Nuclear receptors in health and disease: signaling pathways, biological functions and pharmaceutical interventions

Abstract

Nuclear receptors (NRs) are a large family of ligand-dependent transcription factors that regulate the expression of a wide range of target genes in response to endogenous and exogenous ligands, including steroid hormones, thyroid hormone, vitamin D, retinoic acid, fatty acids, and oxidative steroids. Upon ligand binding, nuclear receptors form dimer complexes with transcriptional cofactors, which interact with specific DNA sequences in the promoter or enhancer regions of target genes to modulate gene expression. This process plays a crucial role in many physiological processes such as reproduction, development, immune responses, metabolism, and homeostasis. Dysregulation of nuclear receptor signaling is implicated in the pathogenesis of numerous diseases, including cancers, metabolic disorders, cardiovascular diseases, and autoimmune conditions. Therefore, understanding the molecular mechanisms underlying nuclear receptor functions is essential for the development of novel therapeutic strategies. This review summarizes the current understanding of nuclear receptors in both physiological and pathological contexts, providing insights into the signaling pathways they regulate. Additionally, we discuss recent advances in drug development targeting nuclear receptors, with a focus on preclinical and clinical studies aimed at improving therapeutic efficacy. By exploring these therapeutic avenues, this article highlights the potential of nuclear receptors as promising targets for future treatments of a variety of human diseases, paving the way for more personalized and effective therapies in clinical medicine.

Introduction

A cell’s ability to detect various extracellular signals depends on the chemical nature of the signaling ligands and the permeability of the plasma membrane to polar compounds, such as polypeptides.^1,2 This necessitates the production of two main types of signaling ligands and receptors. The first type, represented by growth factors, consists of polypeptides that generally cannot penetrate the cell membrane^3,4,5; therefore, their receptors must present sophisticated extracellular binding domains. The second type of nuclear receptor ligand includes small, relatively hydrophobic molecules such as steroid hormones, vitamins, fatty acid derivatives, dexamethasone and enzalutamide.⁶ The hydrophobicity of these ligands allows them to pass through the cell membrane and reach the nucleus to bind to and activate nuclear DNA-binding proteins that then act as transcription factors.⁷

Nuclear receptors (NRs) are a class of ligand-activated transcription factors that sense certain molecules, such as steroids, thyroid hormones and vitamins, to directly bind DNA and modulate gene expression, bypassing the need for cytoplasmic signal cascades that mediate surface receptor and nuclear transcription mechanisms.^8,9,10 They are essential for numerous physiological processes, including development, metabolism, reproduction, and homeostasis. To date, 48 NRs have been identified in the human genome, and 49 have been identified in mice. The typical structure of a nuclear receptor consists of a hinge region, a conserved ligand-binding domain and a DNA-binding domain, which are surrounded by various N- and C-terminal domains.¹¹ While some nuclear receptors are physically connected to chromatin, others remain in the cytoplasm until ligand interactions allow nuclear entry. These receptors bind to a DNA recognition sequence in or close to the promoters of the genes they control once they are attached to chromatin, either as homodimers or heterodimers.^12,13 These recognition sequences are commonly called hormone response elements (HREs) and are composed of two hexanucleotide sequences separated by a variable number of spacer sequences.¹⁴ In addition, NRs can be indirectly recruited to the genome by tethering mechanisms by other DNA-bound transcription factors.¹⁵ Several posttranslational modifications, such as phosphorylation, ubiquitination and SUMOylation, have been reported to modulate the activities of NRs.^16,17,18,19

The regulation of gene expression by nuclear receptors influences the proliferation,²⁰ differentiation²¹ and death^22,23 of many different cell types, thereby playing important roles in the reproduction, development and physiology of metazoans.^24,25,26,27 The characterization of the NR superfamily marked a significant turning point in the field of endocrine physiology by establishing common molecular pathways governing the development and physiology of various animal species. The dysregulation of these genes can lead to cardiovascular disease,²⁸ cancer²⁹ and diabetes.³⁰ Research on NRs began in the mid-1980s when molecular cloning of several hormone receptors revealed their common structural framework.³¹ As a consequence of their central role in governing cell fate, NRs constitute targets for 15–20% of all pharmacologic drugs.^32,33

Drugs that target specific NRs are frequently employed to treat a wide range of illnesses. Tamoxifen and raloxifene, for example, target the estrogen receptor (ER) and are used to treat osteoporosis and breast cancer.^34,35 Enzalutamide is used to treat prostate cancer by targeting the androgen receptor (AR),^36,37 whereas thiazolidinediones are used to treat type 2 diabetes by targeting peroxisome proliferator-activated receptor-gamma (PPARγ).^38,39 Compounds with stronger binding affinities and better specificity are currently under development as new NR-targeted drugs because the available drugs often lack specificity and exhibit significant side effects, including severe heart failure.^40,41 Thus, understanding the mechanism of NR gene selection and the development of specific inhibitors targeting NRs has become a pressing scientific issue in the field of biomedicine.

In this review, we systematically introduce NRs and their members, structure, functions and regulatory signals. We summarize recent findings regarding the function of NRs in regulating physiology and pathology and the relevance of these receptors to clinical drug development. Emphasis is given to research on the targeting of these receptors for disease management, the preclinical and clinical testing and development of novel drugs and the techniques and strategies that facilitate targeting and therapeutic efficacy.

Overview of nuclear receptors

The discovery of hormones dates back to the early 1900s^42,43,44,45 (Fig. 1). In 1905, Ernest Starling coined the term ‘hormone’.^44,45 In 1926, Tadeus Reichstein and Edward Calvin Kendall elucidated the structures of cortisone and thyroxine,⁴⁶ while Adolf Butenandt and Edward Adelbert Doisy first isolated estrogen in 1929.^47,48 became clear only after Elwood Jensen conducted a series of experiments in the late 1950s to determine how estrogen regulates reproductive organ maturation.⁴⁹ The rise of molecular biology in the 1980s led to groundbreaking advances, including the cloning of the human glucocorticoid receptor (GR) and the identification of the first estrogen receptor, ERα, from the ESR1 gene.^50,51,52 In 1985, Ronald Evans successfully cloned the human glucocorticoid receptor (GR),^50,51 while Pierre Chambon’s lab identified the first estrogen receptor, ERα, from the ESR1gene.⁵² They found that these receptors shared similarities with v-erbA, a viral oncogene recognized as a thyroid hormone receptor (TR) transcribed from the THRA gene. This discovery resulted in the placement of steroid and thyroid hormone receptors into a single grouping. A sequence comparison revealed a conserved evolutionary framework, highlighting structural and functional features that predicted the development of the nuclear receptor superfamily. Each receptor contains DNA-binding, ligand-binding, and transactivation domains. Soon after, receptors for other binding factors, such as retinoic acid and vitamin D, were cloned, confirming the existence of a receptor superfamily unified by structure. The formal establishment of the NR superfamily represented a major milestone, bolstering the hypothesis that the development and physiology of all animal species might be regulated by related molecular processes.

Fig. 1

Historical timeline of nuclear receptor expression. Schematic timeline illustrating key milestones in the nuclear receptor research field. The timeline begins with the cloning of the first steroid hormone receptor cDNA and highlights significant advancements, culminating in recent discoveries enabled by “omics” technologies. Major breakthroughs and pivotal discoveries are annotated along the timeline

The therapeutic potential of NRs was recognized in the 1970s when it was shown that the estrogen blocker tamoxifen could inhibit ER-dependent breast cancer cells.^53,54 In prostate cancer, multiple nuclear receptors have been shown to inhibit tumor growth, proliferation, and metastasis, leading to significant interest in targeting these receptors as therapeutic strategies.^55,56,57 Dysfunction of NRs has been associated with specific diseases, such as infertility, obesity, and diabetes.⁵⁸ As key drug targets, NRs are crucial in studying the pathological mechanisms of metabolic diseases and related drug development. Today, they represent a huge family of pharmaceutically targetable proteins. This review discusses the current knowledge on NR-based therapeutic intervention in different types of disease.

Family members

The known sequence of the human genome revealed that forty-eight human NRs detect ligands, such as hormones, and translocate them into the nucleus to function as transcription factors regulating gene expression.⁵⁹ These receptors are classified into three main types on the basis of their ligand types or into eight subgroups on the basis of sequence homology.^11,60 Type I receptors are steroid receptors, including the ER, AR, progesterone receptor (PR), mineralocorticoid receptor (MR) and GR.^61,62 Their ligands are steroid hormones such as sex hormones, glucocorticoids and mineralocorticoids.⁶³ Type II receptors are nonsteroid receptors, such as thyroid hormones (TRα and TRβ), retinoic acid receptors (RARα, β), vitamin D receptors (VDRs) and peroxisome proliferator-activated receptors (PPARα, β and γ).⁶⁴ Type III receptors include orphan receptors whose endogenous ligands are unknown or that do not bind to any ligands, such as the testicular receptor and germ cell nuclear factor.⁶⁵ Alternatively, NRs can be divided into eight subgroups that are similar to classical receptors but differ enough individually, named thyroid hormone receptor-like family, retinoid X receptor-like family, estrogen receptor like family, nerve growth factor IB-like family, steroidogenic factor-like family, germ cell nuclear factor-like family, and those with two DNA-binding domains, as well as recently identified typically structured NR (CgNR8A1) in metazoans such as mollusks, annelids, cnidarians, echinoderms and hemichordates.^66,67

Structure

Except for the dose-sensitive sex reversal-adrenal hypoplasia congenital critical region on the X chromosome, gene 1 (DAX1) and the small heterodimer partner (SHP), all NRs are typically single-chain polypeptides that share four or five functional domains^,68 including the N-terminal transcription activation domain (NTD), the DNA-binding domain (DBD), the ligand-binding domain (LBD), the C-terminal transcription activation domain (CTD) and a hinge domain (H) that connects the DBD and LBD (Fig. 2).

Fig. 2

Diagram of the structural model of nuclear receptors. Nuclear receptors share four functional domains: the N-terminal transcription activation domain (NTD), the DNA binding domain (DBD), the ligand binding domain (LBD), and a hinge domain (H) that connects the DBD and LBD. Some NRs also contain a highly variable C-terminal transcription activation domain (CTD)

The NTD, which is located at the N-terminus and comprises 25–603 amino acids (AAs), contains the first of two transactivation regions (AF-1) and possesses transcriptional activator functions.^69,70 The A/B domain is intrinsically disordered, which makes obtaining full-length 3D representations of the receptor difficult.^71,72 The second identified subunit is the DBD, with 66--68 AAs, including two zinc fingers, which are typically obscured because of lower DNA affinity when the hormone is absent.^73,74,75 Once a hormone is bound, the zinc fingers dock the hormone–receptor complex to hexanucleotide response elements located within NR-regulated promoters that determine the receptor’s regulatory specificity. The DBD also serves as an intermolecular interaction site for receptor dimerization.⁷⁶ The LBD is located at the receptor’s C-terminus and contains 220--250 AAs.⁷⁷ The LBD binds to the cognate hormone or ligand through an interior binding pocket.^78,79 It also has an AF-2 site for recruiting various coactivating proteins, such as heat shock proteins (HSPs), to facilitate interactions with chromatin-remodeling proteins and the transactivation domain.^80,81,82 The LBD plays a crucial role in mediating self-assembly reactions, such as dimerization or tetramerization, which are essential for high-affinity binding to DNA response elements.⁸³ The DBD is connected to the LBD via a flexible domain, the ‘hinge’, which is related primarily to the nuclear localization signal of NRs and may influence the intracellular trafficking and subcellular distribution of the hormone‒receptor complex.^84,85 The hinge region also contains a short NLS, and its phosphorylation is coupled to elevated transactivation.^86,87

However, not all NRs have all four typical domains. Members of the NR0 subfamily, for example, frequently have neither a DBD nor an LBD in their structures.⁸⁸ Among these, NRs with only the LBD and no DBD, such as Dax-1 and SHP, are nonetheless capable of binding to other transcription factors (TFs) and suppressing the expression of genes downstream. Finally, some NRs also possess a short, highly variable C-terminal domain (CTD or F domain) that often has unknown functions.^89,90 However, current research has revealed a critical function of the F domain in the ERα reaction to select ER modulators (SERMs), particularly in SERM-mediated LBD dimerization and AF-1 activity.⁹¹

Origins and evolution

NRs were thought to have evolved approximately 600 million years ago in the common ancestor of bilaterian animals, enabling them to sense and respond to internal and external signals.⁹² This evolution likely involved genetic amplification and mutation, contributing to the functional diversity of the NR superfamily.⁹³ Most NR ligands are small, hydrophobic molecules that pass through cell membranes, although some, such as thyroid hormones, are actively transported into cells.⁹⁴ While NRs were initially termed ligand-binding proteins, it remains debated whether their common ancestor bound ligands or functioned as constitutively active receptors. Over 50% of NRs are orphan receptors lacking known ligands, although some have been shown to bind metabolites, suggesting a role in sensing metabolic changes.^95,96 The evolution of the LBD enabled interactions with small molecules and coregulators, increasing NR versatility.⁹⁷ Gene duplication during early metazoan evolution expanded and specialized the NR superfamily into subfamilies such as steroid hormone receptors, thyroid hormone receptors, and orphan receptors. The coevolution of NRs and their ligands increases their physiological complexity. For example, vertebrate NRs, such as glucocorticoid and estrogen receptors, have evolved high specificity for steroid hormones, which are crucial for the stress response and reproduction.⁹⁸

In 1992, a comparison of the DNA-binding domains of known NRs led to the construction of a phylogenetic tree, suggesting a common ancestor.⁹⁹ By 1997, an alternative hypothesis emerged, suggesting that the original NR was an orphan receptor that gradually gained ligand-binding ability.¹⁰⁰ The earliest NRs are believed to have evolved as orphan receptors that lack defined ligands and are involved in regulating fundamental processes such as metabolism and cellular signaling.¹⁰¹ Over time, orphan receptors adapt to regulate broader metabolic pathways, including lipid homeostasis and detoxification. A recent discovery of the NR7 subfamily has filled a critical gap in the understanding of the evolution of NR dimerization capabilities. Phylogenetically situated between class I NRs (monomers or homodimers) and class II NRs (heterodimers), the NR7 subfamily acts as a “missing link” in the transition from homodimerizing to heterodimerizing nuclear receptors.¹⁰²

Mechanisms of action

Nuclear receptors can modulate gene expression through direct binding to target genes as well as through interactions with other NRs.^103,104 The interplay between NR actions can be described at progressively more detailed levels, with various regulatory modes involved in upstream events that influence downstream gene transcription and crosstalk events at the DNA level that directly influence gene transcription.¹⁰⁵ The existence or lack of physical connections between the relevant NRs could further alter the crosstalk mechanisms at the DNA level.

