Metabolic reprogramming directed by super-enhancers in tumors: An emerging landscape

Abstract

Metabolic reprogramming is an essential hallmark of tumors, and metabolic abnormalities are strongly associated with the malignant phenotype of tumor cells. This is closely related to transcriptional dysregulation. Super-enhancers are extremely active cis-regulatory regions in the genome, and can amalgamate a complex set of transcriptional regulatory components that are crucial for establishing tumor cell identity, promoting tumorigenesis, and enhancing aggressiveness. In addition, alterations in metabolic signaling pathways are often accompanied by changes in super-enhancers. Presently, there is a surge in interest in the potential pathogenesis of various tumors through the transcriptional regulation of super-enhancers and oncogenic mutations in super-enhancers. In this review, we summarize the functions of super-enhancers, oncogenic signaling pathways, and tumor metabolic reprogramming. In particular, we focus on the role of the super-enhancer in tumor metabolism and its impact on metabolic reprogramming. This review also discusses the prospects and directions in the field of super-enhancer and metabolic reprogramming.

Graphical abstract

Zhou and colleagues outline the role of super-enhancers in tumor metabolic reprogramming. Their insights open new horizons for elucidating new epigenetic mechanisms of tumor metabolic reprogramming and for developing innovative strategies in cancer treatment.

Introduction

Metabolic reprogramming is an essential hallmark of tumors.¹ Metabolic reprogramming is the name given to the diverse adaptations in cellular metabolism that tumor cells undergo in response to the influence of surrounding metabolic substrates and tissue cells during tumorigenesis. These adjustments include glucose reprogramming, the dysregulation of lipid metabolism, and other metabolic changes (involving nucleotides and amino acids). Transcriptional regulation of tumor oncogenes and signaling pathways are instrumental in the manipulation of metabolic reprogramming. For instance, c-Myc regulates glycolytic metabolism in tumor cells.² The phosphatidylinositol 3-kinase (PI3K)-AKT pathway controls transcription factors (TFs) that regulate the expression of key components of metabolic pathways.³ KRAS partially mediates the reprogramming of tumor cell metabolism by transcriptionally upregulating several key glycolytic enzymes.⁴ In short, metabolic reprogramming is closely related to transcriptional dysregulation.

Super-enhancer (SE) contributes to transcriptional dysregulation leading to the uncontrolled activity of oncogenes in tumor cells. This dysregulated gene expression creates a dependence on the SE for the regulation of oncogenes, making them susceptible to transcriptional regulators.⁵ Disruption of genes regulating tumor cell metabolism affects the metabolic environment. SE is more sensitive to the perturbation of enhancer components than typical enhancers.⁶ SEs differ from typical enhancers in aspects such as size, length, and function. Table 1 provides a comprehensive summary of these differences and their implications for the relationship between SEs and typical enhancers (Table 1). The SE interacts with the promoter of MYC, thereby promoting its high expression. This interaction is crucial for enhancing glycolysis in tumor cells, reducing lipid and cholesterol synthesis, and boosting nucleotide synthesis.⁷ In addition, the SE modulates lipid metabolism through pathways involving oncogenes. SE-related circuits (KLF15/TCF4/NKX2-2) can regulate critical signaling pathways (PI3K/AKT/MAPK) and lipid metabolism pathways that support tumors.⁸ Therefore, SEs are closely associated with tumor cell metabolism. In this review, we introduce the fundamental structural and functional characteristics of SEs and the relationship between SE-related oncogenic signaling pathways and tumor metabolic reprogramming. We then focus on the role and effects of SEs on tumor metabolic reprogramming. Finally, we discuss the prospects and future research directions for SEs and tumor metabolic reprogramming.

Table 1.

Difference between typical enhancer and SE

Amounts	Typical enhancer	SE
	Single or discrete enhancer	A large set of enhancers
Range of span	200–300 bp	8–20 kb
Extent of histone modifications	Low	High
Transcriptional activity	Low	High
Function	Activating or enhancing gene transcription	Being associated with genes that control key lineage-specific aspects of cell state and differentiation in somatic cells

Structural characteristics and functions of the SE

Hnisz et al. discovered that SEs differ significantly from traditional enhancers in mouse embryonic stem cells.⁹ SE is a large collection of enhancers that regulate the expression of key genes involved in cellular pluripotency. SE aggregates many molecules such as master regulatory TFs (MRTFs), chromatin regulators/markers, cofactors, and RNA polymerases¹⁰ (Figure 1A). The aggregation of these molecules is closely related to the formation process of the SE and can be summarized using a phase-separation model¹¹ (Figure 1B). SEs are closely related to important processes in tumor development and metastasis,^12,13,14,15 such as metabolic reprogramming.^{7,16,17,18,19,20,21}

Figure 1.

