ArticlePDF AvailableLiterature Review

Epigenetic Regulation of Stromal and Immune Cells and Therapeutic Targets in the Tumor Microenvironment

Authors:

Abstract and Figures

The tumor microenvironment (TME) plays a pivotal role in neoplastic initiation and progression. Epigenetic machinery, governing the expression of core oncogenes and tumor suppressor genes in transformed cells, significantly contributes to tumor development at both primary and distant sites. Recent studies have illuminated how epigenetic mechanisms integrate external cues and downstream signals, altering the phenotype of stromal cells and immune cells. This remolds the area surrounding tumor cells, ultimately fostering an immunosuppressive microenvironment. Therefore, correcting the TME by targeting the epigenetic modifications holds substantial promise for cancer treatment. This review synthesizes recent research that elucidates the impact of specific epigenetic regulations—ranging from DNA methylation to histone modifications and chromatin remodeling—on stromal and immune cells within the TME. Notably, we highlight their functional roles in either promoting or restricting tumor progression. We also discuss the potential applications of epigenetic agents for cancer treatment, envisaging their ability to normalize the ecosystem. This review aims to assist researchers in understanding the dynamic interplay between epigenetics and the TME, paving the way for better epigenetic therapy.
Content may be subject to copyright.
Academic Editors: Paolo Fagone,
Dennis R. Grayson and Peixin Dong
Received: 18 November 2024
Revised: 19 December 2024
Accepted: 4 January 2025
Published: 6 January 2025
Citation: Liu, K.; Li, Y.; Shen, M.; Xu,
W.; Wu, S.; Yang, X.; Zhang, B.; Lin, N.
Epigenetic Regulation of Stromal and
Immune Cells and Therapeutic
Targets in the Tumor
Microenvironment. Biomolecules 2025,
15, 71. https://doi.org/10.3390/
biom15010071
Copyright: © 2025 by the authors.
Licensee MDPI, Basel, Switzerland.
This article is an open access article
distributed under the terms and
conditions of the Creative Commons
Attribution (CC BY) license
(https://creativecommons.org/
licenses/by/4.0/).
Review
Epigenetic Regulation of Stromal and Immune Cells and
Therapeutic Targets in the Tumor Microenvironment
Kang Liu 1, 2, , Yue Li 1, 2, , Minmin Shen 1,3, Wei Xu 1,2, Shanshan Wu 1,2, Xinxin Yang 1,2, Bo Zhang 1, 2, * and
Nengming Lin 1,2,4,*
1
College of Pharmaceutical Sciences, Hangzhou First People’s Hospital, Zhejiang Chinese Medical University,
Hangzhou 311402, China; kangliu@zju.edu.cn (K.L.); 202321014011138@zcmu.edu.cn (Y.L.);
20231061@zcmu.edu.cn (M.S.); 202421014011151@zcmu.edu.cn (W.X.); 202211113911046@zcmu.edu.cn (S.W.);
202211113911052@zcmu.edu.cn (X.Y.)
2Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology
Research of Zhejiang Province, Affiliated Hangzhou First People’s Hospital, School of Medicine,
Westlake University, Hangzhou 310006, China
3Department of Drug Clinical Trial Institution, Huzhou Central Hospital, Huzhou 313000, China
4Westlake Laboratory of Life Sciences and Biomedicine of Zhejiang Province, Westlake University,
Hangzhou 310024, China
*Correspondence: zhangbo@hospital.westlake.edu.cn (B.Z.); lnm1013@zju.edu.cn (N.L.)
These authors contributed equally to this work.
Abstract: The tumor microenvironment (TME) plays a pivotal role in neoplastic initiation
and progression. Epigenetic machinery, governing the expression of core oncogenes and tu-
mor suppressor genes in transformed cells, significantly contributes to tumor development
at both primary and distant sites. Recent studies have illuminated how epigenetic mecha-
nisms integrate external cues and downstream signals, altering the phenotype of stromal
cells and immune cells. This remolds the area surrounding tumor cells, ultimately fostering
an immunosuppressive microenvironment. Therefore, correcting the TME by targeting
the epigenetic modifications holds substantial promise for cancer treatment. This review
synthesizes recent research that elucidates the impact of specific epigenetic regulations—
ranging from DNA methylation to histone modifications and chromatin remodeling—on
stromal and immune cells within the TME. Notably, we highlight their functional roles in
either promoting or restricting tumor progression. We also discuss the potential applica-
tions of epigenetic agents for cancer treatment, envisaging their ability to normalize the
ecosystem. This review aims to assist researchers in understanding the dynamic interplay
between epigenetics and the TME, paving the way for better epigenetic therapy.
Keywords: tumor microenvironment; epigenetic modification; epigenetic therapy;
immune therapy
1. Background
Cancer stands as a significant global health threat and the primary cause of mortality.
Despite being a systemic disease, cancer manifests as a multifaceted ecosystem functioning
as a complex ensemble of cancer cells, non-cancerous cells, an extracellular matrix (ECM),
and assorted soluble factors [
1
]. Among the diverse stromal lineages infiltrating the tumor
are cancer-associated fibroblasts (CAFs), endothelial cells (ECs), pericytes, and various
tissue-resident cell types, including adipocytes and stellate cells, etc. Immune cells within
the TME encompass innate immune cells, including tumor-associated macrophages (TAMs),
myeloid-derived suppressor cells (MDSCs), neutrophils, natural killer cells (NKs), and
Biomolecules 2025,15, 71 https://doi.org/10.3390/biom15010071
Biomolecules 2025,15, 71 2 of 25
dendritic cells (DCs), as well as adaptive immune cells such as T lymphocytes and B
lymphocytes [
2
]. These cellular components are increasingly acknowledged as critical
players in cancer initiation and progression [3].
Tumorigenesis entails genetic mutations and epigenetic alterations [
4
]. Coined by
Conrad Waddington, epigenetics denotes the transmission of heritable cellular phenotypes
without DNA sequence changes. Regulators of epigenetic modifications are categorized
as writers, readers, erasers, and remodelers [
5
]. The dysregulated expression or aberrant
activity of these regulators often leads to tumor development and progression [6].
The interaction between tumor cells and other components within the TME fuels the
malignant traits of cancer cells, such as uncontrolled proliferation, aggressive invasion,
and metastasis [
7
]. Recent research has indicated that epigenetic disruptions alter the
phenotype of immune and stromal cells, thereby reshaping the TME [
8
]. In this review,
we aim to comprehensively outline epigenetic modifications within the solid tumor TME.
Additionally, we underscore the therapeutic implications of targeting these epigenetic
regulators within the context of TME remodeling.
2. Fundamental Epigenetic Modifications
Global proteomic and genomic technologies have provided profound insights into the
epigenomic alterations in cancer development, and the process of epigenetic modifications
has been extensively reviewed [
9
11
]. Five key epigenetic mechanisms—DNA methylation,
histone modifications, chromatin remodeling, RNA modifications, and non-coding RNA
(ncRNA) alterations—govern the heritability of gene expression levels. Among these, ncR-
NAs and RNA modifications introduce significant functional changes to the transcriptome
without altering the RNA ribonucleotide sequence, a focus that falls under the emerging
field of epitranscriptomics [
12
,
13
]. Given that epitranscriptomics represents a distinct area
extending beyond the scope of this review, we will center our attention on the classical epi-
genetic regulatory mechanisms: DNA methylation, histone modifications, and chromatin
remodeling (Figure 1).
Biomolecules 2025, 15, x FOR PEER REVIEW 2 of 26
macrophages (TAMs), myeloid-derived suppressor cells (MDSCs), neutrophils, natural
killer cells (NKs), and dendritic cells (DCs), as well as adaptive immune cells such as T
lymphocytes and B lymphocytes [2]. These cellular components are increasingly acknowl-
edged as critical players in cancer initiation and progression [3].
Tumorigenesis entails genetic mutations and epigenetic alterations [4]. Coined by
Conrad Waddington, epigenetics denotes the transmission of heritable cellular pheno-
types without DNA sequence changes. Regulators of epigenetic modications are catego-
rized as writers, readers, erasers, and remodelers [5]. The dysregulated expression or ab-
errant activity of these regulators often leads to tumor development and progression [6].
The interaction between tumor cells and other components within the TME fuels the
malignant traits of cancer cells, such as uncontrolled proliferation, aggressive invasion,
and metastasis [7]. Recent research has indicated that epigenetic disruptions alter the phe-
notype of immune and stromal cells, thereby reshaping the TME [8]. In this review, we
aim to comprehensively outline epigenetic modications within the solid tumor TME.
Additionally, we underscore the therapeutic implications of targeting these epigenetic
regulators within the context of TME remodeling.
2. Fundamental Epigenetic Modications
Global proteomic and genomic technologies have provided profound insights into
the epigenomic alterations in cancer development, and the process of epigenetic modi-
cations has been extensively reviewed [9–11]. Five key epigenetic mechanisms—DNA
methylation, histone modications, chromatin remodeling, RNA modications, and non-
coding RNA (ncRNA) alterations—govern the heritability of gene expression levels.
Among these, ncRNAs and RNA modications introduce signicant functional changes
to the transcriptome without altering the RNA ribonucleotide sequence, a focus that falls
under the emerging eld of epitranscriptomics [12,13]. Given that epitranscriptomics rep-
resents a distinct area extending beyond the scope of this review, we will center our aen-
tion on the classical epigenetic regulatory mechanisms: DNA methylation, histone modi-
cations, and chromatin remodeling (Figure 1).
Figure 1. Schematic model of fundamental epigenetic regulation: DNA methylation, histone modi-
cations, and chromatin remodeling. DNA methylation represents a dynamic process regulated by
DNA methyltransferases, which transfer a methyl group to the cytosine residue. The methyl group
can be actively removed from cytosines by TET enzymes. Histone modications, including histone
Figure 1. Schematic model of fundamental epigenetic regulation: DNA methylation, histone modifi-
cations, and chromatin remodeling. DNA methylation represents a dynamic process regulated by
DNA methyltransferases, which transfer a methyl group to the cytosine residue. The methyl group
can be actively removed from cytosines by TET enzymes. Histone modifications, including
histone methylation and histone acetylation, are dynamic processes catalyzed by histone methyl-
transferases (HMTs) and histone acetyltransferases (HATs), respectively. The methyl and acetyl
Biomolecules 2025,15, 71 3 of 25
groups are added to the histone tails, resulting in chromatin configuration alterations. Chromatin
remodeling is mediated by chromatin complexes that use the energy generated by ATP hydrolysis to
eject, slide, and reposition nucleosomes, leading to the rearrangement of chromatin structure.
2.1. DNA Methylation
DNA methylation is an important epigenetic mark that orchestrates numerous bio-
logical processes, including gene expression, imprinting, chromosome stability, etc. [
14
]. It
refers to the addition of a methyl group to the 5-carbon of cytosine residues (5mC) primarily
within CpG islands located in gene promoters and regulatory elements. Methylated DNA
assumes a closed state, impeding the binding of transcription factors and consequently
suppressing gene expression [15].
DNA methylation is intricately regulated by distinct protein groups. The transfer of
a methyl group from S-adenosyl-L-methionine to DNA’s cytosine residue is catalyzed by
DNA methyltransferases (DNMTs), notably DNMT1, DNMT3A, DNMT3B, and DNMT3L.
DNMT3A and DNMT3B, influenced by DNMT3L, create a methylation pattern on unmethy-
lated DNA, while DNMT1 ensures the preservation of the DNA methylation pattern by
methylating hemimethylated DNA during replication [
16
]. Methyl-binding proteins (MBPs)
bind methylated CpG dinucleotides and interpret various DNA methylation statuses. MBPs
consist of methyl-binding domain proteins, the Kaiso family proteins, and the SET and Ring
finger-associated (SRA) domain proteins [
17
]. TET enzymes facilitate the active removal of
methyl groups from cytosines. These enzymes convert 5mC to
5-hydroxymethyl-cytosine
(5hmC), which can be further oxidized iteratively by TET proteins to 5-formylcytosine (5fC)
and 5-carboxycytosine (5caC) [
18
]. In various cancer types, altered DNMTs, MBPs, and
TET protein expression levels or functional mutations have been repeatedly reported [19].
2.2. Histone Modifications
Post-translational modifications of histones control the structure of chromatin, facili-
tating or hindering transcription factor binding and thereby orchestrating transcriptional
activation and repression [
20
]. Various histone modifications have been discovered on the
N-terminal tails of histone proteins, including acetylation, methylation, phosphorylation,
ubiquitylation, SUMOylation, deamination, and lactylation, among others [
21
]. For brevity,
we will discuss two major modes of histone modifications, methylation and acetylation, in
the following sections.
2.2.1. Histone Methylation
Histone methylation can occur on the side chains of lysine, arginine, and histidine
residues [
22
]. Among various types of histone methylation, methylated modifications
at lysine sites are best studied. This process is meticulously regulated by histone lysine
methyltransferases (HKMTs) and lysine-specific demethylases (LSDs), acting collabora-
tively to add or remove specific methyl groups from critical target residues that regulate
gene expression [
23
]. HKMTs exhibit remarkable substrate specificity for particular lysine
residues and methylation states [
24
]. Histone demethylases are broadly categorized into
two families, LSD and JMJD (JmjC domain-containing demethylase) [
25
]. LSD1 exclusively
removes mono- and di-methylation modifications of H3K4 and H3K9, whereas the JMJD
family targets lysine tri-methylation [
26
]. The outcomes of histone methylation, whether
gene activation or repression, hinge on the site of methylation, the extent of modification,
and the genomic context in which the modification exerts its influence [20].