Crosstalk between nuclear signalings

Nuclear receptors can share overlapping arrays of target genes or regulate distinct genes that are part of the same downstream activity or pathway (Fig. 3). There is a wealth of experimental evidence to support endpoint modifications in gene expression that occur after NR crosstalk. The relationship between ERα and the PR was among the first observed examples of crosstalk between nuclear receptors.¹⁰⁶ Estradiol-stimulated ERα activity was found to be suppressed by liganded PR isoforms, and the ligand, promoter and cell type were demonstrated to influence this suppressive crosstalk.^106,107 Interactions between GRα and PPARα are critical in regulating shared subsets of target genes and different stages of signal transduction cascades involved in inflammatory and metabolic pathways.^108,109 For example, both GRα and PPARγ have been shown to repress genes associated with TLR4- and TLR9-induced innate immune responses in primary peritoneal macrophages.^110,111 However, there are significant differences in how these NRs achieve gene repression, which involves distinct transcriptional corepressor complexes. These variations in regulatory mechanisms highlight the complexity and specificity of gene regulation mediated by GRα and PPARγ in immune and metabolic contexts.

Fig. 3

Crosstalk modes of NR signaling. Various regulatory modes involved in NR signaling influence downstream gene transcription. For example, different types of nuclear receptor signaling can simultaneously regulate the expression of the same gene (Modes 1, 3 and 4) or regulate different genes belonging to the same pathway (Mode 2). Different nuclear receptors may share the same target genes (Mode 5). In addition, crosstalk between two NRs can influence each other’s gene or protein expression (Mode 6)

More complex types of crosstalk, such as reciprocal or unidirectional regulation of the expression of NR genes or proteins and ligand availability, can sometimes occur.^112,113 For example, glucocorticoid-activated GRα was reported to upregulate PPARα mRNA expression.^109,114 Conversely, fenofibrate-activated PPARα was shown to downregulate GRα expression at the posttranscriptional level in a time- and dose-dependent manner.^115,116 In rodent adipocytes, antidiabetic PPARγ ligands increase the expression of PEPCK-C mRNA, which encodes the key glyceroneogenic enzyme EC4.1.1.32.¹¹⁷ In contrast, dexamethasone-activated GRα counteracted this induction at the transcriptional level. These results show that the processes involved in NR crosstalk are not unique; different pairs of nuclear receptors can interact through distinct crosstalk mechanisms according to the stimulus, expression level, cell type, pathway and genes involved. It is probable that many other modes of crosstalk will be uncovered as our knowledge expands to include other intracellular organelles and the shuttling of NRs.

Crosstalk between nuclear receptors at the DNA level

At the DNA level, NR crosstalk can take two primary forms^13,118 (Fig. 4). In one scenario, NRs physically interact to regulate specific target genes (direct crosstalk). In another context, NRs do not actually connect but still engage in unidirectional or bidirectional interactions (indirect crosstalk). When two nuclear receptors interact directly, they can bind to DNA sequences that are either closely positioned or farther apart. Alternatively, they can bind DNA sequences through the action of other transcription factors. A well-known example of this is the peroxisome proliferator-activated receptor PPARs, which are of three types: PPARα, PPARβ/δ and PPARγ. Most of these proteins are heterodimers connected to retinoid X receptors (RXRs) that regulate gene transcription,^119,120 but they can also be fine-tuned by pairing with a different ligand. Multiple coactivators can interact with heterodimer complexes to supplement and stabilize their activity in regulating lipid metabolism, adipogenesis and inflammation.^121,122 Further instances of direct NR connections have been reported for steroid receptors. GRα and AR have many target genes in common due to the recognition of partial palindromic repeats of the sequence 5′-TGTTCT-3′.¹²³ GRα–AR heterodimerization has been proposed as the mechanism underlying the mutual inhibition of the transcriptional activities of these two receptors, allowing for differential regulation of specific genes.^124,125 Furthermore, AR and GR share significant similarities in the dimerization structure of their LBDs, which sheds new light on the previously reported structure of the GR LBD.¹²⁶ The mechanisms of direct crosstalk may allow for dual NR ligand control, but the exact conditions for this process have not been determined. Context-specific influences, such as tissue or cell type and differentiation status, are likely to lead to different interaction patterns, resulting in varied biological responses.^127,128

Fig. 4

Crosstalk modes at the DNA level. At the DNA level, nuclear receptors engage in crosstalk by indirectly or directly interacting with DNA. Part a outlines indirect regulation modes, where no physical interaction occurs, whereas Part b describes regulatory mechanisms involving direct physical interactions among nuclear receptors (NRs). Indirect regulation modes include: NR signaling pathways may compete for overlapping DNA-binding sites; NR heterodimer partners may cause redistribution or squelching; Components of the transcriptional machinery, such as RNA polymerase II (Pol II) and transcriptional coregulators, may cause redistribution or squelching; The alteration of shared coregulators can influence the activity of other NRs. One NR family member can act as a pioneering factor to facilitate chromatin loosening and enable the subsequent binding of other NRs. Direct physical interactions includes: Paired receptors may cooperate for direct DNA binding or through DNA looping; Direct crosstalk can occur with just one partner contacting the DNA; Two nuclear receptors engage in crosstalk through protein-protein interactions with other transcription factors (TFs); The sequestration of one or both NRs (originating from other modes, (f–i) away from the DNA due to heterodimer interactions

In the absence of an actual connection, NR signaling pathways can indirectly influence crosstalk through several mechanisms.^129,130,131 They may compete for overlapping DNA-binding sites by redistributing shared proteins or parts of the transcriptional machinery, such as RNA polymerase II or transcriptional coregulators; by regulating the expression of shared coregulators; and by acting as pioneering factors that loosen chromatin to facilitate the binding of additional NRs. For example, peroxisome proliferator-activated receptor alpha (PPARα) binds to estrogen-related receptor (ERR) target genes in heart tissue through ERR response element motifs via a histone deacetylase SIRT1-dependent mechanism.¹³² RXR, the PPAR partner, can trigger PPAR-independent activities on PPAR response element (RE)-controlled genes via RXR homodimerization, adding another layer of control to an intricate metabolic pathway.¹³³ Members of the PPAR and ERR subfamilies can be further connected through shared coregulators, including PGC1α and PGC1β, as well as through common regulators such as low-energy-sensing AMP kinase.^134,135 For example, during adipocyte differentiation and osteoclastogenesis, PGC1β, a coregulator that is upregulated by ERRα, can be recruited by PPARγ and other transcriptional regulators to enhance their adipogenic properties.¹³⁶ Reduced PGC1β expression levels due to downregulation of ERRα resulted in decreased transcriptional activity of PPARγ. These reports provide evidence for the existence of complex combinations of indirect regulatory modes.

Genomic and nongenomic mechanisms

The function of nuclear receptors can be achieved via genomic or nongenomic pathways (Fig. 5). Genomic mechanisms involve the direct regulation of gene expression through binding to DNA. This mechanism usually plays a critical role in long-term physiological processes, such as development, metabolism, and homeostasis. Nongenomic mechanisms involve rapid, transcription-independent actions of nuclear receptors. These processes occur within minutes and are crucial for swift cellular responses, such as ion channel modulation, cell migration, and acute stress responses.

Fig. 5

Nuclear receptors precisely regulate cell fate and metabolic processes. Nuclear receptors play crucial roles in regulating cell fate by influencing various cellular processes, including proliferation, differentiation, senescence and apoptosis, by acting as transcription factors. Additionally, members of the nuclear receptor family control the synthesis rates of different metabolic enzymes across various tissues, affecting processes such as glucose, lipid and bile acid metabolism, as well as adipocyte differentiation and plasma lipoprotein modulation. By regulating the balance between the storage, utilization and production of these macromolecules, nuclear receptors ensure metabolic flexibility, enabling the organism to adapt to fluctuations in energy availability and demand

Genomic mechanisms

Prior to binding to the specific DNA sequences of target genes known as hormone HREs to control transcription, NRs are typically in an inactive state and require activation through the binding of a cognate ligand.^15,137 With many receptors, in the absence of ligands, molecular chaperone proteins such as heat shock protein 90 (HSP90) and HSP70 anchor them in the cytoplasm in an inactive state.¹³⁸ Upon ligand binding, the NR undergoes a conformational shift that causes it to separate from the heat shock protein and become active.¹³⁹ This allows the hormone–receptor complex to translocate into the cell nucleus after its nuclear localization sequence (NLS) has been revealed.^140,141 Once inside, the complex binds to a specific sequence in the target gene known as an HRE to regulate its transcription. In addition to detaching the HSPs, ligand binding can promote receptor phosphorylation, which further enhances the ability of the receptor to bind to HREs.¹⁴² In general, NRs undergo a change from a non-DNA-binding form to a DNA-binding form upon activation, but some types, such as thyroid hormone receptors, retinoic acid receptors and retinoid X receptors, are retained in the nucleus regardless of their ligand binding status.¹⁴³ They are already bound to HREs but complex with corepressor proteins, which makes them transcriptionally inactive.^144,145 However, upon receiving ligand activation signals, the corepressor dissociates, and coactivator proteins are recruited. The NR/DNA complex then enlists more proteins, such as RNA polymerase, to aid in the transcription of DNA into mRNA.^146,147,148

Nuclear receptors can directly bind DNA via three different modes, namely, homodimers, heterodimers, or monomers, depending on the type of NR.¹³ For example, glucocorticoid receptors (GRs) bind to HREs after forming homodimers.^149,150 In contrast, retinoic acid receptor-related orphan receptor gamma (RORγ) binds as a monomer to the DNA response region to control gene transcription and expression.^151,152 The retinoid X receptor (RXR) can either bind to itself as a homodimer or pair with other nuclear receptors as a heterodimer to activate downstream gene transcription.^153,154,155 To make this process even more complicated, some NRs can form nonclassical heterodimers, which are only activated by outside ligands. Thus, unanticipated adverse effects could appear when developing therapeutics because NRs can operate through nonclassical routes.^{156,157,158,159}

The identification of coregulatory proteins that interact with and control the transcriptional action of NRs in the mid-1990s was another pivotal development in our knowledge of the mechanism of action of NRs.^160,161 These coregulators have a variety of functions, such as chromatin remodeling, which modifies the target gene’s transcriptional accessibility, or bridging, which maintains the binding of other coregulatory proteins.¹⁶² The intrinsic histone acetyltransferase (HAT) activity of coactivator proteins can promote gene transcription by reducing the affinity of histones for DNA.¹⁶³ On the other hand, the recruitment of histone deacetylases (HDACs) by corepressor proteins increases the number of bonds between histones and DNA and suppresses gene transcription.¹⁶⁴ These coactivators or corepressors enable nuclear receptors to function as inducible scaffolds that coordinate large transcriptional complexes, allowing different ligands to induce distinct receptor conformations.^163,165 These changes could expose specific protein–protein interaction surfaces, making them available for coregulator binding. This hypothesis provides an explanation for how structurally different ligands, such as selective estrogen receptor modulators, could influence multiple genes in the same cell via the same receptor or how they could jointly regulate the expression of a single gene. Depending on the tissue-specific location of coregulators, the same ligand can also control specific genes in different tissues or at different developmental stages.^166,167 Nuclear receptor/coregulator complexes that alter chromatin shape and DNA accessibility are produced by receptor-bound coregulators, which can also directly interact with the core RNA polymerase through their enzyme action. In addition, there is no set link between two distinct nuclear receptors, as they can change depending on the target genes and tissues that are engaged. Transcriptional regulation by NRs can be affected by epigenetic variables such as chromatin remodeling, DNA methylation and histone modification.^168,169

Nongenomic mechanisms

In addition to acting as transcription factors in the nucleus to regulate target gene expression (genomic function), NRs can also operate through a molecular mechanism independent of transcriptional activity (nongenomic function)^170,171,172 (Fig. 5, Fig. 6). This nongenomic role requires NRs to be localized to specific subcellular structures,^173,174,175 where they directly interact with various intracellular proteins to rapidly regulate cellular stress responses and signal transduction pathways. Their subcellular translocation can occur either by alternative splicing or posttranslational modifications through free shuttling or with the assistance of other proteins.^176,177 As an example, the plasma membrane is home to a truncated variant of the thyroid hormone receptor. This localization enables them to participate in several biological processes, including the endoplasmic reticulum stress response, apoptosis, autophagy, fatty acid oxidation within mitochondria and the regulation of centrosome homeostasis and cell mitosis. Nongenomic NR signaling frequently involves phosphorylation cascades mediated through pathways associated with AMPK, cAMP/PKA, PI3K/AKT, and Hippo/Yap and signaling via Wnt/β-catenin and MAPK.^{178,179,180,181,182,183}