Structural characteristics of SEs

(A) SE is a tandem collection of enhancers with a high density of TFs and mediator binding. TFs specific to cell types provide a platform for p300, which is recruited to the SE domain. The protein complex includes cohesion, MED1, and BRD4, which forms a loop between the SE and the promoter, and then induces a powerful transcription of the target gene. (B) The SE sites are more prone to a phase separation phenomenon, in which a heterogeneous mixture of proteins and DNA is assembled into a membrane-free organelle-like structure.

Numerous genes and signaling pathways regulated by SE augment the malignant phenotypes of neoplastic cells, such as tumor metastasis^20,22,23 and immune escape.²⁴ Among these, some genes and signaling pathways (KRAS/PI3K/c-MET/MYC)^{16,17,18,19,20} are associated with tumor metastasis. Others (hypoxia-inducible factor 1A [HIF1A] and MYC) have been associated with immune escape.²¹ For instance, SEs upregulate the oncogenes HIF1A and MYC by suppressing the interferon-α/γ pathway genes to inhibit the host immune response. Consequently, it is plausible that SEs may be responsible for tumor metabolic regulation and heightened metabolic competitiveness by reconfiguring conventional metabolic patterns.²⁵ The ability to compete for nutrients is predominantly reflected in the rate of material transportation and the proficiency in processing raw materials. Certain SEs amplify the synthesis of transporters, increase the number of transport channels for materials, and hasten the transportation rate.²⁶ Other SEs stimulate the synthesis of key enzymes, resulting in the faster supply of oxidative energy and nutrients.⁷ The role of SEs in tumor metabolism is extensively examined in the fourth section of this paper.

Oncogenic signaling pathway and metabolic reprogramming

Metabolic reprogramming is a key characteristic of tumors, supporting their growth and proliferation.²⁷ During rapid proliferation, tumors compete for nutrients with other cellular components of the tumor microenvironment, including endothelial, immune, and stromal cells. Based on the balance between catabolic and anabolic metabolism, tumor cells greatly increase their cellular mass, accelerate their own division,²⁸ and seize nutrients from immune cells to suppress the immune system and obtain more space for growth.²⁹

This metabolic difference is reflected in reprogramming changes in tumor cells.³⁰ Some metabolic activities such as aerobic glycolysis, amino acid metabolism, and lipid metabolism are particularly prominent in the reprogramming process of tumor metabolism. Some oncogenes or signaling pathways either enhance the transport of nutrients or regulate the transcription of genes encoding metabolic enzymes. For example, MYC regulates the Warburg effect in tumors by activating or inhibiting certain enzymes and cooperating with HIF to activate several glucose transporters, glycolytic enzymes, lactate dehydrogenase A, and 3′-phosphoinositide-dependent kinase 1 (PDK1),^26,31 which accelerate glucose transport and increase the oxidation rate to meet tumor energy needs. MYC also activates mitochondrial biosynthesis³² and glutamine metabolism, assisting tumors in synthesizing large amounts of proteins. The PI3K-Akt-mammalian target of rapamycin (mTOR) pathway regulates the uptake and utilization of various nutrients, such as glucose, amino acids, nucleotides, and lipids, via posttranslational modifications. In addition, the downstream effectors of this pathway, such as phosphofructokinase-1³³ and FAS-1,³⁴ significantly enhance the activity of metabolic enzymes involved in these processes.³⁵

SE participates in the regulation of cellular metabolism in normal tissues.³⁶ However, proto-oncogenes and signaling pathways regulated by SE activate abnormal metabolic pathways or inhibit normal metabolism, thus becoming initiators of tumor metabolism. Subsequently, tumors or precancerous tissues begin to change their metabolic patterns.