2.2.2. Histone Acetylation
Histone acetylation, catalyzed by histone acetyltransferases (HATs), involves adding
acetyl groups to the
ε
-amino group of histone lysine residues. Three major families of
Biomolecules 2025,15, 71 4 of 25
HATs have been identified to date: the Gcn5-related N-acetyltransferase family (GNAT),
the MYST family (MOZ, Ybf2, Sas2, TIP60), and the orphan family (CBP/EP300 and
nuclear receptors) [
27
]. Acetylation of lysine residues is also a highly reversible process
in which acetyl groups are removed by histone deacetylases (HDACs) [
28
,
29
]. Acetylated
lysines carry a signal that is recognized by various “readers”, including the bromodomain
proteins [30], which collaborate with HATs and HDACs to regulate gene expression.
2.3. Chromatin Remodeling
Covalent modifications of nucleosomes provide a dynamic platform for ATP-
dependent chromatin structure remodeling. This DNA repackaging involves a set of
specialized chromatin remodeling complexes, or remodelers, working in tandem with
diverse factors that engage in chromatin assembly [
31
]. These remodelers are grouped into
four distinct families: the switch/sucrose non-fermentable (SWI/SNF) family, the imitation
switch (ISWI) family, the chromodomain helicase DNA-binding (CHD) family, and the in-
ositol 80 (INO80) family [
32
]. By harnessing the energy generated by ATP hydrolysis, these
complexes eject, slide, and reposition nucleosomes, consequently altering the structure and
accessibility of chromatin DNA [
33
]. Moreover, remodelers could influence nucleosome
stability and transcription initiation by mediating the exchange of the H2A/H2B dimers
with histone variants [34].
3. Basic Cellular Components of the TME
The TME constitutes a diverse array of cells enveloped by secreted factors and extra-
cellular matrix proteins, wielding a pivotal influence on tumor progression [
35
38
]. Prior to
discussing the correlation between epigenetic alterations and the TME, we will first outline
some fundamental cellular constituents that underpin the formation of the TME (Table 1).
These include stromal cells, primarily cancer-associated fibroblasts (CAFs), and immune
cells, specifically tumor-associated macrophages (TAMs), myeloid-derived suppressor cells
(MDSCs), and tumor-infiltrating lymphocytes (TILs).
Table 1. Celular elements of TME.
Cell Type Major Markers Function Reference
CAFs α-SMA, S100A4, FAP,
PDGFRα/β
Enhance tumor cell survival and growth; In specific contexts,
CAFs counteract tumor progression by promoting anticancer
immunity and regulating tumor-inhibitory signaling.
[3943]
TAMs CD68, CD163, ARG1,
CD11b
Promote angiogenesis, metastasis andimmune evasion:
Phagocytosis of cancer cells exerts an anti-tumor effect.
[4449]
MDSCs CD11b, Lin-, CD33, Gr-1 Suppress T-cell activity; Secrete immunosuppressive
cytokines; Facilitate tumor progression.
[5056]
CD8+T
CD8, CD28, CD3, TCR, Tim
3, PD-1
Release perforin and granzymes;
Secrete cytokines like lFN-γ, TNF-α; Kill cancer cells.
[57,58]
CD4+T CD4, CD28, CD3, TCR Th1 subtype promotes the anti-tumoral response; TH2
subtype exerts the pro-tumoral effect.
[59,60]
Treg cells CD4, CD25, FOXP3 Suppress the activity of effector T cells; Expediate tumor
progression.
[61,62]
NK cells CD56, CD16, KIRs, CD94 Recognize and kill tumor cells directly. [63,64]
B cells CD19, CD20, CD22, CD27 Drive the humoral immunity;
Promote the anti-tumoral response.
[65,66]
Biomolecules 2025,15, 71 5 of 25
3.1. Cancer-Associated Fibroblasts
Cancer-associated fibroblasts (CAFs) are central constituents of the tumor stroma,
significantly influencing the TME through extensive interactions with tumor cells and other
cellular components [
39
]. CAFs primarily stem from the activation of resident fibroblasts
or stellate cells in liver and pancreas cancer. However, emerging studies propose that
in certain tumor types, CAFs can also arise from adipocytes, pericytes, endothelial cells,
and bone marrow-derived mesenchymal stem cells [
40
]. Functionally, CAFs wield diverse
mechanisms to regulate tumor growth and progression. For instance, CAFs directly en-
hance tumor cell survival and growth by secreting hepatocyte growth factor (HGF) and
other growth factors [
41
]. Traditionally perceived as pro-tumoral, CAFs shape the immuno-
suppressive tumor microenvironment. However, in specific contexts, CAFs counteract
tumor progression by promoting anticancer immunity and regulating tumor-inhibitory
signaling [
42
]. The functions of CAFs, whether promoting or restraining tumor growth, are
likely tied to their phenotypic heterogeneity and plasticity [43].
3.2. Tumor-Associated Macrophages
Tumor-associated macrophages (TAMs) constitute a significant proportion of immune
cells infiltrating solid tumors, representing up to 50% of a tumor’s mass in certain tumor
types [
44
]. TAMs are mostly originated from bone marrow-derived monocytes. Tumor
cell-secreted chemokines, like CCL2, recruit bone marrow-derived monocytes and promote
their differentiation in the tumor site. Nevertheless, emerging evidence highlights that
the embryonic-derived tissue-resident macrophages could also serve as an alternative
source of TAMs [
45
]. Functionally, macrophages exhibit two activation modes: classically
activated M1 and alternatively activated M2 subtypes. M1-like macrophages elicit pro-
inflammatory responses that favor an anti-tumor phenotype, while M2-like macrophages
trigger anti-inflammatory responses conducive to an immunosuppressive milieu [46].
TAMs play a pivotal role in tumor progression, primarily as promoters and immuno-
suppressors. They drive angiogenesis by secreting angiogenic factors like vascular en-
dothelial growth factor and chemokines, bolstering tumor progression. Moreover, TAMs
contribute to the recruitment of T regulatory cells through the production of chemokines
such as CCL2, CCL3, CCL4, CCL5, and CCL20. These chemokines dampen the activities of
CD8
+
T cells and NK cells, thereby forming an immunosuppressive microenvironment [
47
].
Clinically, TAMs in the TME are associated with poorer prognoses in various types of
cancer, including breast, lung, and gastric cancers [
48
]. Moreover, TAMs are capable of
communicating with a wide range of cell types within the TME, including cancer-associated
fibroblasts, endothelial cells, and other immune cells. These extensive cell–cell interactions
underpin their diverse functional roles [49].
3.3. Myeloid-Derived Suppressor Cells
Myeloid-derived suppressor cells (MDSCs) are a heterogeneous cell population with
common myeloid origin in the TME [
50
]. MDSCs originate from the bone marrow and
migrate to tumor locales, driven by chemokines emanating from tumor cells. There are
two major types of MDSCs: polymorphonuclear MDSCs (PMN-MDSCs), which morpho-
logically and phenotypically resemble neutrophils, and monocytic MDSCs (M-MDSCs),
akin to monocytes [
51
]. MDSCs contribute to an immunosuppressive tumor microenvi-
ronment through diverse mechanisms. These encompass the obstruction of T cell traf-
ficking, the upregulation of negative immune checkpoint molecules, and the generation
of reactive oxygen and nitrogen species [
52
54
]. MDSCs also exert direct influence by
producing immunosuppressive cytokines, such as IL-10 and TGF-
β
, to quell T lymphocyte
function [55,56].
Biomolecules 2025,15, 71 6 of 25
3.4. Tumor-Infiltrating Lymphocytes
Tumor-infiltrating lymphocytes (TILs) comprise diverse populations, including CD8
+
T cells, CD4
+
T cells, B cells, NK cells, and regulatory T cells (Tregs), all exerting significant
impacts on tumor development and progression [
67
]. Notably, CD8
+
T cells, particularly
CD8
+
cytotoxic T lymphocytes (CTLs), have long been regarded as chief immune effectors
against cancer. CTLs recognize aberrant tumor-associated antigens displayed by class I
peptide-major histocompatibility complex (MHC-I) on cancer cells through T cell receptors
(TCR) [
57
]. Upon activation, CTLs eliminate cancer cells via granzyme and perforin-
mediated apoptosis or FASL-FAS-induced cell death. The abundant infiltration of CTLs
within the TME correlates with favorable prognoses in cancer patients [58].
CD4
+
T cells exhibit a bipolar role in the TME. The Th1 subtype promotes the anti-
tumoral response of cytotoxic CD8
+
cells and B cells by secreting interferon
γ
(IFN-
γ
),
interleukin-2 (IL-2), and tumor necrosis factor (TNF-
α
) [
59
]. Conversely, the Th2 subtype
exerts a pro-tumoral effect through the secretion of anti-inflammatory factors [
60
]. Tregs, a
subset of CD4
+
T cells, predominantly curtail anti-tumoral immunity and expedite cancer
progression through diverse mechanisms. Tregs support tumor cell survival both directly,
by producing growth factors, and indirectly, through interactions with stromal cells such as
CAFs and endothelial cells [
61
,
62
]. NK cells possess potent cytotoxic activity against tumors,
serving as primary innate lymphoid cells that control tumor growth and metastasis [
63
,
64
].
B cells, a crucial component of the TME, predominantly drive the humoral immunity. Their
contributions to anti-tumor immune response are gaining recognition [65,66].
The abundance of infiltrated immune cells classifies tumors into three subtypes:
immune-infiltrated, immune-excluded, and immune-silent. While targeting other TILs,
such as B cells, NK cells, and Tregs, can influence tumor growth and complement exist-
ing therapies, invigorating T lymphocytes within the tumor microenvironment remains
the core focus of current immunotherapies [
68
]. Therefore, we will concentrate on the
epigenetic changes in T lymphocytes in this review.
4. Epigenetic Modifications in TME
4.1. Epigenetic Modifications of CAFs
4.1.1. DNA Methylation in CAFs
CAFs exhibit distinct phenotypes, gene expression profiles, and functions within the
TME, despite a scarcity of genetic mutations. This suggests that the phenotypic plasticity of
CAFs stems from underlying epigenetic modifications [
69
,
70
]. Multiple studies report that
CAFs across various tumor types exhibit an identical genome-wide methylation pattern to
that of tumor cells [
71
,
72
]. Within lung, gastric, and colorectal cancer, CAFs show overall
DNA hypomethylation and targeted hypermethylation at specific genomic regions [
73
]. In
contrast, Pidsley et al.’s work with CAFs from prostate cancer contradicts this trend, dis-
covering no global hypomethylation using whole-genome bisulfite sequencing [
74
]. Recent
studies have highlighted that normal fibroblasts undergo substantial DNA methylation
changes upon transiting into CAFs. Specifically, one study identifies the hypomethylation
and subsequent transcriptional activation of RUNX1 as the signaling nexus governing the
epigenetic shift of tumor stroma [
75
]. These findings imply that the methylation pattern of
CAFs may hinge on tumor type and stage.
DNA methylation regulates the conversion of stromal fibroblasts to CAFs [
76
]. Al-
brengues et al. reveal that a transient TGF-
β
stimulus induces a stable preinvasive phe-
notype on fibroblasts in the TME [
77
]. TGF-
β
triggers leukemia inducible factor (LIF)
induction in both tumor cells and stromal cells, orchestrating the phenotypic shift of normal
fibroblasts [
77
]. Notably, LIF prompts the hypermethylation of the protein phosphatase
regulator SHP-1 at its promoter region, driven by increased DNMT3B expression [
77
]. Hy-
Biomolecules 2025,15, 71 7 of 25
permethylation represses SHP-1 expression, leading to the activation of the JAK1/STAT3
signaling pathway, which is sustained by DNMT1 [
78
]. This activation prompts the re-
programming of stroma fibroblasts into pro-invasive CAFs [78]. Interestingly, cancer cells
trigger DNMT1 activation, remolding CAFs into pro-tumor phenotypes via Socs1 gene
methylation in pancreatic cancer [
79
]. Furthermore, CAFs exhibit greater glycolytic ac-
tivity compared to normal fibroblasts [
80
]. The metabolic reprogramming involves DNA
methylation alterations on key metabolic enzymes by unclassified mechanisms under
chronic hypoxia. Thus, further investigations are required to understand the evolution of
tissue-specific DNA methylation in CAFs and its contribution to cancer progression.
4.1.2. Histone Modifications and Chromatin Remodeling in CAFs
Numerous studies highlight the significance of histone modifications and chromatin
remodeling in shaping the functional properties of CAFs. For instance, Tyan et al. revealed
an intriguing connection between the expression level of ADAMTS1 and the behavior of
normal tissue-associated fibroblasts co-cultured with breast tumor cells. This interaction
promotes the invasion of the engaged tumor cells. The elevated ADAMTS1 expression
correlates with the loss of EZH2 binding from its promoter region, leading to reduced
H3K27 methylation [
81
]. In ovarian cancer, the stromal expression of the NNMT protein
was found to be correlated with metastasis. NNMT was proved to be indispensable for the
pro-tumoral traits of CAFs, as silencing NNMT in CAFs curbed ovarian cancer cell invasion
and metastasis
in vivo
. The introduction of NNMT expression into CAFs led to a reduction
in S-adenosyl methionine (SAM), alongside diminished H3K4 and H3K27 methylation on
key genes regulating cytokine secretion and ECM deposition [
82
]. Interestingly, it has been
demonstrated that methionine restriction did not directly result in the alteration of H3K4
methylation in fibroblasts [
83
], suggesting that epigenetic reprogramming might operate
independently from the metabolic switch in CAFs. Taken together, these studies underscore
the role of histone methylation in regulating the tumor-promoting identity of CAFs.
