DNA carries the genetic information necessary for the synthesis of RNA and proteins, and is a biological macro-molecule essential for the development of organisms. DNA damage refers to the abnormal changes in the structure of DNA molecules that occur spontaneously or under the influence of physical, chemical or biological factors during replication, including base mismatches and breaks. Nucleic acids are unstable and susceptible to both endogenous (genomic instability, epigenetic modification, oxidative stress and telomere shortening) and exogenous interference (such as ultraviolet radiation, ionizing radiation and alkylating agents); therefore, DNA damage is a constant threat. Sustained DNA damage triggers a signaling cascade that promotes cellular senescence in order to prevent replication of the damaged genome (61). Notably, super-enhancers serve a key role in this process by interacting with DNA damage repair pathways. Therefore, it is necessary to elucidate the underlying mechanisms and to identify potential targets for the protection against DNA damage. As shown in Fig. 1, the present study explored the molecular mechanisms by which super-enhancers regulate cellular senescence through genomic instability, epigenetic modifications, DNA damage repair, oxidative stress, telomere shortening and the senescence-associated secretory phenotype (SASP) in the DNA damage pathway.

Notably, the genome is unstable and any abnormal changes, such as base substitutions, deletions or insertions and copy number variations, lead to DNA damage, disrupt cell proliferation and reproduction, and hinder cell function. Studies have suggested that super-enhancers can cause DNA damage by regulating the translocation of chromosomes and the mutation of genes within the genome. For example, Meng et al (62) reported that super-enhancers can act on cytidine deaminase-related genes, such as IL4R, IL21R and NSMCE1, causing them to undergo translocation and leading to DNA damage. Glodzik et al (63) revealed that mutations in super-enhancers promote the expression of genes, such as ESR1 and ZNF217, which in turn induce DNA damage (63). In addition, super-enhancers induce activation-induced cytidine deaminase (AID) through recruitment activation, leading to partial mutation of antibody genes and chromosomal translocations (64). Abnormal enrichment of AID in the super-enhancer region may exacerbate DNA damage through antisense transcription (65).

Epigenetic modifications include DNA methylation, histone modifications and chromatin remodeling, which are mostly unstable during the life cycle of somatic cells and are associated with DNA damage and aging (66–68). Previous studies have shown that super-enhancers regulate gene expression through changes in histone modifications, resulting in DNA damage. For example, the Aire factor in H3K27ac-related super-enhancers interacts with topoisomerase 1 to promote DNA damage (69). H3K27ac-related super-enhancers also alter epigenetic modifications by increasing the expression of the PDZK1IP1 gene (38). In addition, Zhang et al (70) demonstrated that deletion of H3K27ac-related super-enhancers can lead to mutations in BRCA1, resulting in DNA damage. In addition to histone modifications that can cause DNA damage, chromatin remodeling can also cause DNA damage. The SWI/SNF complex is a chromatin remodeling factor associated with super-enhancer activity, and aging-related mutations in SWI/SNF subunits, such as SMARCE1, disrupt super-enhancer-driven gene expression, and exacerbate DNA damage accumulation and cell senescence (71). By integrating histone modification and chromatin remodeling, super-enhancers display a dual function in DNA damage response: On the one hand, they drive the expression of repair genes to maintain genome stability, and on the other hand, they may cause genomic instability due to overactive transcription or abnormal recruitment of injury-related enzymes, thereby increasing cell senescence.