SEs and tumor metabolic reprogramming

Oncogenes control the localization, transcription, translation, and posttranslational aspects of tumor cells, which are necessary for regulating metabolism. SEs directly affect oncogene transcription to regulate tumor metabolic reprogramming in different ways: some SEs induce the synthesis of critical metabolic enzymes,⁷ some promote increased fluxes of crucial metabolic cycles,²⁵ and some directly increase metabolic intermediates to boost metabolism.³⁷ In addition, SE-associated core transcriptional regulatory circuitry (CRC) is involved in the metabolic regulation of tumors and modulates many aspects of tumor metabolic reprogramming.⁸

SEs and tumor glucose reprogramming

Glucose metabolism contains the glycolysis pathway, the pentose phosphate pathway (PPP), and the tricarboxylic acid (TCA) cycle in the mitochondria. Abnormal tumor glycolysis is an essential component of metabolic reprogramming in tumors. The Warburg effect, also known as aerobic glycolysis, is a hallmark metabolic pattern of tumor cells. It manifests as enhanced glycolysis in malignant tumors. That is, when oxygen is available, tumor cells obtain more energy by glycolysis than by aerobic respiration.³⁸ According to recent studies, aerobic glycolysis is due in part to the regulation of the transcription of key enzyme genes in the oxidative phosphorylation process. For example, hexokinase 2 is a key enzyme that catalyzes the production of glucose-6-phosphate from glucose and interacts with ATP outside the mitochondrial outer membrane.³⁹ By binding to the voltage-dependent anion channel, it plays a key role in aerobic glycolysis. The overexpression of MYC increases glucose flux and glycolytic enzyme expression in glioblastoma stem cells.²⁵

Glucose is the source of aerobic glycolysis, and its products are an important energy source for tumor cells. By affecting the transcription of transporters or key metabolic enzyme genes (ENO2/ENO3/FUT8/PCK1/SRC), SEs enhance the aerobic glycolysis through two metabolic pathways: (1) it increases the reabsorption of glucose, thus facilitating aerobic glycolysis⁴⁰; and (2) the activation of SE-related oncogenes (including MYC and SRC) enhances the transcription of key enzyme genes related to aerobic glycolysis, thus reprogramming the glucose metabolism pattern^7,41 (Figure 2A).

Figure 2.

The effect of SE on tumor glucose metabolism reprogramming in tumor

(A) The activation of SE-related oncogenes (including MYC and SRC) increases the transcription of glucose metabolism-associated genes (ENO2/ENO3/FUT8/PCK1/SRC) related to aerobic glycolysis, resulting in a reprogramming of the glucose metabolism pattern. (B) The c-Myc protein is involved in metabolic reprogramming by regulating the transcription of key enzyme genes, which affects lipid synthesis, amino acid synthesis, and nucleotide synthesis in tumors. PPP participates in the occurrence of these different reactions.

The regulation of aerobic glycolysis by SEs is not limited to alterations in glycolysis, but it may also affect many metabolic processes, including lipid synthesis (via the TCA cycle), serine synthesis, and nucleotide synthesis in tumors. PPP participates in the occurrence of these different reactions, which provides reducing equivalents of nicotinamide adenine dinucleotide phosphate (NADPH). The total levels of metabolites, including NADPH, NAD, and NADH, were found to be upregulated due to the regulatory effects of SEs.⁷ These ingredients are exactly what the cells need.^40,42 This suggests that SEs not only increase the amount of nutrients required by the cells but also change the way that nutrients are used in the tumor by affecting the key glycolysis enzyme genes (Figure 2B).

SEs and tumor lipid reprogramming

Dysregulation of lipid (fatty acids [FAs] and cholesterol) metabolism is one of the most prominent metabolic alterations in tumors. Lipid metabolism includes FA transport, ab initio synthesis, lipid synthesis, lipid droplet storage, and FA β-oxidation. Lipids are essential energy sources for tumor development. Tumor cells activate adipogenesis in response to their high metabolic demands, even in the presence of exogenous lipid sources.⁴³ Various enzymes such as acetyl coenzyme A carboxylase, FA synthase (FASN), and acyl coenzyme A synthase are involved.⁴⁴ Intracellular cholesterol can act as a secondary messenger to deliver proliferation-related signals, and triphosphorylated phosphatidylinositol helps localize Akt at the cellular membrane. PDK1 and mTORC2 activate Akt⁴⁵ and protein kinase B to regulate two processes of FA synthesis: (1) the intermediate metabolic shuttle provides the carbon source for anabolism and (2) NADPH provides the fuel for lipogenesis.⁴⁶

The SE activation of oncogenic signaling pathways is essential for reprogramming lipid metabolism in tumors. mTORC1 is a complex protein downstream of the PI3K-Akt-mTOR pathway. It regulates lipid biosynthesis by regulating the expression and activity of SREBF1 and SREBF2.⁴⁷ SE-activated genes regulate this pathway to reprogram the lipid metabolism. It was found that SE-bound Kruppel-like factor 6 (KLF6) directly regulates the expression of lipid metabolism genes, promotes the activation of the mTORC1 pathway, and promotes the expression and activity of downstream TFs sterol regulatory element-binding TF1 (SREBF1) and SREBF2, thereby regulating tumor lipid biosynthesis in clear cell renal cell carcinoma (ccRCC) cells⁴⁷ (Figure 3A).