Histone acetylation tightly intertwines with DNA methylation and has been shown
to promote CAF activation and their tumor-promoting functions. Specifically, H3K27
acetylation along with its reader protein BRD4 exhibited significant enrichment within
the promoter and enhancer regions of the Saa1 gene in gastric cancer fibroblasts. This
is necessary for the pro-metastasis capacity of CAFs, and importantly, BRD4 inhibitors
reinstate the anti-tumor phenotypes of CAFs in an SAA1-dependent manner [
84
]. Likewise,
elevated H3K27ac on the promoter regions of Ctgf and Postn was found in hepatic stellate
cells that had undergone myofibroblastic activation. This epigenetic shift, induced by
TGF-
β
1, is responsible for the pro-metastasis behavior of CAFs in murine models of lung,
colorectal, and pancreatic cancer [
85
]. This process relies on canonical histone acetylation
and noncanonical mechanisms mediated by p300 acetyltransferase. Similarly, colorectal
cancer-derived HSPC111 was established to promote liver metastasis through hepatic
stellate cell activation [
86
]. The uptake of HSPC111 causes acetyl-CoA accumulation,
consequently fueling H3K27 acetylation in hepatic stellate cells. H3K27 acetylation elevates
CXCL5 expression and secretion, reciprocally acting on cancer cells to amplify HSPC111
production and enhance liver metastasis [86].
The regulation of CAFs by chromatin remodeling complexes remains less explored.
Increased SATB2 expression was detected in CAFs within endometrial cancer, correlating
with the pro-invasion properties of these CAFs [
87
]. Furthermore, skin cancer stromal cells
showed extensive chromatin remodeling when transcriptional repressors such as ATF3 and
CBF1 were depleted, underpinning the growth-promoting effects of CAFs [
88
]. Tumoral
expression of chromatin remodeler protein HMGA2 is extensively linked to cancer metas-
tasis and therapeutic resistance [
89
]. Intriguingly, the stromal expression of the HMGA2
Biomolecules 2025,15, 71 8 of 25
protein independently predicts poorer clinical outcomes in pancreatic cancer and ampullary
adenocarcinoma patients [90], indicating that parallel chromatin remodeling processes by
HMGA2 occur in both tumoral and stromal compartments of cancers. When overexpressed
in prostatic stromal cells, HMGA2 increases the secretion of WNT ligands, contributing to
hyperplasia and multifocal intraepithelial neoplasia lesions in mouse models [
91
]. These
studies collectively support the critical role of chromatin remodelers in controlling the
pro-tumor phenotypes of CAFs, although the precise underlying mechanisms warrant
further investigation.
4.2. Epigenetic Modulations of TAMs
4.2.1. DNA Methylation in TAMs
DNA methylation is essential for the functional reprogramming of macrophages
within the TME. Studies have indicated that DNA methyltransferases, including DNMT3B
and DNMT1, regulate the phenotypic shift of macrophages in an inflammation setting.
For instance, Yang et al. revealed that DNMT3B functions as a negative regulator for
M2-like macrophage polarization in obese mice [
92
]. The depletion of DNMT3B promotes
the M2-like phenotype in macrophages by mitigating the promoter methylation of the
Ppar
γ
1gene, consequently elevating its mRNA expression [
92
]. Similarly, in another
study, DNMT1-induced hypermethylation of the Socs1 gene in macrophages treated with
lipopolysaccharide (LPS) propels the shift toward an M1-like phenotype by intensifying
the release of proinflammatory factors [
93
]. It would be interesting to examine whether
these mechanisms could be adapted to modulate the polarization of tumor-associated
macrophages. Selective DNA methylation patterns on metabolic genes were recently
reported in M1-like macrophages interacting with pancreatic ductal adenocarcinoma tumor
cells [
94
]. Moreover, these macrophages demonstrate a transition from the M1 to the M2
state and acquire properties that favor cancer progression.
Unsurprisingly, enzymes catalyzing DNA demethylation play a role in macrophage
polarization. Research demonstrates that TET1 activity is required for producing pro-
inflammatory cytokines like TNF-
α
and interleukin-6 (IL-6), crucial for sustaining the M1
macrophage polarization [
95
,
96
]. In contrast, TET2 deficiency results in deleterious NLRP3
inflammasome activation, consequently elevating IL-1
β
secretion from macrophages and
accelerating atherosclerosis development [
97
]. Supporting this, Alyssa H. Cull et al. found
that although LPS stimulation induced TET2 in bone marrow-derived macrophages, it
actually restricted the expression levels of key inflammatory cytokines such as IL-1
β
and IL-
6 [
98
]. TET2 upregulation was shown to recruit HDAC2 to the promoter region, repressing
Il-6 gene transcription through a DNA demethylation impendent mechanism [
99
], suggest-
ing an anti-inflammatory role for TET2 in macrophage differentiation. In melanoma models,
targeted TET2 deletion in myeloid lineage reduced the tumor burden and dampened the
immunosuppressive function of TAMs [
100
]. Collectively, these studies suggest DNA
methylation’s role in macrophage polarization, yet comprehending the precise mechanisms
across diverse tumor microenvironments necessitates future investigation.
4.2.2. Histone Modifications in TAMs
Histone modifications wield a significant impact on macrophage phenotype and func-
tion. For example, Kittan et al. identified the induction of H3K4 methyltransferase SMYD3
during M2-like macrophage differentiation, which consequently promoted the expression
of M2 marker genes [
101
]. Similarly, in the tumor context, cancer cell-derived exosomes or
phosphatidylserine prompts increased expression level of JMJD3 in macrophages, resulting
in M2-like polarization of TAMs and thereby promoting cancer metastasis [
102
]. Further-
more, M2-polarized macrophages showed JMJD3-dependent transcriptional activation
Biomolecules 2025,15, 71 9 of 25
of lysyl oxidase (LOX), which contributes to extracellular matrix remodeling and cancer
metastasis [
103
]. These findings underscore the involvement of histone methylation in the
emergence of M2-like macrophages.
Alterations in histone methylation have also been implicated in reprogramming
macrophages toward an anti-tumor M1-like phenotype. For example, Wang et al. demon-
strated that H3K9 methyltransferase G9a promotes M1-like macrophage polarization
through the negative regulation of the CD36 molecule [
104
]. Lysine-specific histone
demethylase 1A, commonly known as LSD1, appears to exert dual effects on triggering
M1 polarization in macrophages [
105
107
]. On one hand, various groups have suggested
that the genetic or pharmacological inhibition of LSD1 may amplify the inflammation
response of macrophages under diverse conditions [
108
,
109
]. Notably, in breast cancer,
M1-polarized macrophages demonstrated reduced expression levels of LSD1 alongside
nuclear REST corepressor 1 (CoREST1) and the zinc finger protein SNAIL [
110
]. Disrupt-
ing LSD1–CoREST complexes with phenelzine activated H3K4 and H3K9 methylation,
culminating in the transcriptional activation of M1-like marker genes
in vitro
and
in vivo
.
Moreover, a combination of LSD1 inhibitors and chemotherapeutic reagents stimulates
an M1-like antitumor response, significantly reducing the tumor burden in murine breast
cancer models [
111
]. On the other hand, LSD1 has been reported as essential to the pro-
inflammatory effect and the M1-like phenotype of bone marrow-derived macrophages
in multiple studies [
112
,
113
]. The underlying reasons for these seemingly contradictory
findings remain elusive.
Histone acetylation finetunes macrophage functions by regulating the transcription
of critical cytokines. Shinohara et al. found that the extracellular vesicles derived from
colorectal cancer cells contained miR-145, which was taken up by the progenitor cells of
TAMs [
114
]. miR-145 directly binds to the 3
untranslated regions of histone deacetylase
11 (HDAC11) mRNA, suppressing HDAC11 expression in these cells. Consequently,
histone 3 acetylation increases, resulting in the upregulation of IL-10 and downregulation
of IL-12 p40. This epigenetic shift cooperatively promotes an M2-like phenotype in EV-
conditioned macrophages [
114
]. Histone acetylation also influences M2-like polarization
through another cytokine, IL-6. Wang et al. demonstrated that IL-6 sustains the pro-
migrative and angiogenic properties of M2-like TAMs in lung cancer [
115
]. They also
discovered that IL-6 expression was regulated by increased histone-3 acetylation, which
directly arises from stabilized histone acetyltransferase p300 by increased deubiquitinating
enzyme USP24 expression in M2 macrophages [
115
]. It is now well-recognized that the
acetylation of histone proteins couples with macrophage metabolic activities [
116
119
].
As an example, shortly after the TLR4-induced initiation of an inflammatory response,
macrophages exhibited escalated glycolytic and tricarboxylic acid cycle activities, yielding
additional acetyl-coenzyme A. The surplus acetyl-CoA fuels a global increase in histone
acetylation, thus augmenting the pro-inflammatory response of macrophages [119].
4.3. Epigenetic Modulations of MDSCs
4.3.1. DNA Methylation in MDSCs
MDSCs are the main promoters of the immunosuppressive tumor microenvironment
in cancer. Both immune-suppressive MDSCs and immune-stimulating dendritic cells
(DCs) emerge from bone marrow common myeloid progenitor cells. A comparison of
DNA methylation between differentiated MDSCs and DCs reveals that MDSCs exhibit a
global DNA hypomethylation profile with localized hypermethylation gains in specific
DNA regions [
120
]. This pattern closely mirrors the DNA methylation pattern of CAFs
and cancer cells. This similarity led the same study to propose that elevated DNMT3A
activity might underlie the MDSC-specific methylation pattern and connect to MDSC’s
Biomolecules 2025,15, 71 10 of 25
immunosuppressive capacity, particularly in ovarian cancer [
120
]. In another study, Alyssa
et al. reported that the IL-6/STAT3/DNMT signaling axis maintains the DNA methylation
pattern in MDSCs. The activation of this axis leads to the accumulation of MDSCs within
TME by impairing TNF
α
/RIP1-dependent necroptosis that promotes MDSC survival.
Importantly, the use of DNA methyltransferase inhibitor decitabine (DAC) in mouse models
results in the reversal of MDSC accumulation and an upsurge in the infiltration of antigen-
specific cytotoxic T lymphocytes [
121
]. Intriguingly, DNA methylation patterns vary even
in distinct MDSC subsets. For instance, Sasidharan Nair et al. uncovered that an increased
DNA methylation signature was significantly upregulated in infiltrating immature MDSCs,
while PMN-MDSCs showed downregulated methylation in flow cytometry-sorted MDSC
subpopulations of colorectal cancer [
122
]. These findings revealed the influential role of
DNA methylation in shaping the lineage specification and immunosuppressive phenotype
of MDSCs.
4.3.2. Histone Modifications and Chromatin Remodeling in MDSCs
The impacts of histone methylation on MDSC differentiation and function are relatively
less explored. Infiltrating MDSCs are characterized by the overproduction of inducible
nitric oxide synthase (iNOS), contributing to the suppression of the anti-tumor immune
response [
123
,
124
]. Notably, Redd et al. identified a link between histone methyltrans-
ferase SETD1B and iNOS expression in tumor-induced MDSCs. More precisely, within
MDSCs, SETD1B is upregulated and increases the trimethylation of histone H3 lysine 4
(H3K4Me3) at the nos2 promoter, consequently leading to the pathological overproduction
of iNOS. Likewise, significantly enhanced H3K4 trimethylation was detected at the pro-
moter region of the osteopontin (Opn) gene within monocytic MDSCs infiltrating pancreatic
cancer [
125
]. WDR5 recognizes the methylated H3K4 mark and facilitates the dimethylation
and trimethylation processes, ultimately activating the transcription of target genes [
126
].
In mouse models, the use of the WDR5 inhibitor effectively erased H3K4me3 at the Opn
promoter, subsequently decreasing Opn gene expression levels. As a result, the immuno-
suppressive capacity of MDSCs diminished, further leading to reduced tumor growth and
enhanced therapeutic efficacy of anti-PD-1 immunotherapy in pancreatic cancer models
upon WDR5 inhibition. Undoubtedly, other histone methylation modulators that influence
MDSCs accumulation and function could also synergize with immune blockade therapies
for cancer treatment [126].
Numerous studies have highlighted the important role of histone acetylation in driving
MDSC’s pro-tumoral properties. In colorectal cancer, genes related to histone deacetylase
are increased in infiltrating immature MDSCs along with the concurrent upregulation of
DNA methylation genes. This was coupled with a concomitant reduction in histone acetyl-
transferase activity in this MDSCs population. Further insight emerges from exploring
distinct members of the histone deacetylase family, each exerting specific regulatory func-
tions in MDSCs. For instance, Sahakian et al. reported the restraining effect of HDAC11 on
the expansion and immunosuppressive role of MDSCs in the thymoma tumor-bearing mice
model. HDAC11 depletion was required to steer myeloid precursor cells toward mono-
cytic MDSCs, significantly enhancing the immunosuppressive trait of M-MDSCs [127]. In
contrast, Youn et al. proposed that polymorphonuclear MDSCs (PMN-MDSCs) are the
predominant MDSCs population responsible for immunosuppression [
128
]. They also
pointed out the involvement of HDAC2 in the accumulation of PMN-MDSCs in the TME.