The interaction with DNA damage repair is also an important aspect of the regulation of DNA damage by super-enhancers. Super-enhancers have been confirmed to modulate genomic stability in senescent cells by the transcriptional regulation of DNA repair genes or recruitment of repair complexes. However, aberrant over-activation of these repair sites may accelerate replication stress, paradoxically accelerating aging (72). Studies have shown that super-enhancers drive the expression of the DNA repair gene HNRNPF by recruiting transcriptional coactivators such as BRD4, MED1 and P300. HNRNPF further regulates the expression of epigenetic modification enzymes such as PRMT1, thereby synergistically regulating the process of ribosome biogenesis and DNA repair (73). In addition, super-enhancers maintain the open state of chromatin by enriching active histone markers such as H3K27ac and H3K4me1, and promote the rapid recruitment of repair proteins such as 53BP1 and BRCA1 to the damage site. Notably, RCAN1.4 gene expression is dependent on the interaction of enhancers and promoters within topologically associating domains, and disruption of this structure can markedly impair the efficiency of DNA damage repair (74,75). Notably, super-enhancers can also promote recruitment of DNA damage repair factors by binding enhancer RNA (eRNA) produced by transcription to chromatin remodeling complexes. For example, the AT-hook domain of BRG1 can bind eRNA and mediate the enrichment of coactivators such as MLL3/4 and Med1 in the enhancer region, thereby regulating DNA damage response (76). However, studies have thus far mainly focused on the regulatory effects of super-enhancers on repair genes, and it is unclear whether repair pathway-related proteins regulate the activity of super-enhancers through epigenetic modification or chromatin remodeling feedback.

In addition to the aforementioned genomic instability and epigenetic modifications, DNA damage is also affected by a range of other molecular factors such as oxidative stress, telomere shortening and the SASP. The essence of oxidative stress is that free radicals have negative effects on the body and can directly or indirectly oxidize or damage DNA, proteins and lipids; induce gene mutations, protein degeneration and lipid peroxidation; and cause physiological or pathological reactions in cells and tissues (77). Studies have shown that genes such as MUTYH, γH2AX and RNaseH2 are involved in oxidative stress-mediated DNA damage responses, and also promote physiological and pathological changes such as colorectal carcinogenesis, disease progression in chronic myeloid leukemia and the pathogenesis of systemic autoimmune diseases (78–80). In the absence of telomerase, DNA polymerase cannot fully replicate linear DNA, resulting in the gradual shortening of telomeres during karyolysis (81). When telomeres reach a critical length, DNA damage response proteins mistakenly recognize the telomeres and activate DNA damage signals (1,56). Studies have shown that genes such as 53BP1, ATM, γH2AX and TRF2 can cause non-homologous end joining-mediated end-to-end fusion of short telomeres (82–86), which leads to DNA damage. In addition, senescent cells are special intervention targets for a variety of aging-related diseases as they secrete a complex set of pro-inflammatory cytokines, known as the SASP, which on one hand maintains and diffuses senescence, and on the other serves a role in promoting proliferation (87). Super-enhancers drive formation of the SASP by activating transcription programs of pro-inflammatory factors and matrix-remodeling proteins. For example, in DNA damage-induced aging models, super-enhancers recruit transcriptional regulators, such as Zscan4 and TAK1, forming a positive feedback loop that notably enhances the broad-spectrum expression of SASP and promotes the development of aging (88). Notably, to the best of our knowledge, little research has been conducted on whether super-enhancers can mediate DNA damage by regulating the genes involved in oxidative stress and telomere shortening, and the specific mechanisms involved have not yet been elucidated and require further exploration.

Mitochondria are dynamic organelles that produce and transport ATP for energy, and participate in cell differentiation, information transmission, fate determination and other processes (89,90). Mitochondria can malfunction when stimulated by age-related factors, including mitochondrial morphological changes, decreased mitochondrial content, impaired mitochondrial membrane potential (59), reduced electron transport chain complex activity (91), increased mitochondrial outer membrane permeability (92), mitochondrial respiratory chain abnormalities and increased levels of reactive oxygen species (ROS) (93). Mitochondria therefore serve an important role in aging and age-related diseases (59). Recently, several studies have confirmed that super-enhancers are involved in the regulation of mitochondrial function (94–96). Therefore, the present review not only aimed to elucidate the mechanisms by which super-enhancers regulate cellular senescence through the DNA damage pathway, but also to systematically summarize the key role of super-enhancers in regulating mitochondrial functions from the perspectives of mitochondrial respiratory chain function, oxidative phosphorylation (OXPHOS) and mitochondrial autophagy (Fig. 1).

