Sage Journals: Discover world-class research

Abstract

Non-Hodgkin’s lymphomas (NHLs) comprise a diverse group of diseases, either of mature B-cell or of T-cell derivation, characterized by heterogeneous molecular features and clinical manifestations. While most of the patients are responsive to standard chemotherapy, immunotherapy, radiation and/or stem cell transplantation, relapsed and/or refractory cases still have a dismal outcome. Deep sequencing analysis have pointed out that epigenetic dysregulations, including mutations in epigenetic enzymes, such as chromatin modifiers and DNA methyltransferases (DNMTs), are prevalent in both B- cell and T-cell lymphomas. Accordingly, over the past decade, a large number of epigenetic-modifying agents have been developed and introduced into the clinical management of these entities, and a few specific inhibitors have already been approved for clinical use. Here we summarize the main epigenetic alterations described in B- and T-NHL, that further supported the clinical development of a selected set of epidrugs in determined diseases, including inhibitors of DNMTs, histone deacetylases (HDACs), and extra-terminal domain proteins (bromodomain and extra-terminal motif; BETs). Finally, we highlight the most promising future directions of research in this area, explaining how bioinformatics approaches can help to identify new epigenetic targets in B- and T-cell lymphoid neoplasms.

Keywords

BET inhibitors bioinformatics clinical testing DNMT drug combination epigenetics EZH2 HAT HDAC non-Hodgkin’s lymphoma

Introduction

Non-Hodgkin’s lymphoma (NHL) is a common type of hematological malignant tumor, composed of multiple subtypes that originate from B lymphocytes, T lymphocytes, and natural killer (NK) cells. These entities are sub-divided into distinct categories based on the differentiation stage of the malignant cells and on the presence of specific genetic alterations, being diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), T-cell lymphoma (TCL), and NK-T-cell lymphoma (NKTCL) the most common subtypes.

Characteristics of B-NHL

At the origin of roughly 90% of the cases of lymphoma, B-NHLs comprise a heterogeneous group of lymphoid neoplasms originated from either mature or immature B cells, the diagnosis of which is based on morphological, immunophenotypic, and genetic features, and most of them being dictated by the cell of origin¹ (see Figure 1). B-NHL subtypes range in their severity from well-controlled, indolent diseases, to extremely aggressive forms with urgent unmet medical needs that still require the development of novel therapeutic options.

Figure 1.

B- and T-cell lymphomagenesis.

The most common B-NHL subtype is DLBCL, which accounts for 25–35% of all cases. This aggressive disease is characterized by a heterogeneous molecular pathogenesis that can lead to different clinical characteristics.² Despite high-throughput sequencing having recently identified up to seven genetic subtypes,^3–5 gene expression profiling (GEP)-mediated identification of germinal center B-cell (GCB), activated B-cell (ABC), and unclassifiable subgroup⁶ remains widely used in the clinical management of these patients. Patients with ABC-DLBCL or genetic alterations in MYC and BCL2 and/or BCL6, called double hit (DHLs) or triple hit lymphomas (THLs), have generally a poor survival prognosis.

The second most common B-NHL is FL, another germinal center (GC)-derived malignancy that accounts for 20% of all cases. FL is characterized by the t(14;18)(q32;q21) translocation that leads to the overexpression of the BCL2 anti-apoptotic gene.⁷ FL represents a paradigm of dependence on the microenvironment. Seminal microarray studies in lymph node (LN) biopsies from the Leukemia and Lymphoma Profiling Project (LLMPP) series established for the first time that FL prognosis was not given by the tumor cell per se but by the composition of non-malignant cells.⁸ Although the clinical course is mostly indolent, about 20% of patients may relapse or progress to a transformed (more aggressive) form of FL (t-FL).

Burkitt lymphoma (BL) is a third GC-derived lymphoma, which represents 1–5% of all NHL, and which is characterized by the deregulation of MYC due to translocations such as t(8;14)(q23;q32). Three subtypes have been described, namely endemic, sporadic, and immunodeficiency-associated form, which is mostly found in patients infected with the human immunodeficiency virus (HIV).⁹

Originated from mature B-cells of the mantle zone of the LN, mantle cell lymphoma (MCL) accounts for 3–10% of B-NHL, being the t(11;14)(q13;q32) translocation and the expression of the cell cycle regulator cyclin D1 (CCND1), physiologically undetectable in normal B cells, the main characteristics of the disease. Supporting the notion that t(11;14) translocation is an epigenetic event, the Eμ and 3′ Cα cis IgH enhancer elements and the regions upstream of the CCND1 gene are hypomethylated on the translocated allele, and histones surrounding the translocation have shown hyperacetylation.¹⁰ MCL is also characterized by a high genomic instability with a high number of secondary genetic alterations involving cell cycle regulation, DNA damage response, cell death, nuclear factor kappa B (NF-κB), or epigenetic modifiers, with a median number of six secondary events. ATM, CCND1, TP53, and RB1 are among the most recurrently mutated genes.¹¹ MCL has poor prognosis due to diagnosis often at a disseminated stage and an aggressive clinical evolution.

Physiopathology of T-cell lymphoma

Contrasting with B-cell lymphoma, T-cell lymphomas (TCLs) are characterized by numerous T-cell subsets, functional plasticity of which depends on the microenvironment. As a result, appearance of features that do not fit with the cell originating the tumor is common,^12–14 thereby preventing tumor classification and a proper diagnosis of the disease and affecting the clinical management of the patients. Introduction of global GEP technologies are slowly improving our knowledge in the pathological origin of TCLs, but there is still room for improvement.

Mechanisms implicated in TCL development can be intrinsic and imply recurrent mutations leading to: (1) immune evasion, being the most clear example of the nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) oncogene, expressed in ALK+ anaplastic large cell lymphoma (ALCL), which regulates the expression of the immunosuppressive protein programmed death-ligand 1 (PD-L1);¹⁵ (2) alterations within T cell receptor (TCR) signaling pathway, such as mutations affecting the RhoA GTPase¹⁶ or gain-of-function mutations in regulators of T-cell activation and function such as phospholipase C gamma 1 (PLCG1), phosphatidylinositol-3 kinase (PI3K) family, catenin beta-1 (CTNNB1), CD28, caspase recruitment domain family member 11 (CARD11), vav guanine nucleotide exchange factor 1 (VAV1), interferon regulatory factor 4 (IRF4), mainly observed in peripheral T-cell lymphomas (PTCLs), including adult T-cell leukemia/lymphoma (ATLL) and angioimmunoblastic T-cell lymphoma (AITL);^14,17 (3) the implication of whole families of genes or signaling pathways, such as the PI3K-AKT-mTOR axis found to be constitutive activated during TCL pathogenesis,^18,19 or the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway, in which mutations in kinases and transcription activators such as STAT3 or STAT5B, JAK1, JAK3, or JAK5, may not directly induce the lymphoma, but rather confer clinical aggressiveness due to increased cytokine-dependent signaling and consequent promotion of cell growth, immune response, tumor metabolism, and cell death blockade;^17,18,20,21 (4) alteration in transcription factors such as activator protein-1 (AP-1), musculoaponeurotic fibrosarcoma (MAF) and basic leucine zipper ATF-like (BAF) transcription factor families, which are commonly involved in cutaneous T-cell lymphoma (CTCL) and CD30 + PTCL development, by activating the expression of the T-cell growth and survival genes, MYC and CD30, or driving the production of pro-tumoral cytokines;^22,23 (5) PI3K-AKT-mTOR-mediated deregulation or glutamine, nucleotides, and lipid metabolism, and consequent enhancement of lymphoma cell growth;^24,25 (6) altered mitochondrial functions, including a STAT3-mediated deregulation of mitochondrial respiration,^26,27 and as recently described, a glyceraldehyde 3-phosphate dehydrogenase (GAPDH) overexpression-driven development of AITL-like disease;²⁸ and (7) epigenetic deregulation, leading to the silencing of tumor-suppressor genes or the overexpression of several proto-oncogenes (see Figure 1).

Beside these intrinsic mechanisms, a number of extrinsic factors also favor TCLs pathogenesis, such as pro-inflammatory cytokines and chemokines, which build a microenvironment that promote and sustain the survival of the tumor cells, or oncogenic Epstein–Barr virus (EBV)- and T-cell lymphotropic virus type 1 (HTLV-1)-derived viral factors that promote oncogenesis from indolent cutaneous lymphoproliferative diseases to extremely aggressive TCLs such as ATLL.^29,30

Epigenetic deregulations in B- and T-cell lymphoma

A high level of alteration in chromatin state and a frequent deregulation of several epigenetic modulators, are common hallmarks that have been highlighted in most B-NHL subtypes in early 2000s.

Modification of DNA methylation patterns (either hypo- or hyper- DNA methylation status) have been associated for years to somatic mutations in epigenetic regulators of DNA methylation and to a generally repressed conformation of the chromatin in B-NHL.^31,32 Loss-of-function (LOF) mutations (truncation or frameshift mutations) affecting the SET domain of the histone-lysine N-methyltransferase 2D (MLL2/KMT2D) gene is the most frequently epigenetic alteration in DLBCL and FL, occurring, respectively, in about 30% and 90% of the cases, respectively. Inactivation of KMT2D leads to the expansion of GC-derived B cells, impedes class switch recombination and cooperates with the deregulation of BCL2 to increase the incidence of tumors, in association with reduced H3K4 methylated levels.^33–38

While LOF and/or deleterious mutations in the CREB binding protein (CREBBP) and E1A binding protein 300 (EP300) coding for two histone acetyltransferases (HATs) were detected in about 40% of DLBCL and FL cases,^35,39 these two entities also share the presence of point mutations in the myocyte enhancer binding factor 2B (MEF2B) gene codifying for a HAT recruiter (13% of GCB-DLBCL cases and 15% of FL patients).³⁹ From one side, mutant CREBBP and EP300 proteins are deficient in acetylating BCL6 and p53 leading, respectively, to constitutive oncogenic properties and to decreased tumor suppressor activity, thus favoring an increased tolerance for DNA damage mediated by impaired apoptosis triggering and cell cycle arrest.⁴⁰ In parallel, MEF2B mutations decrease the transcriptional activity of this factor, thereby lowering B-cell lymphoma 6 (BCL6) expression levels and leading to decreased activity of the TGFB1 tumor suppressor gene, encoding for transforming growth factor β, together with an increased expression of MYC. The global biological impact of these modifications consists in a reduced inhibition of chemotaxis and in the promotion of B-cell lymphomagenesis.⁴¹

In a lower extent, activating mutations of the enhancer of zeste homolog 2 (EZH2) histone methyltransferase (HMT) gene are specifically found in GC-derived NHL, such as GCB-DLBCL (22% of the patients) and FL (7% of the patients)^42,43 (see Figure 2). Expression of the EZH2^Y641F mutant was associated with the reprogramming of the immunological niche, a process by which the supporting activity of T cells toward GC-B cell development becomes ensured by follicular dendritic cells (FDCs).⁴⁴ Finally, despite genes coding for histone deacetylases (HDACs) remained unmutated in B-NHL patients, an overexpression of HDAC1, HDAC2, and HDAC6 with a consequent global decrease in the activity of the transcription machinery, has been reported in DLBCL cases.⁴⁵ In particular, HDAC6 exerts a crucial role in the response to proteotoxic stress, as it orchestrates the acetylation-dependent stability of heat shock protein of 90 kD (HSP0) and the recruitment of misfolded protein cargo to dynein motors for their transport to intracellular aggresomes.⁴⁶

Figure 2.

Alterations of chromatin states in B- and T-cell lymphoma.

TCLs present a similar mutation spectrum of epigenetic genes than B-cell lymphoma, which includes missense mutations, concomitantly to a general chemo-resistant phenotype.^14,47 Genetic alterations in DNA methylation genes affect Tet methylcytosine dioxygenase 2 (TET2), DNA methyl transferase 3 A (DNMT3A) and isocitrate dehydrogenase 2 (IDH2). These alterations are mainly found in T follicular helper (Tfh) cell-derived PTCLs and constitute the hallmark of AITL, a disease where the three genes are affected simultaneously.⁴⁸ TET2 and DNMT3A deregulations are also found in CTCL.⁴⁷ Similar mutations of TET2 are found in the hematopoietic stem and progenitor cells (HSPCs) of some AITL patients. Notwithstanding, none of these mutations will lead to lymphoma appearance, but will rather favor a premalignant status characterized by a disrupted homeostasis within the hematopoietic stem/progenitor compartment, being the malignant transformation achieved upon the acquisition of further defects in key genes such as RHOA, PLCG1, or NOTCH2.⁴⁹

Modifications in chromatin remodelers such as SET domain containing 2 (SETD2), INO80, involved in DNA repair and cell cycle regulation, and AT-Rich Interaction Domain 1B (ARID1B), have been found in up to 62% of hepatosplenic γδ T-cell lymphoma (HTCL) patients.⁵⁰ SETD2, which acts as a tumor suppressor gene, was the most silenced gene in HTCL and is mutated in monomorphic epitheliotropic intestinal T-cell lymphoma (MEITL). Loss of SETD2 has been further associated with increased cell growth, altered expression of cell cycle genes, and compromised DNA damage response and repair.⁵¹ ARID2, ARID1B, SETD1B mutations are also found in PTCL-NOS.⁵² ARID1A, ARID5B, and SMARCC1 mutations are present in CTCL.⁵³ Finally, ARID1A mutations have been detected in NKTCL.⁵⁴ While ARID1A expression is sufficient to suppress cellular proliferation and tumor growth in mouse models of cancers, in-frame mutations of this gene lead to the nuclear retention of this tumor suppressor, due to its increased degradation and incapacity to stimulate the expression of the cell cycle inhibitor gene, CDKN1A.⁵⁵

