• New reversible oral LSD1is induce efficacious HbF synthesis in vitro and in a SCD mouse model.

  • Combined treatment with a BRD4 degrader rescues an erythroid to myeloid lineage conversion that accompanies LSD1 inhibition.

Abstract

Small molecules that inhibit LSD1 (lysine-specific demethylase 1, KDM1A) have been shown to induce abundant fetal hemoglobin (HbF) levels in red blood cells both in vitro and in vivo, therefore potentially serving as potent and cost-effective therapeutics to treat the β-globinopathies, sickle cell disease (SCD), and β-thalassemia major (TM). However, most LSD1 inhibitors (LSD1is) that induce HbF in vivo are covalent and irreversible, which leads to adverse effects. In this study, we utilized structure-aided drug design to develop potent new reversible LSD1is, leading to robust γ-globin expression in vitro. Moreover, in a mouse model of SCD, oral administration of these novel inhibitors leads to significant HbF elevation and alleviation of multiple features of disease pathology that are the usual consequences of SCD. In addition, we discovered that combined treatment of an LSD1i with a BRD4 degrader (BD-9136) represses the induction of RUNX1 and PU.1, thereby rescuing the erythroid to myeloid lineage conversion that accompanies LSD1is in hematopoiesis. The data indicate that this new generation of LSD1is can effectively induce HbF levels, reduce SCD pathologies, and are well tolerated by oral administration in SCD mice. We anticipate that the combination of these or related binary compounds offer exciting new therapeutic possibilities for treating SCD and TM.

1.
GBD 2021 Sickle Cell Disease Collaborators
.
Global, regional, and national prevalence and mortality burden of sickle cell disease, 2000-2021: a systematic analysis from the Global Burden of Disease study 2021
.
Lancet Haematol
.
2023
;
10
(
8
):
e585
-
e599
.
2.
Xu
J
,
Peng
C
,
Sankaran
VG
, et al
.
Correction of sickle cell disease in adult mice by interference with fetal hemoglobin silencing
.
Science
.
2011
;
334
(
6058
):
993
-
996
.
3.
Bjurström
CF
,
Mojadidi
M
,
Phillips
J
, et al
.
Reactivating fetal hemoglobin expression in human adult erythroblasts through BCL11A knockdown using targeted endonucleases
.
Mol Ther Nucleic Acids
.
2016
;
5
(
8
):
e351
.
4.
Hossain
MA
,
Bungert
J
.
Genome editing for sickle cell disease: a little BCL11A goes a long way
.
Mol Ther
.
2017
;
25
(
3
):
561
-
562
.
5.
Olivieri
NF
,
Weatherall
DJ
.
The therapeutic reactivation of fetal haemoglobin
.
Hum Mol Genet
.
1998
;
7
(
10
):
1655
-
1658
.
6.
Wood
WG
.
Increased HbF in adult life
.
Baillieres Clin Haematol
.
1993
;
6
(
1
):
177
-
213
.
7.
Veith
R
,
Galanello
R
,
Papayannopoulou
T
,
Stamatoyannopoulos
G
.
Stimulation of F-cell production in patients with sickle-cell anemia treated with cytarabine or hydroxyurea
.
N Engl J Med
.
1985
;
313
(
25
):
1571
-
1575
.
8.
Ngo
DA
,
Aygun
B
,
Akinsheye
I
, et al
.
Fetal haemoglobin levels and haematological characteristics of compound heterozygotes for haemoglobin S and deletional hereditary persistence of fetal haemoglobin
.
Br J Haematol
.
2012
;
156
(
2
):
259
-
264
.
9.
Steinberg
MH
,
Lu
ZH
,
Barton
FB
,
Terrin
ML
,
Charache
S
,
Dover
GJ
.
Fetal hemoglobin in sickle cell anemia: determinants of response to hydroxyurea. Multicenter study of hydroxyurea
.
Blood
.
1997
;
89
(
3
):
1078
-
1088
.
10.
Shi
L
,
Cui
S
,
Engel
JD
,
Tanabe
O
.
Lysine-specific demethylase 1 is a therapeutic target for fetal hemoglobin induction
.
Nat Med
.
2013
;
19
(
3
):
291
-
294
.
11.
Cui
S
,
Lim
KC
,
Shi
L
, et al
.
The LSD1 inhibitor RN-1 induces fetal hemoglobin synthesis and reduces disease pathology in sickle cell mice
.
Blood
.
2015
;
126
(
3
):
386
-
396
.
12.