Fig. 6

Platelets are good models for investigating the possible nongenomic impacts of nuclear receptors. Because of their anucleate origin, well-characterized mechanisms, and quick reactions, platelets offer a model system for examining any non-genomic impacts of the NRs. Non-genomic roles of NRs include controlling intracellular calcium levels, ion channel function, kinase and phosphatase activity, and second messenger synthesis. It has been discovered that human platelets contain a number of NRs, and that certain NR agonists have anti-platelet actions through a range of mechanisms

Several NRs have been found to propagate rapid nongenomic effects for cellular protection in addition to their defined genomic effects. Their nongenomic functions operate through the control of kinase/phosphatase activity,^184,185 intracellular calcium levels,^186,187 ion channel function^188,189 and the production of second messengers.¹⁹⁰ Accumulating data indicate that RXRα also possesses extranuclear nongenomic functions. Previous studies have demonstrated that RXRα engages in some nongenomic activities through the creation of heterodimers with Nur77.¹⁹¹ In response to specific apoptotic stimuli, RXRα-Nur77 heterodimers are translocated from the nucleus to the mitochondria, where they regulate apoptosis.¹⁹² Recent research has shown that truncated RXRα (tRXRα) has an important function in the PI3K/AKT signaling pathway, where it interacts with the p85α subunit to increase AKT activation and promote cell proliferation both in vitro and in vivo.^193,194 Notably, glucocorticoids (GCs) manifested nearly instantaneous nongenomic effects through nonspecific interactions with cell membranes and targeted interactions with cytosolic GRs (cGRs) or membrane-bound GRs (mGRs).^124,195,196 This rapid nongenomic action of GCs could also contribute to their anti-inflammatory effects through prolonged genomic processes, particularly in managing inflammatory diseases (Fig. 6).^197,198 For example, recent studies revealed that GCs quickly enhanced the effects of bronchodilators used to treat allergic asthma.¹⁹⁹ Other NRs, including PPARα, LXR and FXR, have also been reported to perform nongenomic functions.^189,191,200 The possibility of turning NR ligands into effective medicines should be explored through the characterization of these extragenomic processes and the discovery of new binding partners and pathways in addition to their known genomic effects.

Platelets are useful models for investigating the potential nongenomic effects of NRs because they lack nuclei and possess well-characterized reactions.^189,201 ERβ, but not ERα, is known to be expressed on human platelets and to affect their function.²⁰² In addition, some studies have shown that platelets isolated from male rats exhibit a stronger aggregation response than those from female rats do, likely due to an increase in androgenic steroids.^203,204 This conclusion was supported by findings that castration reduced platelet aggregation in male rats,²⁰⁵ an effect that was reversed with testosterone treatment.²⁰⁶ LXR and FXR ligands negatively regulate platelet function by inhibiting platelet signaling and the formation of procoagulant-coated platelets.^{207,208,209,210} For example, LXR ligands induce a procoagulant state in platelets, which is marked by the exposure of phosphatidylserine and α-granule contents on the surface of the platelet, coupled with mitochondrial membrane depolarization, reduced calcium mobilization and decreased affinity of integrin αIIbβ3, which ultimately inhibits platelet aggregation.^209,211 Similarly, FXR ligands can cause platelet swelling and transformation into procoagulant-coated platelets, a process dependent on cyclophilin D activity.²¹² FXR ligands also increased cGMP levels, which increased PKG activity and VASP S239 phosphorylation, further suppressing platelet activation.¹⁸⁹ Other studies have identified PPARα as a key mediator of the antiplatelet effects of statins and fenofibrate.²¹³ Treating platelets with PPARα ligands, such as fenofibrate or statins (e.g., simvastatin), inhibited ADP-stimulated platelet activation by increasing intracellular cAMP levels through a PPARα-dependent mechanism.²¹⁴ This role of PPARα was further confirmed by experiments showing that fenofibrate-induced inhibition of platelet activation and prolonged bleeding time were absent in PPARα-deficient mice²¹⁵; the reversion of this inhibitory effect by the PPARα antagonist GW6471 further highlighted its dependence on PPARα.

Subsequent studies revealed the unexpected presence of retinoic acid receptors (RARs) in the cytosol of Sertoli cells, hepatic stellate cells and neurons.^216,217,218 In Sertoli cells, RARα was found to be a substrate for small ubiquitin-like modifier-2 (SUMO-2), and its cytosolic or nuclear localization was influenced by a dynamic process of sumoylation and desumoylation.^219,220 Additionally, in Sertoli and hepatic stellate cells, RARα is retained in the cytosol through interactions with the cytoplasmic adaptor for RAR and TR (CART1) protein or with cytoskeletal proteins that sequester the receptor outside the nucleus.¹⁴⁴ Furthermore, in hippocampal neurons, independent studies have shown that RARα is exported to dendritic RNA granules, where it is associated with a specific subset of mRNAs and RNA-binding proteins.^221,222,223 Interestingly, in response to retinoic acid (RA), this extranuclear pool of RARα rapidly initiates the local translation of the postsynaptic glutamate receptor GluR1, leading to an increase in synaptic strength.^224,225 In light of this growing body of knowledge, understanding these nongenomic mechanisms can lead to the development of new therapeutic strategies that exploit the rapid and diverse roles of nuclear receptors outside of their traditional genomic functions. By targeting the nongenomic pathways of nuclear receptors, it may be possible to create drugs with faster onset times and more specific effects, thereby increasing the efficacy of treatments for various diseases.

Functions in physiology and pathology

Nuclear receptors are of key importance in physiology and pathology because they regulate multiple cellular functions (Fig. 5). For example, NHR-6, the only NR4A-type nuclear receptor in the roundworm Caenorhabditis elegans, has been implicated in the development of the nervous system.²²⁶ During development, the nervous system produces highly specialized neurons with distinct functional characteristics. A prime example is the C. elegans BAG chemosensory neurons.²²⁷ Under certain circumstances, BAG neurons sense the concentration of carbon dioxide in respiratory gas and translate it into reactions of attraction or repulsion; ETS-5 and its target gene NHR-6 are essential for this process.²²⁸ In contrast to ETS-5, which is engaged in both the attraction and avoidance of carbon dioxide, NHR-6 is an NR that is exclusively involved in the attraction process.²²⁹ These findings imply that gene regulatory mechanisms supported by NR subtypes have undergone evolutionary conservation. NHR-6 is necessary for BAGs to exhibit exceptional capacity to adaptively assign positive or negative valences to chemosensory stimuli, and it is a key modulator of the functional plasticity of the neural system.²²⁶ It is clear that NRs are of the greatest importance for the proper functioning of numerous processes in cellular lipid metabolism,^230,231 energy homeostasis²³² and the inflammatory response²³³; cell proliferation and differentiation are critically dependent on nuclear receptors.

Pathological changes in nuclear receptors, such as mutations, altered expression levels, or dysregulated activity, are linked to a wide range of diseases, including cancer, metabolic disorders, inflammation, and cardiovascular conditions. For example, the overexpression of ER in breast cancer drives tumor growth,²³⁴ whereas aberrant AR can cause therapy resistance in prostate cancer.²³⁵ Impaired PPAR function is associated with metabolic disorders such as obesity and type 2 diabetes,²³⁶ whereas dysregulated liver X receptors (LXRs) disrupt cholesterol homeostasis, exacerbating cardiovascular disease.²³⁷ Aberrant GR activity exacerbates inflammatory conditions and may induce corticosteroid resistance. Altered retinoid X receptor (RXR) function has been linked to neurodegenerative diseases such as Alzheimer’s disease. These pathological changes not only hold diagnostic and prognostic value but also serve as therapeutic targets. For example, ER, PR, and HER2 expression levels guide breast cancer classification and treatment, with SERMs such as tamoxifen proving effective in ER-positive patients. AR inhibitors are crucial in prostate cancer, where AR expression levels and mutations influence therapeutic outcomes. Additionally, radiolabeled ligands such as [F-18]-estradiol enable imaging of ER-positive tumors via PET scans,²³⁸ aiding in diagnosis and treatment monitoring. In summary, nuclear receptor alterations play a dual role in clinical practice as both therapeutic targets and biomarkers, underscoring their critical contribution to precision medicine and improved patient outcomes.

Cell fate

Nuclear receptors are essential for regulating cell fate through their function as transcription factors with effects on proliferation,²³⁹ differentiation,²⁴⁰ senescence²⁴¹ and apoptosis.²⁴² Through nongenomic mechanisms, NRs modulate signaling pathways that determine whether a cell will continue to divide, differentiate into a specific cell type, or undergo programmed cell death.²⁴³

The ER has been the most studied ER, mainly because of the estrogen dependence of the growth of certain breast cancer cells. The function of estrogen receptor alpha (ERα/ER) defines the most common type of breast cancer.^244,245 Numerous associated elements that function as regulators of estrogen-driven transcriptional pathways have been discovered, indicating that the ER cannot function solely by itself.²⁴⁶ Enhancer sequences are cis-regulatory ER binding sites that are located mainly away from transcriptional start sites, according to genome-wide profiling of chromatin binding.²⁴⁷ There is growing evidence that global enhancer activation is involved in tumor aneuploidy and carcinogenesis.²⁴⁸ Short DNA enhancer elements are crucial for maintaining a coordinated gene expression program specific to cell types during development and differentiation.²⁴⁹ Other nuclear receptor ligands, such as all-trans retinoic acid (atRA) and 1,25(OH)2D3, induce cell differentiation.^250,251,252 RA, the primary bioactive metabolite of retinol (vit A), has a range of pleiotropic effects on cell growth and differentiation, which are important in adult physiology and embryonic development.²⁵³ Members of the NR class of transactivators, specifically the retinoic acid receptors RARα, RARβ and RARγ, are the main mediators of activity.²⁵⁴ For example, prostate cancer-induced bone formation is decreased, and the endothelial-to-osteoblast transition (EC-to-OSB) is inhibited when the retinoic acid receptor (RAR) is activated.^255,256 Treatment with the RARγ agonist palovarotene, which has been tested for heterotopic ossification in fibrodysplasia ossificans progressiva, inhibited osteoblast mineralization and the EC-to-OSB transition in vitro. It also reduces the growth and formation of tumor-induced bone in several models of osteogenic prostate cancer.²⁵⁵ Compared with mature hepatocytes, hepatocytes induced in a 3D environment exhibited lower activity of the nuclear receptor THRB. The addition of THRB ligands during differentiation upregulated not only the expression of CYP3A4 but also the expression of multiple hepatocyte-related genes and increased histone acetylation; the induced differentiated hepatocytes were more similar to mature hepatocytes.²¹ In addition, the nuclear receptor Nur77 regulates the expression of genes involved in fatty acid absorption and transport, thereby blocking the uptake of exogenous fatty acids by cells and inhibiting the signaling pathways that promote breast cancer cell proliferation.²⁷ These findings highlight the significant role of NRs in controlling cell growth and differentiation.

NRs have also been shown to be involved in cellular senescence and cell death processes. Three members of the NR4A1/Nur77/NGFIB orphan nuclear hormone receptor subfamily (NR4A1, NR4A2 and NR4A3) have been the most studied. NR4A2 was reported to maintain anchorage-independent growth, thereby reducing cell death, known as anoikis, in HeLa cells.²⁵⁷ Following acute kidney injury (AKI), Nur77 and its family members Nurr1 and Nor-1 stimulate epithelial apoptosis. A conformational shift in Bcl2 and an increase in proapoptotic Bcl-xS protein levels are involved in Nur77-mediated kidney damage.²⁵⁸ Furthermore, YAP controls the transcription, phosphorylation and mitochondrial localization of NR4A1 to mediate the proapoptotic and antitumor actions of the Hippo pathway. In turn, NR4A1 acts as a feedback inhibitor of YAP, leading to its destruction, which prevents YAP from participating in carcinogenesis and liver regeneration.²⁵⁹ In addition, Nur77 interacts with DNMT3b, increasing GLS1 promoter methylation and decreasing GLS1 expression and glutaminolysis, which leads to the induction of HSC senescence.²⁶⁰ Hepatocyte nuclear factor 4α (HNF4α, NR2A1), another strongly conserved NR superfamily member, suppresses prostate tumorigenesis by arresting the cell cycle at the G2/M phase and p21-driven cell senescence.²⁶¹ NR subfamily 1 group I member 2 (NR1I2), also called PXR (pregnane-X receptor) or PAR (pregnane-activated receptor), has been implicated in blunting the expression of the proapoptotic genes TP53 and BAK1 (BCL2 antagonist/killer 1) to prevent apoptosis from toxic bile acids.²⁶² The retinoid RXRα has been shown to suppress the production of ITPR2 and control calcium signaling via ITPR2 and the mitochondrial calcium uniporter (MCU). After reducing the degree of DNA damage, the overexpression of RXRα delays replicative senescence.²⁶³ ZBTB17, a zinc finger protein, was shown in another study to interact with RXRα. Notably, ZBTB17 knockdown initiates a series of events, including DNA damage, decreased mitochondrial membrane potential (MMP), RXRα-dependent intracellular calcium signaling and cellular senescence.²⁶⁴ Under metabolic and genotoxic stresses, LXR/CD38 activation promoted lysosomal cholesterol efflux and nicotinamide adenine dinucleotide (NAD⁺) depletion in macrophages, which caused cholesterol-induced macrophage senescence and neurodegeneration.²⁶⁵

Cellular metabolism

Members of the NR family control the pace at which different metabolic enzymes are synthesized in different tissues,²⁶⁶ which affects processes including the metabolism of glucose, lipids and bile acids; adipocyte differentiation; and plasma lipoprotein modulation.^267,268 By influencing the balance between the storage, utilization and production of these macromolecules, NRs ensure metabolic flexibility, allowing the organism to adapt to fluctuations in energy availability and demand (Fig. 7). Their regulatory functions are particularly critical during periods of fasting, stress, or increased physical activity, where their precise control is essential for maintaining overall metabolic health.