The mitochondrial respiratory chain, also known as the mitochondrial electron transport chain, contains a variety of enzyme complexes involved in important biological processes, such as inflammation, thermogenesis, hypoxia tolerance and glycolipid metabolism (97). When there is an insufficient oxygen supply to the cell, a chronic lack of nutrients or mutations in mitochondrial DNA, the mitochondrial respiratory chain is damaged, which leads to mitochondrial dysfunction, causes adverse reactions such as cell aging and eventually leads to aging and age-related diseases of the body. Super-enhancers can affect the mitochondrial respiratory chain by altering the degree of mitochondrial oxidative stress and lipid metabolism. For example, BET) inhibitors can block the action of BRD4-related super-enhancers, and thus reduce the expression of peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α). The reduced level of PGC-1α hinders mitochondrial respiration and its antioxidant stress ability, and it eventually damages the mitochondrial respiratory chain, resulting in the decline or loss of mitochondrial respiratory function (98). Simultaneously, the inhibition of BRD4-related super-enhancers reduces the level of mitochondrial lipid metabolism and destroys complex proteins in the mitochondrial respiratory chain, resulting in excessive accumulation of lipid peroxides and ultimately leading to ferroptosis (99). Through epigenetic regulatory mechanisms, super-enhancers upregulate NADPH oxidase genes, inhibit the expression of antioxidant oxidase genes and increase the levels of mitochondrial ROS, resulting in mitochondrial electron transport chain dysfunction (100). Cytoplasmic and organelle ion signaling also affects mitochondrial respiratory chain function by influencing the formation of respiratory chain complexes (101,102). In addition, it has been shown that communication between mitochondria and other organelles, or between themselves, can impact the uptake and release of ion signals and further affect the mitochondrial respiratory chain (103). However, the effects of super-enhancers on the signal transduction of the aforementioned ion signal transduction and inter-organelle communication in the mitochondria have not been clearly explained.

The process by which mitochondria supply energy to cells depends on OXPHOS. ROS are almost entirely produced during this process and regulate and maintain the normal physiological functions of the body;. however, when the mitochondria are damaged, ROS levels markedly increase, preventing them from functioning normally, thus promoting cell senescence (104,105). It has been demonstrated that super-enhancers are involved in mitochondrial OXPHOS and ROS production, thereby affecting mitochondrial function. For example, histone deactelyase inhibitors can block the H3K27ac super-enhancer action of the c-Myc gene, resulting in abnormal mitochondrial OXPHOS, mitochondrial dysfunction and reduced cell viability (106). By contrast, MLX-related super-enhancers can regulate the SLC7A11 gene to promote the uptake of amino acids by cells, thus causing the production of antioxidants, and maintaining the redox-reduction balance in cells. However, in the case of MLX knockout, the super-enhancer loses its regulatory function in maintaining redox balance, leading to the elevation of intracellular ROS and metabolic disorders, thereby affecting the OXPHOS of mitochondria (107). Notably, substances such as glucose, fatty acids and amino acids produced by glycolysis have key roles in mitochondrial OXPHOS (108). Super-enhancers can change the energy metabolism balance of mitochondria by driving the high expression of genes related to glucose metabolism, lipid metabolism and amino acid metabolism. For example, super-enhancers drive metabolic reprogramming of cells by activating transcription of key glycolytic enzyme genes (such as HK2 and LDHA), which manifests as increased aerobic glycolysis and decreased mitochondrial OXPHOS (96). Super-enhancers increase the uptake of amino acids such as glutamine by upregulating the expression of amino acid transporter alanine-serine-cysteine transporter 2 and glucose transporter 1, thereby promoting the mitochondrial tricarboxylic acid cycle to produce ATP. However, this metabolic reprogramming may exacerbate mitochondrial metabolic stress (96).