Specifically, HDAC2 appeared to play a pivotal role in promoting M-MDSCs differentiation
toward PMN-MDSC. This was achieved through the direct modification of histone acety-
lation on the Rb1 promoter, resulting in the silencing of RB1 expression in diverse mouse
models like 4T1 mammary carcinoma, Lewis lung carcinoma, and EL-4 thymoma [
128
].
Biomolecules 2025,15, 71 11 of 25
Together, these studies indicate the significance of histone acetylation in modulating MDSC
expansion and suppressive functions.
Limited independent research has explored the role of the chromatin remodeler in
MDSCs. Among these, a notable contribution by Almeida Nagata et al. unveiled a link
between chromatin remodeling complexes and histone acetylation in the regulation of
MDSC differentiation and function [
129
]. In their study, the researchers demonstrated that
the activity of CBP/EP300 bromodomain (BRD) dictated the H3K27 acetylation pattern
on cis-elements of pro-tumoral genes in MDSCs. Notably, pharmacological inhibition
of CBP/EP300 BRD induced H3K27 acetylation deposition and thereby reprogramed
the suppressive MDSCs to become inflammatory. This phenotypic change relied on the
inhibition of genes related to the STAT pathway, alongside immunosuppression mediators
such as Arg1 and iNOS [129].
4.4. Epigenetic Modulations of TIL T Cells
4.4.1. DNA Methylation in TIL T Cells
Alterations of DNA methylation patterns directly regulate TIL infiltration and function.
Distinct methylomes have been identified for different subsets of tumor-infiltrating T cells
through genome-wide methylation profiling [
130
]. Notably, reactive T cell populations
simultaneously showed specific demethylated patterns on both tumor-reactive marker
genes and exhaustion-associated genes, indicating that DNA methylation may be linked to
T cell identity.
The trafficking of effector T cells into a tumor relies on the production of Th1-type
chemokines, which is also critical for effective immunotherapy response. Peng et al. demon-
strated that DNMT1-mediated DNA methylation, in coordination with EZH2-mediated
H3K27 trimethylation, suppresses the level of Th1-type chemokines CXCL9 and CXCL10 in
an ovarian cancer model [
131
]. The concurrent inhibition of EZH2 and DNMT1, but not in-
dividual agents, significantly boosts T cell infiltration, slows down tumor progression, and
enhances the therapeutic response to the PD-L1 checkpoint blockade in tumor-bearing mice.
The infiltration of regulatory T cells is often linked to poorer responses to immunother-
apies and other cancer treatments [
132
,
133
]. Tregs necessitate a certain level of Foxp3 gene
expression for development and phenotypic maintenance. Yang et al. [
134
] reported that
TET1 and TET2 catalyze the conversion of 5mC to 5hmC in the Foxp3 gene in a lineage-
specific manner in Tregs, leading to Foxp3 gene hypomethylation and functional Treg
maintenance under immune homeostasis [
134
]. Similarly, reduced Foxp3 gene methylation
was observed in infiltrating Tregs, correlating with their abundance in liver cancer [
135
].
In mouse models, T cell-specific DNMT1 knockdown altered the methylation patterns of
Foxp3 promoter and CpG region and increased the number of infiltrating Tregs [
135
]. These
studies collectively support the critical role of DNA methylation in T cell lineage specifi-
cation and anti-tumor immune response. It is worth noting that the T cell-specific DNA
methylation pattern can serve as a sensitive approach to evaluating long-term survival or
immunotherapy benefits in cancer patients [136,137].
4.4.2. Histone Modifications and Chromatin Remodeling in TIL T Cells
Aberrant methylating patterns of histones correlate with the impaired antitumoral
immune responses of CD8
+
T cells in tumors. For example, in a recent study, Bian et al.
reported that tumor cells outcompete CD8
+
T cells for methionine consumption, resulting
in the loss of H3K79me2 marks in effector T cells [
138
]. This reduction in H3K79me2 levels
led to downregulated STAT5 expression, subsequently impairing T cell immunity against
cancer. Remarkably, methionine supplementation restored the defective H3K79me2–STAT5
axis in tumor-infiltrating CD8
+
T cells and significantly boosted the immune checkpoint
Biomolecules 2025,15, 71 12 of 25
blockade therapy in mouse models with syngeneic tumors [
138
]. Histone methylation can
also indirectly influence the function of CD8
+
T cells. As discussed earlier, the study led by
Peng et al. revealed that combined EZH2 inhibition with DNA methylation inhibition elicits
the secretion of Th1-type chemokines in tumors, amplifying the immune response against
cancer [
131
]. Moreover, another study from the same group found that knocking down
polycomb repressive complex 2 (PRC2) components other than EZH2 or overexpressing
the H3K27-specific demethylase JMJD3 significantly augments the production of Th1-type
chemokines in the TME [
139
]. EZH2 inactivation has been shown to specifically enhance
helper T cell differentiation by modifying H3K27me3 patterns at the promoters of Tbx21
and Gata3 genes [
140
]. SUV39H1, the histone methylase responsible for H3K9me3, has been
shown to be crucial for Th2 lineage identity [
141
]. SUV39H1 deficiency leads to the removal
of H3K9me3 marks at Th1 gene promoters, reducing HP1
α
binding at the same loci. This
event drives the re-expression of the Th1 gene and supports the trans-differentiation of
Th2 cells into Th1 cells [
141
]. Likewise, SETDB1 was demonstrated to regulate the lineage
integrity of helper T cells. SETDB1 knockout removes H3K9me3 marks from a Th1-specific
set of endogenous retroviruses, indirectly boosting Th1 gene expression in helper T cells
and promoting the acquisition of a Th1 phenotype [
142
]. However, whether these findings
can be generalized to tumor-infiltrating helper T cells and guide the optimization of current
immunotherapy remains largely unexplored.
TILs often experience exhaustion due to prolonged exposure to tumor antigens, and
this exhaustion can be attributed in part to acetylated modifications of histone proteins.
For instance, RNA splicing factor SRSF2 was found to be upregulated in exhausted T
cells [
143
]. The acetyl-transferase P300/CBP complex interacts with SRSF2, facilitating
the repositioning of acetylated H3K27 marks near immune checkpoint genes. This rear-
rangement affects STAT3 recruitment to the promoters of these genes, ultimately leading
to TIL exhaustion [
143
]. The fluctuations in cellular acetyl-CoA levels, the main substrate
for histone acetyltransferases, influence histone acetylation, which in turn impacts TIL
exhaustion. For example, in the low-glucose tumor microenvironment, acetate is an alter-
native carbon source for immune cells. Exhausted T cells uptake acetate and convert it
into acetyl-CoA. Acetyl-CoA fuels histone acetylation at restimulation-associated genes,
such as IFN-
γ
, leading to the re-expression of those effector genes and the revitalization
of effector T cells [
144
]. Extracellular potassium can also influence cellular acetyl-CoA
levels. Necrotic tumors release cellular contents, increasing the extracellular potassium
concentration and thereby impeding TIL’s uptake of nutrients [
145
]. This nutrient restric-
tion limits acetyl-CoA production in T cells, resulting in reduced histone acetylation in
genes associated with effector T cells. Interestingly, rather than entering into an exhaustion
phenotype, the authors concluded that the depletion of acetyl-CoA seems to reprogram T
cells toward a stem cell-like phenotype. Likewise, a recent study suggested that CD8
+
T
cells preferentially utilize ketone bodies for the synthesis of acetyl-CoA [
146
]. Effector T
cells exhibit a significant increase in ketolysis activity, which produces more acetyl-CoA.
This surplus acetyl-CoA fuels histone acetylation on effector genes and is required for the
optimal immune response of effector T cells [146].
Chromatin-remodelers also regulate TILs’ function. One example is the essential role
of CHD4, a subunit of the NuRD complex, for T cell development [
147
]. The expression
level of CHD4, also known as Mi-2
β
, is increased during T cell development. Notably, the
conditional knockout of CHD4 impairs various facets of T cell differentiation, including
β
-selection, CD4 lineage specification, and the expansion of mature T cells. While the
NuRD complex generally operates in transcriptional inactivation, CHD4 directly binds
to the enhancer of the Cd4 gene and enables Cd4 gene expression in developing T cells.
The binding of CHD4 facilitates the recruitment of the E-box binding protein HEB and
Biomolecules 2025,15, 71 13 of 25
histone acetyltransferase P300, ultimately creating a hyperacetylated histone H3 landscape
in this enhancer region. Such a landscape is indispensable for CD4 expression and T cell
lineage specification. It remains an intriguing question whether CHD4 functions here
independently of the entire NuRD complex [
147
]. Moreover, a recent study led by Belk et al.
systemically assessed the regulatory mechanisms of T cell exhaustion through genome-
wide CRISPR/Cas9 screening and unexpectedly uncovered the enrichment of subunits of
cBAF and the INO80 complex in this process [
148
]. Subsequent analysis suggested that
depleting these chromatin remodeling factors, particularly ARID1A, significantly improves
the anti-tumor immune response by decreasing exhaustion-related gene expression and
increasing the effector gene expression [148].
5. Epigenetic Therapies Target TME
Epigenetic regulators and their modifications are frequently altered in
cancers [149151]
.
Unlike genetic mutations, these epigenetic changes can often be reversed as enzymes or
chromatin-binding proteins responsible for these modifications are usually targetable. This
makes epigenetic therapy an appealing approach against cancers [
152
,
153
]. There are
various epigenetic therapies that have received FDA approval or are currently undergoing
clinical trials for both hematological and solid tumors [
154
,
155
]. Epigenetic drugs, such as
DNA methyltransferase inhibitors and histone modification inhibitors, hold promise for
transforming the TME from immunosuppressive to antitumoral by influencing stromal and
immune cells (Table 2). Here, we will discuss the prominent mechanisms through which
epigenetic drugs impact these cells in the TME.
Table 2. Epigenetic agents target TME.
Epigenetic Inhibitors Target Cell Type Within TME Reference
DNMT inhibitors
Decitabine+eugenol DNMT1/DNMT3A CAFS [78]
Guadecitabine DNMT1 MDSCs [121]
Decitabine DNMT1/DNMT3B CAFS/MDSCs [156]
5-AZA DNMTS CAFS/TAMs [157]
HKMT inhibitors
CPI-1205 EZH2 Tregs [158,159]
Dzenp EZH2 Tregs [160]
GSK126 EZH2 MDSCs [161]
HDAC inhibitors
Scriptaid HDAC1/3/8 CAFS [162]
CUDC-907 Pan-HDAC CAFS [163,164]
Entinostat Pan-HDAC MDSCs/Tregs [165]
SAHA HDAC1/2/3 CAFS/MDSCs [166,167]
CG-745 Pan-HDAC MDSCS/TAMS [168]
VPA HDAC1 MDSCs [169,170]
BET inhibitors
JQ1 BRD4 CAFs/Tregs [171,172]
CPI203 BRD2/3 Tregs [173]
5.1. DNA Methyltransferase Inhibitor
DNA methyltransferase inhibitors (DNMTi), such as 5-azacitidine (5-Aza), decitabine,
eugenol, and guadecitabine, have shown significant therapeutic potential in reshaping the
DNA methylation landscape of stromal and immune cells within the TME. As an example,
Al-Kharashi et al. demonstrated that treatment with decitabine or eugenol reduced the
proliferation, migration, and pro-tumoral effects of CAFs both
in vitro
and
in vivo
[
156
].
These compounds downregulated the expression of DNMT1 and DNMT3A at both the
Biomolecules 2025,15, 71 14 of 25
mRNA and protein levels in breast CAFs via E2F1 inactivation. Likewise, the DNMT
inhibitor 5-Aza disrupted the epigenetic reprogramming of CAFs in an inflammatory milieu,
restoring the normal fibroblast phenotype
in vivo
[
78
]. These findings suggest that DNMTi
can alter methylation patterns in active CAFs and restrain their pro-tumor phenotypes.
DNMTi could also reverse the immunosuppressive landscape via the repolarization of
TAMs in the TME [157].
In addition, DNMTi has demonstrated potential in preventing MDSC accumulation
in mouse models and cancer patients. Decitabine treatment prompted MDSCs to produce
TNF-
α
, leading to RIP1-dependent necroptosis and consequently reduced MDSC accumu-
lation in colorectal tumor-bearing mice [
174
]. In support of this, guadecitabine inhibited the
systemic accumulation of MDSCs in a murine breast tumor model, enhancing the efficacy
of adaptive immunotherapy by curbing MDSC proliferation and their immunosuppressive
characteristics [
121
]. In an ongoing clinical trial, the combination of guadecitabine with im-
mune checkpoint inhibitors (ICIs) showed durable clinical benefits in certain ovarian cancer
patients [
175
]. In these patients, the combined treatment caused global hypomethylation in
immune cells and the activation of antitumor immunity, as characterized by increased CD4
+
T cells and classical monocytes in tumors. DNMT inhibition can also contract the de novo
DNA methylation responsible for transforming effector T cells into exhausted T cells. By
blocking this process, DNMTi, when combined with the PD-1 blockade, rejuvenates CD8
+
T
cells, leading to a synergized anti-tumor effect by preventing CD8
+
T cell exhaustion [
176
].
Moreover, DNMT inhibition triggers antiviral defense mechanisms in both tumor and
immune cells, boosting type I interferon signaling, remodeling the suppressive immune
environment, and enhancing the efficacy of immune checkpoint blockade [177].