Defects in histone methylation have been associated to mutations in KMT2C, KM2D, and KDM6A genes in PTCL-NOS.⁵² NKTC lymphoma harbors mutations in KMT2D, EZH2, and also in ASXL transcriptional regulator 3 (ASXL3) genes, a phenomenon linked to altered histone deubiquitination.⁵⁴ Histone acetylation genes such as EP300 and CREBBP are mutated in PTCL-NOS⁵² (see Figure 2). Deregulated expression and/or activity of these epigenetic writers, lead to genome-wide DNA and histone modification pattern alterations, modifying the chromatin structure, and thereby leading to cancer development.⁵⁶

Importantly, HDACs have become a promising therapeutic targets (see below) in the context of some TCLs such as CTCL, through their role in the silencing of different BCL-2 proapoptotic family members and in the regulation of autophagy.⁵⁷

Role of epigenetic drugs in B- and T-cell lymphoma

DNA methylation inhibitors

DNA methyltransferases (DNMTs) family includes three major members that have functional methylation activities, namely DNMT1, which mediates maintenance methylation during cell division, and DNMT3A and DNMT3B, that regulate de novo DNA methylation.^58,59 Accumulating evidences have shown that DNMTs regulation of methylation have an important role in normal hematopoiesis.^60,61 On the contrary, aberrant methylation is a key molecular event on the development of hematological malignancies. Indeed, hypermethylation of CDKN2A/p16 is associated with aggressive forms of B-NHL, and can drive progression of T-cell malignancies.^62,63 Considering that an altered methylation pattern is frequently observed in most types of cancers, including B- and T-cell lymphoma, the development of epigenetic drugs to restore methylation levels seems to be an interesting strategy for the treatment of these diseases.⁶⁴

In the 1970s, the nucleoside analogs 5-azacytidine and 5-aza-20-deoxycytidine (or decitabine) appeared in the clinic as a chemotherapeutic option against acute leukemia. Mechanistically, these cytidine analogs are incorporated into DNA, promoting an irreversible blockage of DNMT1, which consequently leads to global demethylation.^65–67 Although azacytidine and decitabine were considered as promising chemotherapeutic agents, the early clinical trials showed a disappointing response and a pronounced toxicity in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) patients.^68–70 Subsequently, in vitro data indicated that low doses of azacytidine can induce a decrease in DNA methylation level, supporting its use as an epigenetic drug.⁷¹ Given the remarkable improvement of the overall survival (OS), and more generally the excellent clinical response of MDS patients to this agent, azacytidine became in 2004 the first drug approved by Food and Drug Administration (FDA) for this indication.^72,73 In B-NHL patients, only two phase I studies using decitabine as a single agent have been completed so far.^74,75 However, until now, the use of DNMT inhibitors (DNMTis) as monotherapy yielded disappointing results in lymphoid malignancies.⁷⁶ Currently, azacytidine and decitabine are being evaluated mostly in combination with other drugs in approximately 95 active clinical trials involving B- and T-cell lymphoma patients. In this review, we will present clinical data from completed or terminated clinical trials (see Table 1).

Table 1.

Clinical evaluation of epidrug and epidrug-based combination therapies in B- and T-cell lymphoma.

Targets	Drug/Regimen	Trial ID	Phase/Status	No. of patients	Diseases	Response	Toxicity	Study
DNMT	Decitabine + Tetrahydrouridine	NCT02846935	I Completed	7	R/R- HL, DLBCL, PTCL, AITL	OR 57%	Grade 3–4 AEs: TP 100%	Hill et al.⁷⁷
DNMT	Azacitidine + Vorinostat +Gemcitabine + Busulfan + Melphalan	NCT01983969	I/II Completed	61	DLBCL, HL, T-cell NHL, FL, MCL	EFS 75%	Not serious AEs: 100%	Clinical trial⁷⁸
DNMT	Azacitidine + Lenalidomide	NCT01121757	II Terminated	9	R/R – FL, MZL	CR 17%	Grade 3–4 AEs: Toxicities 100%, TP 33%	Clinical trial⁷⁹
DNMT	Azacitidine + Vorinostat	NCT01120834	I/II Completed	18	R/R DLBCL	ORR 6.7%	Grade 3–4 AEs: Toxicities 100%, Anemia 7%, TP 33%	Clinical trial⁸⁰
DNMT	Azacitidine + RCHOP	NCT01004991	I/II Completed	12	DLBCL	CR 91.7%	Grade 3–4 AEs: NP 100%	Clinical trial⁸¹
DNMT	Azacitidine + RCHOP	NCT02343536	I Completed	52	DLBCL, FL, tFL	ORR 94.9%, CR 88.1% 1- and 2-year PSF 84.1% and 78.6%	Grade 3–4 AEs: NP 62.7%, febrile NP 25.4%	Martin et al.⁸²
DNMT	Azacitidine + Romidepsin	NCT01998035	I/II Terminated	23	R/R–NHL, HL	ORR 61% CR 48%	Grade 3–4 AEs: TP 48%, NP 40%, LP 32%, anemia 16%	Falchi et al.⁸³ O’Connor et al.⁸⁴
DNMT	Azacitidine + Avelumab + Utomilumab +	NCT02951156	III Terminated	9	R/R DLBCL	ORR 0	No dose-limiting toxicities were reported	Hawkes et al.⁸⁵
DNMT	Vincristine + Prednisone + Etoposide + Thioguanine, Cytarabine + Asparaginase + Methotrexate	NCT00002590	II Completed	86	Children with lymphoma	5-year OS 80% 5-year EFS 68%	Grade 4 AEs: NP 82%, TP 66%, anemia 38%, hepatotoxicity 4%	Lowe et al.⁸⁶
HDAC	Belinostat	NCT00274651	II Terminated	53	R/R cutaneous and peripheral TCL	ORR 25% (PTCL) and 14% (CTCL)	Grade 3–4 AEs: 77%	Johnston et al.⁸⁷
HDAC	Belinostat + CHOP	NCT01839097	II Completed	23	PTCL first line	ORR 86% CR 71%	No additional toxicity was observed with the combination SAEs 43%	Johnston et al.⁸⁸
HDAC	Belinostat	NCT00865969	II Completed	129	R/R PTL	ORR 25.8%	Grade 3–4 AEs 47.29%	Campbell and Thomas⁸⁹
HDAC	Panobinostat + Bortezomib	NCT00901147	II Completed	25	R/R–PTL lymphoma or NK/TCL	ORR 43% CR 22%	Grade 3–4 AEs: TP 68%, NP 20%, diarrhea 20%	Tan et al.⁹⁰
HDAC	Panobinostat	NCT01523834	II Completed	35	DLBCL	ORR 17.1% CR 11.4%	Grade 3–4 AEs: TP >5%	Duvic et al.⁹¹
HDAC	Panobinostat	NCT00425555	II Completed	139	Refractory CTL	PR 21.6% CR 0.7%	Grade 3–4 AEs: 28.8	Duvic et al.⁹¹
HDAC	Panobinostat	NCT01034163	III Completed	41	HL	Not Completed 100%	Grade 3–4 AEs: TP 27%, NP 27%, diarrhea 89%	Clinical trial⁹²
HDAC	Panobinostat + Everolimus	NCT00967044	I/II Completed	31	R/R lymphoma	ORR 10% (TCL, MCL, HL) ORR 43% (HL) CR 15% (HL)	Grade 3–4 AEs: TP 64%, NP 47%, anemia 20%	Oki et al.⁹³
HDAC	Valproic acid + RCHOP	NCT01622439	I/II Completed	495	DLBCL	1-year PFS 97.0%, 2-year PFS 84.7% 1-year OS 100% 2-year OS 96.8%	No toxicity reported	Drott et al.⁹⁴
HDAC	Abexinostat	NCT00724984	I/II Completed	87	R/R lymphoma, NHL, and CLL	ORR 28% CR 5%	Grade 3 AEs: TP 80%, NP 27%, anemia 12%	Evens et al.⁹⁵ and Ribrag et al.⁹⁶
HDAC	Mocetinostat	NCT00358982	II Terminated	51	R/R HL	PR 30% CR 10%	Grade 3–4 AEs: TP 21.5%, NP 13.7%	Younes et al.⁹⁷
HDAC	Fimepinostat + Rituximab, Venetoclax	NCT01742988	I Completed	44	R/R DLBCL, MYC-altered DLBCL	DLBCL ORR 37% CR 11.2% PR 14.6 MYC-altered DLBCL ORR 64% CR 36% PR27%	Grade 3–4 AEs: TP 20%, NP 7%	Younes et al.⁹⁸
HDAC	Vorinostat + Rituximab + Combination chemotherapy	NCT00601718	I/II Completed	29	R/R lymphoma or untreated TNHL, MCL	ORR 70% CR 30%	Grade 3 AEs: gastrointestinal toxicity 33%	Budde et al.⁹⁹
HDAC	Vorinostat + Niacinamide + Etoposide	NCT00691210	I Completed	40	HL, NHL	ORR 24%, CR 10% PR 14% 7.5%. Twelve patients achieved SD (57%).	Grade 3–4 AEs: 27.5%	Amengual et al.¹⁰⁰
HDAC	Vorinostat + Chemotherapy + Rituximab	NCT01193842	I/II Completed	86	HIV-related DLBCL or other aggressive BCL	CR 74% versus 68% for EPOCH versus EPOCH-vorinostat	Grade 4 AEs: NP (47% and 20%), LP (20% and 7%), and TP (29% and 2%) for vorinostat-EPOCH and EPOCH alone, respectively	Ramos et al.¹⁰¹
HDAC	Vorinostat + Fludarabine phosphate + Cyclophosphamide + Rituximab	NCT00918723	I/II Completed	40	CLL 32, SLL 8	ORR 91% CR 74%, PR 11%	Grade 4 AEs: hematologic 36%, electrolyte abnormalities 9%, gastrointestinal 8%, and cardiovascular 6%	Shadman et al.¹⁰²
HDAC	Vorinostat + Cladribine + Rituximab	NCT00764517	I/II Completed	57	MCL, R/R-CLL, or BNHL	ORR 39% in R/R patients, ORR 97%, CR 80% in MCL	Grade 2–3 AEs: NP 67%, TP 42%, anemia 14%	Spurgeon et al.¹⁰³
HDAC	Vorinostat + Bortezomib	NCT00992446	II Completed	27	NHL	ORR 74% CR 42%	Grade 4 AEs: NP 30%	Holmberg et al.¹⁰⁴
HDAC	Vorinostat	NCT00253630	II Completed	35	R/R-FL, MZL, MCL	FL-ORR 47%, CR 23.5%, PR 23.5%, MZL-ORR 22%, CR 11%, PR 11%	Acceptable safety profile	Kirschbaum et al.¹⁰⁵
HDAC	Vorinostat	NCT00875056	II Completed	50	R/R-FL, BNHL, MCL	FL-ORR 49%, CR 10%, PR 31%.	Grade 3–4 AEs: TP 93%, NP 68%	Ogura et al.¹⁰⁶
HDAC	Vorinostat + Rituximab + Cyclophosphamide + Etoposide + Prednisone	NCT00667615	I/II Completed	30	R/R DLBCL	ORR 57%, CR 35%, PR 22%	Grade 3–4 AEs: LP 90%, leucopenia 66%, NP 52%, TP 41%, and anemia 31%	Straus et al.¹⁰⁷
HDAC	Vorinostat + Rituximab	NCT00720876	II Completed	28	iNHL	ORR 41%, CR 27%, PFS 29.2 months	Grade 3–4 AEs: Fatigue 32%, LP 25%	Chen et al.¹⁰⁸
HDAC	Chidamide + CHOP	NCT02809573	I/II Completed	383	PTCL	ORR 39% as chidamide monotherapy, ORR 51% combined therapy	Grade 3–4 AEs: TP 18.1%, NP 12.6%, anemia 7.1%, and fatigue 5.5%	Shi et al.¹⁰⁹
HDAC	Romidepsin	NCT00007345	II Completed	71	TCL, PTCL	ORR 34%, CR 20%	Grade 3–4 AEs TP 47%, leucopenia 47%, granulocytopenia 45%, anemia 40%, LP 17%	Piekarz et al.¹¹⁰
HDAC	Romidepsin + Alisertib	NCT01897012	I Completed	25	R/R aggressive BCL and TCL	ORR 28% CR 12%	Grade 3–4 AEs: TP 40%, NP 24%, anemia 28%	Strati et al.¹¹¹
HDAC	Romidepsin + 5-azacitidine	NCT01998035	I/II Terminated	25	PTCL, FL	PTCL ORR 61%, CR 48%, FL ORR 80%, CR 67%	Grade 3–4 AEs: TP 48%, NP 40%, LP 32%, and anemia 16%	Falchi et al.⁸³
HDAC	Romidepsin	NCT00106431	II Completed	96	R/R CTCL	ORR 34%, CR 8%, DOR of 15.0 months	AEs: 96.2%	Duvic et al.¹¹²
HDAC	Romidepsin	NCT01456039	I/II Completed	40	R/R PTCL	ORR 43%, CR 25%, DFS 5.6 months	Grade 3–4 AEs: TP 98%, LP 88%, leukopenia 84%, NP 80%, and anemia 34%	Maruyama et al.¹¹³
HDAC	Romidepsin	NCT00426764	II Completed	131	Progressive or relapsed PTCL	ORR 25%, CR 15%, DOR 28 months	Grade 3–4 AEs: TP 40%	Foss et al.¹¹⁴
HDAC	Romidepsin + Gemcitabine	NCT01822886	II Completed	20	R/R PTCL	ORR 30%, CR 15%, 2-year OS 50%, PSF 11.2%	Grade 3 AEs: TP 60%, NP 50%, anemia 20%	Pellegrini et al.¹¹⁵
HDAC	Entinostat	NCT00866333	II Terminated	59	R/R HL	PR 12%	Grade 3 AEs: TP 63%, anemia 47%, NP 41%, leukopenia 10%,	Tan et al.¹¹⁶
HDAC	Ricolinostat	NCT02091063	I Completed	21	TCL, HL, PTLD, FL, DLBCL, CTCL	56 days of disease stabilization for 50% of patients	Grade 3–4 AEs: anemia 9.5% and hypercalcemia 9.5%	Amengual et al.¹¹⁷
EZH2	Tazemetostat	NCT03009344	I Completed	10	R/R NHL	ORR 57%, CR 14.3%	Grade 3–4 AEs: TP and dysgeusia 42.9%	Munakata et al.¹¹⁸
EZH2	Tazemetostat	NCT03456726	II Completed	165	R/R BNHL EZH2^mut	ORR 40% (DLBCL EZH2^mut) 18% in patients DLBCL EZH2^wt; ORR 63% ( FL EZH2^mut) 28% (FL EZH2^wt)	Grade 3–4 AEs: 18%	Izutsu et al.¹¹⁹
EZH2	Tazemetostat + Atezolizumab	NCT02220842	I Completed	43	R/R-FL and DLCBL	ORR 16%, CR 5%, PR 12%	Grade 3–4 AEs: anemia 12%, NP 9%, TP 9%	Palomba et al.¹²⁰
EZH2	Tazemetostat	NCT03010982	I Completed	3	BCL	Not reported	Grade 3–4 AEs: 66%	Argon et al.¹²¹
EZH2	Tazemetostat + Fluconazole + Omeprazole + Repaglinide	NCT03028103	I Completed	16	BCL	ORR 15.4%, CR 7.7%, PR 7.7%	Grade 3–4 AEs: 25% tazemetostat-related	Clinical trial¹²²
EZH2	Tazemetostat	NCT01897571	I/II Completed	99	DLBCL EZH2^{wt and mut}	ORR 69% (EZH2^mut) and 35% (EZH2^wt), CR 13% (EZH2^mut) and 4% (EZH2^wt)	Grade 3–4 AEs: TP 3%, NP 3%, anemia 2%	Morschhauser et al.¹²³
EZH2	GSK2816126	NCT02082977	I Terminated	20	R/R DBCL, tFL and NHL	Insufficient evidence of clinical activity	Grade 3–4 AEs: 32%	Yap et al.¹²⁴
BET	Birabresib	NCT01713582	I Completed	17	DLCBL	DOR 17%	Grade 3–4 AEs: TP 58%	Amorim et al.¹²⁵
BET	RO6870810 + Venetoclax + Rituximab	NCT03255096	I Completed	39	DLBCL	ORR 38.5%, CR 20.5, PR 17.9%	Grade 3–4 AEs: NP 28%, anemia and TP 23% each	Dickinson et al.¹²⁶
BET	INCB057643	NCT02711137	I/II Terminated	16	Lymphoma	PR 25%, CR 12.5%	Grade 3–4 AEs: TP 32%	Falchook et al.¹²⁷
BET	INCB054329	NCT02431260	I/II Terminated	4	Lymphoma	Not reported	Grade 3–4 AEs: TP 33%	Falchook et al.¹²⁷
BET	CPI-0610	NCT01949883	I Completed	64	Progressive lymphoma	ORR 7.8%, CR 3%	Grade 3–4 AEs: TP 45%	Blum et al.¹²⁸
BET	FT-1101	NCT02543879	I Completed	10	NHL	SD 33%	Grade 3–4 AEs: pleural effusion 20%	Patel et al.¹²⁹