A decline in mitochondrial autophagy is also an important cause of cellular senescence, in addition to mitochondrial respiratory chain damage and abnormal OXPHOS. Mitochondrial autophagy regulates the number of mitochondria required to meet the energy needs of cells; functionally defective mitochondria are selectively degraded as much as possible which prevents the accumulation of functionally defective mitochondria in the body, which has an important role in maintaining the normal function and shape of cells (109). Decreased or defective mitochondrial autophagy can lead to mitochondrial dysfunction and, if left unchecked, cellular senescence (110). Studies have shown that autophagy in organelles is associated with the regulation of super-enhancers. For example, curcumin promotes the expression of H3K4me1- and H3K27ac-related super-enhancers to promote lysosomal autophagy, thereby reducing the production of ROS, inhibiting the expression of BRD4 and effectively improving inflammation in the body (111,112). In addition, under hypoxia, the circular RNA calmodulin 4 and PURB proteins promote Beclin1 expression through the regulation of H3K27ac-related super-enhancers, thereby regulating endoplasmic reticulum autophagy (113). These findings suggest that super-enhancers are closely related to autophagy in lysosomes, the endoplasmic reticulum and other organelles. However, it is still unclear whether super-enhancers can also regulate mitochondrial autophagy, and this process requires further study.

Atherosclerosis is a chronic cardiovascular disease associated with aging and a common cause of death in older adults. According to the 2023 World Heart Report released by the World Heart Federation, 20.5 million individuals died from cardiovascular diseases worldwide in 2021, accounting for one-third of total global deaths, whereas in 1990 and 2019, the number of deaths from cardiovascular diseases was 12.1 million and 18.6 million, respectively, indicating that the number of deaths from cardiovascular diseases worldwide is increasing (114,115). Atherosclerosis refers to the formation of plaques by lipid deposition on the arterial wall of medium and large arteries, resulting in reduced blood flow or blocked blood outflow (116), which is characterized by the migration and infiltration of macrophages, proliferation of smooth muscle cells, endothelial damage and accumulation of intracellular and extracellular lipids. Although various factors contribute to the development of atherosclerosis, such as chronic inflammation (117), lipid metabolism and accumulation (118), epigenetics (119), immune disorders (120), hypertension, diabetes, smoking, mental health and environmental pollution, aging has been confirmed to be a markedly independent factor when all other factors are controlled. Thus, the present review aimed to explore the effects of super-enhancers on atherosclerosis in terms of the effects of aging and related factors on endothelial cells, smooth muscle cells and macrophages.

Endothelial cells, which cover the inner surface of blood vessels and are composed of a layer of flat cells, complete the metabolic exchange of plasma and interstitial fluid, regulate blood flow in blood vessels, and synthesize and secrete various bioactive substances to control blood pressure, vasoconstriction and relaxation. Endothelial injury is an initial stage of atherosclerosis. After endothelial injury, the integrity and permeability of the vascular intima change (121), and the apoptosis and shedding of endothelial cells promote the adhesion and aggregation of platelets (122). In addition, dysfunctional endothelial cells secrete various growth factors, such as VEGF-A and PDGF (123,124), as well as vasoactive substances, including endothelin-1 and angiotensin II (125,126), in order to stimulate smooth muscle cell proliferation and vascular wall contraction, exacerbating the progression of atherosclerosis. Previous studies have reported that super-enhancers are involved in endothelial cell proliferation, vascular development and formation, regulation of vascular homeostasis and other functions. Mushimiyimana et al (127) revealed that the endothelial cell-specific super-enhancer SE12313 modulates the ADAMTS18 gene to affect endothelial cell proliferation, leading to reduced or shortened endothelial sprouts and decreased cell proliferation. Kalna et al (40) demonstrated that H3K27ac super-enhancers can regulate the expression of ERG and endothelial genes, such as DLL4, CLDN5 and NRARP, to affect the development and generation of blood vessels (Fig. 2A). Endothelial cells not only influence the development of atherosclerosis through growth and proliferation, but also produce nitric oxide (NO), which serves an important role in regulating vascular tone and inhibiting platelet aggregation and leukocyte adhesion. Lubos et al (128) demonstrated that oxidative stress caused by endothelium-derived NO and ROS has a key role in vascular endothelial dysfunction and atherosclerotic thrombosis. Whether super-enhancers can affect the process of atherosclerosis by regulating the ability of endothelial cells to produce NO remains unclear, and further research on the relationship between super-enhancers and endothelial cells to produce NO is required in the future.