5.2. Histone Modification Inhibitors
While histone modification inhibitors are actively evaluated in clinical trials, their
effects on reshaping the TME in preclinical models remain controversial. EZH2 inhibitors,
for instance, have been shown to boost the antitumor immune response by activating
the expression of immunostimulatory factors, including type I IFN genes [
178
], antigen-
presenting machinery [
179
,
180
], and STING [
181
]. EZH2 is critical for the maintenance
of regulatory T cell identity following activation [
158
]. The EZH2 inhibitor CPI-1205
reprograms tumor-infiltrating Tregs into a pro-inflammatory Th1-like phenotype [
159
]. The
EZH2 inhibitor DZNep exerts a similar effect on Tregs, promoting an adaptive antitumor
immune response in nasopharyngeal cancer [
160
]. However, contradictory observations
have arisen regarding the effects of EZH2 inhibition. The EZH2 inhibitor GSK126 was
reported to direct myeloid differentiation and resulted in MDSC accumulation and TIL
exclusion in syngeneic mouse models of lung cancers and colon cancer [
161
]. Importantly,
the methyltransferase activity of EZH2 is required for functional effector T cells according
to a previous report [
182
]. EZH2 activates the Notch signaling pathway and stimulates the
secretion of effector cytokines that promote the survival of tumor-infiltrating CD8
+
T cells.
Thus, the EZH2 inhibitor could inadvertently suppress the function of effector T cells.
Similarly, conflicting findings surround the impact of HDAC inhibitors on the TME in
preclinical models. Scriptaid, an HDAC inhibitor, suppresses the conversion of endothelial
cells into CAFs, thereby impeding CAF-driven tumor growth
in vivo
[
162
]. Other HDAC
inhibitors have also been reported to inhibit CAF activation and tumor growth [
163
,
164
].
A low dose of adjuvant entinostat, combined with Aza, prevents cancer metastasis by
inhibiting MDSC recruitment and disrupting premetastatic niche formation in lung and
breast cancer models [
165
]. Other studies also demonstrate the suppression of MDSC
accumulation and the establishment of immunosuppressive phenotypes by HDAC in-
Biomolecules 2025,15, 71 15 of 25
hibitors [
166
168
]. However, earlier studies also suggest pro-tumoral microenvironmental
changes upon HDAC inhibition [169,170].
5.3. Chromatin Remodeler Modulators
Small molecules that selectively target chromatin remodelers are rare, and the studies
on their efficacy in reshaping TME are limited. For instance, the BET bromodomain inhibitor
JQ1 showed synthetically lethal effects with the HDAC6 inhibitor ricolinostat in preclinical
models of lung cancer [
183
]. This combination therapy enhanced MHC-II expression in
tumor-infiltrating myeloid cells and acted in an NK cell-dependent manner. Later, the same
group reported that JQ1 treatment inhibited the suppressive function of Tregs and therefore
synergized with HDAC inhibition in lung cancer [
171
]. JQ1 treatment was also shown to
reduce pancreatic tumor growth by suppressing the tumor-promoting effects of CAFs [
172
].
The BET inhibitor CPI203 yields similar effects on the stromal content of pancreatic cancer
models, likely by blocking the GLI-SHH paracrine loop [173].
6. Conclusions
There are several reasons why caution must be exercised when applying epigenetic
therapies in real clinical practice. First of all, epigenetic reagents typically target a similar
catalytic domain rather than a specific protein, which may result in inhibitory effects
on multiple proteins with distinct functions. Additionally, the inadvertent targeting of
epigenetic agents to irrelevant proteins is not uncommon. For instance, 5-Aza has been
found to bind directly to the cholesterol transporter ABCA9, reprogramming TAMs through
a DNA methylation-independent mechanism [
184
]. It is even more complicated when
considering the non-canonical functions of epigenetic proteins. For example, the enzymatic
and non-enzymatic activities of the EZH2 protein have been reported to exert contrasting
regulatory effects on TAM polarization [
185
]. Moreover, histone modification enzymes
are known to catalyze lysine methylation or acetylation not only on histone proteins but
also on non-histone proteins, thereby adding an additional layer of regulating mechanisms
within TME [
27
,
186
]. Lastly, while a solitary epigenetic modification can exert certain
functions, the transcriptional regulation of a particular gene often involves combinational
or sequential modifications on local chromatin and distant regulatory elements. This
highlights the necessity of evaluating the impact of combined epigenetic agents for effective
cancer treatment.
Despite the aforementioned limitations, epigenetic enzymes hold significant promise
as targets of novel cancer therapies. Single-cell omics technology has revolutionized our
ability to identify and characterize distinct cellular components, as well as comprehensively
analyze the evolving dynamics of tumor microenvironments. In this review, we have
summarized the well-established knowledge and recent advancements concerning the
epigenetic regulation of major cellular components within tumors (Figure 2). The progress
of cutting-edge technologies and innovative preclinical models is poised to deepen our
understanding of the TME, as well as the spatiotemporal patterns of the epigenome, which
could yield novel insights into the epigenetic regulation of the TME, potentially lead-
ing to optimized epigenetic therapies for cancer treatment. For example, the Assay for
Transposase-Accessible Chromatin using sequencing (ATAC-seq) provides valuable in-
sights into the TME by mapping accessible chromatin regions, which are essential for
understanding epigenetic regulation in cancer [
187
]. By revealing how epigenetic mod-
ifications affect cellular behavior and communication between tumor and stromal cells,
ATAC-seq helps identify potential therapeutic targets [
188
]. This technique enhances the
ability to develop targeted epigenetic therapies by elucidating the intricate relationship be-
tween chromatin structure and gene regulation within the TME, ultimately paving the way
Biomolecules 2025,15, 71 16 of 25
for more effective and personalized cancer treatments [
189
,
190
]. Given the potent impact of
epigenetic agents in normalizing the tumor immune microenvironment, we can anticipate
the emergence of innovative therapeutic paradigms that harness the synergistic potential
of epigenetic agents and immunotherapies, propelling cancer treatment to new heights.
Biomolecules 2025, 15, x FOR PEER REVIEW 16 of 26
have summarized the well-established knowledge and recent advancements concerning
the epigenetic regulation of major cellular components within tumors (Figure 2). The pro-
gress of cuing-edge technologies and innovative preclinical models is poised to deepen
our understanding of the TME, as well as the spatiotemporal paerns of the epigenome,
which could yield novel insights into the epigenetic regulation of the TME, potentially
leading to optimized epigenetic therapies for cancer treatment. For example, the Assay for
Transposase-Accessible Chromatin using sequencing (ATAC-seq) provides valuable in-
sights into the TME by mapping accessible chromatin regions, which are essential for un-
derstanding epigenetic regulation in cancer [187]. By revealing how epigenetic modica-
tions aect cellular behavior and communication between tumor and stromal cells,
ATAC-seq helps identify potential therapeutic targets [188]. This technique enhances the
ability to develop targeted epigenetic therapies by elucidating the intricate relationship
between chromatin structure and gene regulation within the TME, ultimately paving the
way for more eective and personalized cancer treatments [189,190]. Given the potent
impact of epigenetic agents in normalizing the tumor immune microenvironment, we can
anticipate the emergence of innovative therapeutic paradigms that harness the synergistic
potential of epigenetic agents and immunotherapies, propelling cancer treatment to new
heights.
Figure 2. The main mechanisms by which epigenetic modulations remodel the TME. Aberrant epi-
genetic modulations of relevant genes in stroma and immune cells have diverse eects in reframing
the TME. For instance, LIF increases DNMT3B expression to hypermethylate the Shp-1 promoter
[78], thereby activating and maintaining the JAK1/STAT3 pathway via DNMT1 [80]. Proteins such
as NNMT [82], CTGF [85], and HSPC111 [86] regulate CAF activation through histone modica-
tions. Epigenetic factors, including DNMT3B [92], DNMT1 [93], TET1 [95,96], JMJD3 [102,103], LSD1
[108–110], and HDAC11 [114], reprogram macrophages by enhancing the mRNA expression of
PPARγ1 and promoting cytokine secretion. Additionally, DNMT1 [120], DNMT3B [121], CBP [123–
125], SETDB1 [126] and HDAC11 [127] control MDSC accumulation. Together, DNMT1 and EZH2
suppress Th1-type chemokines CXCL9 and CXCL10 [131]. In Tregs, TET1 and TET2 convert 5mC to
Figure 2. The main mechanisms by which epigenetic modulations remodel the TME. Aberrant epige-
netic modulations of relevant genes in stroma and immune cells have diverse effects in reframing the
TME. For instance, LIF increases DNMT3B expression to hypermethylate the Shp-1 promoter [
78
],
thereby activating and maintaining the JAK1/STAT3 pathway via DNMT1 [
80
]. Proteins such
as NNMT [
82
], CTGF [
85
], and HSPC111 [
86
] regulate CAF activation through histone modifica-
tions. Epigenetic factors, including DNMT3B [
92
], DNMT1 [
93
], TET1 [
95
,
96
], JMJD3 [
102
,
103
],
LSD1 [108110]
, and HDAC11 [
114
], reprogram macrophages by enhancing the mRNA expres-
sion of PPAR
γ
1 and promoting cytokine secretion. Additionally, DNMT1 [
120
], DNMT3B [
121
],
CBP [123125]
, SETDB1 [
126
] and HDAC11 [
127
] control MDSC accumulation. Together, DNMT1
and EZH2 suppress Th1-type chemokines CXCL9 and CXCL10 [
131
]. In Tregs, TET1 and TET2
convert 5mC to 5hmC in the Foxp3 gene promoter, ensuring its hypomethylation and functional
integrity [
134
,
135
]. SUV39H1 and SETDB1 regulate T cell differentiation through H3K9me3 modifica-
tions [
141
,
142
]. Furthermore, The P300/CBP complex, interacting with SRSF2, repositions acetylated
H3K27 marks near immune checkpoint genes, which affects STAT3 recruitment and leads to T
cell exhaustion [
143
]. The fluctuations in cellular acetyl-CoA levels, the main substrate for histone
acetyltransferases, influence histone acetylation, which in turn impact TIL exhaustion [
145
,
146
].
Chromatin-remodelers such as NuRD complex [
147
] and ARID1A [
148
] also regulate TILs’ function.
For detailed information on these mechanisms, see the references provided.
Author Contributions: B.Z. and N.L. conceived the study. K.L., Y.L., B.Z. and N.L. wrote the original
manuscript draft. M.S., W.X., S.W. and X.Y. provided some suggestions for the creation of the figures.
All authors have read and agreed to the published version of the manuscript.
Funding: This research received no external funding.
Institutional Review Board Statement: Not applicable.
Biomolecules 2025,15, 71 17 of 25
Informed Consent Statement: Not applicable.
Data Availability Statement: No new data were created or analyzed in this study.
Conflicts of Interest: The authors declare no conflict of interest.
References
1.
Seferbekova, Z.; Lomakin, A.; Yates, L.R.; Gerstung, M. Spatial biology of cancer evolution. Nat. Rev. Genet. 2023,24, 295–313.
[CrossRef] [PubMed]
2.
Xiao, Y.; Yu, D. Tumor microenvironment as a therapeutic target in cancer. Pharmacol. Ther. 2021,221, 107753. [CrossRef]
[PubMed]
3. Arneth, B. Tumor Microenvironment. Medicina 2019,56, 15. [CrossRef]
4. Hanahan, D. Hallmarks of Cancer: New Dimensions. Cancer Discov. 2022,12, 31–46. [CrossRef] [PubMed]
5.
Harvey, Z.H.; Chen, Y.; Jarosz, D.F. Protein-Based Inheritance: Epigenetics beyond the Chromosome. Mol. Cell 2018,69, 195–202.
[CrossRef] [PubMed]
6. Recillas-Targa, F. Cancer Epigenetics: An Overview. Arch. Med. Res. 2022,53, 732–740. [CrossRef] [PubMed]
7.
Mendes, B.B.; Sousa, D.P.; Conniot, J.; Conde, J. Nanomedicine-based strategies to target and modulate the tumor microenviron-
ment. Trends Cancer 2021,7, 847–862. [CrossRef]
8. Bates, S.E. Epigenetic Therapies for Cancer. N. Engl. J. Med. 2020,383, 650–663. [CrossRef]
9.
Yang, J.; Xu, J.; Wang, W.; Zhang, B.; Yu, X.; Shi, S. Epigenetic regulation in the tumor microenvironment: Molecular mechanisms
and therapeutic targets. Signal Transduct. Target. Ther. 2023,8, 210. [CrossRef] [PubMed]
10.
Hogg, S.J.; Beavis, P.A.; Dawson, M.A.; Johnstone, R.W. Targeting the epigenetic regulation of antitumour immunity. Nat. Rev.
Drug Discov. 2020,19, 776–800. [CrossRef] [PubMed]
11.
Dai, E.; Zhu, Z.; Wahed, S.; Qu, Z.; Storkus, W.J.; Guo, Z.S. Epigenetic modulation of antitumor immunity for improved cancer
immunotherapy. Mol. Cancer 2021,20, 171. [CrossRef]
12.
Song, H.; Liu, D.; Dong, S.; Zeng, L.; Wu, Z.; Zhao, P.; Zhang, L.; Chen, Z.-S.; Zou, C. Epitranscriptomics and epiproteomics in
cancer drug resistance: Therapeutic implications. Signal Transduct. Target. Ther. 2020,5, 193. [CrossRef] [PubMed]
13.