Figure 3.

The effect of SE on lipid metabolism reprogramming in tumors

(A) SE-related oncogenes regulate lipid metabolism reprogramming through the mTORC complex. SE-activated KLF6 promotes the transcription of platelet-derived growth factor subunit B in the mTORC1 pathway and downstream target genes SREBF1 and SREBF2, and then activates lipid metabolism reprogramming. (B) The AR activates the expression of genes involved in the SE-mediated FA metabolism pathways (FASN, ACLY, LPL, PI, and SREBP), and then affects tumor lipid metabolism. (C) CRC (e.g., KLF15/TCF4/NKX2-2) regulates lipid metabolism pathways in tumors. (D) The lncRNA, FASRL, under SE control, binds to the ACACA enzyme and promotes FA synthesis, whereas the SE activation of SIRT7 inhibits lipid metabolism.

Abnormal activation of TFs related to SE is indispensable for lipid metabolism reprogramming in tumors. TF androgen receptor (AR) is a major regulator of cellular energy metabolism, including FA β-oxidation and de novo lipid synthesis in lipid-rich prostate cancer (PCA).⁴⁸ Baumgart et al. found that the synthetic androgen R1881 binds to AR and activates the expression of genes involved in the SE-bound FA metabolism pathway (FASN, ATP citrate lyase [ACLY], lipoprotein lipase [LPL], PI, and SREB protein [SREBP]) in PCA cells, thereby affecting tumor lipid metabolism and activating the PI3K-Akt-mTOR pathway⁴⁹ (Figure 3B). In addition, SEs regulate tumor lipid metabolism through CRC, which allows for regulatory interventions in metabolism with the assistance of MRTF. CRC engages in de novo lipid synthesis in tumors. Ma et al. found that in esophageal adenocarcinoma, SEs combined with MRTFs (ELF3/KLF5/GATA6/EHF) to form a transcriptional regulatory circuit, thereby upregulating the expression of genes related to the de novo synthesis of FAs, phospholipids, and sphingolipids.⁵⁰ Shi et al. also identified an SE-related circuit (KLF15/TCF4/NKX2-2) that regulates critical tumor signaling pathways (PI3K-Akt-mTOR and MAPK) and lipid metabolism pathways in Ewing sarcoma.⁸ Li et al. found a CRC between SREBF1, TP63, and KLF5 in esophageal squamous cell carcinoma (ESCC), which is involved in the regulation of FA, sphingolipid, and glycerophospholipid synthesis by signaling pathways, such as mTOR and ErbB, and promotes the invasion and migration of ESCC cells⁵¹ (Figure 3C).

Furthermore, SE also drives the expression of other types of genes besides TFs such as fat synthesis-related genes and long noncoding RNAs (lncRNAs). On the one hand, SEs drive the expression of fat synthesis-related genes to regulate lipid generation in tumors, thereby accelerating tumor growth. For example, SEs activate the fat mass and obesity-associated protein modified by m⁶A demethylase after binding to BRD9, ultimately promoting the growth of ccRCC.⁵² Sirtuins (SIRT1−7) have attracted considerable attention as regulators of metabolism over the past decade. Hepatic SIRT7 controls lipid metabolism in liver by regulating the ubiquitin-proteasome pathway.⁵³ In hepatocellular carcinoma (HCC), SE activation of SIRT7 inhibited some key metabolic and immune regulators,⁵⁴ and the deregulation of SIRT7 has been shown to aggregate hepatic gluconeogenesis and lipid metabolism.⁵³ On the other hand, the SE also drives the transcriptional expression of lncRNA genes, which directly bind to enzymes and inhibit their phosphorylation to enhance enzyme activity. For example, an SE-controlled lncRNA, FASRL, binds to the ACACA enzyme (one of the key limiting enzymes in FA synthesis) and promotes FA synthesis in HCC,⁵⁵ thereby promoting the growth of HCC (Figure 3D).

