Annual Review of Cancer Biology

Transcriptional and Epigenetic

Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

Regulation of T Cell States

in Cancer
Shixin Ma,1,2 Diana C. Hargreaves,1,3
and Susan M. Kaech1
1
NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological
Studies, La Jolla, California, USA; email: skaech@[Link]
2
Institute of Human Immunology, Shenzhen Medical Academy of Research and Translation,
Shenzhen, China
3
Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla,
California, USA

Annu. Rev. Cancer Biol. 2026. 10:461–83 Keywords

First published as a Review in Advance on
T cells, differentiation, transcription, epigenetics, cancer
January 16, 2026

The Annual Review of Cancer Biology is online at Abstract

[Link]
CD8+ T cells are central to effective antitumor immunity, yet in cancer,
[Link]
they often undergo progressive transcriptional, epigenetic, and metabolic
042744
reprogramming that leads to an exhausted state and limits current im-
Copyright © 2026 by the author(s). This work is
munotherapy. A deeper understanding of the molecular mechanisms that
licensed under a Creative Commons Attribution-
NonCommercial-NoDerivatives 4.0 International govern CD8+ T cell differentiation and function within the tumor microen-
License (CC BY-NC-ND 4.0), which permits any vironment is essential to overcome this barrier. This review outlines the
noncommercial use, sharing, distribution, and
current knowledge of the transcriptional and epigenetic programs that shape
reproduction in any medium or format, provided the
original author(s) and source are credited; this T cell heterogeneity in cancer and chronic infection, with a focus on the
license does not permit sharing adapted material formation and maintenance of exhausted T cell subsets. We highlight how
derived from this article or parts of it. Images or
T cell–intrinsic factors such as transcription factors and chromatin regula-
other third-party material in this article are included
in the article’s Creative Commons license unless tors and extrinsic factors such as nutrient availability converge to influence
indicated otherwise; see credit lines for license T cell fate decisions and function, as well as how these are affected in cancer.
information.
Finally, we discuss emerging therapeutic strategies aimed at reprogramming
the epigenome to restore T cell function, offering new avenues to enhance
the efficacy and durability of cancer immunotherapy.

461
 INTRODUCTION
T cell–based immunotherapies, including chimeric antigen receptor (CAR)-T cell therapy and im-
mune checkpoint blockade (ICB), have revolutionized cancer treatment. However, their clinical
efficacy remains limited due to multiple factors including lack of tumor-infiltrating lymphocytes
(TILs), tumor cell evasion of TIL recognition, TIL exhaustion, and other suppressive factors
within the tumor microenvironment (TME). TILs span a spectrum of differentiation and func-
tional states and are broadly categorized into naïve, effector, memory, and exhausted T (TEX)
cells. Notably, specific subsets, such as tissue-resident memory (TRM) and progenitor-like TEX
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

cells, have been associated with improved responses to ICB across multiple tumor types (Giles
et al. 2023, Rausch & Kallies 2025). The diversity of TIL states has prompted researchers to study
which types of T cells are present in tumors, how they differentiate, and what controls their ability
to fight or suppress tumors.
Emerging evidence suggests that distinct T cell subsets arise through the integration of di-
verse environmental cues within the TME, including chronic antigen exposure, inflammatory
cytokines, nutrient availability, and cellular interactions (Giles et al. 2023). Central to this process
is epigenetic regulation, which serves as a key interface linking extracellular signals to the tran-
scriptional programs that establish and maintain T cell identity and function (Belk et al. 2022a,
Franco et al. 2020). While CD4+ T cells also contribute to antitumor immunity, their differen-
tiation pathways and epigenetic regulation within tumors remain less well understood (Baessler
& Vignali 2024). In this review, we focus on CD8+ T cells and examine how their differentiation
states are operationally controlled by their epigenetic landscapes, which are regulated through
changes in chromatin accessibility, transcription factor (TF) networks, histone modifications, and
DNA methylation. We highlight emerging insights into how nutrient-derived metabolic signals
shape these epigenetic programs to direct CD8+ T cell fate and function. Finally, we explore
how targeting epigenetic pathways offers new therapeutic opportunities to reprogram dysfunc-
tional CD8+ T cells and enhance antitumor immune responses. Although our primary focus is on
cancer, we also draw on key insights from chronic infection models, which have provided a foun-
dational understanding of CD8+ T cell differentiation and epigenetic regulation under conditions
of persistent antigen stimulation.

CD8+ T CELL DIFFERENTIATION IN CANCER

Recent advances in single-cell RNA sequencing (scRNA-seq), T cell receptor (TCR) profiling,
and epigenomic analyses have revealed the vast heterogeneity of T cells in tumors and have shown
that they follow a dynamic differentiation process, progressing through multiple states rather than
ending in a single terminal state (Daniel et al. 2022, Hudson & Wieland 2023, Kasmani et al. 2023,
Zheng et al. 2021). Upon antigen encounter, naïve T cells are activated through TCR engagement
with peptide–MHC complexes presented by antigen-presenting cells (APCs), initiating clonal ex-
pansion and differentiation into cytotoxic effector cells (Smith-Garvin et al. 2009). In settings of
acute infection or vaccination, following antigen clearance, most effector cells contract, while a
small subset transitions into long-lived memory cells (Sprent & Surh 2002). In nonlymphoid tis-
sues, most memory cells further adopt a TRM phenotype, enabling local immune surveillance
and rapid recall responses (Christo et al. 2024). In contrast, persistent antigen stimulation, such
as in chronic infections and cancer, drives T cells into a distinct state known as exhaustion to
convey a sense of tiredness. TEX cells are characterized by a progressive loss of effector cytokine
secretion (e.g., IFN, TNF); sustained expression of inhibitory receptors (e.g., PD-1, LAG3, and
TIM-3); and extensive transcriptional, epigenetic, and metabolic reprogramming (McLane et al.
2019). Importantly, these TEX cell populations are heterogeneous, with subsets defined by unique

462 Ma • Hargreaves • Kaech

 transcriptional and epigenetic signatures. Among them, the progenitor-like TEX (TEXprog) sub-
set exhibits self-renewal and proliferative potential (He et al. 2016, Im et al. 2016, Leong et al.
2016, Paley et al. 2012, Utzschneider et al. 2016, Wu et al. 2016) and serves as a reservoir for the
sustained antitumor response. These cells can further differentiate into transitory effector-like
(TEXeff ) cells, characterized by high expression of CX3CR1 and partial cytolytic and IFNg- and
TNF-producing activity, or into terminally exhausted (TEXterm) cells, which adopt a fixed epi-
genetic state and are largely unresponsive to ICB therapy (Hudson et al. 2019, Miller et al. 2019,
Yan et al. 2018, Zander et al. 2019).
These TEX subsets, originally described in mouse models, have also been identified in TILs
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

from cancer patients, including those with colorectal cancer, non-small-cell lung cancer (NSCLC),
and hepatocellular carcinoma (Guo et al. 2018, Zhang et al. 2020, Zheng et al. 2017). Clinically,
higher frequencies of TEXprog cells in patient tumors before ICB are linked to better responses,
whereas more TEXterm cells correlate with poorer outcomes (Im et al. 2016, Sade-Feldman et al.
2018). Similarly, TRM cells have also been associated with improved clinical outcomes in both
human and murine tumors (Clarke et al. 2019, Corgnac et al. 2020, Edwards et al. 2018, Gavil et al.
2024, Luoma et al. 2022). However, the functional contribution of these TRM-like cells in tumor
immunity and their distinction from canonical TEX subsets remain incompletely understood.
Altogether, these findings underscore that CD8+ T cells acquire multiple states in tumors
in response to ever-changing conditions. Identifying which subsets are most protective and
what signals guide their differentiation remains a central challenge in immuno-oncology. Defin-
ing the transcriptional and epigenetic programs of TEX subsets—and the cues that govern
their transitions—will be critical for developing therapies that reprogram T cell states to boost
antitumor immunity.

EPIGENETIC REGULATION AND T CELL DIFFERENTIATION

Seminal studies using assay for transposase-accessible chromatin with high-throughput sequenc-
ing (ATAC-seq) have revealed that TEX cells from chronic viral infections and tumors, in both
murine models and patients, possess a unique chromatin accessibility landscape distinct from that
of effector and memory T cells (Pauken et al. 2016, Philip et al. 2017, Sen et al. 2016). Chro-
matin accessibility is a key determinant of transcriptional potential and reflects the underlying
epigenetic state of a cell. During acute activation, naïve T cells undergo extensive chromatin re-
modeling, gaining accessibility at tens of thousands of regulatory regions that enable effector and
memory cell differentiation (McDonald et al. 2023). During chronic antigen stimulation, over
6,000 open chromatin regions (OCRs) were further changed as compared to effector and mem-
ory cells. In particular, TEX cell OCRs link to exhaustion-related genes such as Cd101 and Cd38
(40) and establish new enhancers that drive sustained expression of inhibitory receptors like Pdcd1
(PD-1) (38). For instance, PD-1 is transiently expressed during acute responses through
conventional enhancer activity, but its persistent expression in TEX cells is maintained by
exhaustion-specific enhancers not found in effector or memory T cells (Pauken et al. 2016).
This exhaustion-specific enhancer circuit reinforces sustained inhibitory receptor signaling and
functional repression, supporting the notion that exhaustion represents a distinct epigenetically
stabilized differentiation state rather than a transient dysfunctional state. Indeed, although PD-1
blockade can transiently reinvigorate TEX cells via transcription of effector genes, their effector
functions often decline once treatment is withdrawn (Angelosanto et al. 2012, Tonnerre et al. 2021,
Utzschneider et al. 2013). It remains unclear, however, whether this limited reinvigoration is due
to their intrinsically fixed epigenetic state or instead reflects a short-term burst of more functional
TEXprog and TEXeff cells.

[Link] • T Cell State Regulation 463

 Nevertheless, the limited durability of responses to PD-1-based therapies may, in part, be at-
tributed to the overall epigenetic stability of TEX cells. For instance, although TEX cells possess
approximately 6,000 unique OCRs compared to effector and memory T cells, only around 600 of
these OCRs are altered following PD-L1 blockade (Pauken et al. 2016). Even within TEXprog
subsets, which are more responsive to ICB therapies, exhaustion-associated chromatin signatures
are already established early in differentiation and impose long-lasting constraints on their poten-
tial to reprogram into effector or memory cells. For example, when TEXprog cells are transferred
into antigen-free conditions, they only partially restore memory-like transcriptional and pheno-
typic features. However, they fail to recover core memory-like epigenetic circuits and instead
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