Turk, A.; ˇ
Ceh, E.; Calin, G.A.; Kunej, T. Multiple omics levels of chronic lymphocytic leukemia. Cell Death Discov. 2024,10, 293.
[CrossRef] [PubMed]
14.
Mattei, A.L.; Bailly, N.; Meissner, A. DNA methylation: A historical perspective. Trends Genet. 2022,38, 676–707. [CrossRef]
[PubMed]
15.
Horvath, S.; Raj, K. DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat. Rev. Genet. 2018,19,
371–384. [CrossRef]
16.
Li, E.; Bestor, T.H.; Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 1992,69,
915–926. [CrossRef] [PubMed]
17. Liu, K.; Shimbo, T.; Song, X.; Wade, P.A.; Min, J. Proteins That Read DNA Methylation. Adv. Exp. Med. Biol. 2022,1389, 269–293.
18.
Bray, J.K.; Dawlaty, M.M.; Verma, A.; Maitra, A. Roles and Regulations of TET Enzymes in Solid Tumors. Trends Cancer 2021,7,
635–646. [CrossRef] [PubMed]
19.
Nishiyama, A.; Nakanishi, M. Navigating the DNA methylation landscape of cancer. Trends Genet. 2021,37, 1012–1027. [CrossRef]
[PubMed]
20.
Zhang, Y.; Sun, Z.; Jia, J.; Du, T.; Zhang, N.; Tang, Y.; Fang, Y.; Fang, D. Overview of Histone Modification. Adv. Exp. Med. Biol.
2021,1283, 1–16.
21.
Neganova, M.E.; Klochkov, S.G.; Aleksandrova, Y.R.; Aliev, G. Histone modifications in epigenetic regulation of cancer: Perspec-
tives and achieved progress. Semin. Cancer Biol. 2022,83, 452–471. [CrossRef]
22.
Mushtaq, A.; Mir, U.S.; Hunt, C.R.; Pandita, S.; Tantray, W.W.; Bhat, A.; Pandita, R.K.; Altaf, M.; Pandita, T.K. Role of Histone
Methylation in Maintenance of Genome Integrity. Genes 2021,12, 1000. [CrossRef]
23.
Li, Y.; Chen, X.; Lu, C. The interplay between DNA and histone methylation: Molecular mechanisms and disease implications.
EMBO Rep. 2021,22, e51803. [CrossRef]
24.
Husmann, D.; Gozani, O. Histone lysine methyltransferases in biology and disease. Nat. Struct. Mol. Biol. 2019,26, 880–889.
[CrossRef] [PubMed]
25.
Hyun, K.; Jeon, J.; Park, K.; Kim, J. Writing, erasing and reading histone lysine methylations. Exp. Mol. Med. 2017,49, e324.
[CrossRef] [PubMed]
26.
Yang, J.; Hu, Y.; Zhang, B.; Liang, X.; Li, X. The JMJD Family Histone Demethylases in Crosstalk Between Inflammation and
Cancer. Front. Immunol. 2022,13, 881396. [CrossRef] [PubMed]
27.
Shvedunova, M.; Akhtar, A. Modulation of cellular processes by histone and non-histone protein acetylation. Nat. Rev. Mol. Cell
Biol. 2022,23, 329–349. [CrossRef]
Biomolecules 2025,15, 71 18 of 25
28.
Minisini, M.; Mascaro, M.; Brancolini, C. HDAC-driven mechanisms in anticancer resistance: Epigenetics and beyond. Cancer
Drug Resist. 2024,7, 46. [CrossRef] [PubMed]
29.
Schizas, D.; Mastoraki, A.; Naar, L.; Tsilimigras, D.I.; Katsaros, I.; Fragkiadaki, V.; Karachaliou, G.-S.; Arkadopoulos, N.; Liakakos,
T.; Moris, D. Histone Deacetylases (HDACs) in Gastric Cancer: An Update of their Emerging Prognostic and Therapeutic Role.
Curr. Med. Chem. 2020,27, 6099–6111. [CrossRef]
30.
Gold, S.; Shilatifard, A. Therapeutic targeting of BET bromodomain and other epigenetic acetylrecognition domain-containing
factors. Curr. Opin. Genet. Dev. 2024,86, 102181. [CrossRef] [PubMed]
31.
Rhodes, D. To slide or not to slide: Key role of the hexasome in chromatin remodeling revealed. Nat. Struct. Mol. Biol. 2024,31,
742–746. [CrossRef]
32.
Mashtalir, N.; D’avino, A.R.; Michel, B.C.; Luo, J.; Pan, J.; Otto, J.E.; Zullow, H.J.; McKenzie, Z.M.; Kubiak, R.L.; Pierre, R.S.; et al.
Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes. Cell 2018,175, 1272–1288.e20.
[CrossRef] [PubMed]
33.
Malone, H.A.; Roberts, C.W.M. Chromatin remodellers as therapeutic targets. Nat. Rev. Drug Discov. 2024,23, 661–681. [CrossRef]
[PubMed]
34.
Kadoch, C. Diverse compositions and functions of chromatin remodeling machines in cancer. Sci. Transl. Med. 2019,11, eaay1018.
[CrossRef]
35.
de Visser, K.E.; Joyce, J.A. The evolving tumor microenvironment: From cancer initiation to metastatic outgrowth. Cancer Cell
2023,41, 374–403. [CrossRef] [PubMed]
36.
Toninelli, M.; Rossetti, G.; Pagani, M. Charting the tumor microenvironment with spatial profiling technologies. Trends Cancer
2023,9, 1085–1096. [CrossRef]
37.
Elhanani, O.; Ben-Uri, R.; Keren, L. Spatial profiling technologies illuminate the tumor microenvironment. Cancer Cell 2023,41,
404–420. [CrossRef]
38.
Polak, R.; Zhang, E.T.; Kuo, C.J. Cancer organoids 2.0: Modelling the complexity of the tumour immune microenvironment. Nat.
Rev. Cancer 2024,24, 523–539. [CrossRef]
39.
Sahai, E.; Astsaturov, I.; Cukierman, E.; DeNardo, D.G.; Egeblad, M.; Evans, R.M.; Fearon, D.; Greten, F.R.; Hingorani, S.R.;
Hunter, T.; et al. A framework for advancing our understanding of cancer-associated fibroblasts. Nat. Rev. Cancer 2020,20,
174–186. [CrossRef]
40.
Desbois, M.; Wang, Y. Cancer-associated fibroblasts: Key players in shaping the tumor immune microenvironment. Immunol. Rev.
2021,302, 241–258. [CrossRef] [PubMed]
41. Tsoumakidou, M. The advent of immune stimulating CAFs in cancer. Nat. Rev. Cancer 2023,23, 258–269. [CrossRef] [PubMed]
42.
Liao, Z.; Tan, Z.W.; Zhu, P.; Tan, N.S. Cancer-associated fibroblasts in tumor microenvironment—Accomplices in tumor malig-
nancy. Cell Immunol. 2019,343, 103729. [CrossRef] [PubMed]
43.
Chen, Y.; McAndrews, K.M.; Kalluri, R. Clinical and therapeutic relevance of cancer-associated fibroblasts. Nat. Rev. Clin. Oncol.
2021,18, 792–804. [CrossRef]
44. Cassetta, L.; Pollard, J.W. Tumor-associated macrophages. Curr. Biol. 2020,30, R246–R248. [CrossRef] [PubMed]
45.
Zhu, Y.; Herndon, J.M.; Sojka, D.K.; Kim, K.W.; Knolhoff, B.L.; Zuo, C.; Cullinan, D.R.; Luo, J.; Bearden, A.R.; Lavine, K.J.; et al.
Tissue-Resident Macrophages in Pancreatic Ductal Adenocarcinoma Originate from Embryonic Hematopoiesis and Promote
Tumor Progression. Immunity 2017,47, 323–338.e6. [CrossRef] [PubMed]
46.
Malik, S.; Sureka, N.; Ahuja, S.; Aden, D.; Zaheer, S.; Zaheer, S. Tumor-associated macrophages: A sentinel of innate immune
system in tumor microenvironment gone haywire. Cell Biol. Int. 2024,48, 1406–1449. [CrossRef] [PubMed]
47.
McWhorter, R.; Bonavida, B. The Role of TAMs in the Regulation of Tumor Cell Resistance to Chemotherapy. Crit. Rev. Oncog.
2024,29, 97–125. [CrossRef]
48.
Li, S.; Sheng, J.; Zhang, D.; Qin, H. Targeting tumor-associated macrophages to reverse antitumor drug resistance. Aging 2024,16,
10165–10196. [CrossRef] [PubMed]
49.
Najafi, M.; Hashemi Goradel, N.; Farhood, B.; Salehi, E.; Nashtaei, M.S.; Khanlarkhani, N.; Khezri, Z.; Majidpoor, J.; Abouzaripour,
M.; Habibi, M.; et al. Macrophage polarity in cancer: A review. J. Cell Biochem. 2019,120, 2756–2765. [CrossRef]
50.
Rajkumari, S.; Singh, J.; Agrawal, U.; Agrawal, S. Myeloid-derived suppressor cells in cancer: Current knowledge and future
perspectives. Int. Immunopharmacol. 2024,142, 112949. [CrossRef]
51.
Lasser, S.A.; Ozbay Kurt, F.G.; Arkhypov, I.; Utikal, J.; Umansky, V. Myeloid-derived suppressor cells in cancer and cancer therapy.
Nat. Rev. Clin. Oncol. 2024,21, 147–164. [CrossRef]
52.
Adeshakin, A.O.; Liu, W.; Adeshakin, F.O.; Afolabi, L.O.; Zhang, M.; Zhang, G.; Wang, L.; Li, Z.; Lin, L.; Cao, Q.; et al.
Regulation of ROS in myeloid-derived suppressor cells through targeting fatty acid transport protein 2 enhanced anti-PD-L1
tumor immunotherapy. Cell Immunol. 2021,362, 104286. [CrossRef]
53.
Jachetti, E.; Sangaletti, S.; Chiodoni, C.; Ferrara, R.; Colombo, M.P. Modulation of PD-1/PD-L1 axis in myeloid-derived suppressor
cells by anti-cancer treatments. Cell Immunol. 2021,362, 104301. [CrossRef] [PubMed]
Biomolecules 2025,15, 71 19 of 25
54.
Zhao, H.; Teng, D.; Yang, L.; Xu, X.; Chen, J.; Jiang, T.; Feng, A.Y.; Zhang, Y.; Frederick, D.T.; Gu, L.; et al. Myeloid-derived
itaconate suppresses cytotoxic CD8+ T cells and promotes tumour growth. Nat. Metab. 2022,4, 1660–1673. [CrossRef]
55.
Azzaoui, I.; Uhel, F.; Rossille, D.; Pangault, C.; Dulong, J.; Le Priol, J.; Lamy, T.; Houot, R.; Le Gouill, S.; Cartron, G.; et al. T-cell
defect in diffuse large B-cell lymphomas involves expansion of myeloid-derived suppressor cells. Blood 2016,128, 1081–1092.
[CrossRef] [PubMed]
56.
Kapor, S.; Radojkovi´c, M.; Santibanez, J.F. Myeloid-derived suppressor cells: Implication in myeloid malignancies and im-
munotherapy. Acta Histochem. 2024,126, 152183. [CrossRef] [PubMed]
57.
Peng, S.; Lin, A.; Jiang, A.; Zhang, C.; Zhang, J.; Cheng, Q.; Luo, P.; Bai, Y. CTLs heterogeneity and plasticity: Implications for
cancer immunotherapy. Mol. Cancer 2024,23, 58. [CrossRef] [PubMed]
58. Maimela, N.R.; Liu, S.; Zhang, Y. Fates of CD8+ T cells in Tumor Microenvironment. Comput. Struct. Biotechnol. J. 2019,17, 1–13.
[CrossRef]
59. Speiser, D.E.; Chijioke, O.; Schaeuble, K.; Münz, C. CD4+T cells in cancer. Nat. Cancer 2023,4, 317–329. [CrossRef]
60.
Ruterbusch, M.; Pruner, K.B.; Shehata, L.; Pepper, M. In Vivo CD4+ T Cell Differentiation and Function: Revisiting the Th1/Th2
Paradigm. Annu. Rev. Immunol. 2020,38, 705–725. [CrossRef] [PubMed]
61.
Li, C.; Jiang, P.; Wei, S.; Xu, X.; Wang, J. Regulatory T cells in tumor microenvironment: New mechanisms, potential therapeutic
strategies and future prospects. Mol. Cancer 2020,19, 116. [CrossRef] [PubMed]
62.
Wang, Y.; Huang, T.; Gu, J.; Lu, L. Targeting the metabolism of tumor-infiltrating regulatory T cells. Trends Immunol. 2023,44,
598–612. [CrossRef]
63.
Kyrysyuk, O.; Wucherpfennig, K.W. Designing Cancer Immunotherapies That Engage T Cells and NK Cells. Annu. Rev. Immunol.
2023,41, 17–38. [CrossRef] [PubMed]
64.
Vivier, E.; Rebuffet, L.; Narni-Mancinelli, E.; Cornen, S.; Igarashi, R.Y.; Fantin, V.R. Natural killer cell therapies. Nature 2024,626,
727–736. [CrossRef]
65.
Ruffin, A.T.; Cillo, A.R.; Tabib, T.; Liu, A.; Onkar, S.; Kunning, S.R.; Lampenfeld, C.; Atiya, H.I.; Abecassis, I.; Kürten, C.H.L.;
et al. B cell signatures and tertiary lymphoid structures contribute to outcome in head and neck squamous cell carcinoma. Nat.
