
,
Martines
C
,
Porro
F
, et al
.
B-cell receptor signaling and genetic lesions in TP53 and CDKN2A/CDKN2B cooperate in Richter transformation
.
Blood
.
2021
;
138
(
12
):
1053
-
1066
.
31.
Seifert
M
,
Sellmann
L
,
Bloehdorn
J
, et al
.
Cellular origin and pathophysiology of chronic lymphocytic leukemia
.
J Exp Med
.
2012
;
209
(
12
):
2183
-
2198
.
32.
Klein
U
,
Tu
Y
,
Stolovitzky
GA
, et al
.
Gene expression profiling of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells
.
J Exp Med
.
2001
;
194
(
11
):
1625
-
1638
.
33.
Puente
XS
,
Bea
S
,
Valdes-Mas
R
, et al
.
Non-coding recurrent mutations in chronic lymphocytic leukaemia
.
Nature
.
2015
;
526
(
7574
):
519
-
524
.
34.
Nellore
A
,
Scharer
CD
,
King
RG
, et al
.
Fcrl5 and T-bet define influenza-specific memory B cells that predict long-lived antibody responses
.
bioRxiv
.
Preprint posted online May 2019
.
35.
Autore
F
,
Strati
P
,
Laurenti
L
,
Ferrajoli
A
.
Morphological, immunophenotypic, and genetic features of chronic lymphocytic leukemia with trisomy 12: a comprehensive review
.
Haematologica
.
2018
;
103
(
6
):
931
-
938
.
36.
Guarini
A
,
Marinelli
M
,
Tavolaro
S
, et al
.
ATM gene alterations in chronic lymphocytic leukemia patients induce a distinct gene expression profile and predict disease progression
.
Haematologica
.
2012
;
97
(
1
):
47
-
55
.
37.
Beekman
R
,
Chapaprieta
V
,
Russinol
N
, et al
.
The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia
.
Nat Med
.
2018
;
24
(
6
):
868
-
880
.
38.
Burger
JA
,
Tsukada
N
,
Burger
M
,
Zvaifler
NJ
,
Dell'Aquila
M
,
Kipps
TJ
.
Blood-derived nurse-like cells protect chronic lymphocytic leukemia B cells from spontaneous apoptosis through stromal cell-derived factor-1
.
Blood
.
2000
;
96
(
8
):
2655
-
2663
.
39.
Pascutti
MF
,
Jak
M
,
Tromp
JM
, et al
.
IL-21 and CD40L signals from autologous T cells can induce antigen-independent proliferation of CLL cells
.
Blood
.
2013
;
122
(
17
):
3010
-
3019
.
40.
Burger
JA
,
Quiroga
MP
,
Hartmann
E
, et al
.
High-level expression of the T-cell chemokines CCL3 and CCL4 by chronic lymphocytic leukemia B cells in nurselike cell cocultures and after BCR stimulation
.
Blood
.
2009
;
113
(
13
):
3050
-
3058
.
41.
Pede
V
,
Rombout
A
,
Vermeire
J
, et al
.
CLL cells respond to B-cell receptor stimulation with a microRNA/mRNA signature associated with MYC activation and cell cycle progression
.
PLoS One
.
2013
;
8
(
4
):
e60275
.
42.
Guarini
A
,
Chiaretti
S
,
Tavolaro
S
, et al
.
BCR ligation induced by IgM stimulation results in gene expression and functional changes only in IgV H unmutated chronic lymphocytic leukemia (CLL) cells
.
Blood
.
2008
;
112
(
3
):
782
-
792
.
43.
Liu
T
,
Zhang
L
,
Joo
D
,
Sun
SC
.
NF-kappaB signaling in inflammation
.
Signal Transduct Target Ther
.
2017
;
2
(
1
):
17023
.
44.
Mitchell
S
,
Mercado
EL
,
Adelaja
A
, et al
.
An NFkappaB activity calculator to delineate signaling crosstalk: type I and II interferons enhance NFkappaB via distinct mechanisms. original research
.
Front Immunol
.
2019
;
10
:
1425
.
45.
Mansouri
L
,
Papakonstantinou
N
,
Ntoufa
S
,
Stamatopoulos
K
,
Rosenquist
R
.
NF-kappaB activation in chronic lymphocytic leukemia: a point of convergence of external triggers and intrinsic lesions
.
Semin Cancer Biol
.
2016
;
39
:
40
-
48
.
46.
Landau
DA
,
Sun
C
,
Rosebrock
D
, et al
.
The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy
.
Nat Commun
.
2017
;
8
(
1
):
2185
.
47.
Burger
JA
,
Sivina
M
,
Jain
N
, et al
.