retain a largely exhausted-like chromatin landscape (Abdel-Hakeem et al. 2021). These epigenetic
scars reflect early and persistent antigen exposure during priming and are stably maintained even
after antigen removal (Burger et al. 2021, Utzschneider et al. 2020). This early epigenetic program-
ming leads to the establishment and gradual reinforcement of exhaustion-associated chromatin
states, involving gene loci such as Tox, Cxcr5, and Cd200, and is shaped by the activities of tran-
scriptional factors including EGR2, T-bet, and TCF (Lan et al. 2024). The limited epigenetic
plasticity of distinct TEX subsets is further demonstrated by minimal changes in chromatin ac-
cessibility following PD-1 blockade, despite substantial shifts in subset frequencies (Giles et al.
2022).
Recent studies have also advanced our understanding of chromatin accessibility in T cell ex-
haustion by revealing opposing roles of SWI/SNF chromatin remodeling complex cBAF and
PBAF in regulating TEX cell differentiation (Baxter et al. 2023, Kharel et al. 2023). PBAF main-
tains the TEXprog cells, and depletion of PBAF subunits Pbrm1 or Arid2 promotes the epigenetic
and transcriptional transition from TEXprog cells to TEXeff cells (Baxter et al. 2023, Kharel
et al. 2023). In contrast, cBAF facilitates early activation of T cells and promotes the transition of
TEX cells from progenitor- to effector-like states (Baxter et al. 2023). Interestingly, knockdown
of the cBAF subunit Arid1a in T cells adoptively transferred into tumor models has been shown
to enhance T cell persistence and improve antitumor immune responses, suggesting a context-
dependent role for cBAF (Belk et al. 2022b, Guo et al. 2022). Relatedly, a CRISPR screen in human
CAR-T cells identified the Mediator complex as a key orchestrator linking enhancer-bound TFs
to the core transcriptional machinery; deletion of MED12, a subunit of the Mediator kinase mod-
ule, resulted in increased H3K27 acetylation and enhancer activation by STAT and AP-1 family
TFs (e.g., BATF), ultimately boosting effector function and persistence (Freitas et al. 2022).
In addition, other layers of epigenetic regulation including DNA methylation and histone
modification further stabilize the exhausted state. DNA methylation patterns progressively di-
verge across naïve, effector, and TEX cells, with TEX cells acquiring unique DNA methylation
patterns that repress effector- and memory-related genes (e.g., Ifng, Ccr7) and TFs (e.g., Tcf7,
Tbx21) (Ghoneim et al. 2017). Notably, deletion of Dnmt3a, a de novo DNA methyltransferase,
alleviates repression of these key effector and memory-associated genes, and pharmacological in-
hibition of DNA methylation using the demethylating agent decitabine significantly enhances
TEX cell responsiveness to PD-1 blockade, suggesting DNA methylation acts as a critical bar-
rier to sustained functional reinvigoration (Ghoneim et al. 2017). Additionally, the methylcytosine
dioxygenase TET2 promotes the differentiation of TEXprog cells toward terminal states (Dimitri
et al. 2024, Fraietta et al. 2018, Kang et al. 2024). Further epigenetic regulation involves ASXL1,
an epigenetic regulator implicated in clonal hematopoiesis. Disruption of Asxl1 supports the main-
tenance of TEXprog cells and enhances anti-PD-L1 responses through ubiquitination of histone
H2A lysine 119 (Kang et al. 2024). Concurrently, global reductions in histone acetylation in TEX
cells reinforce their transcriptionally repressed state, while interventions with histone deacetylase
(HDAC) inhibitors have been shown to restore their global histone H3 acetylation and partially

464 Ma • Hargreaves • Kaech

 rescue their immune functions (Zhang et al. 2014). Collectively, these findings indicate that the
formation and maintenance of TEX cells are associated with gradual and coordinated epigenetic
remodeling involving changes in chromatin accessibility, enhancer activity, DNA methylation,
histone modifications, and TF activity that together enforce a stable, yet potentially targetable,
exhausted state (Beltra et al. 2020, Hudson et al. 2019).

TRANSCRIPTIONAL REGULATION OF EXHAUSTED T CELL

DIFFERENTIATION
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

The distinct epigenetic states of TEX cells are shaped by a core set of TFs—including NFAT,
NR4A family members, and TOX—that act with chromatin remodeling machinery to drive gen-
eral TEX gene expression and subsequently work together with subset-specific TFs to guide
CD8+ T cell differentiation into TEXprog, TEXeff, and TEXterm states (Rausch & Kallies 2025,
Seo et al. 2019). The HMG-box transcription factor TOX was the first key regulator found to be
induced by chronic antigen stimulation. It is essential for establishing and maintaining the epige-
netic landscape and gene networks associated with T cell exhaustion in mice but is not required
for effector or memory T cell formation during acute infection (Alfei et al. 2019, Huang et al.
2025, Khan et al. 2019, Scott et al. 2019, Seo et al. 2019). Importantly, TOX may establish these
TEX cell–specific epigenetic states through direct interactions with chromatin organizing and
remodeling complexes, engaging both activating modifiers, such as the histone acetyltransferase
complex containing KAT7, and repressive regulators such as DNMT1 and SIN3A (Khan et al.
2019). In both chronic infection and tumors, TOX-deficient cells exhibit reduced expression of
inhibitory receptors such as PD-1 and LAG3, along with impaired persistence (Khan et al. 2019,
Scott et al. 2019). While TOX loss enhances cytotoxic effector function including increased TNF,
IFN-γ, and granzyme B expression in chronic infection, this enhancement is only observed in
tumors when both TOX and its paralog TOX2 are deleted (Scott et al. 2019, Seo et al. 2019).
Nonetheless, T cells with partial TOX deficiency exhibit improved tumor control compared to
wild-type cells (Khan et al. 2019), highlighting a dose-dependent role for TOX in balancing T
cell persistence and function. Importantly, TOX and NR4A family members are direct targets
of NFAT, which is activated downstream of calcium and TCR signaling. In the absence of AP-1
family members, NFAT alone drives the expression of exhaustion-associated genes such as TOX,
NR4As, and PD-1, and it fails to effectively control tumors (Martinez et al. 2015, Seo et al. 2019).
Consistently, genetic ablation of NR4As improves T cell effector function and enhances antitu-
mor immunity in preclinical models ( J. Chen et al. 2019). Notably, TOX and NR4As are highly
expressed in intratumoral CD8+ T cells from human cancers, underscoring their conserved role
in establishing and maintaining the TEX program in both mice and humans (Seo et al. 2019).
Evidence also shows that TEX-like programs can transiently arise during acute infection but
are actively suppressed. While early effectors may initiate exhaustion-associated genes like Tox, this
program is quenched by Klf2, which promotes effector differentiation (Chu et al. 2025, McManus
et al. 2025, Yao et al. 2019). Interestingly, in chronic contexts such as tumors, KLF2 also supports
the maintenance of TEXprog cells, highlighting its context-dependent function (Fagerberg et al.
2025). Together, NFAT, NR4A, and TOX form a coordinated transcriptional network that lays
the foundation for progressive commitment to TEX cell fates ( J. Chen et al. 2019, Martinez et al.
2015, Seo et al. 2019).
Exhaustion-specific master regulators cooperate with additional TFs to more selectively
shape the unique functional identities of TEXprog, TEXeff, and TEXterm subsets (Zander &
Cui 2023). Differentiation into TEXprog cells, for example, is governed by TOX along with
BACH2, TCF1, FOXO1, MYB, IKZF1, ID3, and EOMES TFs (Chan et al. 2024, Rausch &
Kallies 2025, Zhou et al. 2023). BACH2 initiates a transcriptional program that limits effector

[Link] • T Cell State Regulation 465

 differentiation and helps establish a progenitor-like epigenetic landscape (Yao et al. 2021). TCF1
further reinforces this state by maintaining chromatin accessibility at memory-like loci and
actively antagonizing terminal differentiation programs (Z. Chen et al. 2019, Jadhav et al. 2019,
Wu et al. 2016). ID3 and EOMES also contribute to sustaining the TEXprog state (Gago
da Graca et al. 2025, Ma et al. 2022, Utzschneider et al. 2020), whereas BCL6 and BLIMP1,
repressed by TCF1, act as negative regulators of TEXprog cells, partly through type I interferon
signaling pathways (Wu et al. 2016). FOXO1, known for its role in memory T cell formation,
also promotes memory-like features during chronic infection and in cancer (Chan et al. 2024,
Kim et al. 2013, Ouyang et al. 2009, Staron et al. 2014, Utzschneider et al. 2018). Additionally,
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

MYB has been identified as a critical TF for precursor progenitor formation and repressing
terminal exhaustion during chronic viral infection (Tsui et al. 2022). Complementary single-cell
CRISPR screens in tumor-infiltrating T cells have identified IKZF1 as a key factor regulating
the transition from precursor TEX cells to TEXprog cells, with IKZF1 depletion impairing
TEXprog formation with increased precursor TEX cells (Zhou et al. 2023). Importantly, many
of these TF-mediated programs are conserved in humans. CRISPR screens in primary human
T cells have demonstrated that disruption of MYB, FOXO1, or BACH2 significantly reduces
the frequency of CCR7+ memory-like CD8+ T cells (McCutcheon et al. 2023). Moreover,
overexpression of BATF3 enhances memory formation, and enforced expression of FOXO1 or
BATF3 has been shown to significantly improve T cell persistence and antitumor activity in
human CAR-T cells in vivo (Chan et al. 2024, Doan et al. 2024, McCutcheon et al. 2023).
As TEXprog cells differentiate, a transcriptional bifurcation emerges that leads to distinct
TEXeff or TEXterm states. On one path, T-bet sustains cytotoxic effector gene expression and
counteracts adoption of TEXterm states mediated by TOX and NR4A family members (Chen
et al. 2021, Fagerberg et al. 2025). ZEB2 further strengthens effector-like lineage commitment,
while BATF facilitates the transition from TEXprog to TEXeff cells by maintaining a permis-
sive chromatin structure and modulating enhancer activity of Tbx21 (which encodes T-bet) and
Klf2 during chronic viral infection (Alfei et al. 2019, J. Chen et al. 2019, Chen et al. 2021, Giles
et al. 2022, Kasmani et al. 2023, Khan et al. 2019, Scott et al. 2019, Seo et al. 2019, Zander & Cui
2023). Consistently, ETS1 has been shown to inhibit TEXeff differentiation in tumors, at least in
part by suppressing BATF expression (Zhou et al. 2023). Consequently, BATF overexpression en-
hances the survival and expansion of tumor-infiltrating CAR-T cells and promotes the generation
of long-lived memory T cells in an IRF4-dependent manner (Seo et al. 2021).
In contrast, TOX-expressing exhausted cells that downregulate TCF1 and T-bet differentiate
into TEXterm cells. This terminal differentiation is driven, at least in part, by type I IFN signaling
in an IRF7-dependent manner during chronic infection (Kasmani et al. 2023). In tumors, the
transcription factor RBPJ has also been shown to promote TEXterm cell differentiation through
activation of IRF1 (Zhou et al. 2023).
Collectively, these studies outline the architectural framework of TEX cell differentiation, in
which a subset of TEX cells retains plasticity and stem-like potential, while others progressively ac-
quire terminally differentiated states. This balance between stemness and terminal differentiation
or specialization is governed by a core transcriptional network, including NFAT, TOX, and NR4A
family members, that establishes the foundational exhaustion program and associated epigenetic
landscape. These master TFs work together with subset-specific TFs (e.g., TCF1, BACH2, T-
bet, BATF) and collaborate closely with chromatin remodelers and histone modifying enzymes
to shape and stabilize distinct TEX states (Figure 1). A deeper understanding of the epigenetic
regulators governing TEX subset differentiation, their cooperation with subset-specific TFs, and
the upstream signals that guide these processes may enable the development of novel T cell–based

466 Ma • Hargreaves • Kaech

 Apoptosis

Acute
stimulation
Naϊve Effector Memory

Ch
ro
TF

nic
:
NF

sti
AT

mu
TF: TBET, ZEB2, BATF, IRF4, ETS1
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

,T
OX

lat

Epi reg: cBAF

ion
,N

TEXeff
R4
A

Tbx21,
TF: BACH2, TCF1, Cx3cr1…
FOXO1, MYB, IKZF1,
ID3, EOMES TEXprog
Epi reg: PBAF
TF: IRF7, RBPJ
Epi reg: DNMT3A, TET2, ASXL1
Tcf7,
Ifn… TEXterm
Pdcd1,
Havcr2…
TUMOR MICROENVIRONMENT

Figure 1
Transcriptional and epigenetic regulation of TEX cell differentiation. Under acute antigen stimulation,
naïve T cells differentiate into effector cells, the majority of which undergo apoptosis, while a subset further
develops into long-lived memory cells. In contrast, chronic antigen stimulation initiates TEX cell
differentiation through master TFs including NFAT, NR4A, and TOX, which establish the core exhaustion
program. These TFs subsequently cooperate with subset-specific TFs (TEXprog: BACH2, TCF1, FOXO1,
MYB, IKZF1, ID3, EOMES; TEXeff: TBET, ZEB2, BATF, IRF4, ETS1; TEXterm: IRF7, RBPJ) and
epigenetic regulators (TEXprog: PBAF; TEXeff: cBAF; TEXterm: DNMT3A, TET2, ASXL1) to guide the
differentiation of TEXeff or TEXterm subsets, with TEXeff subsets capable of further differentiating into
TEXterm cells. Abbreviations: epi reg, epigenetic regulator; TEX, exhausted T; TEXeff, transitory
effector-like TEX; TEXprog, progenitor-like TEX; TEXterm, terminally exhausted; TF, transcription
factor. Figure created in BioRender; Zhou P. 2025. [Link]

immunotherapies that selectively promote TEXprog and TEXeff states while preventing terminal
TEXterm differentiation or even reversing TEXterm cell differentiation.