Commun. 2021,12, 3349. [CrossRef]
66.
Downs-Canner, S.M.; Meier, J.; Vincent, B.G.; Serody, J.S. B Cell Function in the Tumor Microenvironment. Annu. Rev. Immunol.
2022,40, 169–193. [CrossRef]
67.
Qayoom, H.; Sofi, S.; Mir, M.A. Targeting tumor microenvironment using tumor-infiltrating lymphocytes as therapeutics against
tumorigenesis. Immunol. Res. 2023,71, 588–599. [CrossRef] [PubMed]
68.
Farhood, B.; Najafi, M.; Mortezaee, K. CD8
+
cytotoxic T lymphocytes in cancer immunotherapy: A review. J. Cell Physiol. 2019,
234, 8509–8521. [CrossRef] [PubMed]
69.
Saw, P.E.; Chen, J.; Song, E. Targeting CAFs to overcome anticancer therapeutic resistance. Trends Cancer 2022,8, 527–555.
[CrossRef]
70.
Madar, S.; Goldstein, I.; Rotter, V. ‘Cancer associated fibroblasts’—More than meets the eye. Trends Mol. Med. 2013,19, 447–453.
[CrossRef]
71.
Su, S.-F.; Ho, H.; Li, J.-H.; Wu, M.-F.; Wang, H.-C.; Yeh, H.-Y.; Kuo, S.-W.; Chen, H.-W.; Ho, C.-C.; Li, K.-C. DNA methylome and
transcriptome landscapes of cancer-associated fibroblasts reveal a smoking-associated malignancy index. J. Clin. Investig. 2021,
131, e139552. [CrossRef] [PubMed]
72.
Dong, J.; Wang, F.; Gao, X.; Zhao, H.; Zhang, J.; Wang, N.; Liu, Z.; Yan, X.; Jin, J.; Ba, Y.; et al. Integrated analysis of genome-wide
DNA methylation and cancer-associated fibroblasts identified prognostic biomarkers and immune checkpoint blockade in lower
grade gliomas. Front. Oncol. 2022,12, 977251. [CrossRef] [PubMed]
73.
Schmidt, M.; Maié, T.; Cramer, T.; Costa, I.G.; Wagner, W. Cancer-associated fibroblasts reveal aberrant DNA methylation across
different types of cancer. Clin. Epigenet. 2024,16, 164. [CrossRef]
74.
Pidsley, R.; Lawrence, M.G.; Zotenko, E.; Niranjan, B.; Statham, A.; Song, J.; Chabanon, R.M.; Qu, W.; Wang, H.; Richards, M.;
et al. Enduring epigenetic landmarks define the cancer microenvironment. Genome Res. 2018,28, 625–638. [CrossRef]
75.
Halperin, C.; Hey, J.; Weichenhan, D.; Stein, Y.; Mayer, S.; Lutsik, P.; Plass, C.; Scherz-Shouval, R. Global DNA Methylation
Analysis of Cancer-Associated Fibroblasts Reveals Extensive Epigenetic Rewiring Linked with RUNX1 Upregulation in Breast
Cancer Stroma. Cancer Res. 2022,82, 4139–4152. [CrossRef] [PubMed]
76.
Mathot, P.; Grandin, M.; Devailly, G.; Souaze, F.; Cahais, V.; Moran, S.; Campone, M.; Herceg, Z.; Esteller, M.; Juin, P.; et al. DNA
methylation signal has a major role in the response of human breast cancer cells to the microenvironment. Oncogenesis 2017,6,
e390. [CrossRef] [PubMed]
77.
Albrengues, J.; Bourget, I.; Pons, C.; Butet, V.; Hofman, P.; Tartare-Deckert, S.; Feral, C.C.; Meneguzzi, G.; Gaggioli, C. LIF
mediates proinvasive activation of stromal fibroblasts in cancer. Cell Rep. 2014,7, 1664–1678. [CrossRef] [PubMed]
Biomolecules 2025,15, 71 20 of 25
78.
Albrengues, J.; Bertero, T.; Grasset, E.; Bonan, S.; Maiel, M.; Bourget, I.; Philippe, C.; Herraiz Serrano, C.; Benamar, S.; Croce, O.;
et al. Epigenetic switch drives the conversion of fibroblasts into proinvasive cancer-associated fibroblasts. Nat. Commun. 2015,6,
10204. [CrossRef]
79.
Xiao, Q.; Zhou, D.; Rucki, A.A.; Williams, J.; Zhou, J.; Mo, G.; Murphy, A.; Fujiwara, K.; Kleponis, J.; Salman, B.; et al. Cancer-
Associated Fibroblasts in Pancreatic Cancer Are Reprogrammed by Tumor-Induced Alterations in Genomic DNA Methylation.
Cancer Res. 2016,76, 5395–5404. [CrossRef]
80.
Becker, L.M.; O’Connell, J.T.; Vo, A.P.; Cain, M.P.; Tampe, D.; Bizarro, L.; Sugimoto, H.; McGow, A.K.; Asara, J.M.; Lovisa, S.; et al.
Epigenetic Reprogramming of Cancer-Associated Fibroblasts Deregulates Glucose Metabolism and Facilitates Progression of
Breast Cancer. Cell Rep. 2020,31, 107701. [CrossRef] [PubMed]
81.
Tyan, S.-W.; Hsu, C.-H.; Peng, K.-L.; Chen, C.-C.; Kuo, W.-H.; Lee, E.Y.-H.P.; Shew, J.-Y.; Chang, K.-J.; Juan, L.-J.; Lee, W.-H. Breast
cancer cells induce stromal fibroblasts to secrete ADAMTS1 for cancer invasion through an epigenetic change. PLoS ONE 2012,7,
e35128. [CrossRef] [PubMed]
82.
Eckert, M.A.; Coscia, F.; Chryplewicz, A.; Chang, J.W.; Hernandez, K.M.; Pan, S.; Tienda, S.M.; Nahotko, D.A.; Li, G.; Blaženovi´c,
I.; et al. Proteomics reveals NNMT as a master metabolic regulator of cancer-associated fibroblasts. Nature 2019,569, 723–728.
[CrossRef]
83.
Yamamoto, J.; Han, Q.; Inubushi, S.; Sugisawa, N.; Hamada, K.; Nishino, H.; Miyake, K.; Kumamoto, T.; Matsuyama, R.; Bouvet,
M.; et al. Histone methylation status of H3K4me3 and H3K9me3 under methionine restriction is unstable in methionine-addicted
cancer cells, but stable in normal cells. Biochem. Biophys. Res. Commun. 2020,533, 1034–1038. [CrossRef] [PubMed]
84.
Yasukawa, Y.; Hattori, N.; Iida, N.; Takeshima, H.; Maeda, M.; Kiyono, T.; Sekine, S.; Seto, Y.; Ushijima, T. SAA1 is upregulated in
gastric cancer-associated fibroblasts possibly by its enhancer activation. Carcinogenesis 2021,42, 180–189. [CrossRef] [PubMed]
85.
Wang, Y.; Tu, K.; Liu, D.; Guo, L.; Chen, Y.; Li, Q.; Maiers, J.L.; Liu, Z.; Shah, V.H.; Dou, C.; et al. p300 Acetyltransferase Is a
Cytoplasm-to-Nucleus Shuttle for SMAD2/3 and TAZ Nuclear Transport in Transforming Growth Factor
β
-Stimulated Hepatic
Stellate Cells. Hepatology 2019,70, 1409–1423. [CrossRef]
86.
Zhang, C.; Wang, X.-Y.; Zhang, P.; He, T.-C.; Han, J.-H.; Zhang, R.; Lin, J.; Fan, J.; Lu, L.; Zhu, W.-W.; et al. Cancer-derived exosomal
HSPC111 promotes colorectal cancer liver metastasis by reprogramming lipid metabolism in cancer-associated fibroblasts. Cell
Death Dis. 2022,13, 57. [CrossRef]
87.
Aprelikova, O.; Yu, X.; Palla, J.; Wei, B.R.; John, S.; Yi, M.; Stephens, R.; Simpson, R.M.; Risinger, J.I.; Jazaeri, A.; et al. The role of
miR-31 and its target gene SATB2 in cancer-associated fibroblasts. Cell Cycle 2010,9, 4387–4398. [CrossRef] [PubMed]
88.
Kim, D.E.; Procopio, M.-G.; Ghosh, S.; Jo, S.-H.; Goruppi, S.; Magliozzi, F.; Bordignon, P.; Neel, V.; Angelino, P.; Dotto, G.P.
Convergent roles of ATF3 and CSL in chromatin control of cancer-associated fibroblast activation. J. Exp. Med. 2017,214,
2349–2368. [CrossRef]
89.
Campos Gudiño, R.; McManus, K.J.; Hombach-Klonisch, S. Aberrant HMGA2 Expression Sustains Genome Instability That
Promotes Metastasis and Therapeutic Resistance in Colorectal Cancer. Cancers 2023,15, 1735. [CrossRef] [PubMed]
90.
Strell, C.; Norberg, K.J.; Mezheyeuski, A.; Schnittert, J.; Kuninty, P.R.; Moro, C.F.; Paulsson, J.; Schultz, N.A.; Calatayud, D.; Löhr,
J.M.; et al. Stroma-regulated HMGA2 is an independent prognostic marker in PDAC and AAC. Br. J. Cancer 2017,117, 65–77.
[CrossRef]
91.
Zong, Y.; Huang, J.; Sankarasharma, D.; Morikawa, T.; Fukayama, M.; Epstein, J.I.; Chada, K.K.; Witte, O.N. Stromal epigenetic
dysregulation is sufficient to initiate mouse prostate cancer via paracrine Wnt signaling. Proc. Natl. Acad. Sci. USA 2012,109,
E3395–E3404. [CrossRef]
92.
Yang, X.; Wang, X.; Liu, D.; Yu, L.; Xue, B.; Shi, H. Epigenetic regulation of macrophage polarization by DNA methyltransferase
3b. Mol. Endocrinol. 2014,28, 565–574. [CrossRef] [PubMed]
93.
Cheng, C.; Huang, C.; Ma, T.-T.; Bian, E.-B.; He, Y.; Zhang, L.; Li, J. SOCS1 hypermethylation mediated by DNMT1 is associated
with lipopolysaccharide-induced inflammatory cytokines in macrophages. Toxicol. Lett. 2014,225, 488–497. [CrossRef] [PubMed]
94.
Zhang, M.; Pan, X.; Fujiwara, K.; Jurcak, N.; Muth, S.; Zhou, J.; Xiao, Q.; Li, A.; Che, X.; Li, Z.; et al. Pancreatic cancer cells render
tumor-associated macrophages metabolically reprogrammed by a GARP and DNA methylation-mediated mechanism. Signal
Transduct. Target. Ther. 2021,6, 366. [CrossRef]
95.
Huang, Y.; Tian, C.; Li, Q.; Xu, Q. TET1 Knockdown Inhibits Porphyromonas gingivalis LPS/IFN-
γ
-Induced M1 Macrophage
Polarization through the NF-κB Pathway in THP-1 Cells. Int. J. Mol. Sci. 2019,20, 2023. [CrossRef] [PubMed]
96.
Sun, F.; Abreu-Rodriguez, I.; Ye, S.; Gay, S.; Distler, O.; Neidhart, M.; Karouzakis, E. TET1 is an important transcriptional activator
of TNFαexpression in macrophages. PLoS ONE 2019,14, e0218551. [CrossRef]
97.
Fuster, J.J.; MacLauchlan, S.; Zuriaga, M.A.; Polackal, M.N.; Ostriker, A.C.; Chakraborty, R.; Wu, C.-L.; Sano, S.; Muralidharan, S.;
Rius, C.; et al. Clonal hematopoiesis associated with TET2 deficiency accelerates atherosclerosis development in mice. Science
2017,355, 842–847. [CrossRef] [PubMed]
98.
Cull, A.H.; Snetsinger, B.; Buckstein, R.; Wells, R.A.; Rauh, M.J. Tet2 restrains inflammatory gene expression in macrophages. Exp.
Hematol. 2017,55, 56–70.e13. [CrossRef] [PubMed]
Biomolecules 2025,15, 71 21 of 25
99.
Zhang, Q.; Zhao, K.; Shen, Q.; Han, Y.; Gu, Y.; Li, X.; Zhao, D.; Liu, Y.; Wang, C.; Zhang, X.; et al. Tet2 is required to resolve
inflammation by recruiting Hdac2 to specifically repress IL-6. Nature 2015,525, 389–393. [CrossRef]
100.
Pan, W.; Zhu, S.; Qu, K.; Meeth, K.; Cheng, J.; He, K.; Ma, H.; Liao, Y.; Wen, X.; Roden, C.; et al. The DNA Methylcytosine
Dioxygenase Tet2 Sustains Immunosuppressive Function of Tumor-Infiltrating Myeloid Cells to Promote Melanoma Progression.
Immunity 2017,47, 284–297.e5. [CrossRef] [PubMed]
101.
Kittan, N.A.; Allen, R.M.; Dhaliwal, A.; Cavassani, K.A.; Schaller, M.; Gallagher, K.A.; Carson, W.F.; Mukherjee, S.; Grembecka,
J.; Cierpicki, T.; et al. Cytokine induced phenotypic and epigenetic signatures are key to establishing specific macrophage
phenotypes. PLoS ONE 2013,8, e78045. [CrossRef] [PubMed]
102.