Rivers
A
,
Vaitkus
K
,
Jagadeeswaran
R
, et al
.
Oral administration of the LSD1 inhibitor ORY-3001 increases fetal hemoglobin in sickle cell mice and baboons
.
Exp Hematol
.
2018
;
67
:
60
-
64.e2
.
13.
Rivers
A
,
Vaitkus
K
,
Ibanez
V
, et al
.
The LSD1 inhibitor RN-1 recapitulates the fetal pattern of hemoglobin synthesis in baboons (P. anubis)
.
Haematologica
.
2016
;
101
(
6
):
688
-
697
.
14.
Fang
Y
,
Liao
G
,
Yu
B
.
LSD1/KDM1A inhibitors in clinical trials: advances and prospects
.
J Hematol Oncol
.
2019
;
12
(
1
):
129
.
15.
Yang
M
,
Gocke
CB
,
Luo
X
, et al
.
Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase
.
Mol Cell
.
2006
;
23
(
3
):
377
-
387
.
16.
Vianello
P
,
Sartori
L
,
Amigoni
F
, et al
.
Thieno[3,2-b]pyrrole-5-carboxamides as new reversible inhibitors of histone lysine demethylase KDM1A/LSD1. Part 2: structure-based drug design and structure-activity relationship
.
J Med Chem
.
2017
;
60
(
5
):
1693
-
1715
.
17.
Folco
EG
,
Lei
H
,
Hsu
JL
,
Reed
R
.
Small-scale nuclear extracts for functional assays of gene-expression machineries
.
J Vis Exp
.
2012
(
64
):
4140
.
18.
Wang
Y
,
Myers
G
,
Yu
L
, et al
.
TR4 and BCL11A repress γ-globin transcription via independent mechanisms
.
Blood
.
2024
;
144
(
26
):
2762
-
2772
.
19.
Stringer
C
,
Wang
T
,
Michaelos
M
,
Pachitariu
M
.
Cellpose: a generalist algorithm for cellular segmentation
.
Nat Methods
.
2021
;
18
(
1
):
100
-
106
.
20.
Sadafi
A
,
Bordukova
M
,
Makhro
A
,
Navab
N
,
Bogdanova
A
,
Marr
C
.
RedTell: an AI tool for interpretable analysis of red blood cell morphology
.
Front Physiol
.
2023
;
14
:
1058720
.
21.
Yu
L
,
Myers
G
,
Ku
CJ
, et al
.
An erythroid to myeloid cell fate conversion is elicited by LSD1 inactivation
.
Blood
.
2021
;
138
(
18
):
1691
-
1704
.
22.
Kerenyi
MA
,
Shao
Z
,
Hsu
YJ
, et al
.
Histone demethylase Lsd1 represses hematopoietic stem and progenitor cell signatures during blood cell maturation
.
Elife
.
2013
;
2
:
e00633
.
23.
Wang
J
,
Scully
K
,
Zhu
X
, et al
.
Opposing LSD1 complexes function in developmental gene activation and repression programmes
.
Nature
.
2007
;
446
(
7138
):
882
-
887
.
24.
Sun
G
,
Alzayady
K
,
Stewart
R
, et al
.
Histone demethylase LSD1 regulates neural stem cell proliferation
.
Mol Cell Biol
.
2010
;
30
(
8
):
1997
-
2005
.
25.
Chen
Y
,
Yang
Y
,
Wang
F
, et al
.
Crystal structure of human histone lysine-specific demethylase 1 (LSD1)
.
Proc Natl Acad Sci U S A
.
2006
;
103
(
38
):
13956
-
13961
.
26.
Stavropoulos
P
,
Blobel
G
,
Hoelz
A
.
Crystal structure and mechanism of human lysine-specific demethylase-1
.
Nat Struct Mol Biol
.
2006
;
13
(
7
):
626
-
632
.
27.
Kim
SA
,
Zhu
J
,
Yennawar
N
,
Eek
P
,
Tan
S
.
Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate
.
Mol Cell
.
2020
;
78
(
5
):
903
-
914.e4
.
28.
Mathivanan
P
,
Wang
Y
,
White
AD
,
Engel
JD
,
Yu
L
.
Oxygenated heterocyclic LSD-1 inhibitors and related methods of use
.
International patent application
.
27 September 2024
:
PCT/US2024/048808
.
29.
Cui
S
,
Kolodziej
KE
,
Obara
N
, et al
.
Nuclear receptors TR2 and TR4 recruit multiple epigenetic transcriptional corepressors that associate specifically with the embryonic β-type globin promoters in differentiated adult erythroid cells
.