METABOLIC REGULATION OF EPIGENETIC STATES

OF T CELLS IN CANCER
The metabolic state of the cell is integral to the epigenetic status, as many chromatin modifi-
cations depend on the availability of key metabolites such as acetyl-CoA, S-adenosylmethionine
(SAM), α-ketoglutarate (α-KG), and NAD+ , which serve as substrates or cofactors for chromatin-
modifying enzymes (Dai et al. 2020). These metabolites are generated through the metabolism
of both cell-intrinsic and cell-extrinsic nutrients, such as glucose, glutamine, methionine, and lac-
tate. Intrinsically, T cell activation and differentiation are accompanied by profound metabolic
reprogramming to support the bioenergetic and biosynthetic demands of these processes. This
includes increased uptake and utilization of glucose, glutamine, and methionine, which in turn
fuel specific epigenetic programs that govern T cell differentiation and function (S. Ma et al.

[Link] • T Cell State Regulation 467

 2024, Soriano-Baguet & Brenner 2023). Notably, T cell metabolic states are dynamic and vary
across different stages of immune responses and differentiation. For instance, effector T cells rely
heavily on glucose and amino acids (Ho et al. 2015, Nakaya et al. 2014, Sinclair et al. 2013, Wang
et al. 2011), whereas memory T cells are preferentially dependent on fatty acid oxidation (Cui
et al. 2015, O’Sullivan et al. 2014, Pearce et al. 2009). In contrast, TEX cells exhibit diminished
mitochondria function (Bengsch et al. 2016, Gabriel et al. 2021, Scharping et al. 2016, Sukumar
et al. 2016, Yu et al. 2020), increased oxidized lipid uptake (Xu et al. 2021), and heightened re-
liance on glucose metabolism (Reinfeld et al. 2021). Extrinsically, the nutrient availability in the
TME imposes additional constraints on T cell metabolism, epigenetic states, and cell fates. Mass
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

spectrometry–based profiling of tumor interstitial fluid has revealed that T cells in tumors often
face nutrient restrictions, such as low glucose and arginine, along with elevated levels of lactate,
fatty acids, potassium, and hypoxia (Cognet & Muir 2024, Sullivan et al. 2019). These environ-
mental factors impair T cell activation and effector function, at least in part by altering metabolite
availability and metabolic enzyme activity, thereby reshaping the epigenetic landscape and influ-
encing T cell fate decisions (Reina-Campos et al. 2021, Zhao et al. 2021) (Figure 2). However, it
is important to note that most current insights into these metabolic–epigenetic interactions are
derived from studies of bulk TEX populations. A more detailed understanding of how individual
TEX subsets (e.g., TEXprog, TEXeff, TEXterm) differ in their metabolic states and associated
epigenetic landscapes remains an important area for future investigation.

Glucose and Acetate Metabolism

Glucose metabolism generates acetyl-CoA through glycolysis and the tricarboxylic acid (TCA)
cycle, providing the key substrate for histone acetylation. In activated T cells, robust glycolytic
flux supports effector function in part by sustaining acetyl-CoA pools necessary for maintaining
an open chromatin state. For example, LDHA, a key glycolytic enzyme, has been directly linked
to Th1-mediated autoimmunity and the epigenetic regulation of T cell differentiation through
its role in supporting histone acetylation (Peng et al. 2016). However, within tumors, both gly-
colytic metabolism and mitochondria function in T cells are often impaired (Chang et al. 2015,
Ho et al. 2015, Scharping et al. 2016, Siska et al. 2017). In addition, the accumulation of extracel-
lular potassium in the TME further suppresses glycolysis by inducing a metabolically quiescent
state, limiting cytonuclear acetyl-CoA production and constraining chromatin accessibility at key
effector gene loci (Vodnala et al. 2019). As a result, glucose deprivation leads to a global reduction
in histone acetylation and impaired T cell effector function (Ho et al. 2015, Qiu et al. 2019). Inter-
estingly, supplementation with exogenous acetate can restore both histone acetylation and effector
function in T cells under glucose-restricted conditions in vitro (Qiu et al. 2019), highlighting the
metabolic flexibility in adapting to fluctuating nutrient environments.
Emerging evidence further reveals that T cells exhibit dynamic nutrient preferences for acetyl-
CoA production that influence their differentiation and function. In Van Andel Institute–modified
Iscove’s medium (VIM), which closely reflects metabolite concentrations found in mouse serum
compared to regular T cell medium, CD8+ T cells preferentially utilize carbon sources such as
lactate and β-hydroxybutyrate (βOHB) over glucose to generate mitochondria acetyl-CoA and fuel
the TCA cycle. Disruption of lactate metabolism by silencing LDHA impairs T cell proliferation
and effector function during Listeria infection, underscoring the importance of nutrient source of
mitochondrial acetyl-CoA in T cell function (Kaymak et al. 2022).
Beyond mitochondrial metabolism, recent studies indicate that nutrient preferences also shape
nuclear acetyl-CoA availability and thereby influence histone acetylation landscapes in CD8+
T cells. During chronic viral infection and in tumors, CD8+ T cells progressively shift their nutri-
ent preference for acetyl-CoA production from acetate to glucose, driven by differential expression

468 Ma • Hargreaves • Kaech

 EXTRACELLULAR
Lactate Glucose Potassium Acetate Glutamine Methionine TUMOR MICROENVIRONMENT
(Metabolite abundance)
MCT11 Glut1/4

Glucose Acetate Glutamine Methionine SAM

Potassium GLS
ACSS2
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

Lactate Pyruvate Glutamate NUCLEUS

Acetyl-CoA Acetyl-CoA
Lactate

HDACs
ACLY

HATs

INTRACELLULAR
Acetyl-CoA ACSS2 ACLY
T CELL

Citrate P300 KAT2A

Ac Ac Ac Ac
SAM
Succinyl-CoA Havcr2,
TCA Pdcd1…
cycle

JMJC, KDM, TET

Citrate Histone acetylation
IDH

KMT
α-KG

2-HG
Lac Lac Lac Lac Havcr2,
Lactyl-CoA Me Me Me Me
Pdcd1…
Tcf7…

Histone lactylation Histone/DNA methylation

Figure 2
Nutrient-driven epigenetic reprogramming in T cells in cancer. Intrinsic metabolic regulation and altered nutrient availability
(metabolite abundance) within the TME cooperatively shape the epigenetic states of T cells as they transition into exhaustion.
Intrinsically, T cells downregulate ACSS2 while maintaining ACLY activity, thereby shifting their preferred acetyl-CoA source from
acetate to citrate. This nutrient switch differentially regulates histone acetylation at exhaustion-associated loci: ACLY-derived
acetyl-CoA engages with KAT2A to promote TEX-related gene expression, whereas ACSS2-derived acetyl-CoA predominantly
supports p300-mediated effector gene expression. In the TME, nutrient restrictions further influence epigenetic remodeling—limited
glutamine availability, along with a metabolic shift from oxidative glutaminolysis to reductive carboxylation via IDH, impairs the
activity of α-KG-dependent demethylases (e.g., TETs, KDMs), reducing DNA and histone demethylation at TEX-related genes.
Similarly, methionine depletion decreases SAM levels, thereby diminishing methylation-dependent repression. In contrast, elevated
lactate in tumors can enhance histone lactylation or inhibit HDAC activity at stem-like gene promoters to support T cell stemness.
Increased extracellular potassium in the TME further suppresses glycolysis, limiting cytonuclear acetyl-CoA availability and restricting
chromatin accessibility at key effector loci. Abbreviations: α-KG, α-ketoglutarate; ACLY, ATP-citrate lyase; ACSS2, acetyl-CoA
synthetase 2; HDAC, histone deacetylase; IDH, isocitrate dehydrogenase; SAM, S-adenosylmethionine; TCA, tricarboxylic acid; TEX,
exhausted T; TME, tumor microenvironment. Figure created in BioRender; Zhou P. 2025. [Link]

of acetyl-CoA synthetase 2 (ACSS2) and ATP-citrate lyase (ACLY) in TEXprog and TEXterm
cells, respectively. Importantly, ACSS2 and ACLY form functionally distinct protein complexes
with histone acetyltransferases EP300 and KAT2A, respectively, enabling the selective utilization
of acetate- or glucose-derived nuclear acetyl-CoA for histone acetylation at effector/memory-
or exhaustion-associated gene loci. This nutrient-driven remodeling of histone acetylation land-
scapes consequently determines TEXprog or TEXterm cell fates. Functionally, overexpression
of nuclear localized ACSS2 or inhibition of ACLY in CD8+ T cells significantly enhances their
antitumor activity both as monotherapy and in combination with ICB. Importantly, this nutri-
ent preference is conserved in human T cells during chronic antigen stimulation, as depletion
of ACLY in human CAR-T cells promotes TEXprog formation and improves their antitumor
immunity (Ma et al. 2025).

[Link] • T Cell State Regulation 469

 Interestingly, the preferred nutrient source for acetyl-CoA production and its impact on the
epigenome and T cell functional states varies depending on disease context and cell type. For
example, during acute infection, effector T cells primarily rely on glucose-derived acetyl-CoA
via ACLY, with ACSS2 being largely dispensable. However, in the absence of ACLY, the acetate–
ACSS2 axis can compensate to support TCA cycle activity, sustain cytosolic acetyl-CoA pools,
and maintain histone acetylation at effector gene loci, thereby supporting effector T cell function
(Kaymak et al. 2024). Similarly, ACSS2 has also been shown to support histone acetylation and
cell survival in tumor cells lacking ACLY (Zhao et al. 2016), further emphasizing the context-
dependent nature of nutrient utilization and acetyl-CoA metabolism. While targeting these
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

nutrient-driven pathways holds therapeutic promise, their diverse roles across disease contexts
and cell types warrant careful consideration.

Lactate Metabolism
Lactate, a prominent glycolytic byproduct that accumulates in glycolysis-dominant tumors, has
long been viewed as detrimental to T cell effector function, promoting terminal differentiation and
dysfunction within the TME (Llibre et al. 2025, Peralta et al. 2024). However, emerging evidence
has revealed a more complicated role for lactate, demonstrating its potential to support antitumor
T cell responses through epigenetic reprogramming. Mechanistically, lactate can inhibit HDAC
activity, leading to increased histone acetylation (e.g., H3K27ac) at key regulatory loci, includ-
ing the Tcf7 super-enhancer, thereby reinforcing memory and stem-like transcriptional programs
(Barbieri et al. 2023, Feng et al. 2022). Additionally, lactate-derived lactyl-CoA enables histone
lactylation, a recently characterized posttranslational modification associated with enhanced T cell
persistence and stemness (Raychaudhuri et al. 2024, Zhang et al. 2019).
Despite these promising effects, the beneficial epigenetic influence of lactate may be attenuated
by the acidic TME, potentially destabilizing transcriptional programs and impairing T cell func-
tion. Nevertheless, certain T cell subsets, such as regulatory T cells, exhibit remarkable metabolic
flexibility, allowing them to retain functionality even in a lactate-rich TME (Angelin et al. 2017,
Watson et al. 2021), highlighting the importance of adaptive metabolic strategies in maintaining
both epigenetic and functional integrity.