Fig. 7

Examples of nuclear receptors involved in regulating metabolic pathways. Cellular metabolic pathways provide the energy and materials essential for cell survival. Nuclear receptors transcriptionally regulate genes that encode nutrient transporters and metabolic enzymes involved in these processes. The pathways include the following: 1. Glycolysis, 2. Pentose phosphate pathway (PPP), 3. Gluconeogenesis, 4. Lactate oxidation, 5. Autophagy, 6. Amino acid catabolism, 7. Redox homeostasis, 8. Mitochondrial biogenesis/dynamics, 9. Oxidative phosphorylation (OXPHOS), 10. Tricarboxylic acid (TCA) cycle, 11. Ketogenesis/ketolysis, 12. Glutaminolysis, 13. Ca²⁺ homeostasis, 14. Fatty acid oxidation (FAO), 15. Lipolysis

Glucose metabolism and gluconeogenesis

Glucose is the primary metabolic fuel for mammals and plays a crucial role in maintaining energy homeostasis.^269,270 During the fed state, circulating glucose originates primarily from the absorption of nutrients in the intestines.²⁷¹ However, under fasting or energy-demanding conditions, the body relies on two additional sources to maintain glucose levels: the breakdown of stored glycogen through glycogenolysis and the production of new glucose molecules via gluconeogenesis.^272,273,274 These complex metabolic processes are intricately regulated, and NRs play a key role in coordinating them. As molecular sensors, NRs detect changes in the body’s energy status and modulate the expression of genes involved in glucose metabolism.^275,276 The activation of PXR by its ligand, pregnenolone-16α-carbonitrile (PCN), impaired glucose tolerance by dysregulating glucose transporter 2 (GLUT2) function through two distinct mechanisms.²⁷⁷ First, it reduced the expression of GLUT2 in both mouse liver and wild-type hepatocytes. Second, it triggers the transport of GLUT2 from the plasma membrane to the cytosol in the liver, thereby suppressing glucose uptake in primary hepatocytes. Additionally, data mining of published chromatin immunoprecipitation/sequencing results revealed that the Glut2 gene is directly targeted by PXR. These findings may explain the diabetogenic effects of certain medications and environmental contaminants, positioning PXR in a potential novel diabetogenic pathway. At physiological concentrations found in the liver, glucose binds to and activates the transcriptional activity of LXRs, inducing the expression of LXR target genes with similar efficacy to that of oxysterols, which are well-known LXR ligands. Cholesterol homeostasis genes, which depend on LXR for their expression, were upregulated in the liver and intestines of fasted mice after refeeding with a glucose-rich diet,²⁷⁸ suggesting that glucose acted as an endogenous ligand for LXR.

Nuclear orphan receptor subfamily 4 group A member 1 (NR4A1), an important regulator of hepatic glucose homeostasis, was found to interact with the nuclear glycerol kinase Gyk during hepatic gluconeogenesis in the unfed state and in diabetes. Gyk acts as a corepressor of NR4A1, which attenuates the expression of target genes involved in hepatic gluconeogenesis and obstructs blood glucose regulation.²⁷⁹ Nuclear receptor subfamily 5 group A member 2 (NR5A2 or LRH1) and steroidogenic factor 1 (SF1 or NR5A1) work synergistically as key regulators of glucose-sensing systems in hepatic and steroidogenic tissues.²⁸⁰ These receptors are essential for the normal processing of glucose after eating through direct control of GCK and HK1 transcription.²⁸¹ FXR combines signals from PKA and FOXA2 for hepatic glucose metabolism and production through two regulatory arms.²⁸² The first is the phosphorylation of FXR by protein kinase A, which induces glucagon, agonist-activated FXR and CREB to combine and activate gluconeogenic genes. The physical interaction between FXR and the glucagon-activated FOXA2 transcription factor constitutes the second arm, which prevents FXR from stimulating the anti-gluconeogenic nuclear receptor SHP. Foxa2 knockdown did not influence the expression of glucagon-induced or FXR agonist-boosted gluconeogenic genes, suggesting that distinct subsets of FXR-sensitive genes are controlled by the PKA and FOXA2 pathways.²⁸²

NR coregulators play crucial roles in the regulation of glucose metabolism. For example, NR corepressors (NCoRs) operate within multiprotein complexes containing histone deacetylase 3 (HDAC3) to inhibit transcription, primarily through repressive chromatin remodeling at target loci. This process ultimately drives glucocorticoid receptor-dependent activation of hepatic gluconeogenesis. In hepatocytes, the double knockout of both NCoR1 and NCoR2 mimicked the hepatomegaly and fatty liver phenotype observed in HDAC3 knockouts by preventing glucocorticoid receptor binding.²⁸³ Similarly, nuclear receptor coactivator 3 (NCOA3) regulates the transcription of tyrosine-protein kinase (Fyn) in a PPARγ-dependent manner. NCOA3 deficiency was shown to worsen diabetic kidney disease by exacerbating albuminuria, glomerular sclerosis, and podocyte injury and impairing autophagy.²⁸⁴

Bile acid, sterol and lipid metabolism

Increasing evidence suggests that NRs play critical roles not only in glucose metabolism but also in the regulation of sterol, bile acid and lipid metabolism.^285,286,287 The three ERR isoforms, as well as PPARα and PPARδ, are the main transactivators of genes involved in mitochondrial bioenergetics and fatty acid oxidation (FAO) and are viewed as primary controllers of mitochondrial FAO.^288,289 For example, in addition to being a regulator of mitochondrial function, ERRα was established as a major transcriptional regulator of lipid biosynthesis and a promoter of nonalcoholic fatty liver disease (NAFLD/NASH).²⁹⁰ Medium-chain specific acyl-CoA dehydrogenase (ACADM), the first-discovered target gene of ERRα, encodes the initial rate-limiting enzyme in mitochondrial FAO; the promoter is also targeted by PPARα.²⁹¹ In addition, a muscle-specific protein induced by PGC-1 and ERRs, PERM1 (PGC-1/ERR-induced regulator in muscle-1), promoted mitochondrial biogenesis and metabolism in cardiomyocytes. In this study, PERM1 was shown to interact with the proximal regions of PPAR response elements (PPREs) in the endogenous promoters of genes involved in fatty acid oxidation, and further results revealed that PERM1 interacted with PPRE to promote transcription, partly in a PPARα- and PGC-1α-dependent manner.²⁹²

PPARα is also a key regulator of fatty acid oxidation and can induce spontaneous fatty liver and hyperlipidemia in mice fed a standard diet. For example, during the early night, fasting mice exhibited acute PPARα-dependent hepatocyte activity, accompanied by increased circulating free fatty acids that could be further stimulated by adipocyte lipolysis. However, fasting resulted in mild hypoglycemia and hypothermia in PPARα^hep−/− mice, suggesting a role of PPARα activity in nonhepatic tissues.²⁹³ Liver-specific inactivation of Vps15, the essential regulatory subunit of class 3 PI3K, elicited mitochondrial depletion and failure to oxidize fatty acids through blunting of the transcriptional activity of PPARα. Vps15 deficiency led to the accumulation of the PPARα repressors HDAC3 and nuclear receptor corepressor 1 (NCoR1) in the liver due to disrupted autophagy. Activation of PPARα or inhibition of HDAC3 restored mitochondrial biogenesis and FAO in Vps15-deficient hepatocytes, revealing functions for class 3 PI3K and autophagy in the transcriptional coordination of mitochondrial metabolism.²⁹⁴ In addition, hepatic Ncor1 deletion in mice retarded atherosclerosis development by reprogramming bile acid metabolism and enhancing fecal cholesterol excretion, resulting in reduced plasma cholesterol levels and decreased hepatic cholesterol content in liver-specific Ncor1 knockout mice compared with those in controls fed an atherogenic diet for twelve weeks.²⁹⁵

NR4A1 was identified as a previously unrecognized constitutive regulator of adipocyte progenitor (AP) quiescence.²⁹⁶ In ex vivo experiments, NR4A1 gain-of-function reduced adipogenesis, whereas its loss-of-function increased adipogenesis.²⁹⁶ Compared with control mice, NR4A1 knockout mice fed a high-fat diet were more prone to obesity, with increased gene expression of PPARγ and FAS. Conversely, NR4A1 overexpression in 3T3-L1 preadipocytes inhibited adipogenesis. NR4A1 upregulated GATA binding protein 2 (GATA2), which in turn inhibited PPARγ. NR4A1 also suppressed sterol regulatory element-binding protein 1 (SREBP1) and its downstream target fatty acid synthase (FAS) by upregulating p53. Overall, NR4A1 inhibits adipocyte differentiation and lipid accumulation by increasing the expression of GATA2 and p53.²⁹⁷ Nuclear receptor subfamily 0 group B member 2 (NR0B2, also called SHP) is expressed at high levels in the liver and intestine, and its transcriptional activity can be increased by fibroblast growth factor 19 (human FGF19, mouse FGF15) signaling. FGF19 and SHP were observed to inhibit SREBF2 (sterol regulatory element binding transcription factor 2), which led to a reduction in intestinal NPC1L1 expression, cholesterol absorption and hypercholesterolemia.²⁹⁸ Another member of the nuclear receptor family, NR1A1, was reported to influence hepatic autophagy, lipid metabolism and adipocyte homeostasis by interacting with MED1 through a bridge formed by PGC1α.^299,300

The expression of RORα/β/γ and REV-ERBα/β in the liver follows circadian rhythms. The liver genome contains high-order transcriptionally repressive hubs where REV-ERBα condensates are found, and these hubs are strongly associated with circadian gene repression.^301,302,303 In mouse models, RORs bind to ROREs at night, whereas REV-ERBα/β bind to ROREs during the day to decrease lipogenesis. In the liver, REV-ERBα and REV-ERBβ work in concert, increasing the ability of HDAC3 and NCoR to control SREBP activity and maintain lipid homeostasis. They also affect cytochrome P4507A1 expression levels, which helps to maintain the equilibrium of bile acid metabolism.³⁰⁴ RORγ serves as a crucial activator of the entire cholesterol biosynthesis program, controlling SREBP2 by binding to genes involved in cholesterol biosynthesis and facilitating SREBP2 recruitment. At the loci of genes involved in cholesterol production, RORγ inhibition decreases chromatin acetylation and disrupts its connection with SREBP2. In immunocompetent animals and patient-derived xenografts, RORγ antagonists induce tumor regression.³⁰⁵

The regulation of bile acids, sterols and lipids is also associated with many other types of nuclear receptors. Through the regulation of Akr1b7 transcription, the nuclear receptor PXR effectively reduces AKI by increasing reactive oxygen species (ROS) generation, mitochondrial autophagy and mitochondrial dysfunction in lipid metabolism.³⁰⁶ It was recently demonstrated that the function of FXR in BA homeostasis depends on the phosphorylation of Tyr-67 by the FGF15/19 signaling-activated nonreceptor tyrosine kinase Src. According to Byun and colleagues, hepatic FXR phosphorylation by FGF15/19-induced Src preserves cholesterol homeostasis and protects against atherosclerosis.³⁰⁷ PXR activation upregulated intermediates in the Kandutsch–Russell cholesterol synthesis pathway in the liver and induced a number of cholesterol synthesis genes, including the rate-limiting HMRCR. In both mice and humans, PXR activation increased the level of plasma proprotein convertase subtilisin/kexin type 9 (PCSK9), a negative regulator of hepatic LDL absorption. A new regulator of PCSK9 and cholesterol synthesis, the PXR-SREBP2 pathway, also serves as a molecular mechanism for drug- and chemical-induced hypercholesterolemia.³⁰⁸

Mitochondria, OxPhos and the TCA cycle

Mitochondria serve as vital energetic and biosynthetic signaling hubs, taking in substrates from the cytoplasm to generate bioenergetic and biosynthetic building blocks.³⁰⁹ This process is achieved through the coordinated activity of several key metabolic pathways, including the electron transport chain (ETC), oxidative phosphorylation (OxPhos), the tricarboxylic acid (TCA) cycle, glycolysis, glutaminolysis and fatty acid oxidation (FAO). These pathways not only produce ATP but also provide intermediates essential for biosynthesis. Crucially, the function of mitochondria is tightly regulated by various nuclear receptors, which modulate gene expression to ensure proper mitochondrial activity and metabolic balance.

Several nuclear receptors are involved in regulating genes associated with the TCA cycle and OxPhos, including estrogen-related receptor alpha (ERRα), NUR77 (NR6A1) and PPARγ.^310,311,312 One of the first major datasets used to highlight the role of ERRα in OxPhos regulation was a study that integrated PGC1α-induced GW transcriptional profiling with a software approach to identify cis-regulatory sequences.^313,314 Mice lacking both ERRα and ERRγ presented the most extensive and profound disruption in skeletal muscle gene expression, with the ‘mitochondrial function’ pathway genes involved in OxPhos and the TCA cycle being the most significantly affected. Moreover, mice deficient in ERRβ and ERRγ exhibit impairments in lipid metabolism and branched-chain amino acid metabolism, specifically in the soleus muscle.³¹⁵ Similarly, muscle-specific deletion of Esrrg (the gene encoding ERRγ) in mice reduces exercise capacity because of deficient mitochondrial activity.³¹⁶ adipocytes lacking all ERR isoforms exhibited significant downregulation of genes involved in oxidative metabolic pathways, including those controlling the TCA cycle and OxPhos, leading to marked reductions in mitochondrial content and oxidative capacity.³¹⁷ These results suggest that many mitochondrial actions are mediated through the stimulation of ERR expression and activity, underscoring the critical role of ERR in mitochondrial energy metabolism across various tissues.