Vascular smooth muscle cells are the main components of vascular wall tissue and are essential for the maintenance of vascular tension; changes in their structure and function affect the basic function of blood vessels. During atherogenesis, vascular smooth muscle cells proliferate and migrate abnormally, secreting a variety of biologically active molecules, including extracellular matrix components such as collagens, elastin and proteoglycans, as well as cytokines such as MCP-1 and IL-1β, to form a fibrous cap that promotes vessel calcification, subsequently leading to plaque rupture, triggering apoptosis and exacerbating the disease process (129,130). Currently, there are few studies on the controlling role of super-enhancers in vascular smooth muscle cells. Some studies have suggested that super-enhancers can influence the proliferation function of vascular smooth muscle cells. For example, Das et al (39) reported that when H3K27ac- and BRD4-specific super-enhancers were missing, the expression of angiotensin II-induced FGF2, ERG2, TGIF1 and FST was notably reduced, which affected the proliferative and the protective functions of vascular smooth muscle cells (Fig. 2B). However, it is notable that although super-enhancers have been shown to serve a key role in vascular smooth muscle cell proliferation for the development of atherosclerosis, their other functions in the development of this disease have not been clearly elucidated. This provides a new research direction: To explore in depth how super-enhancers contribute to the development of atherosclerosis by influencing other behaviors and functions of vascular smooth muscle cells. Future studies should focus on how super-enhancers promote or inhibit the migration of vascular smooth muscle cells in the vessel wall, the formation of tough and structurally complex fibrous caps, and the promotion of vascular calcification.

Macrophages are immune cells with a strong phagocytic function and antigen-presenting ability that can secrete a large number of cytokines and chemokines. In the early stages of atherosclerosis, monocytes are recruited to the subendothelium to differentiate into macrophages, which further migrate and infiltrate as the disease progresses, and polarize into different subtypes according to the altered microenvironment (131). Studies have shown that super-enhancers recruit monocytes for targeted migration by directly regulating the expression of CXCL1, CCL2 and other chemokines (132,133). In addition, super-enhancers markedly enhance the interaction between macrophages and activated endothelial cells by upregulating adhesion molecules, such asVCAM-1 and ICAM-1, and promote the retention and differentiation of inflammatory cells in plaques (134) (Fig. 2C). In plaques, macrophages absorb lipid deposition particles and transform them into foam cells, thereby inducing an inflammatory response (135). Super-enhancers drive the transformation of macrophages into foam cells by regulating gene networks of glycolysis and lipid metabolism. Specifically, Wang et al (134) showed that super-enhancers activate the SREBP1/2 transcription factor, drive the expression of lipid synthesis genes, and promote the accumulation of intracellular lipid droplets and the formation of foam cells. In addition to regulating the migration and transformation of macrophages, super-enhancers can affect the pathological process of atherosclerosis by mediating the polarization of macrophages. Specifically, super-enhancers have been shown to notably increase the inflammatory response of plaques by driving the expression of pro-inflammatory genes and regulating the polarization of macrophages towards M1 type (111,136,137). Macrophages are also found in a number of other organs and tissues; for example, adipose tissue-associated macrophages, microglia, liver Kupffer cells, alveolar macrophages and renal macrophages (138–140). Recent evidence indicates that adipose tissue-derived exosomes can promote atherosclerosis progression by delivering bioactive molecules to vascular cells (141), and that super-enhancers regulate macrophage polarization and inflammation in atherosclerosis (136). However, the specific molecular mechanism of how super-enhancers regulate adipose tissue macrophages to affect atherosclerosis progression through exosome-mediated remote signaling still needs to be further explored.