Liang, X.; Luo, M.; Shao, B.; Yang, J.; Tong, A.; Wang, R.; Liu, Y.; Jun, R.; Liu, T.; Yi, T.; et al. Phosphatidylserine released from
apoptotic cells in tumor induces M2-like macrophage polarization through the PSR-STAT3-JMJD3 axis. Cancer Commun. 2022,42,
205–222. [CrossRef] [PubMed]
103.
Xun, J.; Du, L.; Gao, R.; Shen, L.; Wang, D.; Kang, L.; Zhang, Z.; Zhang, Y.; Yue, S.; Feng, S.; et al. Cancer-derived exosomal
miR-138-5p modulates polarization of tumor-associated macrophages through inhibition of KDM6B. Theranostics 2021,11,
6847–6859. [CrossRef]
104.
Wang, X.; Chen, S.; He, J.; Chen, W.; Ding, Y.; Huang, J.; Huang, J. Histone methyltransferases G9a mediated lipid-induced M1
macrophage polarization through negatively regulating CD36. Metabolism 2021,114, 154404. [CrossRef] [PubMed]
105.
Fu, J.; Han, Z.; Wu, Z.; Xia, Y.; Yang, G.; Yin, Y.; Ren, W. GABA regulates IL-1
β
production in macrophages. Cell Rep. 2022,41,
111770. [CrossRef]
106.
Tokarz, P.; Płoszaj, T.; Regdon, Z.; Virág, L.; Robaszkiewicz, A. PARP1-LSD1 functional interplay controls transcription of SOD2
that protects human pro-inflammatory macrophages from death under an oxidative condition. Free Radic. Biol. Med. 2019,131,
218–224. [CrossRef]
107.
Sobczak, M.; Strachowska, M.; Gronkowska, K.; Karwaciak, I.; Pułaski, Ł.; Robaszkiewicz, A. LSD1 Facilitates Pro-Inflammatory
Polarization of Macrophages by Repressing Catalase. Cells 2021,10, 2465. [CrossRef]
108.
Mazzarella, L.; Santoro, F.; Ravasio, R.; Fumagalli, V.; Massa, P.E.; Rodighiero, S.; Gavilán, E.; Romanenghi, M.; Duso, B.A.;
Bonetti, E.; et al. Inhibition of the lysine demethylase LSD1 modulates the balance between inflammatory and antiviral responses
against coronaviruses. Sci. Signal 2023,16, eade0326. [CrossRef]
109.
Sun, P.; Zhang, S.-J.; Maksim, S.; Yao, Y.-F.; Liu, H.-M.; Du, J. Epigenetic Modification in Macrophages: A Promising Target for
Tumor and Inflammation-associated Disease Therapy. Curr. Top. Med. Chem. 2019,19, 1350–1362. [CrossRef]
110.
Tan, A.H.Y.; Tu, W.; McCuaig, R.; Hardy, K.; Donovan, T.; Tsimbalyuk, S.; Forwood, J.K.; Rao, S. Lysine-Specific Histone
Demethylase 1A Regulates Macrophage Polarization and Checkpoint Molecules in the Tumor Microenvironment of Triple-
Negative Breast Cancer. Front. Immunol. 2019,10, 1351. [CrossRef]
111.
Boulding, T.; McCuaig, R.D.; Tan, A.; Hardy, K.; Wu, F.; Dunn, J.; Kalimutho, M.; Sutton, C.R.; Forwood, J.K.; Bert, A.G.; et al.
LSD1 activation promotes inducible EMT programs and modulates the tumour microenvironment in breast cancer. Sci. Rep. 2018,
8, 73. [CrossRef]
112.
Zhuo, X.; Wu, Y.; Yang, Y.; Gao, L.; Qiao, X.; Chen, T. Knockdown of LSD1 meliorates Ox-LDL-stimulated NLRP3 activation and
inflammation by promoting autophagy via SESN2-mesiated PI3K/Akt/mTOR signaling pathway. Life Sci. 2019,233, 116696.
[CrossRef]
113.
Doi, K.; Murata, K.; Ito, S.; Suzuki, A.; Terao, C.; Ishie, S.; Umemoto, A.; Murotani, Y.; Nishitani, K.; Yoshitomi, H.; et al. Role
of Lysine-Specific Demethylase 1 in Metabolically Integrating Osteoclast Differentiation and Inflammatory Bone Resorption
Through Hypoxia-Inducible Factor 1αand E2F1. Arthritis Rheumatol. 2022,74, 948–960. [CrossRef] [PubMed]
114.
Shinohara, H.; Kuranaga, Y.; Kumazaki, M.; Sugito, N.; Yoshikawa, Y.; Takai, T.; Taniguchi, K.; Ito, Y.; Akao, Y. Regulated
Polarization of Tumor-Associated Macrophages by miR-145 via Colorectal Cancer-Derived Extracellular Vesicles. J. Immunol.
2017,199, 1505–1515. [CrossRef]
115.
Wang, Y.C.; Wu, Y.S.; Hung, C.Y.; Wang, S.A.; Young, M.J.; Hsu, T.I.; Hung, J.J. USP24 induces IL-6 in tumor-associated
microenvironment by stabilizing p300 and β-TrCP and promotes cancer malignancy. Nat. Commun. 2018,9, 3996. [CrossRef]
116.
Shen, Y.; Wei, W.; Zhou, D.-X. Histone Acetylation Enzymes Coordinate Metabolism and Gene Expression. Trends Plant Sci. 2015,
20, 614–621. [CrossRef]
117.
Covarrubias, A.J.; Aksoylar, H.I.; Yu, J.; Snyder, N.W.; Worth, A.J.; Iyer, S.S.; Wang, J.; Ben-Sahra, I.; Byles, V.; Polynne-Stapornkul,
T.; et al. Akt-mTORC1 signaling regulates Acly to integrate metabolic input to control of macrophage activation. eLife 2016,5,
e11612. [CrossRef] [PubMed]
118.
Noe, J.T.; Rendon, B.E.; Geller, A.E.; Conroy, L.R.; Morrissey, S.M.; Young, L.E.; Bruntz, R.C.; Kim, E.J.; Wise-Mitchell, A.; Rizzo,
M.B.d.S.; et al. Lactate supports a metabolic-epigenetic link in macrophage polarization. Sci. Adv. 2021,7, eabi8602. [CrossRef]
119.
Lauterbach, M.A.; Hanke, J.E.; Serefidou, M.; Mangan, M.S.; Kolbe, C.-C.; Hess, T.; Rothe, M.; Kaiser, R.; Hoss, F.; Gehlen, J.;
et al. Toll-like Receptor Signaling Rewires Macrophage Metabolism and Promotes Histone Acetylation via ATP-Citrate Lyase.
Immunity 2019,51, 997–1011.e7. [CrossRef]
Biomolecules 2025,15, 71 22 of 25
120.
Rodríguez-Ubreva, J.; Català-Moll, F.; Obermajer, N.; Álvarez-Errico, D.; Ramirez, R.N.; Company, C.; Vento-Tormo, R.; Moreno-
Bueno, G.; Edwards, R.P.; Mortazavi, A.; et al. Prostaglandin E2 Leads to the Acquisition of DNMT3A-Dependent Tolerogenic
Functions in Human Myeloid-Derived Suppressor Cells. Cell Rep. 2017,21, 154–167. [CrossRef] [PubMed]
121.
Luker, A.J.; Graham, L.J.; Smith, T.M.; Camarena, C.; Zellner, M.P.; Gilmer, J.-J.S.; Damle, S.R.; Conrad, D.H.; Bear, H.D.; Martin,
R.K. The DNA methyltransferase inhibitor, guadecitabine, targets tumor-induced myelopoiesis and recovers T cell activity to
slow tumor growth in combination with adoptive immunotherapy in a mouse model of breast cancer. BMC Immunol. 2020,21, 8.
[CrossRef]
122.
Sasidharan Nair, V.; Saleh, R.; Toor, S.M.; Taha, R.Z.; Ahmed, A.A.; Kurer, M.A.; Murshed, K.; Alajez, N.M.; Abu Nada, M.;
Elkord, E. Transcriptomic profiling disclosed the role of DNA methylation and histone modifications in tumor-infiltrating
myeloid-derived suppressor cell subsets in colorectal cancer. Clin. Epigenet. 2020,12, 13. [CrossRef]
123.
Cartwright, A.N.; Suo, S.; Badrinath, S.; Kumar, S.; Melms, J.; Luoma, A.; Bagati, A.; Saadatpour, A.; Izar, B.; Yuan, G.C.; et al.
Immunosuppressive Myeloid Cells Induce Nitric Oxide-Dependent DNA Damage and p53 Pathway Activation in CD8
+
T Cells.
Cancer Immunol. Res. 2021,9, 470–485. [CrossRef] [PubMed]
124.
Jayaraman, P.; Parikh, F.; Lopez-Rivera, E.; Hailemichael, Y.; Clark, A.; Ma, G.; Cannan, D.; Ramacher, M.; Kato, M.; Overwijk,
W.W.; et al. Tumor-expressed inducible nitric oxide synthase controls induction of functional myeloid-derived suppressor cells
through modulation of vascular endothelial growth factor release. J. Immunol. 2012,188, 5365–5376. [CrossRef] [PubMed]
125.
Lu, C.; Liu, Z.; Klement, J.D.; Yang, D.; Merting, A.D.; Poschel, D.; Albers, T.; Waller, J.L.; Shi, H.; Liu, K. WDR5-H3K4me3
epigenetic axis regulates OPN expression to compensate PD-L1 function to promote pancreatic cancer immune escape. J.
Immunother. Cancer 2021,9, e002624. [CrossRef]
126.
Wysocka, J.; Swigut, T.; Milne, T.A.; Dou, Y.; Zhang, X.; Burlingame, A.L.; Roeder, R.G.; Brivanlou, A.H.; Allis, C.D. WDR5
associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 2005,121,
859–872. [CrossRef] [PubMed]
127.
Sahakian, E.; Powers, J.J.; Chen, J.; Deng, S.L.; Cheng, F.; Distler, A.; Woods, D.M.; Rock-Klotz, J.; Sodre, A.L.; Youn, J.-I.; et al.
Histone deacetylase 11: A novel epigenetic regulator of myeloid derived suppressor cell expansion and function. Mol. Immunol.
2015,63, 579–585. [CrossRef] [PubMed]
128.
Youn, J.-I.; Kumar, V.; Collazo, M.; Nefedova, Y.; Condamine, T.; Cheng, P.; Villagra, A.; Antonia, S.; McCaffrey, J.C.; Fishman, M.;
et al. Epigenetic silencing of retinoblastoma gene regulates pathologic differentiation of myeloid cells in cancer. Nat. Immunol.
2013,14, 211–220. [CrossRef]
129.
de Almeida Nagata, D.E.; Chiang, E.Y.; Jhunjhunwala, S.; Caplazi, P.; Arumugam, V.; Modrusan, Z.; Chan, E.; Merchant, M.; Jin,
L.; Arnott, D.; et al. Regulation of Tumor-Associated Myeloid Cell Activity by CBP/EP300 Bromodomain Modulation of H3K27
Acetylation. Cell Rep. 2019,27, 269–281.e4. [CrossRef]
130.
Yang, R.; Cheng, S.; Luo, N.; Gao, R.; Yu, K.; Kang, B.; Wang, L.; Zhang, Q.; Fang, Q.; Zhang, L.; et al. Distinct epigenetic features
of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis. Genome Biol.
2019,21, 2. [CrossRef]
131.
Peng, D.; Kryczek, I.; Nagarsheth, N.; Zhao, L.; Wei, S.; Wang, W.; Sun, Y.; Zhao, E.; Vatan, L.; Szeliga, W.; et al. Epigenetic
silencing of TH1-type chemokines shapes tumour immunity and immunotherapy. Nature 2015,527, 249–253. [CrossRef] [PubMed]
132. Tanaka, A.; Sakaguchi, S. Regulatory T cells in cancer immunotherapy. Cell Res. 2017,27, 109–118. [CrossRef]
133.
Tay, C.; Tanaka, A.; Sakaguchi, S. Tumor-infiltrating regulatory T cells as targets of cancer immunotherapy. Cancer Cell 2023,41,
450–465. [CrossRef]
134.
Yang, R.; Qu, C.; Zhou, Y.; Konkel, J.E.; Shi, S.; Liu, Y.; Chen, C.; Liu, S.; Liu, D.; Chen, Y.; et al. Hydrogen Sulfide Promotes
Tet1- and Tet2-Mediated Foxp3 Demethylation to Drive Regulatory T Cell Differentiation and Maintain Immune Homeostasis.
Immunity 2015,43, 251–263. [CrossRef] [PubMed]
135.
Liu, Q.; Du, F.; Huang, W.; Ding, X.; Wang, Z.; Yan, F.; Wu, Z. Epigenetic control of Foxp3 in intratumoral T-cells regulates growth
of hepatocellular carcinoma. Aging 2019,11, 2343–2351. [CrossRef]
136.
Zou, Q.; Wang, X.; Ren, D.; Hu, B.; Tang, G.; Zhang, Y.; Huang, M.; Pai, R.K.; Buchanan, D.D.; Win, A.K.; et al. DNA methylation-
based signature of CD8+ tumor-infiltrating lymphocytes enables evaluation of immune response and prognosis in colorectal
cancer. J. Immunother. Cancer 2021,