Glutamine Metabolism
In addition to glucose, glutamine is another critical nutrient that supports T cell activation and dif-
ferentiation, in part through its epigenetic influence (E.H. Ma et al. 2024). However, its availability
is often markedly reduced in the TME due to high consumption by tumor cells. Glutamine serves
as a major source of α-KG, a critical cofactor for DNA and histone demethylases such as TET en-
zymes and JmjC-domain-containing demethylases. Through oxidative metabolism–derived α-KG
production, glutamine metabolism promotes Th1 and CD8+ T cell effector function by enhancing
chromatin accessibility via DNA demethylation and histone modifications, including H3K27me3
(Chisolm et al. 2017). While glutamine metabolism is essential for the proliferation of both tu-
mor and T cells, inhibition of glutamine metabolism by pan-glutamine antagonist DON or its
prodrug JHU083 has been shown to enhance T cell–mediated antitumor immunity by inducing
distinct metabolic reprogramming in each cell type (Leone et al. 2019, Nabe et al. 2018). In tu-
mor cells, DON broadly represses glycolysis and oxidative phosphorylation, compromising cell
viability. In contrast, T cells under DON treatment exhibit metabolic flexibility by increasing
oxidative phosphorylation fueled by glucose and acetate, which promotes effector/memory-like
gene expression (e.g., Cd62l, Cd127, Tbx21, Eomes) and cytotoxicity. Concurrently, DON-induced
reductions in α-KG and corresponding increases in global histone methylation (e.g., H3K4me3,

470 Ma • Hargreaves • Kaech

 H3K27me3, H3K36me3) may further reinforce expression of effector- and memory-associated
genes in T cells by limiting demethylase activity and enhancing chromatin accessibility, either
directly or indirectly, at these loci (Leone et al. 2019).
However, the timing and specificity of glutamine inhibition are critical. Pan-glutamine block-
ade with DON during early T cell activation impairs α-KG-dependent demethylation, reduces
histone modifications, and compromises T cell persistence and antitumor responses, whereas
glutaminase-specific inhibition or glutamine depletion has minimal effect (Madden et al. 2023).
T cells also exhibit metabolic and epigenetic plasticity in how they utilize glutamine. Effec-
tor T cells engage both oxidative metabolism and reductive carboxylation (RC), while memory
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

T cells predominantly rely on oxidation. Inhibiting RC by depleting isocitrate dehydrogenase 2

(IDH2) enhances oxidative metabolism and promotes memory gene expression, thereby improv-
ing CAR-T cell function ( Jaccard et al. 2023). This effect may result from the accumulation of
TCA cycle intermediates, such as succinate, fumarate, malate, and 2-hydroxyglutarate (2-HG),
which compete with α-KG and inhibit demethylases like KDM5, preserving H3K4me3 at naïve
and memory-associated genes ( Jaccard et al. 2023). Supporting this, 2-HG treatment promotes a
memory-like phenotype by inhibiting UTX and TET-mediated histone and DNA demethylation,
enhancing T cell persistence and antitumor capacity (Tyrakis et al. 2016). Notably, IDH2 is tran-
scriptionally induced by HIF1α, suggesting that hypoxia within the TME may favor RC activity in
TILs, promote repressive chromatin states, and drive TEXterm cell differentiation ( Jaccard et al.
2023). Together, these findings highlight the capacity of the T cell epigenome to actively interpret
and integrate distinct glutamine metabolic pathways. The source, timing, and downstream fate of
glutamine metabolism shape the chromatin landscape in a context-dependent manner, guiding
T cell differentiation toward effector, memory, or exhausted states.

Methionine Metabolism
Methionine metabolism represents another axis through which tumors can metabolically and
epigenetically influence T cell function. Upon activation, T cells increase methionine uptake to
fuel the one-carbon cycle, generating S-adenosylmethionine (SAM), the universal methyl donor
required for RNA, DNA, and histone methylation (Xiao & Locasale 2021). This supports key
histone modifications (e.g., H3K4me3) at loci critical for effector gene expression and T cell lin-
eage commitment (Roy et al. 2020, Sinclair et al. 2019). In the TME, however, tumor cells often
upregulate methionine transporters such as SLC43A2, allowing them to outcompete T cells for
extracellular methionine (Bian et al. 2020). This competition leads to reduced SAM levels in TILs,
impairing DOT1L-mediated H3K9me2 methylation, particularly at STAT5 loci, a TF essential
for effector function, and ultimately compromising T cell effector activity and survival. Methio-
nine supplementation in both mouse models and colorectal cancer patients has been shown to
restore T cell effector function.
Paradoxically, methionine restriction can also exert antitumor effects in certain contexts. In
patient-derived chemotherapy-resistant colorectal cancer and mouse autochthonous soft-tissue
sarcoma models, dietary methionine restriction improved treatment responses (Gao et al. 2019).
Additionally, methionine restriction reduced tumor expression of PD-L1 and VISTA by modu-
lating m6A RNA methylation, and high levels of the m6A reader YTHDF1 were associated with
poor prognosis and reduced immunotherapy response (T. Li et al. 2023). These findings highlight
the dual role of methionine metabolism in regulating both T cell fitness and tumor immune eva-
sion via transcriptional and posttranscriptional epigenetic mechanisms and emphasize the need
for context-specific strategies when considering methionine-targeted interventions in clinic.
Collectively, these findings highlight the T cell epigenome as a finely tuned sensor of cellular
metabolism and nutrient fluctuations within the TME. By integrating signals from metabolic

[Link] • T Cell State Regulation 471

 alterations, the epigenome translates nutrient cues into distinct epigenetic landscapes that govern
the transcriptional and functional states of T cells in cancer. Future research is needed to dissect
nutrient metabolism and its epigenetic regulation across distinct TEX subsets, particularly in
human samples, which will be essential for the development of metabolic- and epigenetic-based
immunotherapies.

HARNESSING EPIGENETIC REGULATION TO ENHANCE T CELL

IMMUNITY IN CANCER
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

The expanding understanding of epigenetic regulation in T cells offers a powerful framework for
advancing cancer immunotherapy. While transformative approaches such as CAR-T cell therapy,
TCR-engineered T cells, and ICB have significantly improved outcomes for some patients, their
efficacy is often limited by barriers including inadequate infiltration into tumor sites, poor T cell
persistence, and T cell exhaustion. These functional limitations are increasingly recognized to be
governed, at least in part, by epigenetic programs that integrate environmental cues within the
TME and shape T cell differentiation and function. As such, the ability to decode and therapeu-
tically reprogram the epigenome represents a promising strategy to overcome these barriers and
enhance the efficacy, durability, and breadth of T cell–based cancer therapies.

EPIGENETIC REPROGRAMMING IN ADOPTIVE T CELL THERAPIES

Among adoptive cell therapies (ACTs), CAR-T and TCR-T cells have demonstrated remarkable
clinical success in hematologic malignancies. However, their broader application in solid tumors
remains limited, in part due to their inability to persist long-term or function effectively within
immunosuppressive environments ( June et al. 2018). Recent work has underscored the critical role
of epigenetic regulation in shaping these outcomes and opens the door to manipulating epigenetic
modifiers and TFs to rewire T cell fate and function in clinically meaningful ways (Akbari et al.
2021).
Several studies have highlighted that targeting epigenetic enzymes in CAR-T cells can reshape
their chromatin landscape, promote persistence, and enhance antitumor efficacy. For example,
deletion of TET2, a DNA demethylase, extends CAR-T cell functional longevity by preserving a
stem-like epigenetic state, which supports enhanced expansion and memory potential in murine
models (Dimitri et al. 2024, Kang et al. 2024). Clinically, this was supported by a report in which a
patient with chronic lymphocytic leukemia achieved long-term remission following CD19 CAR-
T cell therapy. In this case, the infused CAR-T cells carried a disruption in the TET2 locus that
originated predominantly from a single clone, highlighting that even a single epigenetically re-
programmed T cell can undergo robust expansion and be sufficient to drive durable therapeutic
success (Fraietta et al. 2018). Similarly, depletion of other hematopoietic-associated epigenetic
regulators such as DNMT3A and ASXL1 has been shown to enhance CAR-T cell functionality by
promoting a less differentiated state, likely through modulation of DNA methylation and histone
ubiquitination, respectively (Kang et al. 2024).
In addition to DNA methylation, histone methylation represents another critical aspect of
epigenetic regulation in CAR-T cells. For instance, knockout of SUV39H1, which catalyzes the
deposition of the repressive H3K9me3 mark, improves early expansion, long-term persistence,
and antitumor efficacy of human CAR-T cells. This is accompanied by increased expression of
memory-associated genes regulated by TFs such as TCF1 and LEF1, reinforcing a stem-like
transcriptional program ( Jain et al. 2024). EZH2, the catalytic subunit of Polycomb repressive
complex 2 (PRC2), mediates H3K27me3 and has been shown to prevent hematopoietic stem
cell exhaustion (Kamminga et al. 2006). It also plays a crucial role in T cell differentiation,

472 Ma • Hargreaves • Kaech

 memory maintenance, and antitumor immunity (Gray et al. 2017, He et al. 2017). Notably, recent
studies comparing continuously stimulated CAR-T cells with those given a rest period revealed
that transient rest enables epigenetic and transcriptional reprogramming, leading to improved
functionality and persistence. This reinvigoration was dependent on EZH2 activity and was
accompanied by repression of exhaustion-associated genes such as TBX21, NFATC1, and the
AP-1 family members FOS, FOSB, and JUNB (Weber et al. 2021).
Transcription factors that orchestrate T cell fate are also emerging as promising targets to en-
hance CAR-T efficacy. FOXO1 (Doan et al. 2024), a key regulator of memory-associated genes
such as Tcf7 and Ccr7, plays a critical role in memory T cell formation in both mice and hu-
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

mans (Fabre et al. 2008, Hess Michelini et al. 2013, Kim et al. 2013, Utzschneider et al. 2018).
Overexpression of FOXO1 in CAR-T cells from both healthy donors and patients enhances a
stem-like phenotype, mitochondrial fitness, persistence, and therapeutic efficacy in vivo, with-
out impairing the epigenetic flexibility required for activation and effector function (Chan et al.
2024). In contrast, the NR4A family has been identified as critical mediators of T cell exhaus-
tion. Triple knockout of Nr4a1/2/3 in CAR-T cells reinvigorates effector gene expression and
enhances tumor control in mouse models ( J. Chen et al. 2019). Mechanistically, this is associ-
ated with increased accessibility at NF-κB and AP-1 binding motifs, key transcriptional factors
involved in T cell activation and inflammation. Additionally, engineered expression of constitu-
tively active STAT5 (CA-STAT5), a downstream effector of cytokine signaling (e.g., IL-7, IL-15),
has been shown to further boost CAR-T cell survival and proliferation in both CD4+ and CD8+
T cells. By sustaining the transcription of genes linked to homeostasis and effector function, CA-
STAT5 expression promotes robust antitumor responses, enhances persistence in mouse models,
and shows functional relevance in human T cells (Ding et al. 2020).
While genetic reprogramming offers durable and cell-intrinsic approaches, in vitro precondi-
tioning offers a more immediately translatable and scalable strategy to influence T cell epigenetic
states prior to infusion. Cytokine-based preconditioning with IL-7, IL-15, or IL-21 during
T cell expansion helps maintain a less-differentiated phenotype, enriching for central memory-
like populations that exhibit improved persistence in vivo (Alizadeh et al. 2019, Giuffrida et al.
2020, Loschinski et al. 2018, Xu et al. 2014). This effect is likely mediated through the induction
of key TFs such as TCF1, BCL2, FOXO1, and STAT5, which promote survival, homeostasis,
and chromatin accessibility at effector and memory-associated loci (Chan et al. 2024, Ding et al.
2020). Notably, T cells expanded under these cytokine conditions also exhibit improved oxidative
metabolism, which further supports their durable antitumor capacity.
Metabolic preconditioning offers a complementary approach that could epigenetically
program T cells before infusion during ACTs or CAR-T therapies. For example, acetate sup-
plementation increases intracellular acetyl-CoA levels, promoting histone acetylation at loci
associated with effector and memory functions (Ma et al. 2025, Qiu et al. 2019). Similarly, inhibi-
tion of glycolysis using 2-deoxyglucose (2-DG) during T cell priming has been shown to enhance
T cell proliferation and antitumor activity (Sukumar et al. 2013), potentially by promoting reliance
on acetate-derived acetyl-CoA and reinforcing effector- or memory-related epigenetic landscapes
(Ma et al. 2025). Although lactate exhibits paradoxical effects on T cell function in tumors in vivo,
pretreatment of T cells with lactate in vitro has shown promising results. Lactate preconditioning
enhances T cell persistence and promotes a stem-like phenotype by inducing histone lactyla-
tion or inhibiting HDACs, thereby supporting favorable transcriptional programs and improving
antitumor efficacy upon transfer (Barbieri et al. 2023, Feng et al. 2022, Raychaudhuri et al. 2024).
Together, these findings demonstrate that targeted manipulation of the epigenetic and tran-
scriptional landscapes holds immense potential to enhance CAR-T cell fitness, longevity, and
antitumor efficacy, particularly within the immunosuppressive microenvironment of solid tumors.