Alzheimer's disease is a progressive neurodegenerative disease and is one of the most common causes of dementia in elderly individuals worldwide. Characteristic pathological changes include cerebral cortex atrophy, continuous proliferation of microglia, reduction in the number of memory neurons, formation of age plaques, β-amyloid deposition and neurofibrillary tangles (142). According to the United Nations Department of Economic and Social Affairs, the global proportion of individuals aged ≥65 years increased from ~7% in 2000 and is projected to reach 12% by 2030. Furthermore, according to the Centers for Disease Control and Prevention, the incidence of Alzheimer's disease approximately doubles every 5 years after 65 years of age. A total of 50% of individuals aged ≥ 85 years in the United States have Alzheimer's disease (143–145). Therefore, aging is considered the greatest risk factor for Alzheimer's disease (146–148). The present review discusses the influence of super-enhancers on Alzheimer's disease resulting from aging and its related factors on the continuous proliferation of microglia, and the formation of neurofibrillary tangles and amyloid plaques.

Microglia, which reside in the central nervous system, are mononuclear macrophages that are widely distributed throughout the brain and spinal cord, and are important for maintaining nervous system homeostasis. Microglia, the main regulators of neuroinflammation, are more sensitive to inflammation during aging, and their continuous proliferation is considered a hallmark of Alzheimer's disease (149,150). During aging, persistent inflammation and overexposure to oxidative environments results in microglia being continuously activated, leading to neurodegeneration, neuroinflammation and neurotoxicity (151,152). Previous studies have reported that microglial super-enhancers serve an important role in the risk of developing Alzheimer's disease. For example, Nott et al (153) revealed that H3K27ac super-enhancers can regulate genes, such as BIN1, PICALM and SORL1, to promote microglial proliferation, thereby increasing the risk of Alzheimer's disease. Jansen et al (154) demonstrated that H3K27ac super-enhancers can regulate TREM2, TOMM40, APOE and other genes to activate microglia, leading to neurodegeneration (Fig. 3). In Alzheimer's disease, microglia undergo sustained proliferation, abnormally phagocytose synapses and mediate synaptic loss. Lipid signaling in neuron-glia interactions is a key factor in this process, which involves relevant receptors or lipids such as TREM2, GM1 ganglioside and ApoE (155). Therefore, whether super-enhancers can modulate lipid signaling between neurons and glial cells, and thus the process of phagocytosis of synapses by the microglia, needs to be investigated in depth in the future.

Two pathological markers of Alzheimer's disease are the formation of neurofibrillary tangles and amyloid plaques (148,156). Neurofibrillary tangle formation is caused by the accumulation of tau proteins via hyperphosphorylation in cells. Tau protein is a soluble microcore-related protein that mainly stabilizes microtubules by phosphorylation. However, it loses its biological activity and becomes an insoluble protein under hyperphosphorylation, subsequently aggregating to form neurofibrillary tangles (157). Tau protein phosphorylation can promote the aging of brain cells, causing memory decline and neuropathological changes in Alzheimer's disease (158). Studies on neurofibrillary tangles have mainly focused on the relationship between the tau protein and BIN1. Chapuis et al (159) demonstrated that a genetic change caused by a 3-bp insertion in the 5′ regulatory region of the BIN1 gene (~28 kb upstream of BIN1) can cause upregulation of BIN1 in vivo, which can increase the risk of Alzheimer's disease by interfering with tau biology. Furthermore, Nott et al (153) found that super-enhancers in microglia can regulate the level of the genetically determined BIN1 gene, increase the expression of the BIN1 gene and thus increase the risk of Alzheimer's disease, as well as the neuroinflammatory response and the activity of specific cell signaling pathways that promote the formation of neurofibrillary tangles (Fig. 3). Super-enhancers may reduce the neuroinflammatory response by modulating the activity of glial cells or inhibiting the release of inflammatory factors, thereby decreasing the extent of neurofibrillary tangles and reducing the risk of Alzheimer's disease (160–162). Specific cell signaling pathways also serve key roles in the formation of neurofibrillary tangles. Super-enhancers may reduce the formation of neurofibrillary tangles by modulating the activity of signaling pathways, such as the Wnt or nerve growth factor signaling pathways, in order to affect the function and structure of neurons (15,163,164). Research into the mechanisms by which these super-enhancers regulate the formation of neurofibrillary tangles is required.