Randomized trial of ibrutinib vs ibrutinib plus rituximab in patients with chronic lymphocytic leukemia
.
Blood
.
2019
;
133
(
10
):
1011
-
1019
.
48.
Sun
C
,
Nierman
P
,
Kendall
EK
, et al
.
Clinical and biological implications of target occupancy in CLL treated with the BTK inhibitor acalabrutinib
.
Blood
.
2020
;
136
(
1
):
93
-
105
.
49.
Herman
SE
,
Mustafa
RZ
,
Gyamfi
JA
, et al
.
Ibrutinib inhibits BCR and NF-kappaB signaling and reduces tumor proliferation in tissue-resident cells of patients with CLL
.
Blood
.
2014
;
123
(
21
):
3286
-
3295
.
50.
Lam
V
,
Best
S
,
Kittai
A
, et al
.
Proapoptotic and immunomodulatory effects of SYK inhibitor entospletinib in combination with obinutuzumab in patients with chronic lymphocytic leukaemia
.
Br J Clin Pharmacol
.
2022
;
88
(
2
):
836
-
841
.
51.
Gobessi
S
,
Laurenti
L
,
Longo
PG
, et al
.
Inhibition of constitutive and BCR-induced Syk activation downregulates Mcl-1 and induces apoptosis in chronic lymphocytic leukemia B cells
.
Leukemia
.
2009
;
23
(
4
):
686
-
697
.
52.
Efremov
DG
,
Turkalj
S
,
Laurenti
L
.
Mechanisms of B cell receptor activation and responses to B cell receptor inhibitors in B cell malignancies
.
Cancers (Basel)
.
2020
;
12
(
6
):
1396
.
53.
Blatte
TJ
,
Machnicki
MM
,
Glodkowska-Mrowka
E
, et al
.
Gene expression profiling predicts sensitivity of chronic lymphocytic leukemia cells to dasatinib
.
Hemasphere
.
2021
;
5
(
1
):
e514
.
54.
Bonato
A
,
Chakraborty
S
,
Bomben
R
, et al
.
NFKBIE mutations are selected by the tumor microenvironment and contribute to immune escape in chronic lymphocytic leukemia
.
Leukemia
.
Published online 15 March 2024
.
55.
Iwata
S
,
Mikami
Y
,
Sun
HW
, et al
.
The transcription factor T-bet limits amplification of type I IFN transcriptome and circuitry in T helper 1 cells
.
Immunity
.
2017
;
46
(
6
):
983
-
991.e4
.
56.
Herbst
SA
,
Vesterlund
M
,
Helmboldt
AJ
, et al
.
Proteogenomics refines the molecular classification of chronic lymphocytic leukemia
.
Nat Commun
.
2022
;
13
(
1
):
6226
.
57.
Dietrich
S
,
Oles
M
,
Lu
J
, et al
.
Drug-perturbation-based stratification of blood cancer
.
J Clin Invest
.
2018
;
128
(
1
):
427
-
445
.
58.
Massoni-Badosa
R
,
Aguilar-Fernández
S
,
Nieto
JC
, et al
.
An atlas of cells in the human tonsil
.
Immunity
.
2024
;
57
(
2
):
379
-
399.e18
.
59.
Gao
X
,
Cockburn
IA
.
The development and function of CD11c(+) atypical B cells - insights from single cell analysis
.
Front Immunol
.
2022
;
13
:
979060
.
60.
King
HW
,
Orban
N
,
Riches
JC
, et al
.
Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics
.
Sci Immunol
.
2021
;
6
(
56
):
eabe6291
.
61.
Van de Sande
B
,
Flerin
C
,
Davie
K
, et al
.
A scalable SCENIC workflow for single-cell gene regulatory network analysis
.
Nat Protoc
.
2020
;
15
(
7
):
2247
-
2276
.
62.
Seufert
I
,
Sant
P
,
Bauer
K
,
Syed
AP
,
Rippe
K
,
Mallm
J-P
.
Enhancing sensitivity and versatility of Tn5-based single cell omics
.
Front Epigenet Epigenom
.
2023
;
1
:
1245879
.
63.
Mallm
JP
,
Iskar
M
,
Ishaque
N
, et al
.
Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks
.
Mol Syst Biol
.
2019
;
15
(
5
):
e8339
.
64.
Muckenhuber
M
,
Seufert
I
,
Muller-Ott
K
, et al
.
Epigenetic signals that direct cell type-specific interferon beta response in mouse cells
.
Life Sci Alliance
.
2023
;
6
(
4
):
e202201823
.
65.
Kardava
L
,
Yang
Q
,
St Leger
A
, et al
.
The B lineage transcription factor E2A regulates apoptosis in chronic lymphocytic leukemia (CLL) cells
.