AEs, adverse effects; AITL, angioimmunoblastic T-cell lymphoma; BCL, B-cell lymphoma; BET, bromodomain and extra-terminal motif; CLL, chronic lymphocytic leukemia; CR, complete response; CTCL, cutaneous T-cell lymphoma; DLBCL, diffuse large B-cell lymphoma; DOR, duration of response; FL, follicular lymphoma; HDAC, histone deacetylase; MCL, mantle cell lymphoma; MM, multiple myeloma; MZL, marginal zone lymphoma; NA, not available; NHL, non-Hodgkin’s lymphoma; NP, neutropenia; ORR, overall response rate; OS, overall survival; PD, progressive disease; PFS, progression-free survival; PR, partial response; PTCL, peripheral T-cell lymphoma; R/R, relapsed and refractory; SD, stable disease; TP, thrombopenia.

Azacytidine was evaluated, in a phase II clinical study (NCT01998035), in combination with the HDAC inhibitor (HDACi) romidepsin. This combination was safe and demonstrated to be an effective regimen for treatment-naïve patients and R/R PTCL cases. The reported overall response (ORR) and complete response (CR) rates were 61% and 48%, respectively, therefore supporting the use of oral azacytidine and romidepsin in both first-line and R/R settings, including as a bridging therapy.^83,84 The mechanism of action underlying this combinatorial activity might be related to the enhanced expression of several cancer-testis antigens involved in the promotion of tumor immunogenicity.¹³⁰ The combination of azacytidine with avelumab (anti-PD-L1 antibody) and utomilumab (4-1BB/CD137 agonist) was evaluated in R/R DLBCL patients. However, due to insufficient clinical activity, the study was prematurely discontinued.⁸⁵

High levels of cytidine deaminase (CDA) were reported to decrease the half-life of decitabine and azacytidine.^131,132 Based on this observation, the effect of tetrahydrouridine (THU), a CDA inhibitor, was evaluated in relapsed B- and T-cell malignancies (NCT02846935, see Table 1). The overall results indicated a significant reduction in tumor burden, together with subjective improvements in symptoms in 57% of the patients; however, these effects were lost upon treatment interruptions consequent to neutropenia.⁷⁷ Decitabine was also evaluated in treatment-naïve DLBCL patients prior to receiving R-CHOP. The results from this clinical trial (NCT02951728) indicated that 86% of the patients responded to the treatment, with 74% CR and 11% PR.¹³³

Besides the above-described FDA-approved DNA methylation inhibitors, over the last decades several new DNMTis have been developed, showing promising results in pre-clinical models of hematological disorders. Among them it is worth to highlight the thioguanine [2-amino-1,7-dihydro-6H-purine-6-thione (6-tG)] that was FDA-approved for the treatment of AML patients.¹³⁴ Thioguanine is currently included in the NHL-BFM90 protocol.¹³⁵ The main findings reported by the large European network applying this protocol for the management of childhood and adolescent NHL, indicated that the 5-year event-free survival (EFS) was in the range 82–90% (NCT00275106 and NCT00004228, respectively, see Table 1), while 5-year OS was in the range 87–96%.¹³⁶

HDAC inhibitors

As commented above, HDACs play a crucial role in the control of cell proliferation and growth, and angiogenesis. Accordingly, their overregulation promotes the occurrence of cancer, making the use of HDACis an efficient anticancer approach as these agents can trigger apoptosis, cell cycle arrest or even regulate the immune system.^57,137,138 Among the growing list of clinical trials exploring the possible therapeutic application of HDACi (see Table 1), the most successful ones are depicted below.

Vorinostat is a hydroxamic acid presenting inhibitory activity against classes I and II HDACs.¹³⁹ It has been used successfully in monotherapy in different subtypes of B-NHL, including FL and MCL,^106,140 and has been approved in 2006 by FDA to treat R/R CTCL.¹⁴¹ This agent has also been tested with success in combination with multiple drugs such as the anti-CD20 monoclonal antibody rituximab, cladribine, fludarabine phosphate, cyclophosphamide, niacinamide, prednisone, or etoposide, for the treatment of indolent or aggressive B-NHL, including relapsed cases, in R/R CLL cases and in previously untreated T-NHL.^{99,107,108,142–145}

Mocetinostat, a selective HDAC class I and IV inhibitor developed by Methylgene has also been approved for R/R CTCL,¹⁴⁶ while its therapeutic effect in the context of R/R Hodgkin’s lymphoma (HL) managed to control the disease evolution in half of the treated patients.⁹⁷

Belinostat is a sulfonamide-hydroxamic acid acting as a pan-HDACi¹⁴⁷ developed by TopoTarget. While its use has been approved for the treatment of R/R PTCL, it also demonstrated remarkable activity when assessed in CTCL patients.^87,89,148 Conversely, this agent exhibited poor activity as monotherapy in B-cell lymphoma patients. Interestingly, when combined to CHOP chemotherapeutic regimen as a first-line treatment for PTCL patient, it achieved a significant CR rate.¹⁴⁹

Chidamide is a selective HDAC class I inhibitor¹⁵⁰ currently approved by the China Food and Drug Administration (CFDA) as a treatment for R/R PTCL, alone or in combination with CHOP regimen. A new clinical trial involving refractory extranodal NKTCL patients, and the results of which will be released in 2023, has already shown promising results.¹⁵¹ Its applicability to the management of AITL is also under evaluation. Several clinical trials aiming at evaluating chidamide as a therapeutic strategy for B-NHL treatment alone or in combination with R-GDP, DICE, R-CHOP have been registered and are in recruiting processes.

Ricolinostat, a selective HDAC6 inhibitor,¹⁵² exerted a synergic antitumor effect in combination with the BTK inhibitor ibrutinib, the alkylating agent bendamustine, the ALK inhibitor crizotinib and the proteasome inhibitor carfilzomib, in preclinical models of DLBCL and MCL, but possible translation into human subjects is still under evaluation.⁵⁷ In a clinical study including patients with R/R B/T-lymphomas, this agent harbored lower toxicity compared with other pan-HDACis and achieved the stabilization of half of the patients, although in the absence of CR or partial response (PR).¹⁴⁵

Fimepinostat, which dually targets HDAC and PI3K, has been tested in combination with rituximab in relapsed DLBCL and MYC-altered DLBCL patients.^98,153 Response to treatment was achieved most notably in MYC-altered DLBCL (64% versus 37% in non-MYC-altered).

Romidepsin is a depsipeptide from bacterial origin able to inhibit Class I HDACs.¹⁵⁴ While its use has been approved for R/R CTCL and PTCL,^{114,155–158} it also showed additive effect when combined with other agents employed for the treatment of PTCL, FL, or R/R T-cell lymphomas, such as the nucleoside analog gemcitabine, 5-azacitidine or the aurora kinase inhibitor alisertib.^159–161

Panobinostat, a hidroxamic acid with therapeutic activity as pan-HDAC inhibitory, has been evaluated up to phase III clinical trials in R/R HL patients. Unfortunately, it failed to achieve the therapeutic effect expected from previous phases.¹⁶² Similarly, phase II clinical trials involving R/R DLBCL patients demonstrated a modest activity of the drug.¹⁶³ In T-cell lymphoma and HL, some degree of clinical response was observed when associating this agent with the mTOR inhibitor everolimus.⁹³ Further drug assessment in HL, but not in CTCL patients, employing panobinostat in combination with ICE, also showed initial positive response.^164,165 Panobinostat was also administered to R/R HL patients in combination with the immunomodulatory drug lenalidomide, showing good tolerances but low therapeutic activity.¹⁶⁶ Finally, this HDACi has been tested in combination with bortezomib for the treatment of R/R TCL, providing a good response rate, but also producing serious adverse effects (AEs) in almost half of the cases.¹⁶⁷

Entinostat is a HDAC I and III inhibitor, therapeutic effect of which has been tested in R/R HL. Different dosages were tested, achieving an ORR of 12%, and a mean tumor size reduction of 58%.¹¹⁶

Abexinostat, a pan-HDAC inhibitor, has been tested in a subset of R/R NHL and CLL patients. A phase II trial demonstrated that it can be successfully considered for the treatment of FL, TCL, and DLBCL,⁹⁵ with ORRs in the 56–31% range (see Table 1).

Valproic acid, an organic weak acid previously used as anticonvulsant, also exhibits HDAC inhibition properties. Several clinical trials aimed at evaluating its effect in lymphoma patients have been carried out, showing that it significantly improved the efficacy of the R-CHOP chemo-immunotherapy as a first-line treatment for DLBCL, as shown by a reduced rate of relapsed disease and a 96.8% OS at 2 years.⁹⁴

HMT inhibitors

Currently, the development of HMT inhibitors is mainly focused on EZH2 targeting. This gene encodes an HMT that forms the catalytic subunit of the polycomb repressive complex 2, which mediates gene silencing via the addition of methyl groups to H3K27. EZH2 overexpression has been correlated with poor prognosis in several tumor types including hematological malignancies.^168–171 Moreover, it has been shown that the gain-of-function mutation at Y641 residue of EZH2, leads to its enzymatic activity converting mono- or di-methylated H3K27 to the tri-methylated state, promoting the repression of cell differentiation and the downregulation of tumor suppressor genes.¹⁷² Interestingly, these gain-of-function EZH2 mutations has been frequently associated with the presence of BCL2 rearrangement in both FL (28%) and GCB-DLBCL groups (33%), and it has been shown to be a crucial regulator of MYC-associated lymphomagenesis in B cells.^173–175 Thus, EZH2 activity is currently a potential therapeutic strategy to treat B-NHL.

In this context, several selective EZH2 inhibitors have been developed in the last decade, for the treatment of hematological patients. Among these molecules, GSK126 demonstrated an improved inhibitory capacity toward mutant EZH2 in preclinical studies.^176,177 However, its clinical evaluation in R/R patients, including cases with DLBCL, transformed tFL, MM, and other NHL, (NCT02082977) was stopped prematurely due to insufficient therapeutic activity.¹²⁴ Another small molecule called CPI-1205, which showed promising activity in xenograft mouse models and in human B-NHL cell lines,¹⁷⁸ is currently being evaluated in a phase I trial involving DLBCL patients (NCT02395601). At this time, no data have been released regarding the efficacy and the safety of this agent in these heavily pretreated patients. Antitumoral effects of EZH2 inhibitors have been also reported in TCL cell lines.¹⁷⁹ The use of EZH1/2 inhibitor, valemetostat, has been evaluated in clinical trial including B- and T-NHL subtypes (NCT02732275). The observed ORR was 53% in a phase I trial involving 15 patients, being the cases with TCL by far the best responders (80% ORR).¹⁸⁰

Tazemetostat, a potent and selective EZH2 inhibitor, first demonstrated encouraging preclinical activity, in both in vitro and in vivo models (including xenografts) of EZH2-mutant NHL.¹⁸¹ An initial phase I study showed that tazemetostat, as single agent, was safe and exerted notable antitumor activity (OR = 38%) in patients with refractory B-NHL.¹⁸² Based on pharmacodynamic and toxicity profiling, a phase II study including EZH2^mut and EZH2^wt R/R FL patients was carried out. Surprisingly, an ORR of 69% was observed among EZH2^mut patients, and 35% in EZH2^wt cohort.¹²³ Based on these data, FDA granted accelerated approval of this agent for R/R-FL patients with EZH2^mut. Similarly, two independent cohorts of R/R DLBCL and FL patients corroborated that tazemetostat was effective in R/R EZH2^mut FL patients.^118,119 Tazemetostat was also evaluated in combination with the anti-PD-L1 antibody atezolizumab in R/R DLBCL patients (NCT02220842). However, this combination did not provide additional efficacy.¹²⁰ Thus, further clinical trials are needed to establish new drug combinations based on HMT inhibitors to improve the OS of the patients.