The accumulation of amyloid plaques is also a hallmark of Alzheimer's disease. In a degenerative disease state, β-secretase and γ-secretase break down amyloid precursor protein (APP), causing β-amyloid protein (Aβ) to produce Aβ40 and Aβ42 insoluble oligomers, which deposit amyloid plaques outside the cell and ultimately lead to neuronal death (165). Similar to tau phosphorylation, increased β-amyloid deposition promotes the aging of brain cells via mechanisms such as oxidative stress, DNA damage and activation of the p16/p21 senescence pathways, which in turn serves a key role in Alzheimer's disease (166,167). Thus far, research on amyloid plaques has mainly focused on APP gene mutations that lead to the development of Alzheimer's disease. Tanzi et al (168) reported that mutations in the APP, PSEN1 and PSEN2 genes alter the sequence of the APP exon encoding β-amyloid, demonstrating that mutations in these genes can affect chromosomal genetics. Although studies have determined that mutations in APP affect amyloid plaque formation, there is no evidence of a relationship between super-enhancers and APP or amyloid plaques (169–171). Furthermore, the aggregation and clearance of β-amyloid and transport of proteins within neurons also affect amyloid plaque formation (172,173). Notably, super-enhancers may affect the aggregation and clearance process of β-amyloid; they may reduce β-amyloid deposition by promoting β-amyloid degradation, for example by activating autophagy and proteasome pathways within cells, thereby reducing the formation of amyloid plaques (174,175). Abnormal intra-neuronal transport may also lead to abnormal aggregation of β-amyloid within neurons, thereby promoting amyloid plaque formation. Super-enhancers may regulate protein transport within neurons by affecting intracellular molecular mechanisms, thereby reducing the aggregation of β-amyloid within neurons and lowering the formation of amyloid plaques (15,176,177). An in-depth study of the aforementioned mechanisms of super-enhancers in regulating the formation of amyloid plaques will further promote the understanding of Alzheimer's disease and provide novel options for its treatment.

Osteoporosis is a bone disease closely related to aging, characterized by bone mass loss, bone structure damage and increased bone brittleness, ultimately leading to a notable increase in the risk of fractures (178). As global population aging increases, osteoporosis has become one of the important causes of disability and death among the elderly. Under normal physiological conditions, the bones maintain skeletal homeostasis through the dynamic balance between bone formation by osteoblasts and bone resorption by osteoclasts (179). However, during the aging process, changes in hormone levels, such as estrogen and androgens, oxidative stress responses, chronic inflammation, dysregulation of epigenetic regulation and decreased differentiation ability of mesenchymal stem cells, all disrupt this bone homeostasis (180–183). In recent years, more evidence has shown that super-enhancers serve a key role in determining the fate of bone formation by osteoblasts and bone resorption by osteoclasts (22,26,184). Therefore, clarifying the regulatory network of super-enhancers in osteoporosis is expected to provide new targets for the treatment of osteoporosis, an aging-related disease.

In the process of bone formation by osteoblasts, super-enhancers directly affect the function of osteoblasts by regulating key transcription factors and signaling pathways involved in osteoblast differentiation. Yu et al (26) revealed that, during osteoblast differentiation, osteoblast-related genes such as ZBTB16, RUNX2 and SP7 are enriched around a large number of H3K27ac super-enhancers. Among them, the enhanced activity of super-enhancers targeting ZBTB16 was shown to markedly upregulate the expression of the ZBTB16 gene, promote osteoblast differentiation and increase the formation of mineralized nodules (26). Additionally, BRD4, as a key cofactor of super-enhancers, collaboratively drives the transcription of genes such as Runx2 and Osterix (also known as SP7) with H3K27ac super-enhancers during osteoblast bone formation, and the use of BRD4 inhibitors can notably inhibit osteoblast differentiation (185,186). However, there is a lack of dynamic mapping analysis at the single-cell level in aging bone tissue regarding how super-enhancers integrate upstream signals from estrogen deficiency or oxidative stress.