Int Immunol
.
2011
;
23
(
6
):
375
-
384
.
66.
Hodson
DJ
,
Shaffer
AL
,
Xiao
W
, et al
.
Regulation of normal B-cell differentiation and malignant B-cell survival by OCT2
.
Proc Natl Acad Sci U S A
.
2016
;
113
(
14
):
E2039
-
E2046
.
67.
Asghar
U
,
Witkiewicz
AK
,
Turner
NC
,
Knudsen
ES
.
The history and future of targeting cyclin-dependent kinases in cancer therapy
.
Nat Rev Drug Discov
.
2015
;
14
(
2
):
130
-
146
.
68.
Sun
C
,
Chen
YC
,
Martinez Zurita
A
, et al
.
The immune microenvironment shapes transcriptional and genetic heterogeneity in chronic lymphocytic leukemia
.
Blood Adv
.
2023
;
7
(
1
):
145
-
158
.
69.
Strati
P
,
Shanafelt
TD
.
Monoclonal B-cell lymphocytosis and early-stage chronic lymphocytic leukemia: diagnosis, natural history, and risk stratification
.
Blood
.
2015
;
126
(
4
):
454
-
462
.
70.
Kretzmer
H
,
Biran
A
,
Purroy
N
, et al
.
Preneoplastic alterations define CLL DNA methylome and persist through disease progression and therapy
.
Blood Cancer Discov
.
2021
;
2
(
1
):
54
-
69
.
71.
Ten Hacken
E
,
Sewastianik
T
,
Yin
S
, et al
.
In vivo modeling of CLL transformation to Richter syndrome reveals convergent evolutionary paths and therapeutic vulnerabilities
.
Blood Cancer Discov
.
2023
;
4
(
2
):
150
-
169
.
72.
Nadeu
F
,
Royo
R
,
Massoni-Badosa
R
, et al
.
Detection of early seeding of Richter transformation in chronic lymphocytic leukemia
.
Nat Med
.
2022
;
28
(
8
):
1662
-
1671
.
73.
Burgler
S
,
Gimeno
A
,
Parente-Ribes
A
, et al
.
Chronic lymphocytic leukemia cells express CD38 in response to Th1 cell-derived IFN-gamma by a T-bet-dependent mechanism
.
J Immunol
.
2015
;
194
(
2
):
827
-
835
.
74.
Hodgson
K
,
Ferrer
G
,
Montserrat
E
,
Moreno
C
.
Chronic lymphocytic leukemia and autoimmunity: a systematic review
.
Haematologica
.
2011
;
96
(
5
):
752
-
761
.
75.
Hervé
M
,
Xu
K
,
Ng
YS
, et al
.
Unmutated and mutated chronic lymphocytic leukemias derive from self-reactive B cell precursors despite expressing different antibody reactivity
.
J Clin Invest
.
2005
;
115
(
6
):
1636
-
1643
.
76.
Tomic
J
,
Lichty
B
,
Spaner
DE
.
Aberrant interferon-signaling is associated with aggressive chronic lymphocytic leukemia
.
Blood
.
2011
;
117
(
9
):
2668
-
2680
.
77.
Luo
TY
,
Shi
Y
,
Wang
G
,
Spaner
DE
.
Enhanced IFN sensing by aggressive chronic lymphocytic leukemia cells
.
J Immunol
.
2022
;
209
(
9
):
1662
-
1673
.
78.
Montserrat
E
,
Villamor
N
,
Urbano-Ispizua
A
,
Ribera
JM
,
Rozman
C
.
alpha Interferon in chronic lymphocytic leukaemia
.
Eur J Cancer
.
1991
;
27
(
Suppl 4
):
S74
-
S77
.
79.
Lu
Y
,
Qu
H
,
Qi
D
, et al
.
OCT4 maintains self-renewal and reverses senescence in human hair follicle mesenchymal stem cells through the downregulation of p21 by DNA methyltransferases
.
Stem Cell Res Ther
.
2019
;
10
(
1
):
28
.
80.
Penter
L
,
Gohil
SH
,
Lareau
C
, et al
.
Longitudinal single-cell dynamics of chromatin accessibility and mitochondrial mutations in chronic lymphocytic leukemia mirror disease history
.
Cancer Discov
.
2021
;
11
(
12
):
3048
-
3063
.
81.
Gutierrez
A
,
Tschumper
RC
,
Wu
X
, et al
.
LEF-1 is a prosurvival factor in chronic lymphocytic leukemia and is expressed in the preleukemic state of monoclonal B-cell lymphocytosis
.
Blood
.
2010
;
116
(
16
):
2975
-
2983
.
You do not currently have access to this content.
Sign in via your Institution