Although the clinical development of HMT inhibitors is centered on the targeting of EZH2 in B-NHL patients, other indirect strategies have shown encouraging results in preclinical models of the disease. Among these approaches, the carbocyclic adenosine analog 3-deazaneplanocin A (DZNep), is an inhibitor of S-adenosylhomocysteine hydrolase (AdoHcyase), that triggers intracellular accumulation of 5-adenosylhomocystein, followed by the blockade of several methyltransferases, including EZH2. Despite a strong apoptogenic effect in different preclinical cancer models, DZNep antitumor effect was not restricted to EZH2-mutated cases and may involve EZH2-independent targets, therefore, hinting as potential undesired effects in patients.¹⁸³ Blockade of the transfer of a methyl group from S-adenosyl methionine (SAM) to a lysine or arginine residue can also be achieved upon exposure to 2-chloro-2′-deoxyadenosine (2-CdA, cladribine), a drug that inactivates S-adenosyl-L-homocysteine hydrolase (SAH), thereby impairing the capacity of genomic DNA (gDNA) to accept methyl groups. Although cladribine was shown to efficiently reduce the level of methylated cytosines in myeloid cells,¹⁸⁴ its clinical activity as single agent in lymphoid malignancies, including CLL, MCL, hairy cell leukemia, and marginal zone lymphoma (MZL), was initially associated to its capacity, as a purine analog, to selectively target and suppress lymphocyte growth.¹⁸⁵ However, in MCL, induction therapy associating a purine analog to rituximab and cyclophosphamide demonstrated a lower response rate than standard R-CHOP regimen,¹⁸⁶ contrasting with the impressive 97% ORR observed in patients receiving a cladribine-containing immuno-epigenetic combo.¹⁴² Therefore, it is highly plausible that, at least in MCL patients, the remarkable clinical activity of cladribine is derived from its epigenetic modulatory properties.

Bromodomain inhibitors

Bromodomain-containing family of proteins comprise 46 members, including nuclear proteins with HAT or HMT activity, chromatin remodelers, helicases, transcription co-activators, and mediators or scaffold proteins. Undoubtedly most of the scientific attention was focused on BRD2, BRD3, and BRD4.¹⁸⁷ Interestingly, these proteins have a bromodomain and extra-terminal motif (BET) domain, which is responsible for protein–protein interactions,^187,188 that acts as DNA enhancers for oncogene regulation.¹⁸⁹ BET bromodomains are important regulators of several players with a central role in several cancers, including hematological malignancies, such as MYC, cell cycle regulators, and NF-κB-related genes.¹⁹⁰ Thus, in early 2000s, the development of BET inhibitors (BETi) rapidly gained a growing attention as a promising anticancer strategy.

The first BETi to enter into clinical development was birabresib. The data from the initial dose-escalation, open-label, phase I trial (NCT01713582) indicated that, when used as monotherapy, birabresib achieved a 47% CR rate in 17 R/R DLBCL patients, while durable OR was reported for only 18% of them.¹²⁵ A dose exploration study of this drug, involving DLBCL and AML patients (NCT02698189), was closed prematurely due to a lack of efficacy.

Others BETis, INCB054329 and INCB057643, were evaluated as monotherapy in a small cohort of patients with hematologic malignancies (NCT02431260 and NCT02711137, respectively). In both cases, the clinical trial was terminated due to a lack of responses and notable toxicity.¹²⁷

CPI-0610 is another BETi, which was evaluated in B-NHL patients, reaching a modest 7% OR rate (NCT01949883). Mechanistically, the analysis of BET target genes demonstrated a dose-dependent decrease (2–8 h post-dose) in interleukin-8 (IL8) and C-C motif chemokine receptor 1 (CCR1) transcript levels.¹²⁸

FT-1101, is a small molecule that presents a potent anti-proliferative activity in vitro, which was subsequently confirmed in B-NHL patients in a phase I clinical trial (NCT02543879). Although this agent showed an acceptable safety profile, a modest clinical activity was observed.¹²⁹

Given the strong synergy between BET and BCL-2 inhibitors in vitro,¹⁹¹ a phase Ib trial evaluated the effects of RO6870810 combined to the BCL2 antagonist, venetoclax, with or without rituximab in R/R DLBCL patients. ORR was 38.5%, including 20.5% CR and 17.9% PR. A stable disease (SD) was observed in 15.4% of the patients, whereas 30.8% maintained a progressive disease (PD). Although the triple combination resulted in higher response rates when compared with single agents, authors concluded to a lack of synergistic effect of this combinatorial approach.¹²⁶

Future perspectives: paving the way for precision medicine with epidrugs in B- and T-cell lymphoma and implementing bioinformatics approaches to identify new epigenetic targets in hematological cancers

Personalized epigenome targeting in NHL

The identification of recurrent mutations in NHL provides a rationale to introduce epigenetic drugs for the design of selective and personalized therapies for these patients. Supported by promising results obtained in preclinical and clinical trials, the notion that epigenetic alterations can be used for lymphoma diagnosis and as valuable clinical biomarkers of response to therapy, represents a game changer for the clinical management of these patients.

Several preclinical studies have already shown that a genetic or epigenetic alteration could be specifically targeted by a particular drug. As described in the section ‘HMT inhibitors’, EZH2 inhibitors have demonstrated enhanced preclinical and clinical activity against EZH2-mutated B-NHL. Preclinical studies evaluating the safety and efficacy of a new class of LSD1 inhibitors showed that this class of agents had a very potent activity against proliferation of MLL-rearranged leukemia cells, with EC50 values in the nanomolar range. These cell-permeable molecules were found to significantly increase the levels of H3K4me2 in MLL-rearranged leukemic cells, to significantly reduce tumor burden, and to expand the life expectancy of leukemic mice, demonstrating the potential of this class of compounds to become clinically useful for MLL-rearranged leukemia.¹⁹²

In a different context, HDAC3 inhibition using the novel molecule BRD3308 led to the upregulation of the cell cycle inhibitor, p21, resulting in cell cycle blockade and in proliferation arrest exclusively in CBP/p300-mutated DLBCL cells, characterized by the presence of BCL6–HDAC3 complexes that repress the transcription of the p21-encoding gene, CDKN1A.¹⁹³

Despite these significant advances in the design of personalized treatments that could target a specific epigenetic alteration by means of one or several epidrugs, until recently efforts were still to be made to elaborate the best treatment approach for a determined patient with altered epigenome. The implementation of massive sequencing in early 2000s, followed by the standardization of big data processing, responded partly to these crucial needs.

In silico epigenetic profiling: basic concepts

Bioinformatics tools have enabled the interpretation of complex and dynamic phenomena, such as epigenetics, as well as the development of large-scale (big data), highly selective (e.g. single cell chip), and high-throughput modern molecular biology techniques.¹⁹⁴ These latter are aimed at facilitating the prediction of epigenetic events such as DNA methylation, chromatin conformation changes, histone modifications and non-coding RNA activity, and their relationship with other sources of biological information (e.g. phenotype, transcriptomic, and proteomic), with the final objective to improve the diagnosis and prognosis of different diseases,¹⁹⁵ and the design of effective and safe epidrugs,¹⁹⁶ and breeding strategies.¹⁹⁷ Epigenomic data, defined as the set of variations in certain genes, regions, or in the whole genome,¹⁹⁸ can be evaluated by methods that vary according to (1) the analytical platform used for data collection (e.g. array, sequencing, immunoprecipitation)^199–201, (2) the stage of analysis (e.g. preprocessing of raw data, statistical comparison, variable selection, functional analysis, and drug-target structural analysis),²⁰² or (3) the objective of the study (e.g. multiomics, single cell, drug repurposing).^203–205

Epigenetics-based drug therapy is primarily aimed at reversing aberrant gene expression that may be found in the development and progression of lymphoma and understanding the potential to affect multiple cellular processes. These bioinformatics targets can be found by directly affecting regulatory regions of genes, such as in the methylome or DNA methylation information sets, or by altering histone proteins and related structures.²⁰⁶ The methylome can be profiled experimentally by bisulfite sequencing, while the main technique for identifying histone alteration profiles is immunoprecipitation of these proteins.

Computational validation of epigenetic alterations in B- and T-cell lymphoma

The first stages of bioinformatics analysis of epigenetic data are data acquisition, quality control, and preprocessing. At these levels, the characteristics of the bioinformatics methods depend on the particularities of the experimental techniques. Chromatin immunoprecipitation (ChIP), followed by DNA identification by microarray (ChIP-on-chip) or sequencing (ChIP-seq), and mass spectrometry (MS) are the most common experimental approaches to profile histone post-translational modifications. ChIP-on-chip data require the normalization of hybridized fragment intensities, followed by the selection of representative peaks, and the merging of overlapping overrepresented regions.²⁰⁷ Many packages have been developed for this purpose such as Ringo,²⁰⁸ Tilescope,²⁰⁹ HMMTiling,²¹⁰ among others. ChIP-seq analyses require mapping short histone-associated DNA fragments to reference genomes. This step constitutes a challenge in both ChIP-on-chip and ChIP-seq. This so-called peak calling step needs more attention and quality control to avoid false overrepresentation and to map sequences that are actually in contact with our protein of interest (e.g. histones). Several open source (e.g. Bowtie, BLAT, or EpiChip)^211–213 or proprietary (e.g. Broad Institute sequencing platform)²¹⁴ programs or packages have been developed for reference alignment. In addition, packages such as SAMtools can be used for removal of duplicate reads due to amplification artifacts, to finally perform peak calling using some of the available approaches that best fit the experimental design.²¹⁵ In this sense, Peakzilla uses predefined cutoff values,²¹⁶ while MACS uses Poisson model to analyze the distribution of reads,²¹⁷ and JAMM retrieves information from biological replicates to determine the amplitude of enriched sites.²¹⁸ There are several studies using the ChIP technique to confirm whether alterations in chromatin structure and expression of certain genes are restored after epidrug treatment.^219–221

MS has been used to determine the altered structure of proteins of interest, although there are limitations in recognizing the large number of ions inherent to histones or other cellular proteins. Different algorithms have been developed depending on the integrity of the quantified protein (total, peptides or amino acids), THRASH being one of the most versioned although it still depends on the structural reference database.²²² These MS methods have recently been used to accurately target EZH2 and HDAC in lymphoma.²²³

The methylome encompasses information on DNA methylation at the genomic level, a well-studied phenomenon for which there are analytical methods based on bisulfite modification followed by sequencing²⁰⁰ or microarray²²⁴ analysis, and enrichment methods such as methylated DNA immunoprecipitation (MeDIP) or methyl-binding domain proteins (MethylCap) followed by DNA sequencing.^225,226 Bisulfite sequencing is based on the quantification of cytosines sequenced as thymines, after interaction with bisulfites that do not affect methylated bases. The bioinformatics algorithms used in the data generated by this technique have, as their main objective, the correct alignment to a reference genome and the calculation of the rate of cytosines and thymines that represent the methylation level of the genome studied. In addition to the previously mentioned methods for ChIP-seq, there are specific approaches that consider cytosine mismatches implemented, such as RRBSMAP²²⁷ or Segemehl,²²⁸ among others, that consider a three-base alignment (T, G, and A) such as MethylCoder or BRAT-nova.^229,230 With the sequences already aligned, it is possible to quantify the frequency of cytosines and thymines in certain regions of the genomes using probabilistic algorithms such as Bis-SNP and MethylExtract.^231,232

Different databases have compiled and organized the data of epigenetic modifications and the information related to each deposited project. These platforms provide information for planning future projects and facilitate meta-analyses that may lead to new conclusions not seen in individual studies.²³³ Databases such as NCBI epigenomics and ENCODE collect data from several large-scale projects.^234,235 MethDB and Methbank, among others, provide data exclusively on DNA methylation, while ChromatinDB and HHMD contain information on histone post-translational modifications for different species.^236–239

The epigenetic alterations evaluated in previous steps can be used to define a differential profile that can be related to other types of omics data, especially gene expression data that are directly affected by such phenomena. As an example, the relationship between differential gene expression and binding analysis was used to point out the reversion of CREBBP mutations by HDAC3 selective inhibitors.¹⁹³ Programs such as diffReps²⁴⁰ allow the detection of differential sites in ChIP-seq data where differences in the transcriptomic profile generated in those same regions are expected to be seen. Although it is often difficult to determine this association due to the variability of peak callers, some studies have shown its importance in, for example, defining genes and pathways associated with doxorubicin resistance.²⁴¹ Some studies have successfully used data on DNA sequence variations (e.g. in the differentiation of MCL subtypes),²⁴² protein or metabolite abundance, and clinical information.²⁴³ This approach was also used to determine the association between metabolic and sensitivity to HDACis,²⁴⁴ and to establish the relevance of phosphoproteomics data, gene expression and protein–protein interaction for the deciphering of a novel mechanism of regulation of KMT2D.²⁴⁵ These types of associations could allow the reconstruction of multilevel regulatory networks.²⁴⁶ The methods used to analyze this integration can vary greatly depending on the type of data used, between probabilistic models,²⁴⁷ machine learning²⁴⁸ (i.e. a model of protein-compound interaction with epigenetic targets using different machine learning methods),²⁴⁹ coexpression networks²⁵⁰ (i.e. differential coexpression and regulation networks to propose therapeutic factor for adult T-cell LL),²⁵¹ based on dimensionality reduction and clusterization,²⁵² integrated as networks based on quantitative relationships or described in previous literature, among others. Finally, we can use the structural information of the proteins responsible for modulating epigenetic marks in nucleosomes and their activity in the covalent bonds that generate these modifications. These data may help in the discovery of new epidrugs and epiprobes.²⁵³ The main computer-aided drug design (CADD) methods in this area include druggability prediction,²⁵⁴ virtual screening,²⁵⁵ pharmacophore modeling,²⁵⁶ and molecular dynamics simulations.²⁵⁷