In terms of osteoclastic bone resorption, super-enhancers also affect the occurrence and development of osteoporosis by regulating osteoclast differentiation and function. Bae et al (22) discovered that, during the osteoclast differentiation induced by RANKL, multiple genes related to osteoclasts, such as NFATC1, C-FOS, ACP5 and CTSK, form new super-enhancers around them. The establishment of these super-enhancers depends on BRD4 and p300. Notably, RANKL shows a marked dose-dependent effect on super-enhancers in osteoclasts: Low concentrations of RANKL only activate ordinary enhancers, whereas high concentrations of RANKL or the formation of a chronic inflammatory microenvironment can induce the formation of super-enhancers, leading to excessive activation of osteoclasts (22). However, the distribution of osteoclast super-enhancers in aged bone tissue within the body and their interaction with osteoblast super-enhancers still require further investigation. Osteoclast-secreted exosomes are emerging as critical mediators of intercellular communication in the bone microenvironment, capable of delivering bioactive cargoes such as proteins and miRNAs to regulate the function of recipient cells (187). Additionally, whether super-enhancers can remotely inhibit osteoblast function by regulating exosomes secreted by osteoclasts remains unexplored.

Although super-enhancers have shown notable regulatory potential in osteoporosis, current research still faces a number of unanswered questions and knowledge gaps. On one hand, super-enhancers exhibit opposite regulatory characteristics in different environments. For example, ZBTB16-related super-enhancers can promote osteoblastic bone formation, while super-enhancers related to the NF-κB signaling pathway promote osteoclastic bone resorption and inhibit osteoblastic bone formation (185). On the other hand, the heterogeneity of super-enhancers in different types of bone cells, such as osteoblasts, osteocytes and osteoprogenitor cells, has not yet been systematically mapped. In osteoporosis, bone marrow mesenchymal stem cells exhibit an imbalanced differentiation pattern, with increased adipogenic differentiation at the expense of osteogenic differentiation, leading to bone marrow adiposity accumulation and reduced bone formation (15,188). Future research on super-enhancers in osteoporosis should focus on developing in vivo super-enhancer tracing techniques, clarifying the heterogeneity of super-enhancers in different bone cell types and assessing the role of metabolic reprogramming, such as glycolytic reprogramming, regulated by super-enhancers in the determination of osteogenic and adipogenic differentiation.

T2D is a chronic metabolic disease characterized by insulin resistance and impairment of islet β-cell function, which accounts for 90–95% of all diabetes cases. Insulin resistance is a key feature of T2D; over time, the pancreas may produce less insulin in response to the body's needs, leading to hyperglycemia. The pathogenesis of T2D is complex, involving the interaction between multiple organs and systems. The main mechanisms include epigenetic regulation, insulin resistance and functional defects of islet β cells (189).

As a key element of epigenetic regulation, super-enhancers notably affect the progression of T2D by regulating the function of islet β cells, and insulin synthesis and secretion. Suzuki et al (190) showed that a T2D risk variant (rs231361) located in the KCNQ1 locus disrupts the interaction between the super-enhancer and the INS gene, ultimately triggering insulin secretion dysfunction. Notably, their single-cell chromatin accessibility analysis further revealed that the super-enhancers of T2D risk genes are enriched in islet β cells and can affect their transcriptional regulatory networks (189,190). Recent studies have suggested that the understanding of the pathogenesis of T2D needs to break through the traditional single-organ perspective and turn to multi-organ interaction network analysis at the level of systems biology. Super-enhancers may serve a role in the interaction between intestinal, fat, liver, muscle and islet β cells through dynamic regulation of metabolic organ core functions and cross-tissue signal transduction, thus driving the pathological process of T2D (191–194).

In addition, some clinical studies have revealed that non-coding single nucleotide polymorphisms (SNPs) serve an important role in T2D. Sun et al (51) demonstrated through 3D genomics analysis that T2D SNPs re mostly enriched in space-adjacent super-enhancers, and participate in chromatin interaction to regulate and affect transcription factor binding. Such SNP-super-enhancer interaction modules are markedly enriched in the Wnt signaling pathway, which may provide novel insights into the pathogenesis of T2D (51). Future studies may combine single-cell epigenomics and gene-editing techniques to further elucidate the dynamic regulatory mechanisms of super-enhancers in multi-organ interactions.