The nuclear receptor Nur77 (also known as TR3 or NGFI-B), encoded by Nr4a1, belongs to the steroid/thyroid/retinoid superfamily and serves as a key regulator of energy metabolism. Nur77 is phosphorylated by ERK2 and translocated to the mitochondria upon glucose deprivation. Mitochondrial Nur77 binds to TPβ, a rate-limiting enzyme in FAO, to protect it from oxidation. This promoted the metabolic adaptation of melanoma cells by evading ROS-induced cell death.³¹⁸ Ubiquitinated mitochondrial Nur77 interacts with the ubiquitin-binding domain of p62/SQSTM1 to form condensates capable of sequestering damaged mitochondria. An additional interaction between the N-terminal intrinsically disordered region (IDR) of Nur77 and the N-terminal PB1 domain of p62/SQSTM1 allows tethering of clustered mitochondria to the autophagy machinery, which endows Nur77-p62/SQSTM1 condensates with the magnitude and liquidity to act on the mitochondria.³¹⁹ In response to the pathological accumulation of α-synuclein (α-syn) fibrils in Parkinson’s disease (PD), Nur77 is translocated from the cytoplasm to the mitochondria to improve PHB-mediated mitophagy by regulating c-Abl phosphorylation. Nur77 overexpression alleviated the expression of pS129-α-syn and protected dopamine (DA) neurons from the loss of α-syn in PD.³²⁰

NR1D1 (nuclear receptor subfamily 1 group D member 1) is the most highly upregulated nuclear receptor in abdominal aortic aneurysm (AAA) tissues. Knockout of Nr1d1 in vascular smooth muscle cells (VSMCs), but not in endothelial or myeloid cells, led to significant inhibition of AAA formation. Mechanistic investigations revealed that ACO2 (aconitase-2), a key enzyme in the TCA cycle, is a direct transcriptional target of NR1D1. By repressing ACO2, NR1D1 modulates mitochondrial metabolism. In the absence of NR1D1, ACO2 expression is restored, which subsequently corrects mitochondrial dysfunction during the early stages of Ang II infusion, even prior to the onset of AAA development.³²¹

Catabolism of amino acids

Amino acid catabolism is vital during starvation to sustain glucose levels and provide alternative carbon sources, primarily in the liver but also in the kidneys, muscles and adipose tissue.³²² This process involves transamination and oxidative deamination in the cytoplasm, producing metabolites such as α-ketoglutarate, pyruvate and acetyl-CoA, which feed into the TCA cycle.³²³ An essential NR in AA catabolism is ERRα, which is active in regulating genes involved in amino acid uptake and branched-chain amino acid metabolism.³²⁴ ERRα is also linked to reduced leucine oxidation under energy-demanding conditions.³²⁵ PPARα and HNF4α also regulate amino acid utilization. PPARα, in the presence of RXRα, inhibited HNF4α activity, suppressing serine dehydratase expression by promoting HNF4α degradation via the proteasome pathway. In PPARα-knockout mice, HNF4α levels and amino acid catabolizing enzyme (AACE) expression are elevated.³²⁶ In response to amino acid deficiency (AAD), MEF2D (myocyte enhancer factor 2D) and NR4A1 induce FAM134B2 expression and promote FAM134B2-mediated reticulophagy to maintain intracellular amino acid levels.³²⁷

Inflammation and immunity

Compelling evidence suggests that NRs can regulate inflammation and immunity, contributing to the pathogenesis of human diseases. For example, Nur77 binds to LPS, acting as an LPS receptor protein and playing a role in macrophage pyroptosis. Further research indicated that Nur77-LPS interactions activated NLRP3, resulting in the formation of an atypical inflammasome. These findings demonstrated that Nur77 promotes NLRP3 inflammasome activation, enhancing the host immune response to endotoxins.¹⁷⁴ Similarly, Nur77 was identified as a key transcriptional regulator of the proinflammatory metabolic switch in macrophages. IDH expression was not downregulated in Nur77-deficient macrophages, which led to increased levels of succinate and other TCA cycle metabolites, independent of glutamine, resulting in increased nitric oxide and proinflammatory cytokine production in an SDH-dependent manner. Thus, Nur77 promotes an anti-inflammatory metabolic state in macrophages, offering protection against chronic inflammatory diseases such as atherosclerosis.³²⁸ Another nuclear receptor, RORα, regulates hepatic macrophage polarization and inflammation by inducing kruppel-like factor 4 (KLF4) expression. In myeloid-specific RORα-deficient animals, Kupffer cells (KCs) and bone marrow-derived macrophages fail to undergo M2 polarization, rendering them more susceptible to high-fat-diet-induced nonalcoholic steatohepatitis (NASH).³²⁹ Additionally, the orphan nuclear receptor TLX directly bound to the CD274 (PD-L1) gene promoter, showing a strong positive correlation with PD-L1 overexpression. Suppressing TLX significantly reduced the in vivo growth of glioma allografts and xenografts, preserved the antitumor immune response and markedly decreased the number of PD-L1-positive cells and glioma-associated macrophages.³³⁰ Nuclear receptor subfamily 1 group D member 1 (NR1D1) acts as a transcriptional repressor and plays a key role in regulating inflammation. The activation of NR1D1 decreased the expression of proinflammatory cytokines and matrix metalloproteinases (MMPs), whereas NR1D1 silencing had the opposite effect. Additionally, NR1D1 activation reduces ROS production and increases the generation of Nrf2-associated antioxidant enzymes.³³¹

NRs also play crucial roles in modulating immune responses by directly regulating the function and activity of immune cells, such as influencing their development, differentiation and activation. For example, overexpression of NR4A1 inhibited the development of effector T cells through binding to the transcription factor AP-1 and inhibited its promotion of the expression of effector genes. NR4A1 binding encouraged the acetylation of histone 3 at lysine 27 (H3K27ac), which activated genes linked to tolerance. Deletion of NR4A1 increases immunity against tumors and chronic viruses, overcomes T-cell tolerance and enhances effector function.³³² Similarly, another study revealed that NR4A triple knockout CAR-T lymphocytes presented traits and gene expression profiles typical of CD8⁺ effector T cells. The chromatin regions in these cells were enriched in binding motifs for transcription factors involved in T-cell activation, such as NF-κB and AP-1.³³³ These studies suggest that NR4A is a major regulator involved in the induction of T-cell dysfunction and that NR4A inhibition is a promising approach for cancer immunotherapy.

RARs and RA signaling play crucial roles in immune responses, influencing immune tolerance, tissue homing, lymph node formation and protective immunity.³³⁴ RARs include RARα, RARβ and RARγ, which are encoded by different genes with unique transcriptional variants and isoforms. In the resting state, RARα binds to transcriptional repressors to inhibit gene expression. However, upon binding to RA, RARα tends to bind to transcriptional activators, promoting gene expression³³⁴ RAR signaling has been shown to regulate immunity. For example, following TCR stimulation, extranuclear RARα is rapidly phosphorylated and recruited to the TCR signalosome. RA disrupted extranuclear RARα signaling, leading to reduced TCR activation and increased conversion of FOXP3+ regulatory T cells. RA is translocated to the nucleus by CRABP2, which is upregulated by TCR activation. Deletion of Crabp2 resulted in increased cytoplasmic RA, disrupting signalosome-associated RARα and consequently weakening autoimmune responses while diminishing antipathogen immunity.³³⁵

Temporal expression changes

The expression of nuclear receptors is not only related to tissue, sex, and disease but also varies across different age groups within the same individual.³³⁶ These variations reflect developmental needs, metabolic changes, hormonal shifts, and adaptations to aging-related physiological demands. Generally, developmental NRs such as RARs, PPARs and RXRs are highly expressed during embryogenesis and early development to support rapid growth, differentiation, and development.³³⁷ During adolescence, ARs, ERα and ERβ are elevated to correlate with puberty and the onset of secondary sexual characteristics, whereas GRs act to moderate stress responses and energy metabolism during periods of rapid physical and emotional development. PPARs, LXRs, and FXRs live in adult individuals to maintain lipid and glucose homeostasis, supporting metabolic stability during peak years of physical activity and reproductive capability. Diet, exercise, and stress significantly modulate NR expression, affecting metabolic and endocrine balance during this period. The expression of these NRs decreases with increasing age, which causes impaired lipid metabolism and insulin sensitivity, cholesterol and bile acid metabolism, and calcium homeostasis and immune function, leading to an increased risk of metabolic syndrome, compromised organ function and chronic inflammation. For example, Nr4a1 is reduced in peripheral blood mononuclear cells and CA1 pyramidal neurons with aging, which impairs cognition and excitatory synaptic function.³³⁸ Monitoring age-specific NR expression patterns could guide personalized therapies to optimize metabolic health and prevent age-related diseases.

Degradation and metabolic cycling

The metabolic cycling process of NRs, including their synthesis, activation, degradation, and recycling, is integral to maintaining homeostasis and ensuring that NRs can adapt to changing physiological demands. Since the activation and transcriptional regulation of nuclear receptors have been discussed above, we mainly emphasize their degradation and recycling. The degradation of nuclear receptors is a highly regulated process that involves proteasomal and lysosomal pathways, ensuring the dynamic control of receptor levels in response to physiological and environmental cues. Ligand binding can either stabilize or destabilize NRs by inducing conformational changes that influence ubiquitination.^339,340 In addition, posttranslational modifications (PTMs), such as phosphorylation,³⁴¹ SUMOylation³⁴² and acetylation,³⁴³ modify NR degradation rates by altering their interaction with ubiquitin ligases or stabilizing proteins. Moreover, many NRs, such as REV-ERBs and PPARs, exhibit circadian cycling, with their expression and activity oscillating in a 24-hour rhythm to align with metabolic needs.^344,345 These rhythms are coregulated by core circadian clock genes (e.g., CLOCK and BMAL1), which synchronize metabolic functions with environmental cycles such as light and feeding. Altogether, cycling of NRs ensures appropriate receptor levels, preventing excessive or prolonged signaling that could lead to cellular dysfunction.

Alterations cause by aging

With aging, the efficiency of key regulatory pathways declines, leading to altered NR turnover, disrupted signaling, and increased susceptibility to age-related diseases.³⁴⁶ Proteasomal dysfunction, a hallmark of aging, impairs the degradation of damaged or misfolded proteins, including NRs. This results in the accumulation of inactive or malfunctioning receptors, which disrupt signaling and contribute to metabolic and endocrine dysregulation, key features of aging. These disruptions play a central role in the development of diseases such as obesity, diabetes, cardiovascular conditions, and neurodegenerative disorders.^347,348 Additionally, aging reduces autophagic flux, hindering the clearance of damaged proteins, including aggregated NRs. As autophagy becomes less efficient with age, NR aggregates persist, disrupting receptor signaling and promoting chronic inflammation, mitochondrial dysfunction, and cellular stress.^349,350 These factors are implicated in the progression of age-related diseases like Alzheimer’s, diabetes, and frailty. Oxidative stress also contributes to aging-related cellular damage by directly modifying NRs. ROS cause conformational changes in NRs, preventing their proper ubiquitination and degradation. This oxidation makes NRs resistant to degradation, leading to the accumulation of damaged receptors and further dysfunction in signaling pathways.³⁵¹ Understanding these age-related changes offers valuable insights for developing targeted therapies to restore NR homeostasis and mitigate aging-associated disorders.

Targeting nuclear receptors for disease management

Given the critical role of NRs in physiological and pathological processes, they constitute a highly significant and privileged class of intracellular druggable targets for treating various diseases.^{52,352,353,354} By modulating these receptors, it is possible to influence a wide range of conditions, from metabolic disorders such as diabetes and obesity to immune-related diseases such as autoimmune disorders and inflammatory conditions (Tables 1, 2). NRs are central to cancer progression and hormone regulation, making them prime targets for oncology and hormone therapies. The ability to design drugs that specifically interact with nuclear receptors enhances their potential for precision medicine, offering more targeted treatments with fewer side effects across a broad spectrum of diseases.

Table 1 Summary of completed clinical trials of nuclear receptor-targeted drugs

Table 2 Summary of ongoing clinical trials of nuclear receptor-targeted drugs

Targeting nuclear receptors in cancer

NRs, especially those that bind to three steroid hormones, namely, estrogen, progesterone and androgen, play a significant role in the development of human malignancies, particularly breast cancer,^355,356 ovarian cancer³⁵⁷ and prostate cancer.³⁵⁸ In recent years, NR-targeted drugs have attracted widespread attention as novel therapeutic strategies^359,360,361 that play a significant role in inhibiting the growth and progression of many types of cancer.