Conclusion and future perspectives

In the last decade, the advances in high-throughput sequencing technologies have provided multitude of information on the role of both genomic and epigenomic deregulations in malignant transformation and in the physiopathology of B and T lymphoid neoplasms. Besides helping the characterization of some lymphoma subtypes considered so far unclassifiable, the identification of recurrent mutations affecting epigenetic enzymes with crucial functions in the determination of B and T cell fate, fostered the development and evaluation of several epigenetic drugs, which rapidly showed high degree of efficacy, first in preclinical settings, and further in clinical trials essentially in relapsed NHL patients. Single agents and combination therapies involving HDAC inhibition or DNMT blockade have shown remarkable activity in specific subsets of B-cell and T-cell lymphoma, which remained unresponsive to or relapsed after chemo-immunotherapeutic regimens. However, beside general inhibitors of acetylation and demethylase, specific epigenetic drugs, including class-specific HDACi, EZH2 inhibitors or BET antagonists are showing significant clinical activity and have already been broadly implemented in the clinical management of determined subtypes of NHL patients. In combination therapy, some of these agents have demonstrated their ability to facilitate the response of B-NHL patients to anti-CD20 treatment. Among them, vorinostat was able to improve the outcomes of R/R FL, MCL, and MZL patients when associated to rituximab;²⁵⁸ however, this effect seemed barely additive and the combined use of additional chemotherapeutic combo such as ICE or CHOP may be a prerequisite to achieve synergistic antitumor activity (NCT00601718, NCT00972478). Other HDACis such as panobinostat, fimepinostat, belinostat, or valproic acid either failed to exhibit such combinatorial activity with rituximab-based regimens or were associated with important AEs that limited their clinical development.^94,153,259 Within the family of methylation modulators, cladribine also exhibits combinatorial activity with rituximab, as MCL patients receiving this combination presented a superior CR rate than the group of patients treated with cladribine alone (52% versus 42%, respectively).²⁶⁰ In previously untreated patients, the observed responses were even higher when vorinostat was added to this doublet (97% ORR and 80% CR).¹⁴² Importantly, these last studies showed a plateau in PFS and OS as well as a prolonged PFS, implying potential curative potential for cladribine–rituximab based regimens. In the case of EZH2 inhibitors, the first results of the phase Ib Epi-R-CHOP study combining tazemetostat to rituximab-CHOP suggested that this combo, although generally well tolerated, does not appear to substantially improve rituximab-CHOP toxicity and efficacy profiles.²⁶¹ Thus, in determined but limited conditions, epidrug therapy may significantly improve the outcome of NHL patients receiving anti-CD20-based regimens.

Despite these outstanding advances, further field of development include the identification of ad hoc biomarkers that may facilitate patient selection for their inclusion in clinical trials, and the design of rationally based combination regimens, may help reaching the final aim of establishing selective and personalized therapies for this subgroup of patients. One of the latest and most promising approach, which will help selecting the most relevant targeted therapies in the near future, is the multiomic characterization of each patient sample. However, the considerable volume of information provided by the latest technologies, including single-cell proteogenomics, requires a rigorous and reproducible analytical workflow that is nowadays within our reach, thanks to the recent improvements in bioinformatic data analysis. These approaches will allow us to be closer to the complete mapping of B- and T-cell lymphoma and, therefore, will empower the design of optimal therapeutic scheme, including new epigenetic drug combinations.

Footnotes

Acknowledgements

The authors thank Josep Carreras Leukaemia Research Institute and CERCA Programme/Generalitat de Catalunya for institutional support.

Declarations

ORCID iDs

Salvador Sánchez Vinces

Gael Roué

References

Seifert

Scholtysik

Küppers

. Origin and pathogenesis of B cell lymphomas. Methods Mol Biol 2013; 971: 1–25.

Sehn

Salles

. Diffuse large B-cell lymphoma. N Engl J Med 2021; 384: 842.

Chapuy

Stewart

Dunford

, et al. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med 2018; 24: 679–690.

Schmitz

Wright

Huang

, et al. Genetics and pathogenesis of diffuse large B-cell lymphoma. N Engl J Med 2018; 378: 1396–1407.

Wright

Huang

Phelan

, et al. A probabilistic classification tool for genetic subtypes of diffuse large B cell lymphoma with therapeutic implications. Cancer Cell 2020; 37: 551–568.e14.

Alizadeh

Elsen

Davis

, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nat 2000; 403: 503–511.

Mozas

Rivero

López-Guillermo

. Past, present and future of prognostic scores in follicular lymphoma. Blood Rev 2021; 50: 100865.

Kline

Godfrey

Ansell

. The immune landscape and response to immune checkpoint blockade therapy in lymphoma. Blood 2020; 135: 523–533.

Roschewski

Staudt

Wilson

. Burkitt’s lymphoma. N Engl J Med 2022; 387: 1111–1122.

10.

Hasanali

Sharma

Epner

. Flipping the cyclin D1 switch in mantle cell lymphoma. Best Pract Res Clin Haematol 2012; 25: 143–152.

11.

Saleh

Cheminant

Chiron

, et al. Tumor microenvironment and immunotherapy-based approaches in mantle cell lymphoma. Cancers 2022; 14: 3229.

12.

De Leval

Jaffe

. Lymphoma classification. Cancer J 2020; 26: 176–185.

13.

Elenitoba-Johnson

KSJ

Lim

. New insights into lymphoma pathogenesis. Annu Rev Pathol 2018; 13: 193–217.

14.

Fiore

Cappelli

Broccoli

, et al. Peripheral T cell lymphomas: from the bench to the clinic. Nat Rev Cancer 2020; 20: 323–342.

15.

Kasprzycka

Marzec

Liu

, et al. Nucleophosmin/anaplastic lymphoma kinase (NPM/ALK) oncoprotein induces the T regulatory cell phenotype by activating STAT3. Proc Natl Acad Sci USA 2006; 103: 9964–9969.

16.

Cortes

Ambesi-Impiombato

Couronne

, et al. RHOA G17V induces T follicular helper cell specification and promotes lymphomagenesis. Cancer Cell 2018; 33: 259–273.e7.

17.

Vallois

Dobay

Morin

, et al. Activating mutations in genes related to TCR signaling in angioimmunoblastic and other follicular helper T-cell-derived lymphomas. Blood 2016; 128: 1490–1502.

18.

Pechloff

Holch

Ferch

, et al. The fusion kinase ITK-SYK mimics a T cell receptor signal and drives oncogenesis in conditional mouse models of peripheral T cell lymphoma. J Exp Med 2010; 207: 1031–1044.

19.

Heavican

Bouska

, et al. Genetic drivers of oncogenic pathways in molecular subgroups of peripheral T-cell lymphoma. Blood 2019; 133: 1664–1676.

20.

Witzig

Offer

, et al. Epigenetic mechanisms of protein tyrosine phosphatase 6 suppression in diffuse large B-cell lymphoma: implications for epigenetic therapy. Leukemia 2014; 28: 147–154.

21.

Zhang

Wang

Wei

, et al. Cutaneous T cell lymphoma expresses immunosuppressive CD80 (B7-1) cell surface protein in a STAT5-dependent manner. J Immunol 2014; 192: 2913–2919.

22.

Schleussner

Merkel

Costanza

, et al. The AP-1-BATF and -BATF3 module is essential for growth, survival and TH17/ILC3 skewing of anaplastic large cell lymphoma. Leukemia 2018; 32: 1994–2007.

23.

Marzec

Zhang

Goradia

, et al. Oncogenic kinase NPM/ALK induces through STAT3 expression of immunosuppressive protein CD274 (PD-L1, B7-H1). Proc Natl Acad Sci USA 2008; 105: 20852–20857.

24.

McDonnell

Hwang

Basrur

, et al. NPM-ALK signals through glycogen synthase kinase 3beta to promote oncogenesis. Oncogene 2012; 31: 3733–3740.

25.

Lien

Lyssiotis

Cantley

. Metabolic reprogramming by the PI3K-Akt-mTOR pathway in cancer. Recent Results Cancer Res 2016; 207: 39–72.

26.

McDonnell

Hwang

Rolland

, et al. Integrated phosphoproteomic and metabolomic profiling reveals NPM-ALK-mediated phosphorylation of PKM2 and metabolic reprogramming in anaplastic large cell lymphoma. Blood 2013; 122: 958–968.

27.

Gough

Corlett

Schlessinger

, et al. Mitochondrial STAT3 supports Ras-dependent oncogenic transformation. Science 2009; 324: 1713–1716.

28.

Mondragon

Mhaidly

De Donatis

, et al. GAPDH overexpression in the T cell lineage promotes angioimmunoblastic T cell lymphoma through an NF-κB-dependent mechanism. Cancer Cell 2019; 36: 268–287.e10.

29.

Kim

Montes-Mojarro

Fend

, et al. Epstein-Barr virus-associated T and NK-cell lymphoproliferative diseases. Front Pediatr 2019; 7: 71.

30.

Watanabe

. Adult T-cell leukemia: molecular basis for clonal expansion and transformation of HTLV-1-infected T cells. Blood 2017; 129: 1071–1081.

31.

Hassler

Schiefer

Egger

. Combating the epigenome: epigenetic drugs against non-Hodgkin’s lymphoma. Epigenomics 2013; 5: 397–415.

32.

Blecua

Martinez-Verbo

Esteller

. The DNA methylation landscape of hematological malignancies: an update. Mol Oncol 2020; 14: 1616–1639.

33.

Shilatifard

. Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation. Curr Opin Cell Biol 2008; 20: 341–348.

34.

Morin

Mendez-Lago

Mungall

, et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 2011; 476: 298–303.

35.

Pasqualucci

Trifonov

Fabbri

, et al. Analysis of the coding genome of diffuse large B-cell lymphoma. Nat Genet 2011; 43: 830–837.

36.

Lohr

Stojanov

Lawrence

, et al. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci USA 2012; 109: 3879–3884.

37.

Reddy

Zhang

Davis

, et al. Genetic and functional drivers of diffuse large B cell lymphoma. Cell 2017; 171: 481–494.e15.

38.

Ortega-Molina

Boss

Canela

, et al. The histone lysine methyltransferase KMT2D sustains a gene expression program that represses B cell lymphoma development. Nat Med 2015; 21: 1199–1208.

39.

Morin

Mendez-Lago

Mungall

, et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 2011; 476: 298–303.

40.

Pasqualucci

Dominguez-Sola

Chiarenza

, et al. Inactivating mutations of acetyltransferase genes in B-cell lymphoma. Nature 2011; 471: 189.

41.

Pon

Wong

Saberi

, et al. MEF2B mutations in non-Hodgkin lymphoma dysregulate cell migration by decreasing MEF2B target gene activation. Nat Commun 2015; 6: 7953.

42.

Morin

Johnson

Severson

, et al. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet 2010; 42: 181–185.

43.

Serganova

Chakraborty

Yamshon

, et al. Epigenetic, metabolic, and immune crosstalk in germinal-center-derived B-cell lymphomas: unveiling new vulnerabilities for rational combination therapies. Front Cell Dev Biol 2022; 9: 3626.

44.

Béguelin

Teater

Meydan

, et al. Mutant EZH2 induces a pre-malignant lymphoma Niche by reprogramming the immune response. Cancer Cell 2020; 37: 655–673.e11.

45.

Marquard

Poulsen

Gjerdrum

, et al. Histone deacetylase 1, 2, 6 and acetylated histone H4 in B- and T-cell lymphomas. Histopathology 2009; 54: 688–698.

46.

Cosenza

Pozzi

. The therapeutic strategy of HDAC6 inhibitors in lymphoproliferative disease. Int J Mol Sci 2018; 19: 2337.

47.

Cortes

Palomero

. Biology and molecular pathogenesis of mature T-cell lymphomas. Cold Spring Harb Perspect Med 2021; 11: a035402.

48.

Cortés

Palomero

. The curious origins of angioimmunoblastic T-cell lymphoma. Curr Opin Hematol 2016; 23: 434–443.

49.

Quivoron

Couronné

Della Valle

, et al. TET2 inactivation results in pleiotropic hematopoietic abnormalities in mouse and is a recurrent event during human lymphomagenesis. Cancer Cell 2011; 20: 25–38.

50.

McKinney

Moffitt

Gaulard

, et al. The genetic basis of hepatosplenic T-cell lymphoma. Cancer Discov 2017; 7: 369–379.

51.

Mar

Chu

Kahn

, et al. SETD2 alterations impair DNA damage recognition and lead to resistance to chemotherapy in leukemia. Blood 2017; 130: 2631–2641.

52.

Palomero

Couronné

Khiabanian

, et al. Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas. Nat Genet 2014; 46: 166–170.

53.

Choi

Goh

Walradt

, et al. Genomic landscape of cutaneous T cell lymphoma. Nat Genet 2015; 47: 1011–1019.

54.

Choi

Kim

, et al. Mutational analysis of extranodal NK/T-cell lymphoma using targeted sequencing with a comprehensive cancer panel. Genomics Inf 2016; 14: 78–84.

55.