Mol Cell Biol
.
2011
;
31
(
16
):
3298
-
3311
.
30.
Xu
J
,
Bauer
DE
,
Kerenyi
MA
, et al
.
Corepressor-dependent silencing of fetal hemoglobin expression by BCL11A
.
Proc Natl Acad Sci U S A
.
2013
;
110
(
16
):
6518
-
6523
.
31.
Liu
N
,
Hargreaves
VV
,
Zhu
Q
, et al
.
Direct promoter repression by BCL11A controls the fetal to adult hemoglobin switch
.
Cell
.
2018
;
173
(
2
):
430
-
442.e17
.
32.
Tanabe
O
,
Katsuoka
F
,
Campbell
AD
, et al
.
An embryonic/fetal beta-type globin gene repressor contains a nuclear receptor TR2/TR4 heterodimer
.
Embo J
.
2002
;
21
(
13
):
3434
-
3442
.
33.
Hu
J
,
Hu
B
,
Xu
F
, et al
.
Precise conformational control yielding highly potent and exceptionally selective BRD4 degraders with strong antitumor activity
.
J Med Chem
.
2023
;
66
(
12
):
8222
-
8237
.
34.
Mill
CP
,
Fiskus
W
,
DiNardo
CD
, et al
.
RUNX1-targeted therapy for AML expressing somatic or germline mutation in RUNX1
.
Blood
.
2019
;
134
(
1
):
59
-
73
.
35.
Fiskus
W
,
Mill
CP
,
Nabet
B
, et al
.
Superior efficacy of co-targeting GFI1/KDM1A and BRD4 against AML and post-MPN secondary AML cells
.
Blood Cancer J
.
2021
;
11
(
5
):
98
.
36.
Wu
LC
,
Sun
CW
,
Ryan
TM
,
Pawlik
KM
,
Ren
J
,
Townes
TM
.
Correction of sickle cell disease by homologous recombination in embryonic stem cells
.
Blood
.
2006
;
108
(
4
):
1183
-
1188
.
37.
Woodard
KJ
,
Doerfler
PA
,
Mayberry
KD
, et al
.
Limitations of mouse models for sickle cell disease conferred by their human globin transgene configurations
.
Dis Model Mech
.
2022
;
15
(
6
):
dmm049463
.
38.
Chen
K
,
Liu
J
,
Heck
S
,
Chasis
JA
,
An
X
,
Mohandas
N
.
Resolving the distinct stages in erythroid differentiation based on dynamic changes in membrane protein expression during erythropoiesis
.
Proc Natl Acad Sci U S A
.
2009
;
106
(
41
):
17413
-
17418
.
39.
Alvarez-Argote
J
,
Dlugi
TA
,
Sundararajan
T
, et al
.
Pathophysiological characterization of the Townes mouse model for sickle cell disease
.
Transl Res
.
2023
;
254
:
77
-
91
.
40.
Wu
Y
,
Zeng
J
,
Roscoe
BP
, et al
.
Highly efficient therapeutic gene editing of human hematopoietic stem cells
.
Nat Med
.
2019
;
25
(
5
):
776
-
783
.
41.
Rivers
A
,
Jagadeeswaran
R
,
Lavelle
D
.
Potential role of LSD1 inhibitors in the treatment of sickle cell disease: a review of preclinical animal model data
.
Am J Physiol Regul Integr Comp Physiol
.
2018
;
315
(
4
):
R840
-
r847
.
42.
Jagadeeswaran
R
,
Vazquez
BA
,
Thiruppathi
M
, et al
.
Pharmacological inhibition of LSD1 and mTOR reduces mitochondrial retention and associated ROS levels in the red blood cells of sickle cell disease
.
Exp Hematol
.
2017
;
50
:
46
-
52
.
43.
Wang
J
,
Tran
J
,
Wang
H
, et al
.
mTOR Inhibition improves anaemia and reduces organ damage in a murine model of sickle cell disease
.
Br J Haematol
.
2016
;
174
(
3
):
461
-
469
.
44.
Hollebecque
A
,
Salvagni
S
,
Plummer
R
, et al
.
Clinical activity of CC-90011, an oral, potent, and reversible LSD1 inhibitor, in advanced malignancies
.
Cancer
.
2022
;
128
(
17
):
3185
-
3195
.
45.
Raouf
YS
.
Covalent inhibitors: to infinity and beyond
.
J Med Chem
.
2024
;
67
(
13
):
10513
-
10516
.
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