Within the nuclear receptor superfamily, ERs were the first nuclear receptors to be described. Breast cancer is the most common cancer in women, with ER⁺ breast cancer accounting for approximately 75% of all cases. Numerous studies have confirmed that ERα plays a causative role in carcinogenesis. As a result, an increasing number of ERα-based targeted medicines have entered preclinical and clinical trials (Table 1), and some have even received FDA approval. This includes directly antagonizing the estrogen receptor via SERMs and selective estrogen receptor degraders (SERDs). These drugs include ER antagonists, selective ER modulators and aromatase inhibitors.³⁶² ER antagonists competitively inhibit the ER, whereas selective ER modulators function as partial agonists or antagonists on the basis of their tissue affinity. Aromatase inhibitors decrease estrogen production by blocking aromatase in tissues such as the ovaries and adipose tissue.^363,364 Tamoxifen is the most widely used antiestrogen for hormone-dependent breast cancer and is indicated for various treatment settings. Evidence shows that patients with estrogen receptor-positive tumors are more likely to benefit from tamoxifen. FDA-approved treatments include treating breast cancer in both females and males, providing adjuvant therapy after surgery and radiation, treating female patients with ductal carcinoma in situ (DCIS) postsurgery and radiation to lower the risk of invasive breast cancer and reduce the risk of breast cancer in certain high-risk patients.^365,366 In addition to tamoxifen, many other SERMs, including raloxifene, lasofoxifene, bazedoxifene and fulvestrant, have been developed and used for breast cancer treatment.³⁶³ These drugs have also been used to treat other tumors with high estrogen expression. In addition to hormone-dependent breast cancer, antiestrogen medications such as tamoxifen and aromatase inhibitors have shown efficacy in managing conditions such as endometrial cancer and certain types of ovarian cancer.^367,368 Although estrogen levels are low in prostate tissue, ER expression has been detected in some prostate cancer patients.³⁶⁹ ER activation is believed to be associated with the proliferation and metastasis of prostate cancer cells.³⁷⁰ Thus, antiestrogen therapy targeting the ER has also been proposed as a new treatment strategy for prostate cancer. For example, in males with advanced prostate cancer, an ERα agonist, GTx-758, has been shown to lower testosterone with fewer side effects associated with androgen-deprivation therapy.³⁷¹

Bidedoxifene is the most recent generation of SERMs. Fanning and colleagues demonstrated that bazedoxifene works in concert with palbociclib, a CDK4/6b inhibitor, and is more effective than tamoxifen against specific ERα mutants, such as Y537S and D538G. A phase II clinical trial in patients with ductal carcinoma in situ [NCT02694809] and a phase I/II clinical trial on bazedoxifene in combination with palbociclib in hormone receptor-positive breast cancer [NCT02448771] are two examples of the numerous clinical trials that have examined bazedoxifene across a variety of cancer types. Degradation of this receptor by SERDs is another tactic to target ERs. Fulvestrant is the most researched SERD, and its clinical application has been growing. Clinical trials have combined fulvestrant with CDK4/6 inhibitors, such as ribociclib in men and postmenopausal women with advanced breast cancer [NCT02422615] and palbociclib in hormone receptor+HER2-metastasized breast cancer after endocrine failure [NCT01942135], as well as phosphatidylinositol 3-kinasitol kinase (PI3K)/AKT/mTOR pathway inhibitors, such as pictilisib, in advanced or metastatic breast cancer in participants resistant to aromatase inhibitor therapy [NCT01437566].

The abnormal expression of AR in prostate cancer cells makes anti-AR drugs a logical treatment strategy.³⁷² These drugs inhibit AR function through various mechanisms, reducing androgen stimulation of tumor cells. Among the most common anti-AR agents are AR antagonists such as abiraterone and enzalutamide. These drugs competitively bind to the AR, preventing androgen attachment and inhibiting receptor activity. Abiraterone has been shown to prolong survival in patients with metastatic castration-resistant prostate cancer (mCRPC).³⁷³ In the context of metastatic castration-sensitive prostate cancer (mCSPC), a combination treatment involving abiraterone, prednisone and docetaxel has favorable effects.³⁷⁴ Furthermore, for metastasis-free survival, combining enzalutamide with leuprolide has shown superior outcomes compared with leuprolide alone in high-risk patients with biochemical recurrence. Additionally, enzalutamide monotherapy has outperformed leuprolide monotherapy.³⁶ The prostate cancer community has recently focused much attention on a number of newly created AR proteolysis-targeting chimeras (PROTACs), which were created as SARDs. ARV-110 [NCT03888612], the first AR PROTAC to reach clinical trials, is now being used in patients with metastatic CRPC and is undergoing a phase I/II clinical trial. In contrast to clinically licensed AR antagonists, ARD-61, a novel AR PROTAC, has been shown to efficiently promote on-target AR degradation, elicit more potent antiproliferative and proapoptotic effects, and reduce downstream AR target gene expression in prostate cancer cells. The most effective AR PROTACs may eventually be utilized extensively in cancer patients, and we expect more advancements to the clinical trial stage.

Additionally, RARs and their heterodimer partners, such as PPARs and RXR, which are involved in vitamin A metabolism, cell differentiation and immune regulation, also have therapeutic potential.^375,376 Aberrant RXR signaling can promote cancer development by disrupting normal cellular homeostasis and enhancing oncogenic processes. RXR agonists have shown potential in treating various advanced cancers in clinical trials. IRX4204, in combination with erlotinib, is under investigation for previously treated advanced non-small cell lung cancer (NSCLC) [NCT02991651]. NRX194204 is being studied for its efficacy in castration- and taxane-resistant prostate cancer [NCT01540071] and advanced NSCLC [NCT00964132]. Additionally, bexarotene is being evaluated for the treatment of metastatic breast cancer and relapsed or refractory cutaneous T-cell lymphoma in patients with stage III or IV disease [NCT00003752, NCT00514293, NCT01134341, NCT00316030]. These studies underscore the therapeutic potential of RXR agonists in managing resistant and advanced malignancies. PPAR agonists have shown promising antitumor effects across a range of cancers, either as standalone treatments or in combination therapies. Troglitazone has shown efficacy in prostate cancer and liposarcoma [NCT00003058], whereas pioglitazone is being studied for advanced solid tumors [NCT02133625], pancreatic cancer [NCT01838317], and thyroid cancer [NCT01655719], often with chemotherapy. Inolitazone combined with paclitaxel is under investigation for advanced anaplastic thyroid cancer [NCT02152137]. Rosiglitazone is being explored for the treatment of liposarcoma [NCT00004180], metastatic thyroid cancer [NCT00098852], and androgen-dependent prostate cancer [NCT00182052]. These trials demonstrate the therapeutic potential of PPAR agonists in treating challenging malignancies. Retinoic acid, a natural RAR agonist, regulates the expression of genes related to cell growth. Studies suggest that RAR/RXR agonists may have antitumor effects on prostate cancer. For example, the RAR agonist adapalene has been shown to induce a tumor-suppressive senescence-associated secretory phenotype (SASP) in prostate cancer cells. In combination with docetaxel, adapalene enhanced tumor suppression and improved natural killer (NK) cell-mediated clearance in preclinical models. This approach also increased the efficacy of NK cell infusion in mice with human prostate cancer, leading to greater tumor suppression.³⁷⁷

REV-ERBs, including REV-ERBα (NR1D1) and REV-ERBβ (NR1D2), are key regulators of the circadian clock. Notably, many tumor types exhibit elevated expression of REV-ERBβ, regardless of ERBB2 or ER status, whereas nonmalignant mammary epithelial cells primarily express REV-ERBα. High levels of REV-ERBβ in cancer cells have been linked to reduced sensitivity to chloroquine via the modulation of autophagy, suggesting a role in therapy resistance. REV-ERB agonists, such as SR9009 and SR9011, selectively target cancer cells and oncogene-induced senescent cells, such as melanocytic naevi, without impacting normal cell viability. These agonists have shown promising anticancer effects, including reduced glioblastoma growth and improved survival in mice, without causing significant toxicity.³⁷⁸

Targeting nuclear receptors in metabolic-related diseases

Metabolic diseases such as nonalcoholic fatty liver disease (NAFLD), obesity, type 2 diabetes and atherosclerosis represent a growing global health burden.^379,380 These conditions are frequently associated with dysregulated lipid or glucose metabolism.^381,382 NRs play crucial roles in maintaining metabolic homeostasis by controlling the expression of genes involved in lipid, glucose and energy metabolism. Among NRs, PPARs, farnesoid X receptor (FXR), liver X receptor (LXR) and pregnane X receptor (PXR) have been identified as promising therapeutic targets. Drugs that modulate these receptors, such as PPAR agonists and FXR agonists, have demonstrated promising activity in clinical trials for the treatment of metabolic disorders, particularly NAFLD. Here, we explore current and emerging therapies that target these receptors.

One of the most well-known nuclear receptors is the PPAR family. PPAR agonists, such as pioglitazone and rosiglitazone, can increase insulin sensitivity in individuals with T2D. By activating PPARγ, these drugs enhance glucose uptake and lipid storage, which helps to lower blood sugar levels and improve metabolic control. However, these drugs are associated with certain risks, such as weight gain and fluid retention, necessitating careful patient management. PPARα agonists, such as fibrates, have been used clinically for 35 years to regulate blood lipids and prevent atherosclerosis.³⁸³ Pemafibrate was introduced in Japan in June 2018 and has since been demonstrated to be effective in inhibiting VLDL secretion and enhancing triglyceride (TG) clearance by activating LPL.³⁸⁴ In mice fed a high-fat diet, it suppressed postprandial hyperlipidemia by downregulating the mRNA expression of the intestinal cholesterol transporter NPC1L1 and upregulating genes involved in β-oxidation to inhibit VLDL secretion from the liver. In a 4-week trial with dyslipidemic patients (0.4 mg/day), pemafibrate significantly reduced fasting and nonfasting serum TG, RemL-C, and apo B-48 levels, with a marked reduction in the postprandial TG AUC, indicating improved postprandial hypertriglyceridemia.³⁸⁵ Similar results were observed in diabetic patients treated with pemafibrate.³⁸⁶ PPARγ and PPARδ regulate energy utilization and insulin sensitivity in skeletal muscle and adipose tissue. High insulin levels accelerate the development of NAFLD through a PPARγ-dependent pathway.³⁸⁷ PPARγ agonists, thiazolidinediones, have been used as insulin sensitizers in diabetic patients.³⁸⁸ PPARδ agonists improved the pathological manifestations of nonalcoholic steatohepatitis (NASH) without affecting body weight. The dual PPARα/δ agonist elafibranor (GFT505) improved glycemic and lipid metabolism in NASH patients in a phase II clinical trial, reduced liver inflammation and did not exacerbate fibrosis, demonstrating good tolerability. Phase III clinical trials targeting NASH patients [NCT02704403] are ongoing. A phase II clinical trial of the dual PPARα/γ agonist Saroglitazar [NCT03061721] in NASH patients was completed in April 2020. Midterm reports revealed not only regression of NASH tissue lesions but also decreased serum ALT levels, indicating improved liver function. The Indian pharmaceutical company Zydus Cadila has submitted a marketing application for this drug.

Another good NR drug target is FXR, which regulates bile acid metabolism and lipid homeostasis. FXR activation improves lipid metabolism and reduces liver inflammation, offering a new avenue for managing metabolic liver disorders.^389,390,391 Obeticholic acid, an FXR agonist also known as INT-747, is approved for treating NAFLD and NASH³⁹² [NCT02548351]. Owing to its ability to lower ALP levels and combat cholestasis and fibrosis, obeticholic acid (Ocaliva) was initially approved as a treatment for primary biliary cholangitis. In a phase III clinical trial for NASH [NCT02548351], obeticholic acid improved liver function and reduced tissue pathology, although it exhibited some side effects, such as pruritus and increased low-density lipoprotein levels. Given that pruritus can be managed symptomatically and that dyslipidemia can be addressed by the concomitant use of statins, the United States Food and Drug Administration has approved obeticholic acid as the primary treatment for NASH. Several other FXR agonists with diverse physicochemical characteristics, including bile acid derivatives, nonbile acid-derived steroidal FXR agonists, nonsteroidal FXR agonists and partial FXR agonists, are also progressing through advanced stages of clinical development. The noncarboxylic acid steroidal FXR agonist EDP-305 has been shown to modulate many pathways that trigger antilipogenic, anti-inflammatory and antifibrotic gene signatures. This resulted in hepatoprotective and antisteatotic effects in a mouse model of NASH.³⁹³ Patients with intestinal failure require more complicated care when they have parenteral nutrition (PN)-associated cholestasis (PNAC). By restoring hepatic FXR signaling, GW4064 protected animals against PNAC by increasing the expression of sterol and phospholipid transporters and canalicular bile and suppressing the recruitment and activation of macrophages. These findings suggest that increasing FXR activity could be used as a therapeutic approach to treat or prevent PNAC.³⁹⁴

In addition to PPAR and FXR, LXR is involved in cholesterol metabolism and can be targeted for atherosclerosis treatment. LXR agonists have been shown to increase cholesterol efflux and reduce the development of atherosclerotic plaques in preclinical models.³⁹⁵ However, treating patients with medications that increase cholesterol is not a practical option for metabolic illnesses; instead, methods for separating the advantageous effects of LXR ligands from unfavorable side effects must be investigated. Taken together, these examples highlight the growing potential of NR-targeted drugs in addressing the underlying causes of metabolic disorders, offering more precise and effective treatments than traditional approaches do.

Targeting nuclear receptors in cardiovascular diseases

The targeting of NRs for the treatment of cardiovascular diseases has gained significant attention because of the pivotal role these receptors play in regulating the expression of genes involved in metabolic, inflammatory and lipid processes.^{361,396,397,398} Nuclear receptors, such as PPARs, LXR and FXR, are key regulators of lipid metabolism, glucose homeostasis and inflammation, all of which are critical factors in the development of cardiovascular diseases. By modulating these receptors, it is possible to control pathological processes such as atherosclerosis, hypertension and other cardiovascular disorders.