Guan

Gao

, et al. Functional analysis of in-frame indel ARID1A mutations reveals new regulatory mechanisms of its tumor suppressor functions. Neoplasia 2012; 14: 986–993.

56.

Yamagishi

. The role of epigenetics in T-cell lymphoma. Int J Hematol 2022; 116: 828.

57.

Chen

Sethy

Liou

. Recent update of HDAC inhibitors in lymphoma. Front Cell Dev Biol 2020; 8: 576391.

58.

Belinsky

Klinge

Stidley

, et al. Inhibition of DNA methylation and histone deacetylation prevents murine lung cancer. Cancer Res 2003; 63: 7089–7093.

59.

Hermann

Goyal

Jeltsch

. The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites. J Biol Chem 2004; 279: 48350–48359.

60.

Shaknovich

Cerchietti

Tsikitas

, et al. DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood 2011; 118: 3559–3569.

61.

Lai

Mav

Shah

, et al. DNA methylation profiling in human B cells reveals immune regulatory elements and epigenetic plasticity at Alu elements during B-cell activation. Genome Res 2013; 23: 2030–2041.

62.

Nosaka

Maeda

Tamiya

, et al. Increasing methylation of the CDKN2A gene is associated with the progression of adult T-cell leukemia. Cancer Res 2000; 60: 1043–1048.

63.

Martinez-Delgado

Fernandez-Piqueras

Garcia

, et al. Hypermethylation of a 5’ CpG island of p16 is a frequent event in non-Hodgkin’s lymphoma. Leukemia 1997; 11: 425–428.

64.

Azad

Zahnow

Rudin

, et al. The future of epigenetic therapy in solid tumours – lessons from the past. Nat Rev Clin Oncol 2013; 10: 256–266.

65.

Ghoshal

Datta

Majumder

, et al. 5-Aza-deoxycytidine induces selective degradation of DNA methyltransferase 1 by a proteasomal pathway that requires the KEN box, bromo-adjacent homology domain, and nuclear localization signal. Mol Cell Biol 2005; 25: 4727–4741.

66.

Juttermann

Jaenisch

. Toxicity of 5-aza-2’-deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation. Proc Natl Acad Sci USA 1994; 91: 11797–11801.

67.

Almstedt

Blagitko-Dorfs

Duque-Afonso

, et al. The DNA demethylating agent 5-aza-2’-deoxycytidine induces expression of NY-ESO-1 and other cancer/testis antigens in myeloid leukemia cells. Leuk Res 2010; 34: 899–905.

68.

Vogler

Miller

Keller

. 5 Azacytidine (NSC102816): a new drug for the treatment of myeloblastic leukemia. Blood 1976; 48: 331–337.

69.

Saiki

McCredie

Vietti

, et al. 5-azacytidine in acute leukemia. Cancer 1978; 42: 2111–2114.

70.

Levi

Wiernik

. A comparative clinical trial of 5-azacytidine and guanazole in previously treated adults with acute nonlymphocytic leukemia. Cancer 1976; 38: 36–41.

71.

Jones

Taylor

. Cellular differentiation, cytidine analogs and DNA methylation. Cell 1980; 20: 85–93.

72.

Silverman

Demakos

Peterson

, et al. Randomized controlled trial of azacitidine in patients with the myelodysplastic syndrome: a study of the cancer and leukemia group B. J Clin Oncol 2002; 20: 2429–2440.

73.

Fenaux

Mufti

Hellstrom-Lindberg

, et al. Efficacy of azacitidine compared with that of conventional care regimens in the treatment of higher-risk myelodysplastic syndromes: a randomised, open-label, phase III study. Lancet Oncol 2009; 10: 223–232.

74.

Stewart

Issa

Kurzrock

, et al. Decitabine effect on tumor global DNA methylation and other parameters in a phase I trial in refractory solid tumors and lymphomas. Clin Cancer Res 2009; 15: 3881–3888.

75.

Blum

Liu

Lucas

, et al. Phase I trial of low dose decitabine targeting DNA hypermethylation in patients with chronic lymphocytic leukaemia and non-Hodgkin lymphoma: dose-limiting myelosuppression without evidence of DNA hypomethylation. Br J Haematol 2010; 150: 189–195.

76.

Kuendgen

Müller-Thomas

Lauseker

, et al. Efficacy of azacitidine is independent of molecular and clinical characteristics-an analysis of 128 patients with myelodysplastic syndromes or acute myeloid leukemia and a review of the literature. Oncotarget 2018; 9: 27882–27894.

77.

Hill

Jagadeesh

Pohlman

, et al. A pilot clinical trial of oral tetrahydrouridine/decitabine for noncytotoxic epigenetic therapy of chemoresistant lymphoid malignancies. Semin Hematol 2021; 58: 35–44.

78.

Aza-SAHA-GBM with AutoSCT for refractory lymphoma – study results. ClinicalTrials.gov, https://clinicaltrials.gov/ct2/show/results/NCT01983969 (accessed 16 January 2023).

79.

Epigenetic modulation in relapsed/refractory follicular lymphoma and marginal zone lymphoma – study results. ClinicalTrials.gov, https://clinicaltrials.gov/ct2/show/results/NCT01121757 (accessed 16 January 2023).

80.

Study of 5-azacitidine in combination with vorinostat in patients with relapsed or refractory diffuse large B cell lymphoma (DLBCL) – study results. ClinicalTrials.gov, https://clinicaltrials.gov/ct2/show/results/NCT01120834 (accessed 16 January 2023).

81.

Phase I/II trial of R-CHOP + azacytidine in diffuse large B cell lymphoma – study results. ClinicalTrials.gov, https://clinicaltrials.gov/ct2/show/results/NCT01004991 (accessed 16 January 2023).

82.

Martin

Bartlett

Chavez

, et al. Phase 1 study of oral azacitidine (CC-486) plus R-CHOP in previously untreated intermediate- to high-risk DLBCL. Blood 2022; 139: 1147–1159.

83.

Falchi

Klein

, et al. Combined oral 5-azacytidine and romidepsin are highly effective in patients with PTCL: a multicenter phase 2 study. Blood 2021; 137: 2161–2170.

84.

O’Connor

Falchi

Lue

, et al. Oral 5-azacytidine and romidepsin exhibit marked activity in patients with PTCL: a multicenter phase 1 study. Blood 2019; 134: 1395–1405.

85.

Hawkes

Phillips

Budde

, et al. Avelumab in combination regimens for relapsed/refractory DLBCL: results from the phase Ib JAVELIN DLBCL study. Target Oncol 2021; 16: 761–771.

86.

Lowe

Sposto

Perkins

, et al. Intensive chemotherapy for systemic anaplastic large cell lymphoma in children and adolescents: final results of children’s cancer group study 5941. Pediatr Blood Cancer 2009; 52: 335–339.

87.

Foss

Advani

Duvic

, et al. A phase II trial of belinostat (PXD101) in patients with relapsed or refractory peripheral or cutaneous T-cell lymphoma. Br J Haematol 2015; 168: 811–819.

88.

Johnston

Cashen

Nikolinakos

, et al. Belinostat in combination with standard cyclophosphamide, doxorubicin, vincristine and prednisone as first-line treatment for patients with newly diagnosed peripheral T-cell lymphoma. Exp Hematol Oncol 2021; 10: 15.

89.

Campbell

Thomas

. Belinostat for the treatment of relapsed or refractory peripheral T-cell lymphoma. J Oncol Pharm Pr 2017; 23: 143–147.

90.

Tan

Phipps

Hwang

WYK

, et al. Panobinostat in combination with bortezomib in patients with relapsed or refractory peripheral T-cell lymphoma: an open-label, multicentre phase 2 trial. Lancet Haematol 2015; 2: e326–e333.

91.

Duvic

Dummer

Becker

, et al. Panobinostat activity in both bexarotene-exposed and -naïve patients with refractory cutaneous T-cell lymphoma: results of a phase II trial. Eur J Cancer 2013; 49: 386–394.

92.

A phase III randomized, double blind, placebo controlled multi-center study of panobinostat for maintenance of response in patients with Hodgkin’s Lymphoma (HL) – study results. ClinicalTrials.gov, https://clinicaltrials.gov/ct2/show/results/NCT01034163 (accessed 16 January 2023).

93.

Oki

Buglio

Fanale

, et al. Phase I study of panobinostat plus everolimus in patients with relapsed or refractory lymphoma. Clin Cancer Res 2013; 19: 6882–6890.

94.

Drott

Hagberg

Papworth

, et al. Valproate in combination with rituximab and CHOP as first-line therapy in diffuse large B-cell lymphoma (VALFRID). Blood Adv 2018; 2: 1386–1392.

95.

Evens

Balasubramanian

Vose

, et al. A phase I/II multicenter, open-label study of the oral histone deacetylase inhibitor abexinostat in relapsed/refractory lymphoma. Clin Cancer Res 2016; 22: 1059–1066.

96.

Ribrag

Kim

Bouabdallah

, et al. Safety and efficacy of abexinostat, a pan-histone deacetylase inhibitor, in non-Hodgkin lymphoma and chronic lymphocytic leukemia: results of a phase II study. Haematologica 2017; 102: 903–909.

97.

Younes

Oki

Bociek

, et al. Mocetinostat for relapsed classical Hodgkin’s lymphoma: an open-label, single-arm, phase 2 trial. Lancet Oncol 2011; 12: 1222–1228.

98.

Younes

Berdeja

Patel

, et al. Safety, tolerability, and preliminary activity of CUDC-907, a first-in-class, oral, dual inhibitor of HDAC and PI3K, in patients with relapsed or refractory lymphoma or multiple myeloma: an open-label, dose-escalation, phase 1 trial. Lancet Oncol 2016; 17: 622–631.

99.

Budde

Zhang

Shustov

, et al. A phase I study of pulse high-dose vorinostat (V) plus rituximab (R), ifosphamide, carboplatin, and etoposide (ICE) in patients with relapsed lymphoma. Br J Haematol 2013; 161: 183–191.

100.

Amengual

Clark-Garvey

Kalac

, et al. Sirtuin and pan-class I/II deacetylase (DAC) inhibition is synergistic in preclinical models and clinical studies of lymphoma. Blood 2013; 122: 2104–2113.

101.

Ramos

Sparano

Chadburn

, et al. Impact of Myc in HIV-associated non-Hodgkin lymphomas treated with EPOCH and outcomes with vorinostat (AMC-075 trial). Blood 2020; 136: 1284–1297.

102.

Shadman

Gopal

Press

, et al. Fludarabine, cyclophosphamide, rituximab (FCR) and vorinostat followed by rituximab and vorinostat maintenance therapy in patients with previously untreated chronic lymphocytic leukemia (CLL) or small lymphocytic leukemia (SLL) – final results of a phase. Blood 2016; 128: 4396.

103.

Spurgeon

Sharma

Claxton

, et al. Phase 1–2 study of vorinostat (SAHA), cladribine and rituximab (SCR) in relapsed B-cell non-Hodgkin lymphoma and previously untreated mantle cell lymphoma. Br J Haematol 2019; 186: 845–854.

104.

Holmberg

Green

Libby

, et al. Bortezomib and vorinostat therapy as maintenance therapy after autologous transplant for multiple myeloma. Acta Haematol 2020; 143: 146–154.

105.

Kirschbaum

Frankel

Popplewell

, et al. Phase II study of vorinostat for treatment of relapsed or refractory indolent non-Hodgkin’s lymphoma and mantle cell lymphoma. J Clin Oncol 2011; 29: 1198–1203.

106.

Ogura

Ando

Suzuki

, et al. A multicentre phase II study of vorinostat in patients with relapsed or refractory indolent B-cell non-Hodgkin lymphoma and mantle cell lymphoma. Br J Haematol 2014; 165: 768–776.

107.

Straus

Hamlin

Matasar

, et al. Phase I/II trial of vorinostat with rituximab, cyclophosphamide, etoposide and prednisone as palliative treatment for elderly patients with relapsed or refractory diffuse large B-cell lymphoma not eligible for autologous stem cell transplantation. Br J Haematol 2015; 168: 663–670.

108.

Chen

Frankel

Popplewell

, et al. A phase II study of vorinostat and rituximab for treatment of newly diagnosed and relapsed/refractory indolent non-Hodgkin lymphoma. Haematologica 2015; 100: 357–362.

109.

Shi

Jia

, et al. Chidamide in relapsed or refractory peripheral T cell lymphoma: a multicenter real-world study in China. J Hematol Oncol 2017; 10: 69.

110.

Piekarz

Frye

Prince

, et al. Phase 2 trial of romidepsin in patients with peripheral T-cell lymphoma. Blood 2011; 117: 5827–5834.

111.

Strati

Nastoupil

Davis

, et al. A phase 1 trial of alisertib and romidepsin for relapsed/refractory aggressive B-cell and T-cell lymphomas. Haematologica 2020; 105: e26–e28.

112.

Duvic

Bates

Piekarz

, et al. Responses to romidepsin in patients with cutaneous T-cell lymphoma and prior treatment with systemic chemotherapy. Leuk Lymphoma 2018; 59: 880–887.

113.

Maruyama

Tobinai

Ogura

, et al. Romidepsin in Japanese patients with relapsed or refractory peripheral T-cell lymphoma: a phase I/II and pharmacokinetics study. Int J Hematol 2017; 106: 655–665.

114.

Foss

Pro

Miles Prince

, et al. Responses to romidepsin by line of therapy in patients with relapsed or refractory peripheral T-cell lymphoma. Cancer Med 2017; 6: 36–44.

115.

Pellegrini

Dodero

Chiappella

, et al. A phase II study on the role of gemcitabine plus romidepsin (GEMRO regimen) in the treatment of relapsed/refractory peripheral T-cell lymphoma patients. J Hematol Oncol 2016; 9: 38.

116.

Batlevi

Kasamon

Bociek

, et al. ENGAGE-501: phase II study of entinostat (SNDX-275) in relapsed and refractory Hodgkin lymphoma. Haematologica 2016; 101: 968–975.