[Link] • T Cell State Regulation 473

 Moreover, modulating upstream signals such as cytokine signaling and cellular metabolism offers a
more dynamic and adaptable approach to reprogram T cell states, enabling context-specific tuning
of their epigenetic and functional states for improved therapeutic outcomes.

COMBINING EPIGENETIC THERAPY AND IMMUNE THERAPY

US Food and Drug Administration (FDA)-approved epigenetic drugs, such as DNA methyltrans-
ferase (DNMT) inhibitors (e.g., 5-azacytidine, decitabine), EZH2 inhibitors (e.g., tazemetostat),
and HDAC inhibitors (e.g., romidepsin, vorinostat, belinostat, panobinostat), have already demon-
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

strated clinical efficacy in hematologic malignancies. In parallel, at least 10 additional classes

of epigenetic modulators, including inhibitors of SWI/SNF chromatin remodeling complexes,
lysine-specific demethylase 1 (LSD1), and bromodomain and extraterminal domain (BET) pro-
teins, are currently being evaluated in clinical trials (Mabe et al. 2024, Tolu et al. 2025, Yu et al.
2024). While originally developed to disrupt oncogenic transcriptional programs in tumor cells,
these agents are now increasingly recognized for their ability to modulate the immune system, in-
cluding T cells, highlighting their potential for synergistic combinations with immunotherapies
such as ICB and adoptive T cell therapies (Van Acker et al. 2021).
For example, histone deacetylase inhibitors (HDACi) have been shown in preclinical mod-
els to enhance antitumor immunity through multiple mechanisms. These include upregulating
MHC class I and II molecules to increase tumor antigen presentation, promoting chemokine ex-
pression for T cell recruitment, and reactivating effector gene programs in TEX cells (Khan &
Tomasi 2008, Magner et al. 2000, Woods et al. 2013). In early-phase clinical trials, the combina-
tion of the HDACi entinostat with the anti-PD-1 antibody pembrolizumab has demonstrated
a favorable safety profile and preliminary signs of clinical activity in patients with NSCLC
(Hellmann et al. 2021). Additional clinical trials are ongoing to evaluate HDACi and ICB combi-
nations across a range of solid tumors ([Link] identifiers NCT03812796
and NCT02453620) (Cartwright et al. 2024, Roussos Torres et al. 2024). HDACi have also been
combined with DNA methyltransferase inhibitors (DNMTi) for their synergistic effect with
ICB (NCT01928576). DNMTi agents may complement HDACi by demethylating endogenous
retroviral elements, thereby inducing a type I interferon response in tumors, and by removing
DNA methylation at key effector loci in T cells (Chiappinelli et al. 2015, Ghoneim et al. 2017,
Topper et al. 2017). These combinations not only increase tumor immunogenicity but also restore
T cell functionality, contributing to enhanced responses to ICB. Similarly, SWI/SNF inhibitors
(SWI/SNFi) have been shown to induce type I interferon responses in tumors, potentially con-
verting cold tumors into hot tumors, mimicking the SWI/SNF mutant tumors (Brodeur et al.
2024, Maxwell et al. 2024). Additionally, SWI/SNFi have been shown to enhance CAR-T activ-
ity in solid tumors (Battistello et al. 2023, Guo et al. 2022), positioning them as dual-function
agents that both sensitize tumors to immune attack and bolster adoptive T cell therapies. How-
ever, further investigation is needed to evaluate their potential off-target toxicities and risk of
tumorigenicity.
BET inhibitors represent another promising class of epigenetic drugs for combination im-
munotherapy (Doroshow et al. 2017). These agents target acetyl-lysine reader proteins that
regulate transcriptional elongation at key oncogenic and immune regulatory loci. BET inhibi-
tion, such as with the compound JQ1, remodels suppressive TME, promotes the expansion of
CD8+ T cells with stem-like and central memory phenotypes by suppressing BATF, a TF that
drives effector memory differentiation, and enhances the efficacy of CAR-T and TCR-T ther-
apies (Adeegbe et al. 2018, Kagoya et al. 2016, Wang et al. 2022). Early-phase clinical trials of
novel BET inhibitors, such as INCB054329, have demonstrated synergistic tumor suppression in

474 Ma • Hargreaves • Kaech

 multiple syngeneic murine models, underscoring their potential for broader clinical applications
(Koblish et al. 2016).
Collectively, ongoing preclinical and clinical evaluations of various epigenetic therapies
combined with ICB highlight a promising strategy to enhance immunotherapy efficacy. By re-
programming both tumor and immune cells, these combinatorial approaches have the potential
to overcome immunosuppression and significantly improve antitumor responses across a broad
range of malignancies.

CONCLUDING REMARKS
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

The T cell epigenome functions as a dynamic sensor of environmental cues, such as nutrient
availability, metabolic flux, and inflammatory signals, enabling the modulation of epigenetic states
and T cell fates through metabolic reprogramming and nutrient-based therapies. Indeed, dietary
interventions and metabolic reprogramming strategies may offer flexible and powerful approaches
to fine-tune the immune epigenome and T cell function in a context- and patient-specific manner
(Zhao et al. 2021).
Looking ahead, T cells represent an ideal test bed for predicting genomic function and gene
regulation using emerging machine learning approaches such as AlphaGenome. Their well-
defined developmental trajectories, plastic yet progressively restricted differentiation states, and
dynamic response to environmental cues, particularly within tumors, make them a powerful model
system. Advances in single-cell and spatial multiomics technologies, including integrated scRNA-
seq, single-cell ATAC-seq, single-cell chromatin immunoprecipitation sequencing (scChIP-seq),
and spatial transcriptomics augmented with epigenetic layers, are now enabling high-resolution
mapping of T cell states and regulatory programs across diverse tumor ecosystems (Hudson &
Wieland 2023).
Meanwhile, CRISPR-based functional epigenomics is transforming our capacity to systemat-
ically identify and validate chromatin regulators essential for T cell differentiation and function.
High-throughput pooled and single-cell CRISPR screens are accelerating the discovery of key
epigenetic regulators, offering a road map for prioritizing therapeutic targets (Xiang et al. 2024).
Moreover, the integration of artificial intelligence (AI) and machine learning with multiomics
and CRISPR screen datasets holds significant potential for identifying context-specific epige-
netic regulators and optimizing rational combination strategies tailored to the tumor and immune
epigenome (Lin et al. 2025). Complementing these, locus-specific epigenetic editing tools, such
as dCas9 fused to epigenetic writers and erasers (e.g., dCas9-DNMT3A, dCas9-TET1, dCas9-
p300), provide unprecedented precision for modulating gene expression at specific loci (Hilton
et al. 2015, Morita et al. 2016, Pflueger et al. 2018). Furthermore, emerging tools like proteolysis-
targeting chimera (PROTAC) and degron-based systems allow for temporally controlled and
reversible perturbation of chromatin regulators, facilitating causal dissection of epigenetic circuits
in T cell fate decisions and providing greater flexibility for therapeutic timing and modulation
(Kim et al. 2024, S. Li et al. 2023).
Together, these advances are paving the way for a new generation of rationally designed epige-
netic immunotherapies. By integrating personalized epigenomic profiling, functional genomics,
programmable editing technologies, and AI-based predictive modeling, we are moving toward
precise, context-dependent modulation of the T cell epigenome with spatial, temporal, and molec-
ular resolution. This approach will enable the selective expansion and preservation of TEXprog
cells for ACT and CAR-T therapies. Importantly, as we gain deeper mechanistic understanding
of locus-specific epigenetic regulation in TEX cell differentiation, such as nutrient-driven his-
tone codes, it may become possible to reprogram the TEXterm cells and restore their antitumor
capacity.

[Link] • T Cell State Regulation 475

 DISCLOSURE STATEMENT
The authors are not aware of any affiliations, memberships, funding, or financial holdings that
might be perceived as affecting the objectivity of this review.

ACKNOWLEDGMENTS
We thank Thomas H. Mann, H. Kay Chung, and Bryan McDonald from the Kaech lab for their
constructive comments and discussions. We apologize for not being able to cite all of the out-
standing studies in this area due to space limitations and gratefully acknowledge the valuable
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

contributions these works have made to advancing knowledge in this field.

LITERATURE CITED
Abdel-Hakeem MS, Manne S, Beltra JC, Stelekati E, Chen Z, et al. 2021. Epigenetic scarring of exhausted
T cells hinders memory differentiation upon eliminating chronic antigenic stimulation. Nat. Immunol.
22:1008–19
Adeegbe DO, Liu S, Hattersley MM, Bowden M, Zhou CW, et al. 2018. BET bromodomain inhibition co-
operates with PD-1 blockade to facilitate antitumor response in Kras-mutant non-small cell lung cancer.
Cancer Immunol. Res. 6:1234–45
Akbari B, Ghahri-Saremi N, Soltantoyeh T, Hadjati J, Ghassemi S, Mirzaei HR. 2021. Epigenetic strategies
to boost CAR T cell therapy. Mol. Ther. 29:2640–59
Alfei F, Kanev K, Hofmann M, Wu M, Ghoneim HE, et al. 2019. TOX reinforces the phenotype and longevity
of exhausted T cells in chronic viral infection. Nature 571:265–69
Alizadeh D, Wong RA, Yang X, Wang D, Pecoraro JR, et al. 2019. IL15 enhances CAR-T cell antitumor ac-
tivity by reducing mTORC1 activity and preserving their stem cell memory phenotype. Cancer Immunol.
Res. 7:759–72
Angelin A, Gil-de-Gomez L, Dahiya S, Jiao J, Guo L, et al. 2017. Foxp3 reprograms T cell metabolism to
function in low-glucose, high-lactate environments. Cell Metab. 25:1282–93.e7
Angelosanto JM, Blackburn SD, Crawford A, Wherry EJ. 2012. Progressive loss of memory T cell potential
and commitment to exhaustion during chronic viral infection. J. Virol. 86:8161–70
Baessler A, Vignali DAA. 2024. T cell exhaustion. Annu. Rev. Immunol. 42:179–206
Barbieri L, Velica P, Gameiro PA, Cunha PP, Foskolou IP, et al. 2023. Lactate exposure shapes the metabolic
and transcriptomic profile of CD8+ T cells. Front. Immunol. 14:1101433
Battistello E, Hixon KA, Comstock DE, Collings CK, Chen X, et al. 2023. Stepwise activities of mSWI/SNF
family chromatin remodeling complexes direct T cell activation and exhaustion. Mol. Cell 83:1216–36.e12
Baxter AE, Huang H, Giles JR, Chen Z, Wu JE, et al. 2023. The SWI/SNF chromatin remodeling com-
plexes BAF and PBAF differentially regulate epigenetic transitions in exhausted CD8+ T cells. Immunity
56:1320–40.e10
Belk JA, Daniel B, Satpathy AT. 2022a. Epigenetic regulation of T cell exhaustion. Nat. Immunol. 23:848–60
Belk JA, Yao W, Ly N, Freitas KA, Chen YT, et al. 2022b. Genome-wide CRISPR screens of T cell exhaustion
identify chromatin remodeling factors that limit T cell persistence. Cancer Cell 40:768–86.e7
Beltra JC, Manne S, Abdel-Hakeem MS, Kurachi M, Giles JR, et al. 2020. Developmental relationships of
four exhausted CD8+ T cell subsets reveals underlying transcriptional and epigenetic landscape control
mechanisms. Immunity 52:825–41.e8
Bengsch B, Johnson AL, Kurachi M, Odorizzi PM, Pauken KE, et al. 2016. Bioenergetic insufficiencies due
to metabolic alterations regulated by the inhibitory receptor PD-1 are an early driver of CD8+ T cell
exhaustion. Immunity 45:358–73
Bian Y, Li W, Kremer DM, Sajjakulnukit P, Li S, et al. 2020. Cancer SLC43A2 alters T cell methionine
metabolism and histone methylation. Nature 585:277–82
Brodeur MN, Dopeso H, Zhu Y, Longhini ALF, Gazzo A, et al. 2024. Interferon response and epigenetic
modulation by SMARCA4 mutations drive ovarian tumor immunogenicity. Sci. Adv. 10:eadk4851