SEs and tumor amino acid reprogramming

Both tumor cells and immune cells need amino acids. On the one hand, immune cells need amino acids to enhance their killing ability on tumor cells; on the other hand, tumor cells need amino acids to form proteins for cellular proliferation, cooperative growth, and synthesis of key enzymes. Glutamine is the amino acid with the highest uptake rate by tumor cells. Tumor cells replenish large amounts of carbon intermediates via glutamine catabolism to assemble the required macromolecules. Tumor cells usually rely on the uptake of exogenous glutamine through cytosolic drinking.⁵⁶ mTORC1 pathway regulation contributes to the differential uptake of amino acids.⁵⁷ This pathway enhances this difference by activating the transcription of metabolic- and transport-related enzymes. SEs increase glutamine transport in tumor cells in vivo,⁵⁸ and heat shock factor-1 enhances the transcription of its binding genes (including LINC00857) by stimulating SE activity, providing metabolic support for cancer development (Figure 4A).

Figure 4.

The effect of SE on amino acid metabolism reprogramming in tumors

(A) SE decreases glutamine transportation in tumor cells by stimulating the transcriptional activity of LINC00857. (B) SE drives the transcription of COL1A2 and increases collagen levels. (C) SE also drives the expression of oncogene XBP1, thus restoring protein synthesis.

Collagen, one of the most abundant proteins in the body, is produced by fibroblasts and is prevalent in the extracellular matrix. The extracellular matrix structure is closely related to the dormant-reviving state of tumor cells.⁵⁹ In pancreatic ductal cell carcinoma, the SE drives genes (MYC, BRD4, RNA polymerase II, and COL1A2) that activate the TP53 pathway and inhibit the KRAS pathway, ultimately increasing collagen levels in tumor cells, indicating that SE is involved in the synthesis of collagen in tumor cells⁶⁰ (Figure 4B).

In addition, SEs indirectly regulate the expression of genes related to the unfolded protein response (UPR) in tumor cells, which improves the efficiency of tumor protein synthesis. For example, SE drives the expression of oncogene XBP1 (X-box binding protein 1) in leukemic stem cells, which activates the expression of a series of UPR-related proteins and restores protein synthesis in the endoplasmic reticulum.^61,62 In PCA cells, SEs also regulate the protein-folding efficiency of tumor cells through the AR, thereby affecting protein synthesis^49,63(Figure 4C).

Summary, challenges, and prospects

In the present review, we systematically generalized the role of the SE in tumor metabolism and its impact on metabolic reprogramming. In recent years, major studies on tumor metabolism have focused on specific tumors with specific metabolic patterns, but the role of SEs in tumor metabolism remain uninvestigated or less studied. Moreover, most of the studies on SEs have focused only on the correlation between SEs and metabolic genes. There is still a lack of understanding of the mechanism and specific processes of the role of SEs in tumor metabolism-related enzymes or genes, such as how certain master TFs are recruited to SEs in tumor metabolism.

The number of tumor amino acid- and nucleotide-related metabolic reprogramming studies is very small. In particular, the relationship between SEs and metabolic reprogramming of amino acids or nucleotides is worth exploring. An increasing number of studies on the Warburg effect have been published in recent years. The Warburg effect is not only related to glucose metabolism but it also exists as an important intermediate in biosynthesis, affecting lipid and amino acid synthesis. SEs manipulate the Warburg effect in tumor cells by directly regulating the transcription of key enzymes or transporter genes in the metabolic process. This raises the question of whether there is a “Warburg effect” in lipid or amino acid metabolism being driven by SEs, which may be an important direction in metabolic research. However, it is a challenging and complicated task that needs to be explored further. Single-cell sequencing technology may be useful for investigating relevant therapeutic targets and identifying new mechanisms of action for SE.⁶⁴

In the future, additional SEs-associated key metabolic enzymes and molecules will be found in different types of tumors, as well as the relationship between the abnormal expression of key SEs-related metabolic genes and enzymes, and the development of various tumors will be identified, which will provide new ideas for tumor prevention, diagnosis, treatment, and research on related mechanisms.

SE is a collection of enhancers, and BRD4 and MED1 are two key transcriptional coactivators and participate in the composition of phase-separated condensates in the regulatory regions controlled by SE.⁶⁵ Related inhibitors have been effectively applied to tumor treatment. Since the SE-associated transcription complex has many components, more drugs targeting SEs will be available in the future.