117.

Amengual

Lue

, et al. First-in-class selective HDAC6 inhibitor (ACY-1215) has a highly favorable safety profile in patients with relapsed and refractory lymphoma. Oncologist 2021; 26: 184-e366.

118.

Munakata

Shirasugi

Tobinai

, et al. Phase 1 study of tazemetostat in Japanese patients with relapsed or refractory B-cell lymphoma. Cancer Sci 2021; 112: 1123–1131.

119.

Izutsu

Ando

Nishikori

, et al. Phase II study of tazemetostat for relapsed or refractory B-cell non-Hodgkin lymphoma with EZH2 mutation in Japan. Cancer Sci 2021; 112: 3627–3635.

120.

Palomba

Cartron

Popplewell

, et al. Safety and clinical activity of atezolizumab in combination with tazemetostat in relapsed or refractory diffuse large B-cell lymphoma: primary analysis of a phase 1B study. Hematol Oncol 2019; 37: 517–519.

121.

Argon

Nguyen

Rajarethinam

, et al. Abstract CT170: phase 1 study to characterize the pharmacokinetics and safety of tazemetostat in b-cell lymphomas or advanced solid tumors. Cancer Res 2020; 80: CT170.

122.

Open-label, multicenter, two-part, phase 1 study to characterize effects of a moderate CYP3A inhibitor on PK of tazemetostat, effects of tazemetostat on PK of CYP2C8 and CYP2C19 substrates, and effect of increased gastric pH on PK of tazemetostat in B-cell lymphoma or advanced solid tumor patients – study results. ClinicalTrials.gov, https://clinicaltrials.gov/ct2/show/results/NCT03028103 (accessed 16 January 2023).

123.

Morschhauser

Tilly

Chaidos

, et al. Tazemetostat for patients with relapsed or refractory follicular lymphoma: an open-label, single-arm, multicentre, phase 2 trial. Lancet Oncol 2020; 21: 1433–1442.

124.

Yap

Winter

Giulino-Roth

, et al. Phase I study of the novel enhancer of zeste homolog 2 (EZH2) inhibitor GSK2816126 in patients with advanced hematologic and solid tumors. Clin Cancer Res 2019; 25: 7331–7339.

125.

Amorim

Stathis

Gleeson

, et al. Bromodomain inhibitor OTX015 in patients with lymphoma or multiple myeloma: a dose-escalation, open-label, pharmacokinetic, phase 1 study. Lancet Haematol 2016; 3: e196–e204.

126.

Dickinson

Briones

Herrera

, et al. Phase 1b study of the BET protein inhibitor RO6870810 with venetoclax and rituximab in patients with diffuse large B-cell lymphoma. Blood Adv 2021; 5: 4762–4770.

127.

Falchook

Rosen

LoRusso

, et al. Development of 2 bromodomain and extraterminal inhibitors with distinct pharmacokinetic and pharmacodynamic profiles for the treatment of advanced malignancies. Clin Cancer Res 2020; 26: 1247–1257.

128.

Blum

Abramson

Maris

, et al. 41OA phase I study of CPI-0610, a bromodomain and extra terminal protein (BET) inhibitor in patients with relapsed or refractory lymphoma. Ann Oncol 2018; 29: iii7–iii9.

129.

Patel

Garcia-Manero

Paquette

, et al. Phase 1 dose escalation and expansion study to determine safety, tolerability, pharmacokinetics, and pharmacodynamics of the BET inhibitor FT-1101 as a single agent in patients with relapsed or refractory hematologic malignancies. Blood 2019; 134: 3907.

130.

Marchi

Zullo

Amengual

, et al. The combination of hypomethylating agents and histone deacetylase inhibitors produce marked synergy in preclinical models of T-cell lymphoma. Br J Haematol 2015; 171: 215–226.

131.

Ebrahem

Mahfouz

, et al. High cytidine deaminase expression in the liver provides sanctuary for cancer cells from decitabine treatment effects. Oncotarget 2012; 3: 1137–1145.

132.

Liu

Xie

, et al. Characterization of in vitro and in vivo hypomethylating effects of decitabine in acute myeloid leukemia by a rapid, specific and sensitive LC-MS/MS method. Nucleic Acids Res 2007; 35: e31.

133.

Zhang

Cheng

, et al. Decitabine plus R-chop in patients with newly diagnosed diffuse large B-cell lymphoma: interim results of a phase I/II study. Hematol Oncol 2019; S2: 380–382.

134.

Munshi

Lubin

Bertino

. 6-thioguanine: a drug with unrealized potential for cancer therapy. Oncologist 2014; 19: 760–765.

135.

Reiter

Schrappe

Ludwig

, et al. Intensive ALL-type therapy without local radiotherapy provides a 90% event-free survival for children with T-cell lymphoblastic lymphoma: a BFM group report. Blood 2000; 95: 416–421.

136.

Landmann

Burkhardt

Zimmermann

, et al. Results and conclusions of the European intergroup EURO-LB02 trial in children and adolescents with lymphoblastic lymphoma. Haematologica 2017; 102: 2086–2096.

137.

Zhang

Wang

Chen

, et al. Histone deacetylases (HDACs) guided novel therapies for T-cell lymphomas. Int J Med Sci 2019; 16: 424–442.

138.

Wang

Qin

Huo

, et al. Advances in targeted therapy for malignant lymphoma. Signal Transduct Target Ther 2020; 5: 15.

139.

Marks

Breslow

. Dimethyl sulfoxide to vorinostat: development of this histone deacetylase inhibitor as an anticancer drug. Nat Biotechnol 2007; 25: 84–90.

140.

Kirschbaum

Frankel

Popplewell

, et al. Phase II study of vorinostat for treatment of relapsed or refractory indolent non-Hodgkin’s lymphoma and mantle cell lymphoma. J Clin Oncol 2011; 29: 1198–1203.

141.

Duvic

. Vorinostat: a new oral histone deacetylase inhibitor approved for cutaneous T-cell lymphoma. Expert Opin Investig Drugs 2007; 16: 1111–1120.

142.

Spurgeon

Sharma

Claxton

143.

Shadman

Gopal

Press

, et al. 642. CLL: therapy, excluding Transplantation: poster III. Fludarabine, cyclophosphamide, rituximab (FCR) and vorinostat followed by rituximab and vorinostat maintenance therapy in patients with previously untreated chronic lymphocytic leukemia (CLL) or SMA. Blood 2016; 128: 4396.

144.

Ramos

Sparano

Chadburn

, et al. Impact of Myc in HIV-associated non-Hodgkin lymphomas treated with EPOCH and outcomes with vorinostat (AMC-075 trial). Blood 2020; 136: 1284–1297.

145.

Amengual

Lue

, et al. First-in-class selective HDAC6 inhibitor (ACY-1215) has a highly favorable safety profile in patients with relapsed and refractory lymphoma. Oncologist 2021; 26: 184-e366.

146.

Boumber

Younes

Garcia-Manero

. Mocetinostat (MGCD0103): a review of an isotype-specific histone deacetylase inhibitor. Exp Opin Investig Drugs 2011; 20: 823–829.

147.

Chowdhury

Howell

Teggart

, et al. Histone deacetylase inhibitor belinostat represses survivin expression through reactivation of transforming growth factor beta (TGFbeta) receptor II leading to cancer cell death. J Biol Chem 2011; 286: 30937–30948.

148.

Poole

. Belinostat: first global approval. Drugs 2014; 74: 1543–1554.

149.

Johnston

Cashen

Nikolinakos

150.

Shi

Jia

, et al. Chidamide in relapsed or refractory peripheral T cell lymphoma: a multicenter real-world study in China. J Hematol Oncol 2017; 10: 69.

151.

Yan

Bing

, et al. 624. Hodgkin lymphoma and T/NK cell lymphoma-clinical studies: poster II. Chidamide, oral subtype-selective histone deacetylase inhibitor (HDACI) monotherapy was effective on the patients with relapsed or refractory extranodal natural killer (NK)/T-cell L. Blood 2017; 130: 2797.

152.

Santo

Hideshima

Kung

, et al. Preclinical activity, pharmacodynamic, and pharmacokinetic properties of a selective HDAC6 inhibitor, ACY-1215, in combination with bortezomib in multiple myeloma. Blood 2012; 119: 2579–2589.

153.

Oki

Kelly

Flinn

, et al. CUDC-907 in relapsed/refractory diffuse large B-cell lymphoma, including patients with MYC-alterations: results from an expanded phase I trial. Haematologica 2017; 102: 1923–1930.

154.

Ueda

Nakajima

Hori

, et al. Action of FR901228, a novel antitumor bicyclic depsipeptide produced by Chromobacterium violaceum no. 968, on Ha-ras transformed NIH3T3 cells. Biosci Biotechnol Biochem 1994; 58: 1579–1583.

155.

Reddy

. Romidepsin for the treatment of relapsed/refractory cutaneous T-cell lymphoma (mycosis fungoides/Sezary syndrome): use in a community setting. Crit Rev Oncol Hematol 2016; 106: 99–107.

156.

Maruyama

Tobinai

Ogura

, et al. Romidepsin in Japanese patients with relapsed or refractory peripheral T-cell lymphoma: a phase I/II and pharmacokinetics study. Int J Hematol 2017; 106: 655–665.

157.

Whittaker

Demierre

M-F

Kim

, et al. Final results from a multicenter, international, pivotal study of romidepsin in refractory cutaneous T-cell lymphoma. J Clin Oncol 2010; 28: 4485–4491.

158.

Piekarz

Frye

Prince

, et al. Phase 2 trial of romidepsin in patients with peripheral T-cell lymphoma. Blood 2011; 117: 5827–5834.

159.

Falchi

Klein

, et al. Combined oral 5-azacytidine and romidepsin are highly effective in patients with PTCL: a multicenter phase 2 study. Blood 2021; 137: 2161–2170.

160.

Pellegrini

Dodero

Chiappella

, et al. A phase II study on the role of gemcitabine plus romidepsin (GEMRO regimen) in the treatment of relapsed/refractory peripheral T-cell lymphoma patients. J Hematol Oncol 2016; 9: 38.

161.

Strati

Nastoupil

Davis

, et al. A phase 1 trial of alisertib and romidepsin for relapsed/refractory aggressive B-cell and T-cell lymphomas. Haematologica 2020; 105: e26–e28.

162.

https://www.clinicaltrialsregister.eu/ctr-search/trial/2009-014846-26/results

163.

Zaja

Salvi

Rossi

, et al. Single-agent panobinostat for relapsed/refractory diffuse large B-cell lymphoma: clinical outcome and correlation with genomic data. A phase 2 study of the Fondazione Italiana Linfomi. Leuk Lymphoma 2018; 59: 2904–2910.

164.

Panobinostat plus ifosfamide, carboplatin, and etoposide (ICE) compared with ICE for relapsed Hodgkin lymphoma – study results. ClinicalTrials.gov, https://clinicaltrials.gov/ct2/show/results/NCT01169636 (accessed 16 January 2023).

165.

Duvic

Dummer

Becker

, et al. Panobinostat activity in both bexarotene-exposed and -naive patients with refractory cutaneous T-cell lymphoma: results of a phase II trial. Eur J Cancer 2013; 49: 386–394.

166.

Maly

Christian

Zhu

, et al. A phase I/II trial of panobinostat in combination with lenalidomide in patients with relapsed or refractory Hodgkin lymphoma. Clin Lymphoma Myeloma Leuk 2017; 17: 347.

167.

Tan

Phipps

Hwang

168.

Varambally

Dhanasekaran

Zhou

, et al. The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature 419: 624–629.

169.

Kleer

Cao

Varambally

, et al. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc Natl Acad Sci USA 2003; 100: 11606–11611.

170.

Visser

HPJ

Gunster

. The polycomb group protein EZH2 is upregulated in proliferating, cultured human mantle cell lymphoma. Br J Haematol 2001; 112: 950–958.

171.

Abd

Kader

Oka

Takata

, et al. In aggressive variants of non-Hodgkin lymphomas, Ezh2 is strongly expressed and polycomb repressive complex PRC1.4 dominates over PRC1.2. Virchows Arch 2013; 463: 697–711.

172.

Morin

Johnson

Severson

, et al. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet 2010; 42: 181–185.

173.

Zhang

Zhao

Fiskus

, et al. Coordinated silencing of MYC-mediated miR-29 by HDAC3 and EZH2 as a therapeutic target of histone modification in aggressive B-cell lymphomas. Cancer Cell 2012; 22: 506–523.

174.

Ryan

RJH

Nitta

Borger

, et al. EZH2 codon 641 mutations are common in BCL2-rearranged germinal center B cell lymphomas. PLoS ONE 2011; 6: 1–7.

175.

Zhao

Lwin

Zhang

, et al. Disruption of the MYC-miRNA-EZH2 loop to suppress aggressive B-cell lymphoma survival and clonogenicity. Leukemia 2013; 27: 2341–2350.

176.

Lue

Prabhu

Liu

, et al. Precision targeting with EZH2 and HDAC inhibitors in epigenetically dysregulated lymphomas. Clin Cancer Res 2019; 25: 5271–5283.

177.

McCabe

Ott

Ganji

, et al. EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations. Nature 2012; 492: 108–112.

178.

Vaswani

Gehling

Dakin

, et al. Identification of (R)-N-((4-Methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-2-methyl-1-(1-(1-(2,2,2-trifluoroethyl)piperidin-4-yl)ethyl)-1H-indole-3-carboxamide (CPI-1205), a potent and selective inhibitor of histone methyltransferase EZH2, suitable for phase I clinical trials for B-cell lymphomas. J Med Chem 2016; 59: 9928–9941.

179.

Whittaker

. Global patterns of methylation in sézary syndrome provide insight into the role of epigenetics in cutaneous T-Cell lymphoma. J Invest Dermatol 2016; 136: 1753–1754.

180.