The NRs RORα and REV-ERBα are key components of the circadian system and regulate biological rhythms, glucose metabolism, lipid metabolism, vascular inflammation and fibrinolysis.³⁹⁹ RORα is instrumental in endothelial progenitor cell (EPC) differentiation and promotes angiogenesis, tissue repair and vascular stability by inducing erythropoietin production and activating AMPK.⁴⁰⁰ RORα mediates the protective effects of melatonin, including its anti-inflammatory, antioxidant and antiapoptotic effects, making it a potential therapeutic target for atherosclerosis and endothelial dysfunction.^401,402 In hypertensive rats, melatonin altered clock gene expression patterns, maintaining high levels of REV-ERBα mRNA, which regulated blood pressure rhythms. This effect is linked to melatonin receptor activity and may involve posttranslational mechanisms.⁴⁰³ Increased RORα expression, which is stimulated by melatonin and the sympathetic nervous system, also protects against programmed hypertension. A number of small-molecule agonists for RORα and REV-ERBα, such as the pharmacological agents SR9009 and GSK4112 for REV-ERBα, have been developed⁴⁰⁴ and are available for use in cellular and animal experiments, but prospective studies on the impact of stable circadian rhythms on CHD and heart failure are still limited.^405,406 When considered collectively, the bulk of current research points to considerable clinical value and therapeutic potential for medications that target RORα and REV-ERBα to treat hypertension and atherosclerosis.

Several studies have highlighted the function of RXRs in cardiovascular disease. Treatment with 9cRA or the synthetic RXR agonist LGD1069 (bexarotene) has been shown to reduce oxidative stress-induced cell damage and preserve the mitochondrial membrane potential.⁴⁰⁷ In heart failure, oxidative stress activates angiotensin-II (AngII), leading to harmful cardiac remodeling and dysfunction. Bexarotene treatment of cultured rat aortic smooth muscle cells inhibited AngII-driven inflammation and p38 MAPK activation, suggesting that RXR activation has protective effects on cardiac disease.⁴⁰⁸ ERRα and ERRγ are essential for normal postnatal cardiovascular function, whereas ERRβ supports maximal ATP generation in contracting cardiomyocytes. ERR agonists help maintain oxidative metabolism, which protects the heart against pressure overload-induced heart failure (HF) in vivo. Using a structure-based design, Xu and colleagues synthesized two pan-ERR agonists, SLU-PP-332 and SLU-PP-915, each of which significantly improved the ejection fraction, reduced fibrosis and enhanced survival in models of pressure overload-induced HF without affecting cardiac hypertrophy.⁴⁰⁹ Targeting other nuclear receptors, such as RARs, PPARs, and LXRs, has also shown promise for ameliorating cardiovascular disease.^410,411 These findings provide strong pharmacological evidence supporting the potential of targeting NRs for cardiovascular disease management.

Targeting nuclear receptors in central nervous system disorders

Alzheimer’s disease (AD), PD, Huntington’s disease (HD), multiple sclerosis (MS), cerebral ischemia, stroke and other conditions are common central nervous system disorders that currently affect approximately one hundred million people worldwide. Compelling evidence suggests that nuclear receptors are important in these disorders and that targeting these receptors has significant therapeutic potential.³⁵³

Liver X receptor LXRs are key regulators of cholesterol trafficking in the central nervous system (CNS), working with ApoE to facilitate cholesterol recycling and efflux, which are essential for maintaining CNS homeostasis. Dysregulation of LXR signaling is linked to neurodegenerative diseases such as AD, PD and Niemann‒Pick type C disease. LXR activation offers therapeutic potential by modulating neuroinflammation in CNS disorders. In AD models, LXR agonists such as T0901317 reduce inflammation associated with amyloid-beta (Aβ) deposition and tau tangles by suppressing microglial activation and the expression of inflammatory markers such as iNOS, COX-2, and NF-κB. Similar effects are observed in PD models, where T0901317 decreases iNOS and COX-2 levels. In Niemann–Pick type C disease, LXR activation promotes cholesterol clearance, reduces cerebellar inflammation, and extends lifespan. LXRs also enhance blood‒brain barrier (BBB) integrity by increasing the expression of ABC transporters such as ABCB1, which prevents toxin entry into the brain. Natural LXR agonists (e.g., oxysterols) and RXR activation (e.g., with bexarotene) improve BBB function in coculture models, whereas LXR agonists support tissue regeneration in ischemic stroke by stabilizing the BBB and reducing inflammatory cytokines. Although preclinical results are promising, the clinical translation of LXR agonists is hindered by side effects, including elevated triglycerides and LDL cholesterol.²⁸⁴ Efforts to mitigate these issues include the development of selective LXRβ agonists, regional drug delivery, and the targeting of specific downstream pathways, making LXRs promising therapeutic targets for CNS diseases.

PPARs, particularly PPARγ, play pivotal roles in neuroprotection by regulating neuroinflammation, mitochondrial function, and antioxidant defenses. It is expressed in various CNS cell types, including neurons, astrocytes, oligodendrocytes, and microglia. Dysregulation of PPARs is associated with neurodegenerative diseases characterized by inflammation, such as AD and amyotrophic lateral sclerosis (ALS). PPARγ agonists, including endogenous ligands such as OA and synthetic compounds such as rosiglitazone and pioglitazone, have shown promise in preclinical models because they reduce inflammatory cytokines, increase IL-10 levels, and enhance mitochondrial function in conditions such as stroke, ischemia, and traumatic brain injury. Moreover, PPARγ activation has exhibited potential benefits in neuropsychiatric disorders (e.g., depression, anxiety, and mood disorders) and neurodegenerative diseases, with ongoing clinical trials exploring its applications in AD, PD, MS, and bipolar disorder⁴¹² [NCT00982202, NCT00736996, NCT00265148, NCT00733785, NCT00688207, NCT01280123]. However, mixed clinical outcomes highlight gaps in understanding the mechanisms of PPARγ within the CNS.⁴¹³ Further research aimed at optimizing PPARγ activity may unlock its full therapeutic potential for treating neurodegenerative and neuropsychiatric conditions.

The GR also plays a critical role in neuroinflammation, neuroprotection, and brain homeostasis. Its anti-inflammatory effects in the brain are mediated through interactions with AP-1 and NF-κB, limiting their transcriptional activity.⁴¹⁴ GR also regulates brain-derived neurotrophic factor (BDNF), promotes neurogenesis, neuronal survival, and synaptic plasticity, and contributes to memory, aging, and behavior. Additionally, GR supports BBB integrity by upregulating tight junction proteins and establishing metabolic barriers to xenobiotics.^415,416 GR dysfunction has been implicated in various neuropathologies, including AD, HD and epilepsy. Abnormal GR expression in AD is correlated with hippocampal overexpression, impaired cortisol feedback, and memory deficits.⁴¹⁷ Similarly, GR overexpression in epilepsy has been associated with reactive gliosis and coregulation with PXR in epileptic brain endothelial cells. GR dysregulation also affects HD-related changes, such as increased cortisol secretion and muscular atrophy, alongside reduced GR expression in the hypothalamic and pituitary regions. GR abnormalities also underlie mood disorders such as depression and anxiety, as dysfunction in GR and MR signaling leads to maladaptive stress responses, dendritic retraction, and impaired serotonin activity.^418,419 GR dysregulation in the prefrontal cortex and hippocampus has been linked to anxiety and depression-like behaviors in animal models. Pharmacological modulation of the GR provides therapeutic opportunities. GR agonists, such as dexamethasone and methylprednisolone, are widely used to treat neurological conditions such as gliomas, MS, and traumatic brain injuries. Dexamethasone reduces edema, prevents cerebrovascular leakage, and upregulates tight junction proteins at the BBB.^420,421 Methylprednisolone improves memory and long-term potentiation at low doses but has dose-dependent effects, with high doses alleviating motor deficits in MS models but not cognition.^422,423 GR antagonists, such as mifepristone and relacorilant, have shown efficacy in treating mood disorders, neurodegenerative conditions, and PTSD. Mifepristone restores serotonin signaling and alleviates depression-like behaviors, whereas relacorilant is undergoing phase II and III trials for conditions such as Cushing syndrome and prostate cancer^424,425 [NCT036748142019, NCT036971092019]. These findings underscore the potential of targeting GRs in a range of CNS disorders.

Estrogens and their receptors play critical roles in neuroprotection and the regulation of inflammatory and neurodegenerative processes in the CNS. Owing to their antiapoptotic, antioxidative, and anti-inflammatory properties, estrogens provide early protection against ischemic injury. ERα and ERβ agonists, such as diarylpropionitrile (DPN), have demonstrated neuroprotective effects by mitigating damage in ischemic models, including the caudate nucleus and CA1 region of ovariectomized mice and the striatum of male mice. The membrane receptor GPER-1 also contributes to ischemic protection, with its agonist G1 offering estrogen-like neuroprotection, particularly in males, as suggested by sex-dependent differences in GPER-1 expression. In addition to estrogens, NRs such as Nr4a2 and bile acid receptors play vital roles in alleviating neuroinflammation and neuropathic pain. Nr4a2 helps regulate depressive-like behaviors by preventing structural and functional damage to anterior cingulate cortex (ACC) microglia and excitatory neurons during chronic neuroinflammation.⁴²⁶ Its upregulation through the dopaminergic agonist pramipexole has demonstrated neuroprotective effects on dopaminergic neurons in Parkinson’s disease.⁴²⁷ Similarly, bile acids activate TGR5 and FXR, alleviating mechanical hyperalgesia by reducing glial activation and neuronal sensitization in the spinal dorsal horn. The presence of bile acid synthesis enzymes in spinal astrocytes suggests an endogenous mechanism for decreasing nociceptive neuron transmission and mechanical hypersensitivity, emphasizing bile acid receptors as promising targets for neuropathic pain relief.⁴²⁸ In MS, Th17-driven inflammation is aggravated by RORγt overexpression, which promotes Th17 cell differentiation. By suppressing RORγt, vitamin A has shown therapeutic potential for MS⁴²⁹[NCT01225289]. Collectively, these findings highlight the diverse and pivotal roles of estrogens and nuclear receptors in neuroprotection, inflammation regulation, and the development of innovative therapeutic strategies.

Targeting nuclear receptors in infectious diseases

In recent decades, global spending on infectious diseases has increased significantly, with treatment costs rising faster than those for other diseases. Infectious diseases caused by bacteria, viruses, fungi, and parasites include common conditions such as pneumonia, influenza, gastroenteritis, hepatitis, malaria, and dengue fever, as well as diseases such as HIV/AIDS, tuberculosis, and COVID-19. NRs play a key role in regulating immune responses by modulating genes involved in inflammation, pathogen defense, and immune cell function, thus influencing the outcome of both bacterial and viral infections. Given the increasingly appreciated roles of NRs in the context of infections, targeting NRs may provide a new, largely unexplored area for infectious disease treatment.⁴³⁰

The role of FXR extends to hepatitis C virus (HCV) infection, where it, along with other NRs, such as HNF4α, PPARα, and PXR, reprograms hepatocyte metabolism, influencing glycolysis, ketogenesis, and drug metabolism.⁴³¹ The targeting of FXR or PPARα in HCV infection has shown complex antiviral effects, with receptor inhibition reducing viral replication by reversing HCV-induced metabolic shifts. Furthermore, FXR agonists such as GW4064 have demonstrated potential in alleviating inflammation and preserving intestinal barrier function in experimental colitis, primarily through the modulation of NF-κB signaling.^432,433 In addition, GW4064 has been reported to downregulate scavenger receptors via FXR and indirectly inhibits HCV entry into cells.⁴³⁴

In addition to their roles in viral infections, NRs are essential in bacterial infection. For example, PPARγ signaling is crucial for resolving Staphylococcus aureus (MRSA) infections and improving outcomes in sepsis models by modulating inflammation.⁴³⁵ PPARγ agonists such as pioglitazone have been shown to restore mitochondrial function and reduce oxidative stress in macrophages, highlighting their potential in treating inflammatory and infectious diseases.⁴³⁶ LXRs are involved in macrophage phagocytic responses, particularly during Salmonella Typhimurium infections.⁴³⁷ In a mouse model, LXR agonist treatment ameliorated clinical signs of Salmonella infection in a CD38-dependent manner.⁴³⁸ Recent transcriptomic studies investigating susceptibility to dengue virus in a Cuban cohort of African ancestry revealed increased gene expression of RXR in individuals who were more resistant to infection and suggested a protective role for LXR/RXR against dengue virus.⁴³⁹ In the case of tuberculosis (TB), NRs such as Nur77 and Nor1 are upregulated in response to Mycobacterium tuberculosis infection. Interestingly, the first-line TB drug rifampicin activates PXR, which can impair its effectiveness in infected macrophages, underscoring the complex interactions between NRs and drug efficacy.^440,441 Rifampicin, a first-line anti-tuberculosis (TB) drug, is a potent activator of PXRs, which in turn compromises the effect of rifampicin in M. tuberculosis-infected human macrophages.⁴⁴²

NRs also influence fungal infections, with PPARγ playing a central role in defending against Candida albicans in the gastrointestinal tract. PPARγ ligands reduce fungal colonization through a dectin-1-dependent mechanism. Sepsis models have revealed a critical role for PPARγ in controlling inflammation and improving overall disease outcomes. PPARγ gene expression was downregulated in freshly isolated peripheral blood mononuclear cells (PBMCs) from human sepsis patients as well as in the lungs in a murine sepsis model.⁴⁴³ Treatment with PPARγ agonists improved sepsis outcomes, decreased proinflammatory cytokine levels, increased IL-10 levels, and improved mouse survival.⁴⁴⁴ Other PPAR isoforms have also been linked to decreased severity of sepsis through the downregulation of inflammation. In a cecal ligation and puncture rat sepsis model, treatment with a PPARβ/δ agonist inhibited signal transducer and activator of transcription 3 (STAT3) activation in AMs, reduced the inflammatory response, and prolonged rat survival.^445,446