476 Ma • Hargreaves • Kaech

 Burger ML, Cruz AM, Crossland GE, Gaglia G, Ritch CC, et al. 2021. Antigen dominance hierarchies shape
TCF1+ progenitor CD8 T cell phenotypes in tumors. Cell 184:4996–5014.e26
Cartwright E, Slater S, Saffery C, Tran A, Turkes F, et al. 2024. Phase II trial of domatinostat (4SC-202)
in combination with avelumab in patients with previously treated advanced mismatch repair proficient
oesophagogastric and colorectal adenocarcinoma: EMERGE. ESMO Open 9:102971
Chan JD, Scheffler CM, Munoz I, Sek K, Lee JN, et al. 2024. FOXO1 enhances CAR T cell stemness,
metabolic fitness and efficacy. Nature 629:201–10
Chang CH, Qiu J, O’Sullivan D, Buck MD, Noguchi T, et al. 2015. Metabolic competition in the tumor
microenvironment is a driver of cancer progression. Cell 162:1229–41
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

Chen J, Lopez-Moyado IF, Seo H, Lio CJ, Hempleman LJ, et al. 2019. NR4A transcription factors limit CAR
T cell function in solid tumours. Nature 567:530–34
Chen Y, Zander RA, Wu X, Schauder DM, Kasmani MY, et al. 2021. BATF regulates progenitor to cytolytic
effector CD8+ T cell transition during chronic viral infection. Nat. Immunol. 22:996–1007
Chen Z, Ji Z, Ngiow SF, Manne S, Cai Z, et al. 2019. TCF-1-centered transcriptional network drives an
effector versus exhausted CD8 T cell-fate decision. Immunity 51:840–55.e5
Chiappinelli KB, Strissel PL, Desrichard A, Li H, Henke C, et al. 2015. Inhibiting DNA methylation causes
an interferon response in cancer via dsRNA including endogenous retroviruses. Cell 162:974–86
Chisolm DA, Savic D, Moore AJ, Ballesteros-Tato A, Leon B, et al. 2017. CCCTC-binding factor translates
interleukin 2- and α-ketoglutarate-sensitive metabolic changes in T cells into context-dependent gene
programs. Immunity 47:251–67.e7
Christo SN, Park SL, Mueller SN, Mackay LK. 2024. The multifaceted role of tissue-resident memory
T cells. Annu. Rev. Immunol. 42:317–45
Chu T, Wu M, Hoellbacher B, de Almeida GP, Wurmser C, et al. 2025. Precursors of exhausted T cells are
pre-emptively formed in acute infection. Nature 640:782–92
Clarke J, Panwar B, Madrigal A, Singh D, Gujar R, et al. 2019. Single-cell transcriptomic analysis of tissue-
resident memory T cells in human lung cancer. J. Exp. Med. 216:2128–49
Cognet G, Muir A. 2024. Identifying metabolic limitations in the tumor microenvironment. Sci. Adv.
10:eadq7305
Corgnac S, Malenica I, Mezquita L, Auclin E, Voilin E, et al. 2020. CD103+ CD8+ TRM cells accumulate in
tumors of anti-PD-1-responder lung cancer patients and are tumor-reactive lymphocytes enriched with
Tc17. Cell Rep. Med. 1:100127
Cui G, Staron MM, Gray SM, Ho PC, Amezquita RA, et al. 2015. IL-7-induced glycerol transport and TAG
synthesis promotes memory CD8+ T cell longevity. Cell 161:750–61
Dai Z, Ramesh V, Locasale JW. 2020. The evolving metabolic landscape of chromatin biology and epigenetics.
Nat. Rev. Genet. 21:737–53
Daniel B, Yost KE, Hsiung S, Sandor K, Xia Y, et al. 2022. Divergent clonal differentiation trajectories of
T cell exhaustion. Nat. Immunol. 23:1614–27
Dimitri AJ, Baxter AE, Chen GM, Hopkins CR, Rouin GT, et al. 2024. TET2 regulates early and
late transitions in exhausted CD8+ T cell differentiation and limits CAR T cell function. Sci. Adv.
10:eadp9371
Ding ZC, Shi H, Aboelella NS, Fesenkova K, Park EJ, et al. 2020. Persistent STAT5 activation reprograms the
epigenetic landscape in CD4+ T cells to drive polyfunctionality and antitumor immunity. Sci. Immunol.
5:eaba5962
Doan AE, Mueller KP, Chen AY, Rouin GT, Chen Y, et al. 2024. FOXO1 is a master regulator of memory
programming in CAR T cells. Nature 629:211–18
Doroshow DB, Eder JP, LoRusso PM. 2017. BET inhibitors: a novel epigenetic approach. Ann. Oncol.
28:1776–87
Edwards J, Wilmott JS, Madore J, Gide TN, Quek C, et al. 2018. CD103+ tumor-resident CD8+ T cells are
associated with improved survival in immunotherapy-naive melanoma patients and expand significantly
during anti-PD-1 treatment. Clin. Cancer Res. 24:3036–45
Fabre S, Carrette F, Chen J, Lang V, Semichon M, et al. 2008. FOXO1 regulates L-selectin and a network of
human T cell homing molecules downstream of phosphatidylinositol 3-kinase. J. Immunol. 181:2980–89

[Link] • T Cell State Regulation 477

 Fagerberg E, Attanasio J, Dien C, Singh J, Kessler EA, et al. 2025. KLF2 maintains lineage fidelity and
suppresses CD8 T cell exhaustion during acute LCMV infection. Science 387:eadn2337
Feng Q, Liu Z, Yu X, Huang T, Chen J, et al. 2022. Lactate increases stemness of CD8 + T cells to augment
anti-tumor immunity. Nat. Commun. 13:4981
Fraietta JA, Nobles CL, Sammons MA, Lundh S, Carty SA, et al. 2018. Disruption of TET2 promotes the
therapeutic efficacy of CD19-targeted T cells. Nature 558:307–12
Franco F, Jaccard A, Romero P, Yu YR, Ho PC. 2020. Metabolic and epigenetic regulation of T-cell exhaustion.
Nat. Metab. 2:1001–12
Freitas KA, Belk JA, Sotillo E, Quinn PJ, Ramello MC, et al. 2022. Enhanced T cell effector activity by
targeting the Mediator kinase module. Science 378:eabn5647
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

Gabriel SS, Tsui C, Chisanga D, Weber F, Llano-Leon M, et al. 2021. Transforming growth factor-beta-
regulated mTOR activity preserves cellular metabolism to maintain long-term T cell responses in
chronic infection. Immunity 54:1698–714.e5
Gago da Graca C, Sheikh AA, Newman DM, Wen L, Li S, et al. 2025. Stem-like memory and precursors of
exhausted T cells share a common progenitor defined by ID3 expression. Sci. Immunol. 10:eadn1945
Gao X, Sanderson SM, Dai Z, Reid MA, Cooper DE, et al. 2019. Dietary methionine influences therapy in
mouse cancer models and alters human metabolism. Nature 572:397–401
Gavil NV, Cheng K, Masopust D. 2024. Resident memory T cells and cancer. Immunity 57:1734–51
Ghoneim HE, Fan Y, Moustaki A, Abdelsamed HA, Dash P, et al. 2017. De novo epigenetic programs inhibit
PD-1 blockade-mediated T cell rejuvenation. Cell 170:142–57.e19
Giles JR, Globig AM, Kaech SM, Wherry EJ. 2023. CD8+ T cells in the cancer-immunity cycle. Immunity
56:2231–53
Giles JR, Ngiow SF, Manne S, Baxter AE, Khan O, et al. 2022. Shared and distinct biological circuits in effector,
memory and exhausted CD8+ T cells revealed by temporal single-cell transcriptomics and epigenetics.
Nat. Immunol. 23:1600–13
Giuffrida L, Sek K, Henderson MA, House IG, Lai J, et al. 2020. IL-15 preconditioning augments CAR T
cell responses to checkpoint blockade for improved treatment of solid tumors. Mol. Ther. 28:2379–93
Gray SM, Amezquita RA, Guan T, Kleinstein SH, Kaech SM. 2017. Polycomb repressive complex 2-mediated
chromatin repression guides effector CD8+ T cell terminal differentiation and loss of multipotency.
Immunity 46:596–608
Guo A, Huang H, Zhu Z, Chen MJ, Shi H, et al. 2022. cBAF complex components and MYC cooperate early
in CD8+ T cell fate. Nature 607:135–41
Guo X, Zhang Y, Zheng L, Zheng C, Song J, et al. 2018. Global characterization of T cells in non-small-cell
lung cancer by single-cell sequencing. Nat. Med. 24:978–85
He R, Hou S, Liu C, Zhang A, Bai Q, et al. 2016. Follicular CXCR5-expressing CD8+ T cells curtail chronic
viral infection. Nature 537:412–28
He S, Liu Y, Meng L, Sun H, Wang Y, et al. 2017. Ezh2 phosphorylation state determines its capacity to
maintain CD8+ T memory precursors for antitumor immunity. Nat. Commun. 8:2125
Hellmann MD, Janne PA, Opyrchal M, Hafez N, Raez LE, et al. 2021. Entinostat plus pembrolizumab
in patients with metastatic NSCLC previously treated with anti-PD-(L)1 therapy. Clin. Cancer Res.
27:1019–28
Hess Michelini R, Doedens AL, Goldrath AW, Hedrick SM. 2013. Differentiation of CD8 memory T cells
depends on Foxo1. J. Exp. Med. 210:1189–200
Hilton IB, D’Ippolito AM, Vockley CM, Thakore PI, Crawford GE, et al. 2015. Epigenome editing by a
CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat. Biotechnol.
33:510–17
Ho PC, Bihuniak JD, Macintyre AN, Staron M, Liu X, et al. 2015. Phosphoenolpyruvate is a metabolic
checkpoint of anti-tumor T cell responses. Cell 162:1217–28
Huang YJ, Ngiow SF, Baxter AE, Manne S, Park SL, et al. 2025. Continuous expression of TOX safeguards
exhausted CD8 T cell epigenetic fate. Sci. Immunol. 10:eado3032
Hudson WH, Gensheimer J, Hashimoto M, Wieland A, Valanparambil RM, et al. 2019. Proliferating transi-
tory T cells with an effector-like transcriptional signature emerge from PD-1+ stem-like CD8+ T cells
during chronic infection. Immunity 51:1043–58.e4