Maruyama

Tobinai

Makita

, et al. First-in-human study of the EZH1/2 dual inhibitor DS-3201b in patients with relapsed or refractory non-Hodgkin lymphomas – preliminary results. Blood 2017; 130: 4070–4070.

181.

Knutson

Kawano

Minoshima

, et al. Selective inhibition of EZH2 by EPZ-6438 leads to potent antitumor activity in EZH2-mutant non-Hodgkin lymphoma. Mol Cancer Ther 2014; 13: 842–854.

182.

Italiano

Soria

Toulmonde

, et al. Tazemetostat, an EZH2 inhibitor, in relapsed or refractory B-cell non-Hodgkin lymphoma and advanced solid tumours: a first-in-human, open-label, phase 1 study. Lancet Oncol 2018; 19: 649–659.

183.

Akpa

Kleo

Lenze

, et al. DZNep-mediated apoptosis in B-cell lymphoma is independent of the lymphoma type, EZH2 mutation status and MYC, BCL2 or BCL6 translocations. PLoS ONE 2019; 14: e0220681.

184.

Wyczechowska

Fabianowska-Majewska

. The effects of cladribine and fludarabine on DNA methylation in K562 cells. Biochem Pharmacol 2003; 65: 219–225.

185.

Sigal

Miller

Schram

, et al. Beyond hairy cell: the activity of cladribine in other hematologic malignancies. Blood 2010; 116: 2884–2896.

186.

Kluin-Nelemans

Hoster

Hermine

, et al. Treatment of older patients with mantle-cell lymphoma. N Engl J Med 2012; 367: 520–531.

187.

Padmanabhan

Mathur

Manjula

, et al. Bromodomain and extra-terminal (BET) family proteins: new therapeutic targets in major diseases. J Biosci 2016; 41: 295–311.

188.

Delmore

Issa

Lemieux

, et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 2011; 146: 904–917.

189.

Lovén

Hoke

Lin

, et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 2013; 153: 320–334.

190.

Yang

Yik

JHN

Chen

, et al. Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4. Mol Cell 2005; 19: 535–545.

191.

Johnson-Farley

Veliz

Bhagavathi

, et al. ABT-199, a BH3 mimetic that specifically targets Bcl-2, enhances the antitumor activity of chemotherapy, bortezomib and JQ1 in ‘double hit’ lymphoma cells. Leuk Lymphoma 2015; 56: 2146–2152.

192.

Feng

Yao

Zhou

, et al. Pharmacological inhibition of LSD1 for the treatment of MLL-rearranged leukemia. J Hematol Oncol 2016; 9: 24.

193.

Mondello

Tadros

Teater

, et al. Selective inhibition of HDAC3 targets synthetic vulnerabilities and activates immune surveillance in lymphoma. Cancer Discov 2020; 10: 440–459.

194.

Yang

Lee

. Application of bioinformatics in cancer epigenetics. Ann N Y Acad Sci 2004; 1020: 67–76.

195.

Ching

Huang

, et al. Using epigenomics data to predict gene expression in lung cancer. BMC Bioinformatics 2015; 16(Suppl. 5): S10.

196.

Mai

Altucci

. Epi-drugs to fight cancer: from chemistry to cancer treatment, the road ahead. Int J Biochem Cell Biol 2009; 41: 199–213.

197.

Springer

. Epigenetics and crop improvement. Trends Genet 2013; 29: 241–247.

198.

Mullard

. The roadmap epigenomics project opens new drug development avenues. Nat Rev Drug Discov 2015; 14: 223–225.

199.

Schumacher

Kapranov

Kaminsky

, et al. Microarray-based DNA methylation profiling: technology and applications. Nucleic Acids Res 2006; 34: 528–542.

200.

Booth

Branco

Ficz

, et al. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 2012; 336: 934–937.

201.

Furey

. ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions. Nat Rev Genet 2012; 13: 840–852.

202.

Gautam

Goswami

Mishra

, et al. The role of bioinformatics in epigenetics. In: Wadhwa

Shanmughavel

Singh

, et al. (eds) Current trends in bioinformatics: an insight. Singapore: Springer Singapore, 2018, pp. 39–53.

203.

Pettini

Visibelli

Cicaloni

, et al. Multi-omics model applied to cancer genetics. Int J Mol Sci 2021; 22: 5751.

204.

Meir

Mukamel

Chomsky

, et al. Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells. Nat Genet 2020; 52: 709–718.

205.

Montalvo-Casimiro

González-Barrios

Meraz-Rodriguez

, et al. Epidrug repurposing: discovering new faces of old acquaintances in cancer therapy. Front Oncol 2020; 10: 605386.

206.

Liu

, et al. The status and prospects of epigenetics in the treatment of lymphoma. Front Oncol 2022; 12: 874645–874623.

207.

Bock

Lengauer

. Computational epigenetics. Bioinformatics 2008; 24: 1–10.

208.

Toedling

Sklyar

Huber

. Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinform 2007; 8: 221.

209.

Zhang

Rozowsky

Lam

, et al. Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol 2007; 8: R81.

210.

Meyer

Liu

. A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics 2005; 21(Suppl. 1): i274–i282.

211.

Langmead

Trapnell

Pop

, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10: R25.

212.

Kent

. BLAT – the BLAST-like alignment tool. Genome Res 2002; 12: 656–664.

213.

Hebenstreit

Haider

, et al. EpiChIP: gene-by-gene quantification of epigenetic modification levels. Nucleic Acids Res 2011; 39: e27–e27.

214.

Mikkelsen

Jaffe

, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007; 448: 553–560.

215.

Handsaker

Wysoker

, et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009; 25: 2078–2079.

216.

Bardet

Steinmann

Bafna

, et al. Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bioinformatics 2013; 29: 2705–2713.

217.

Zhang

Liu

Meyer

, et al. Model-based analysis of ChIP-seq (MACS). Genome Biol 2008; 9: R137.

218.

Ibrahim

Lacadie

Ohler

. JAMM: a peak finder for joint analysis of NGS replicates. Bioinformatics 2015; 31: 48–55.

219.

Wang

Zhang

, et al. Primary effusion lymphoma enhancer connectome links super-enhancers to dependency factors. Nat Commun 2020; 11: 6318.

220.

Xue

J-C

X-Y

, et al. Chidamide triggers BTG1-mediated autophagy and reverses the chemotherapy resistance in the relapsed/refractory B-cell lymphoma. Cell Death Dis 2021; 12: 900.

221.

Wang

Yang

, et al. TRIB3 promotes MYC-associated lymphoma development through suppression of UBE3B-mediated MYC degradation. Nat Commun 2020; 11: 6316.

222.

Horn

Zubarev

McLafferty

. Automated reduction and interpretation of. J Am Soc Mass Spectrom 2000; 11: 320–332.

223.

Lue

Prabhu

Liu

, et al. Precision targeting with EZH2 and HDAC inhibitors in epigenetically dysregulated lymphomas. Clin Cancer Res 2019; 25: 5271–5283.

224.

Bibikova

Barnes

Tsan

, et al. High density DNA methylation array with single CpG site resolution. Genomics 2011; 98: 288–295.

225.

Down

Rakyan

Turner

, et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 2008; 26: 779–785.

226.

Aberg

Xie

Chan

, et al. Evaluation of methyl-binding domain based enrichment approaches revisited. PLoS ONE 2015; 10: e0132205.

227.

Bock

Müller

, et al. RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. Bioinformatics 2012; 28: 430–432.

228.

Otto

Stadler

Hoffmann

. Fast and sensitive mapping of bisulfite-treated sequencing data. Bioinformatics 2012; 28: 1698–1704.

229.

Pedersen

Hsieh

T-F

Ibarra

, et al. MethylCoder: software pipeline for bisulfite-treated sequences. Bioinformatics 2011; 27: 2435–2436.

230.

Harris

Ounit

Lonardi

. BRAT-nova: fast and accurate mapping of bisulfite-treated reads. Bioinformatics 2016; 32: 2696–2698.

231.

Liu

Siegmund

Laird

, et al. Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol 2012; 13: R61.

232.

Barturen

Rueda

Oliver

, et al. MethylExtract: high-quality methylation maps and SNV calling from whole genome bisulfite sequencing data. F1000Res 2014; 2: 217.

233.

Küpers

Monnereau

Sharp

, et al. Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight. Nat Commun 2019; 10: 1893.

234.

Fingerman

Zhang

Ratzat

, et al. NCBI epigenomics: what’s new for 2013. Nucleic Acids Res 2012; 41: D221–D225.

235.

Dunham

Kundaje

Aldred

, et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012; 489: 57–74.

236.

Grunau

. MethDB – a public database for DNA methylation data. Nucleic Acids Res 2001; 29: 270–274.

237.

Liang

, et al. MethBank 3.0: a database of DNA methylomes across a variety of species. Nucleic Acids Res 2018; 46: D288–D295.

238.

O’Connor

Wyrick

. ChromatinDB: a database of genome-wide histone modification patterns for Saccharomyces cerevisiae. Bioinformatics 2007; 23: 1828–1830.

239.

Zhang

Liu

, et al. HHMD: the human histone modification database. Nucleic Acids Res 2010; 38(Database issue): D149–D154.

240.

Shen

Shao

N-Y

Liu

, et al. diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS ONE 2013; 8: e65598.

241.

Hsu

C-H

Tomiyasu

Liao

C-H

, et al. Genome-wide DNA methylation and RNA-seq analyses identify genes and pathways associated with doxorubicin resistance in a canine diffuse large B-cell lymphoma cell line. PLoS ONE 2021; 16: e0250013.

242.

Nadeu

Martin-Garcia

Clot

, et al. Genomic and epigenomic insights into the origin, pathogenesis, and clinical behavior of mantle cell lymphoma subtypes. Blood 2020; 136: 1419–1432.

243.

Zaghlool

Kühnel

Elhadad

, et al. Epigenetics meets proteomics in an epigenome-wide association study with circulating blood plasma protein traits. Nat Commun 2020; 11: 15.

244.

Shen

Boccuto

Pauly

, et al. Genome-scale network model of metabolism and histone acetylation reveals metabolic dependencies of histone deacetylase inhibitors. Genome Biol 2019; 20: 49.

245.

Saffie

Zhou

Rolland

, et al. FBXW7 triggers degradation of KMT2D to favor growth of diffuse large B-cell lymphoma cells. Cancer Res 2020; 80: 2498–2511.

246.

Evans

Parker

Rutteman

, et al. Multi-omics approach identifies germline regulatory variants associated with hematopoietic malignancies in retriever dog breeds. PLoS Genet 2021; 17: e1009543.

247.

Schadt

Friend

Shaywitz

. A network view of disease and compound screening. Nat Rev Drug Discov 2009; 8: 286–295.

248.

Cai

Poulos

Liu

, et al. Machine learning for multi-omics data integration in cancer. iScience 2022; 25: 103798.

249.

Sánchez-Cruz

Medina-Franco

. Epigenetic target fishing with accurate machine learning models. J Med Chem 2021; 64: 8208–8220.

250.

Langfelder

Horvath

. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008; 9: 559.

251.

Ghobadi

Emamzadeh

Mozhgani

. Deciphering microRNA-mRNA regulatory network in adult T-cell leukemia/lymphoma; the battle between oncogenes and anti-oncogenes. PLoS ONE 2021; 16: e0247713.

252.

Singh

Shannon

Gautier

, et al. DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays. Bioinformatics 2019; 35: 3055–3062.

253.

Zhang

Jiang

, et al. Computer-aided drug design in epigenetics. Front Chem 2018; 6: 57.

254.

Fauman

Rai

Huang

. Structure-based druggability assessment – identifying suitable targets for small molecule therapeutics. Curr Opin Chem Biol 2011; 15: 463–468.

255.

Chen

, et al. Identification of novel disruptor of telomeric silencing 1-like (DOT1L) inhibitors through structure-based virtual screening and biological assays. J Chem Inf Model 2016; 56: 527–534.

256.

Güner

Clement

Kurogi

. Pharmacophore modeling and three dimensional database searching for drug design using catalyst: recent advances. Curr Med Chem 2004; 11: 2991–3005.

257.

Caulfield

Medina-Franco

. Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A. J Struct Biol 2011; 176: 185–191.

258.

Chen

Frankel

Popplewell

, et al. A phase II study of vorinostat and rituximab for treatment of newly diagnosed and relapsed/refractory indolent non-Hodgkin lymphoma. Haematologica 2015; 100: 357–362.

259.

Assouline

Nielsen

, et al. Phase 2 study of panobinostat with or without rituximab in relapsed diffuse large B-cell lymphoma. Blood 2016; 128: 185–194.

260.

Inwards

Fishkin

PAS

Hillman

, et al. Long-term results of the treatment of patients with mantle cell lymphoma with cladribine (2-CDA) alone (95-80-53) or 2-CDA and rituximab (N0189) in the North Central Cancer Treatment Group. Cancer 2008; 113: 108–116.

261.

Sarkozy

Morschhauser

Dubois

, et al. A LYSA phase Ib study of tazemetostat (EPZ-6438) plus R-CHOP in patients with newly diagnosed diffuse large B-cell lymphoma (DLBCL) with poor prognosis features. Clin Cancer Res 2020; 26: 3145–3153.

Epigenetic targets in B- and T-cell lymphomas: latest developments

Abstract

Keywords

Introduction

Characteristics of B-NHL

Physiopathology of T-cell lymphoma

Epigenetic deregulations in B- and T-cell lymphoma

Role of epigenetic drugs in B- and T-cell lymphoma

DNA methylation inhibitors

HDAC inhibitors

HMT inhibitors

Bromodomain inhibitors

Future perspectives: paving the way for precision medicine with epidrugs in B- and T-cell lymphoma and implementing bioinformatics approaches to identify new epigenetic targets in hematological cancers

Personalized epigenome targeting in NHL

In silico epigenetic profiling: basic concepts

Computational validation of epigenetic alterations in B- and T-cell lymphoma

Conclusion and future perspectives

Footnotes

Acknowledgements

Declarations

ORCID iDs

References