478 Ma • Hargreaves • Kaech

 Hudson WH, Wieland A. 2023. Technology meets TILs: deciphering T cell function in the -omics era. Cancer
Cell 41:41–57
Im SJ, Hashimoto M, Gerner MY, Lee J, Kissick HT, et al. 2016. Defining CD8+ T cells that provide the
proliferative burst after PD-1 therapy. Nature 537:417–21
Jaccard A, Wyss T, Maldonado-Perez N, Rath JA, Bevilacqua A, et al. 2023. Reductive carboxylation
epigenetically instructs T cell differentiation. Nature 621:849–56
Jadhav RR, Im SJ, Hu B, Hashimoto M, Li P, et al. 2019. Epigenetic signature of PD-1+ TCF1+ CD8
T cells that act as resource cells during chronic viral infection and respond to PD-1 blockade. PNAS
116:14113–18
Jain N, Zhao Z, Koche RP, Antelope C, Gozlan Y, et al. 2024. Disruption of SUV39H1-mediated H3K9
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

methylation sustains CAR T-cell function. Cancer Discov. 14:142–57

June CH, O’Connor RS, Kawalekar OU, Ghassemi S, Milone MC. 2018. CAR T cell immunotherapy for
human cancer. Science 359:1361–65
Kagoya Y, Nakatsugawa M, Yamashita Y, Ochi T, Guo T, et al. 2016. BET bromodomain inhibition enhances
T cell persistence and function in adoptive immunotherapy models. J. Clin. Investig. 126:3479–94
Kamminga LM, Bystrykh LV, de Boer A, Houwer S, Douma J, et al. 2006. The Polycomb group gene Ezh2
prevents hematopoietic stem cell exhaustion. Blood 107:2170–79
Kang TG, Lan X, Mi T, Chen H, Alli S, et al. 2024. Epigenetic regulators of clonal hematopoiesis control
CD8 T cell stemness during immunotherapy. Science 386:eadl4492
Kasmani MY, Zander R, Chung HK, Chen Y, Khatun A, et al. 2023. Clonal lineage tracing reveals mechanisms
skewing CD8+ T cell fate decisions in chronic infection. J. Exp. Med. 220:e20220679
Kaymak I, Luda KM, Duimstra LR, Ma EH, Longo J, et al. 2022. Carbon source availability drives nutrient
utilization in CD8+ T cells. Cell Metab. 34:1298–311.e6
Kaymak I, Watson MJ, Oswald BM, Ma S, Johnson BK, et al. 2024. ACLY and ACSS2 link nutrient-dependent
chromatin accessibility to CD8 T cell effector responses. J. Exp. Med. 221:e20231820
Khan AN, Tomasi TB. 2008. Histone deacetylase regulation of immune gene expression in tumor cells.
Immunol. Res. 40:164–78
Khan O, Giles JR, McDonald S, Manne S, Ngiow SF, et al. 2019. TOX transcriptionally and epigenetically
programs CD8+ T cell exhaustion. Nature 571:211–18
Kharel A, Shen J, Brown R, Chen Y, Nguyen C, et al. 2023. Loss of PBAF promotes expansion and effector
differentiation of CD8+ T cells during chronic viral infection and cancer. Cell Rep. 42:112649
Kim MS, Bhargava HK, Shavey GE, Lim WA, El-Samad H, Ng AH. 2024. Degron-based bioPROTACs for
controlling signaling in CAR T cells. Preprint, bioRxiv. [Link]
2024.02.16.580396v1
Kim MV, Ouyang W, Liao W, Zhang MQ, Li MO. 2013. The transcription factor Foxo1 controls central-
memory CD8+ T cell responses to infection. Immunity 39:286–97
Koblish HK, Hansbury M, Hall L, Wang L-C, Zhang Y, et al. 2016. The BET inhibitor INCB054329
enhances the activity of checkpoint modulation in syngeneic tumor models. Cancer Res. 76(14
Suppl.):4904
Lan X, Mi T, Alli S, Guy C, Djekidel MN, et al. 2024. Antitumor progenitor exhausted CD8+ T cells are
sustained by TCR engagement. Nat. Immunol. 25:1046–58
Leone RD, Zhao L, Englert JM, Sun IM, Oh MH, et al. 2019. Glutamine blockade induces divergent metabolic
programs to overcome tumor immune evasion. Science 366:1013–21
Leong YA, Chen Y, Ong HS, Wu D, Man K, et al. 2016. CXCR5+ follicular cytotoxic T cells control viral
infection in B cell follicles. Nat. Immunol. 17:1187–96
Li S, Chen T, Liu J, Zhang H, Li J, et al. 2023. PROTACs: novel tools for improving immunotherapy in
cancer. Cancer Lett. 560:216128
Li T, Tan YT, Chen YX, Zheng XJ, Wang W, et al. 2023. Methionine deficiency facilitates antitumour
immunity by altering m6 A methylation of immune checkpoint transcripts. Gut 72:501–11
Lin M, Guo J, Gu Z, Tang W, Tao H, et al. 2025. Machine learning and multi-omics integration: advancing
cardiovascular translational research and clinical practice. J. Transl. Med. 23:388
Llibre A, Kucuk S, Gope A, Certo M, Mauro C. 2025. Lactate: a key regulator of the immune response.
Immunity 58:535–54

[Link] • T Cell State Regulation 479

 Loschinski R, Bottcher M, Stoll A, Bruns H, Mackensen A, Mougiakakos D. 2018. IL-21 modulates memory
and exhaustion phenotype of T-cells in a fatty acid oxidation-dependent manner. Oncotarget 9:13125–38
Luoma AM, Suo S, Wang Y, Gunasti L, Porter CBM, et al. 2022. Tissue-resident memory and circulating
T cells are early responders to pre-surgical cancer immunotherapy. Cell 185:2918–35.e29
Ma C, Wang L, Liao W, Liu Y, Mishra S, et al. 2022. TGF-β promotes stem-like T cells via enforcing their
lymphoid tissue retention. J. Exp. Med. 219:e20211538
Ma EH, Dahabieh MS, DeCamp LM, Kaymak I, Kitchen-Goosen SM, et al. 2024. 13 C metabolite tracing
reveals glutamine and acetate as critical in vivo fuels for CD8 T cells. Sci. Adv. 10:eadj1431
Ma S, Dahabieh MS, Mann TH, Zhao S, McDonald B, et al. 2025. Nutrient-driven histone code determines
exhausted CD8+ T cell fates. Science 387:eadj3020
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

Ma S, Ming Y, Wu J, Cui G. 2024. Cellular metabolism regulates the differentiation and function of T-cell
subsets. Cell Mol. Immunol. 21:419–35
Mabe NW, Perry JA, Malone CF, Stegmaier K. 2024. Pharmacological targeting of the cancer epigenome.
Nat. Cancer 5:844–65
Madden MZ, Ye X, Chi C, Fisher EL, Wolf MM, et al. 2023. Differential effects of glutamine inhibition
strategies on antitumor CD8 T cells. J. Immunol. 211:563–75
Magner WJ, Kazim AL, Stewart C, Romano MA, Catalano G, et al. 2000. Activation of MHC class I, II, and
CD40 gene expression by histone deacetylase inhibitors. J. Immunol. 165:7017–24
Martinez GJ, Pereira RM, Aijo T, Kim EY, Marangoni F, et al. 2015. The transcription factor NFAT promotes
exhaustion of activated CD8+ T cells. Immunity 42:265–78
Maxwell MB, Hom-Tedla MS, Yi J, Li S, Rivera SA, et al. 2024. ARID1A suppresses R-loop-mediated STING-
type I interferon pathway activation of anti-tumor immunity. Cell 187:3390–408.e19
McCutcheon SR, Swartz AM, Brown MC, Barrera A, McRoberts Amador C, et al. 2023. Transcriptional and
epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens.
Nat. Genet. 55:2211–23
McDonald B, Chick BY, Ahmed NS, Burns M, Ma S, et al. 2023. Canonical BAF complex activity shapes the
enhancer landscape that licenses CD8+ T cell effector and memory fates. Immunity 56:1303–19.e5
McLane LM, Abdel-Hakeem MS, Wherry EJ. 2019. CD8 T cell exhaustion during chronic viral infection and
cancer. Annu. Rev. Immunol. 37:457–95
McManus DT, Valanparambil RM, Medina CB, Scharer CD, McGuire DJ, et al. 2025. An early precursor
CD8+ T cell that adapts to acute or chronic viral infection. Nature 640:772–81
Miller BC, Sen DR, Al Abosy R, Bi K, Virkud YV, et al. 2019. Subsets of exhausted CD8+ T cells differentially
mediate tumor control and respond to checkpoint blockade. Nat. Immunol. 20:326–36
Morita S, Noguchi H, Horii T, Nakabayashi K, Kimura M, et al. 2016. Targeted DNA demethylation in vivo
using dCas9-peptide repeat and scFv-TET1 catalytic domain fusions. Nat. Biotechnol. 34:1060–65
Nabe S, Yamada T, Suzuki J, Toriyama K, Yasuoka T, et al. 2018. Reinforce the antitumor activity of CD8+
T cells via glutamine restriction. Cancer Sci. 109:3737–50
Nakaya M, Xiao Y, Zhou X, Chang JH, Chang M, et al. 2014. Inflammatory T cell responses rely on amino acid
transporter ASCT2 facilitation of glutamine uptake and mTORC1 kinase activation. Immunity 40:692–
705
O’Sullivan D, van der Windt GJ, Huang SC, Curtis JD, Chang CH, et al. 2014. Memory CD8+ T cells
use cell-intrinsic lipolysis to support the metabolic programming necessary for development. Immunity
41:75–88
Ouyang W, Beckett O, Flavell RA, Li MO. 2009. An essential role of the Forkhead-box transcription factor
Foxo1 in control of T cell homeostasis and tolerance. Immunity 30:358–71
Paley MA, Kroy DC, Odorizzi PM, Johnnidis JB, Dolfi DV, et al. 2012. Progenitor and terminal subsets of
CD8+ T cells cooperate to contain chronic viral infection. Science 338:1220–25
Pauken KE, Sammons MA, Odorizzi PM, Manne S, Godec J, et al. 2016. Epigenetic stability of exhausted
T cells limits durability of reinvigoration by PD-1 blockade. Science 354:1160–65
Pearce EL, Walsh MC, Cejas PJ, Harms GM, Shen H, et al. 2009. Enhancing CD8 T-cell memory by
modulating fatty acid metabolism. Nature 460:103–7
Peng M, Yin N, Chhangawala S, Xu K, Leslie CS, Li MO. 2016. Aerobic glycolysis promotes T helper 1 cell
differentiation through an epigenetic mechanism. Science 354:481–84

480 Ma • Hargreaves • Kaech

 Peralta RM, Xie B, Lontos K, Nieves-Rosado H, Spahr K, et al. 2024. Dysfunction of exhausted T cells is
enforced by MCT11-mediated lactate metabolism. Nat. Immunol. 25:2297–307
Pflueger C, Tan D, Swain T, Nguyen T, Pflueger J, et al. 2018. A modular dCas9-SunTag DNMT3A
epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A
constructs. Genome Res. 28:1193–206
Philip M, Fairchild L, Sun L, Horste EL, Camara S, et al. 2017. Chromatin states define tumour-specific
T cell dysfunction and reprogramming. Nature 545:452–56
Qiu J, Villa M, Sanin DE, Buck MD, O’Sullivan D, et al. 2019. Acetate promotes T cell effector function
during glucose restriction. Cell Rep. 27:2063–74.e5
Rausch L, Kallies A. 2025. Molecular mechanisms governing CD8 T cell differentiation and checkpoint
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

inhibitor response in cancer. Annu. Rev. Immunol. 43:515–43

Raychaudhuri D, Singh P, Chakraborty B, Hennessey M, Tannir AJ, et al. 2024. Histone lactylation drives
CD8+ T cell metabolism and function. Nat. Immunol. 25:2140–51
Reina-Campos M, Scharping NE, Goldrath AW. 2021. CD8+ T cell metabolism in infection and cancer. Nat.
Rev. Immunol. 21:718–38
Reinfeld BI, Madden MZ, Wolf MM, Chytil A, Bader JE, et al. 2021. Cell-programmed nutrient partitioning
in the tumour microenvironment. Nature 593:282–88
Roussos Torres ET, Ho WJ, Danilova L, Tandurella JA, Leatherman J, et al. 2024. Entinostat, nivolumab
and ipilimumab for women with advanced HER2-negative breast cancer: a phase Ib trial. Nat. Cancer
5:866–79
Roy DG, Chen J, Mamane V, Ma EH, Muhire BM, et al. 2020. Methionine metabolism shapes T helper cell
responses through regulation of epigenetic reprogramming. Cell Metab. 31:250–66.e9
Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, et al. 2018. Defining T cell states associated
with response to checkpoint immunotherapy in melanoma. Cell 175:998–1013.e20
Scharping NE, Menk AV, Moreci RS, Whetstone RD, Dadey RE, et al. 2016. The tumor microenviron-
ment represses T cell mitochondrial biogenesis to drive intratumoral T cell metabolic insufficiency and
dysfunction. Immunity 45:374–88
Scott AC, Dundar F, Zumbo P, Chandran SS, Klebanoff CA, et al. 2019. TOX is a critical regulator of tumour-
specific T cell differentiation. Nature 571:270–74
Sen DR, Kaminski J, Barnitz RA, Kurachi M, Gerdemann U, et al. 2016. The epigenetic landscape of T cell
exhaustion. Science 354:1165–69
Seo H, Chen J, Gonzalez-Avalos E, Samaniego-Castruita D, Das A, et al. 2019. TOX and TOX2 transcription
factors cooperate with NR4A transcription factors to impose CD8+ T cell exhaustion. PNAS 116:12410–
15. Erratum. 2019. PNAS 116:19761
Seo H, Gonzalez-Avalos E, Zhang W, Ramchandani P, Yang C, et al. 2021. BATF and IRF4 cooperate to
counter exhaustion in tumor-infiltrating CAR T cells. Nat. Immunol. 22:983–95
Sinclair LV, Howden AJ, Brenes A, Spinelli L, Hukelmann JL, et al. 2019. Antigen receptor control of
methionine metabolism in T cells. eLife 8:e44210
Sinclair LV, Rolf J, Emslie E, Shi YB, Taylor PM, Cantrell DA. 2013. Control of amino-acid transport by
antigen receptors coordinates the metabolic reprogramming essential for T cell differentiation. Nat.
Immunol. 14:500–8
Siska PJ, Beckermann KE, Mason FM, Andrejeva G, Greenplate AR, et al. 2017. Mitochondrial dysregulation
and glycolytic insufficiency functionally impair CD8 T cells infiltrating human renal cell carcinoma. JCI
Insight 2:e93411
Smith-Garvin JE, Koretzky GA, Jordan MS. 2009. T cell activation. Annu. Rev. Immunol. 27:591–619
Soriano-Baguet L, Brenner D. 2023. Metabolism and epigenetics at the heart of T cell function. Trends
Immunol. 44:231–44
Sprent J, Surh CD. 2002. T cell memory. Annu. Rev. Immunol. 20:551–79
Staron MM, Gray SM, Marshall HD, Parish IA, Chen JH, et al. 2014. The transcription factor FoxO1 sus-
tains expression of the inhibitory receptor PD-1 and survival of antiviral CD8+ T cells during chronic
infection. Immunity 41:802–14
Sukumar M, Liu J, Ji Y, Subramanian M, Crompton JG, et al. 2013. Inhibiting glycolytic metabolism enhances
CD8+ T cell memory and antitumor function. J. Clin. Investig. 123:4479–88

[Link] • T Cell State Regulation 481

 Sukumar M, Liu J, Mehta GU, Patel SJ, Roychoudhuri R, et al. 2016. Mitochondrial membrane potential
identifies cells with enhanced stemness for cellular therapy. Cell Metab. 23:63–76
Sullivan MR, Danai LV, Lewis CA, Chan SH, Gui DY, et al. 2019. Quantification of microenvironmental
metabolites in murine cancers reveals determinants of tumor nutrient availability. eLife 8:e44235
Tolu SS, Viny AD, Amengual JE, Pro B, Bates SE. 2025. Getting the right combination to break the epigenetic
code. Nat. Rev. Clin. Oncol. 22:117–33
Tonnerre P, Wolski D, Subudhi S, Aljabban J, Hoogeveen RC, et al. 2021. Differentiation of exhausted
CD8+ T cells after termination of chronic antigen stimulation stops short of achieving functional
T cell memory. Nat. Immunol. 22:1030–41
Topper MJ, Vaz M, Chiappinelli KB, DeStefano Shields CE, Niknafs N, et al. 2017. Epigenetic therapy ties
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

MYC depletion to reversing immune evasion and treating lung cancer. Cell 171:1284–300.e21
Tsui C, Kretschmer L, Rapelius S, Gabriel SS, Chisanga D, et al. 2022. MYB orchestrates T cell exhaustion
and response to checkpoint inhibition. Nature 609:354–60
Tyrakis PA, Palazon A, Macias D, Lee KL, Phan AT, et al. 2016. S-2-Hydroxyglutarate regulates CD8+ T-
lymphocyte fate. Nature 540:236–41
Utzschneider DT, Charmoy M, Chennupati V, Pousse L, Ferreira DP, et al. 2016. T cell factor 1-expressing
memory-like CD8+ T cells sustain the immune response to chronic viral infections. Immunity 45:415–27
Utzschneider DT, Delpoux A, Wieland D, Huang X, Lai CY, et al. 2018. Active maintenance of T cell memory
in acute and chronic viral infection depends on continuous expression of FOXO1. Cell Rep. 22:3454–67
Utzschneider DT, Gabriel SS, Chisanga D, Gloury R, Gubser PM, et al. 2020. Early precursor T cells establish
and propagate T cell exhaustion in chronic infection. Nat. Immunol. 21:1256–66
Utzschneider DT, Legat A, Fuertes Marraco SA, Carrie L, Luescher I, et al. 2013. T cells maintain an
exhausted phenotype after antigen withdrawal and population reexpansion. Nat. Immunol. 14:603–10
Van Acker HH, Ma S, Scolaro T, Kaech SM, Mazzone M. 2021. How metabolism bridles cytotoxic CD8+
T cells through epigenetic modifications. Trends Immunol. 42:401–17
Vodnala SK, Eil R, Kishton RJ, Sukumar M, Yamamoto TN, et al. 2019. T cell stemness and dysfunction in
tumors are triggered by a common mechanism. Science 363:eaau0135
Wang H, Liu G, Jin X, Song S, Chen S, et al. 2022. BET inhibitor JQ1 enhances anti-tumor immunity and
synergizes with PD-1 blockade in CRC. J. Cancer 13:2126–37
Wang R, Dillon CP, Shi LZ, Milasta S, Carter R, et al. 2011. The transcription factor Myc controls metabolic
reprogramming upon T lymphocyte activation. Immunity 35:871–82
Watson MJ, Vignali PDA, Mullett SJ, Overacre-Delgoffe AE, Peralta RM, et al. 2021. Metabolic support of
tumour-infiltrating regulatory T cells by lactic acid. Nature 591:645–51
Weber EW, Parker KR, Sotillo E, Lynn RC, Anbunathan H, et al. 2021. Transient rest restores functionality
in exhausted CAR-T cells through epigenetic remodeling. Science 372:eaba1786
Woods DM, Woan K, Cheng F, Wang H, Perez-Villarroel P, et al. 2013. The antimelanoma activity of the his-
tone deacetylase inhibitor panobinostat (LBH589) is mediated by direct tumor cytotoxicity and increased
tumor immunogenicity. Melanoma Res. 23:341–48
Wu T, Ji Y, Moseman EA, Xu HC, Manglani M, et al. 2016. The TCF1-Bcl6 axis counteracts type I interferon
to repress exhaustion and maintain T cell stemness. Sci. Immunol. 1:eaai8593
Xiang M, Li H, Zhan Y, Ma D, Gao Q, Fang Y. 2024. Functional CRISPR screens in T cells reveal new
opportunities for cancer immunotherapies. Mol. Cancer 23:73
Xiao Z, Locasale JW. 2021. Epigenomic links from metabolism-methionine and chromatin architecture. Curr.
Opin. Chem. Biol. 63:11–18
Xu S, Chaudhary O, Rodriguez-Morales P, Sun X, Chen D, et al. 2021. Uptake of oxidized lipids by the scav-
enger receptor CD36 promotes lipid peroxidation and dysfunction in CD8+ T cells in tumors. Immunity
54:1561–77.e7
Xu Y, Zhang M, Ramos CA, Durett A, Liu E, et al. 2014. Closely related T-memory stem cells correlate with
in vivo expansion of CAR.CD19-T cells and are preserved by IL-7 and IL-15. Blood 123:3750–59
Yan Y, Cao S, Liu X, Harrington SM, Bindeman WE, et al. 2018. CX3CR1 identifies PD-1 therapy-responsive
CD8+ T cells that withstand chemotherapy during cancer chemoimmunotherapy. JCI Insight 3:e97828
Yao C, Lou G, Sun HW, Zhu Z, Sun Y, et al. 2021. BACH2 enforces the transcriptional and epigenetic
programs of stem-like CD8+ T cells. Nat. Immunol. 22:370–80

482 Ma • Hargreaves • Kaech

 Yao C, Sun HW, Lacey NE, Ji Y, Moseman EA, et al. 2019. Single-cell RNA-seq reveals TOX as a key regulator
of CD8+ T cell persistence in chronic infection. Nat. Immunol. 20:890–901
Yu X, Zhao H, Wang R, Chen Y, Ouyang X, et al. 2024. Cancer epigenetics: from laboratory studies and
clinical trials to precision medicine. Cell Death Discov. 10:28
Yu YR, Imrichova H, Wang H, Chao T, Xiao Z, et al. 2020. Disturbed mitochondrial dynamics in CD8+ TILs
reinforce T cell exhaustion. Nat. Immunol. 21:1540–51
Zander R, Cui W. 2023. Exhausted CD8+ T cells face a developmental fork in the road. Trends Immunol.
44:276–86
Zander R, Schauder D, Xin G, Nguyen C, Wu X, et al. 2019. CD4+ T cell help is required for the formation of a
cytolytic CD8+ T cell subset that protects against chronic infection and cancer. Immunity 51:1028–42.e4
Downloaded from [Link]. Guest (guest) IP: [Link] On: Sun, 03 May 2026 17:57:40

Zhang D, Tang Z, Huang H, Zhou G, Cui C, et al. 2019. Metabolic regulation of gene expression by histone
lactylation. Nature 574:575–80
Zhang F, Zhou X, DiSpirito JR, Wang C, Wang Y, Shen H. 2014. Epigenetic manipulation restores functions
of defective CD8+ T cells from chronic viral infection. Mol. Ther. 22:1698–706
Zhang L, Li Z, Skrzypczynska KM, Fang Q, Zhang W, et al. 2020. Single-cell analyses inform mechanisms of
myeloid-targeted therapies in colon cancer. Cell 181:442–59.e29
Zhao S, Peralta RM, Avina-Ochoa N, Delgoffe GM, Kaech SM. 2021. Metabolic regulation of T cells in the
tumor microenvironment by nutrient availability and diet. Semin. Immunol. 52:101485
Zhao S, Torres A, Henry RA, Trefely S, Wallace M, et al. 2016. ATP-citrate lyase controls a glucose-to-acetate
metabolic switch. Cell Rep. 17:1037–52
Zheng C, Zheng L, Yoo JK, Guo H, Zhang Y, et al. 2017. Landscape of infiltrating T cells in liver cancer
revealed by single-cell sequencing. Cell 169:1342–56.e16
Zheng L, Qin S, Si W, Wang A, Xing B, et al. 2021. Pan-cancer single-cell landscape of tumor-infiltrating
T cells. Science 374:abe6474
Zhou P, Shi H, Huang H, Sun X, Yuan S, et al. 2023. Single-cell CRISPR screens in vivo map T cell fate
regulomes in cancer. Nature 624:154–63

[Link] • T Cell State Regulation 483