Parasitic worms are among the global health threats to billions of humans worldwide.^447,448 Although several anthelmintic drugs, including benzimidazole, levamisole/morantel and ivermectin, have been used to treat these parasites, resistance frequently occurs. Therefore, identifying novel therapeutic targets in parasitic diseases is urgently needed. Nuclear receptors, which are well-known therapeutic targets in humans, are currently being investigated in parasitic worms because of their widespread distribution and important functions in controlling transcriptional networks involved in metabolism and development.⁴⁴⁹ Among them, DAF-12 is a nuclear receptor that is necessary for the typical development of nematodes, including the crucial infectious stage. In free-living nematodes such as C. elegans, a lack of DAF-12 ligands (such as dafachronic acid (DA)) under stress conditions promotes entry into the L3d (dauer diapause) state, whereas supplementation with DAF-12 ligands in prosperous environments leads to their exit from L3d and the beginning of reproductive development.⁴⁵⁰ In contrast, in parasitic nematodes such as S. stercoralis, the absence of a DAF-12 ligand leads to an L3d ortholog stage, termed the infectious L3 (iL3) stage, during preinfection, whereas the presence of a DAF-12 ligand in the definitive host can resume reproductive development.⁴⁵¹

The mechanism underlying DAF-12-mediated cell fate decisions is similar to that of other nuclear receptors. Briefly, under favorable conditions or in a host-specific environment, DAF-12 binds with its ligand and is thus activated, which induces the transcription of target genes that facilitate metabolism and development. In contrast, under stress conditions, DAF-12 is inactive without ligand binding, resulting in transcriptional repression and subsequent development arrest and infection. Thus, strategies targeting DAF-12 or its ligands have potential for the treatment of parasitic diseases. In addition to exogenous DA, endogenous Δ7-DA was recently reported as a novel ligand of DAF-12 in S. stercoralis. The abundance of Δ7-DA is regulated by several enzymes, including DAF-36, DHS-16, and DAF-9, which govern the on/off switch of the reproduction, infection and development processes in this parasitic nematode.⁴⁵² In addition to receptors and ligands, other components, such as cofactors, can also be potential targets for the manipulation of the life cycle of parasitic nematodes. For example, DAF-12 interacting protein-1 (DIP-1) was recently identified as a coactivator of DAF-12, which is indispensable for the ligand-activated transcriptional activity of DAF-12 in Strongyloides spp.⁴⁵³ Together, this evidence suggests that the nuclear receptor DAF-12 is a promising target for the treatment of parasitic diseases.

Targeting nuclear receptors in reproductive diseases

Polycystic ovary syndrome (PCOS) is a type of reproductive disease that affects 5–18% of women worldwide who are of reproductive age.⁴⁵⁴ Interestingly, patients with PCOS are frequently associated with metabolic syndrome, such as obesity, dyslipidemia, impaired glucose tolerance or increased fasting insulin,⁴⁵⁵ which is closely linked to an abnormal gut microbiome. A recent study revealed that PCOS can be induced by alterations in the gut microbiome via the activation of the nuclear receptor FXR.⁴⁵⁶ Mechanistically, agmatine produced by B. vulgatus can activate FXR, which in turn prevents L cells from secreting glucagon-like peptide-1 (GLP-1), suggesting that FXR is a possible therapeutic target for the treatment of PCOS.⁴⁵⁶ Moreover, PPAR is a large nuclear receptor superfamily related to energy metabolism and is thus involved in the progression of PCOS. In fact, all three PPAR family members, including PPARα, PPARβ/δ and PPARγ, play critical roles in PCOS via multiple mechanisms, such as the regulation of lipogenesis; glucose homeostasis; and fatty acid oxidation, synthesis and storage.⁴⁵⁷ Given the important function of PPARs in PCOS pathogenesis, modulating the activity of PPARs profoundly affects the development of PCOS. For example, the activation of PPARγ by a polyphenolic compound, sinapic acid, was shown to ameliorate metabolic dysfunction and attenuate PCOS phenotypes in rats.⁴⁵⁸ Another study focusing on the downstream mechanism underlying PPAR-mediated alleviation of PCOS indicated that PPARα can bind to the promoter of FADS2, a ferroptosis-related gene, thus increasing FADS2 transcription. This event inhibits ferroptosis of granulosa cells in a dehydroepiandrosterone (DHEA)-induced PCOS mouse model, suggesting that PPARα alleviates PCOS by protecting granulosa cells from ferroptosis.⁴⁵⁹

Uterine leiomyomas, another name for uterine fibroids, are benign tumors of the fibrotic smooth muscle in the reproductive system. The ovarian steroid hormone estrogen, as well as its receptor ER, are involved in this disease.⁴⁶⁰ In addition, other nuclear receptors, such as the NR4A protein family, may also participate in the progression of uterine fibroids.⁴⁶¹ NR4A restricts the proliferation of primary leiomyoma smooth muscle cells by modeling the extracellular matrix, whereas low expression of NR4A contributes to the pathogenesis of uterine fibroids. Moreover, leuprolide acetate, a GnRH analog used to treat uterine fibroids, can restore the expression of NR4A1 and NR4A3 in clinical samples, suggesting that these two NR4A family members might be additional targets of leuprolide acetate in addition to sex steroid receptors.

Targeting nuclear receptors in renal diseases

While NRs are intimately involved in proper kidney function, they are also implicated in a variety of renal diseases, such as diabetes, acute kidney injury, and other conditions, such as aging. In the last 10 years, our understanding of renal disease etiology and progression has been greatly shaped by knowledge regarding how NRs are dysregulated in these conditions. Importantly, NRs have also become attractive therapeutic targets for the attenuation of renal diseases, and their modulation for this purpose has been the subject of intense investigation. Here, we review the roles of six key renal NRs, including PPAR, ERR, FXR, ER, LXR, and VDR, in health and disease, with an emphasis on recent findings over the last decade.

PPARs are involved in various renal diseases, both acute and chronic. PPARα-null mice treated with streptozotocin (STZ) exhibit accelerated diabetic nephropathy, including worsened albuminuria, glomerular sclerosis, mesangial matrix expansion, collagen deposition, and macrophage infiltration. PPARα agonists have been studied as potential treatments for diabetic nephropathy (DN) in rodents, with evidence supporting their renoprotective effects. Recent research by Chung et al.demonstrated that impairment of PPARα and fatty acid oxidation exacerbates kidney fibrosis during aging, with reduced PPARα expression and lipid accumulation in tubular cells.⁴⁶² PPARα-null mice also exhibit more severe renal aging and fibrosis. Jao et al.reported that ATF6 downregulates PPARα transcription, leading to decreased fatty acid oxidation and increased lipotoxicity in proximal tubule cells, whereas ATF6-deficient mice exhibit increased PPARα expression and decreased lipid accumulation.⁴⁶³ In addition to PPARα, PPARγ has also been studied in DN, with evidence suggesting that its activity is suppressed in this disease. Unlike other PPAR family members, PPARβ/δ is ubiquitously expressed in both cortical and medullary cells. Recent studies have highlighted a potential role for PPARβ/δ in renal homeostasis. For example, Kirkby et al. demonstrated that activation of renal PPARβ/δ by endogenous prostacyclin induces vasodilation and improves blood flow, a process regulated by cyclooxygenase-2 (COX-2).⁴⁶⁴ This COX-2/prostacyclin/PPARβ/δ axis offers new insights into kidney vascular physiology and therapeutic possibilities. Additionally, activation of PPARβ/δ has been shown to improve renal dysfunction in a lupus mouse model by lowering blood pressure, reducing renal hypertrophy, decreasing albuminuria, and preventing renal injury.⁴⁶⁵

Additionally, other nuclear receptors play key roles in kidney health. ERRs are crucial regulators in the kidneys, where they help maintain metabolic balance, regulate monovalent cation homeostasis, and control blood pressure.⁴⁶⁶ The importance of ERRs is further highlighted by the fact that the deletion of ERRγ leads to significant mitochondrial dysfunction and progressive renal failure.⁴⁶⁷ For example, ERRα has been shown to protect against AKI in tubular epithelial cells, particularly in cases of cisplatin-induced AKI in mice.⁴⁶⁸ Compared with those in wild-type mice, in ERRα-null mice subjected to cisplatin treatment, tubular injury, a reduced mitochondrial content, abnormal mitochondrial morphology, and increased oxidative stress were observed. A recent study demonstrated that Nr4a1 was upregulated in the kidneys of mice with unilateral ureteral obstruction (UUO), and its expression was positively correlated with the degree of interstitial kidney injury and the level of fibrotic proteins. Nr4a1 may contribute to renal fibrosis by activating the p38 MAPK pathway, as treatment with the p38 MAPK inhibitor SB203580 successfully inhibited fibrotic protein expression and p38 MAPK phosphorylation.¹⁸⁴ Furthermore, VDR has been shown to exert a renoprotective effect by inhibiting fibrosis. VDR translocates into the nucleus to form the VDR:RXR heterodimer, which inhibits fibrogenic gene expression in HK-2 cells exposed to high glucose and reduces fibrogenic gene expression in proximal renal tubules.⁴⁶⁹ In the aging kidney, the expression of FXR and TGR5 is decreased. However, a dual agonist of FXR and TGR5, INT-767, has been found to reverse age-related kidney disease in mice, demonstrating the therapeutic potential of targeting these receptors in renal aging.⁴⁷⁰ In conclusion, nuclear receptors play vital roles in regulating kidney function and protecting against kidney injury and fibrosis. Understanding their mechanisms and interactions could open new avenues for therapeutic strategies to treat kidney diseases, particularly those related to aging and fibrosis.

Application of emerging technologies in NR research

Several challenges remain in targeting NRs therapeutically due to the complexity of NR signaling, tissue specificity, and the need for precise drug design. However, recent advancements in genomics, proteomics, imaging, and computational modeling have enabled more precise exploration of NR function, regulation, and their involvement in various physiological and pathological processes.

Technologies such as ChIP-chip, ChIP-Seq, and GRO-Seq have enabled unbiased, genome-wide profiling of NR binding sites, revealing new insights into NR mechanisms and their regulatory networks in breast cancer. These genomic methods have highlighted the dynamic interactions between NRs and the chromatin landscape. It is increasingly clear that chromatin, in its varying states of condensation, both regulates and is regulated by NR activity, with NR-chromatin interactions playing a major role in cell type-specific transcriptional regulation.⁴⁷¹ Single-cell RNA sequencing (scRNA-seq) has further advanced our understanding of NR function by enabling gene expression analysis at the single-cell level. This technology is invaluable for investigating tissue-specific NR roles and identifying distinct signaling pathways in various cell populations, which is crucial for understanding their contributions to tissue homeostasis, development, and diseases like cancer and metabolic disorders.⁴⁷² For instance, single-cell transcriptomics revealed the involvement of a previously uncharacterized retinoic acid receptor family member, SmRAR, in reproductive development in Schistosoma mansoni.⁴⁷³ CRISPR-Cas9 technology has revolutionized NR research by allowing precise manipulation of genes in vitro and in vivo. This has facilitated studies of NR roles in diseases such as type 2 diabetes, neurodegeneration, and cancer, and provide reversible and tunable control of NR expression, enabling dynamic investigation of NR function.^474,475

Recent advances in proteomics, particularly mass spectrometry (MS), have enabled the identification and quantification of NR interactomes, providing insights into the molecular mechanisms regulating NR activity. MS also helps identify post-translational modifications like phosphorylation, acetylation, and SUMOylation, which are crucial for NR activation and signaling.³⁰⁶ Cryo-EM has emerged as a powerful tool for visualizing the 3D structure of proteins, including NRs, at near-atomic resolution. This technique has provided key insights into the conformational changes NRs undergo upon ligand binding and co-factor recruitment, essential for drug discovery, as many NRs are targeted by small molecules in diseases like cancer, diabetes, and inflammation.⁴⁷⁶ For example, cryo-EM has elucidated the assembly of the AR:coactivator complex and its role in coactivator assembly and transcriptional regulation.⁷⁰ Additionally, the cryo-EM structure of the NCOA4-FTH1 interface revealed key amino acids crucial for interaction, paving the way for developing ferritinophagy modulators.⁴⁷⁷ These technologies, including cryo-EM and omics, have advanced our understanding of NR activation, NR-chromatin interactions, transcriptional regulation, and non-genomic effects, offering new avenues for therapeutic development.

Artificial intelligence (AI) and machine learning (ML) are increasingly applied in NR research to predict receptor-ligand interactions, identify novel signaling pathways, and design drugs targeting specific NR subtypes. These technologies analyze large datasets to uncover hidden patterns within complex biological systems, enhancing our understanding of NRs in health and disease. For example, chemical language models combined with beam search algorithms have been used for automated molecule design, leading to the development of novel inverse agonists for retinoic acid receptor-related orphan receptors (RORs) with low micromolar to nanomolar potency.⁴⁷⁸ AI and deep docking methodologies have also facilitated the development of VPC-260724, a novel ER-AF2 binder that inhibits ER activity and exhibits antiproliferative effects in ER-positive breast cancer models.⁴⁷⁹ Additionally, AI has been applied to create an adverse outcome pathway (AOP) network for chemical-induced cholestasis, facilitating automated data collection and the identification of key molecular events.⁴⁸⁰ Moreover, Bhimsaria and colleagues identified previously hidden binding sites of human NRs via high-throughput SELEX and a novel MinSeq Find algorithm, revealing new biological roles of NRs and their involvement in disease-associated genetic variations while providing a valuable resource for drug repurposing and precision medicine.⁴⁸¹ With AI and ML, high-throughput screening (HTS) has become more efficient, enabling better prediction of drug candidates and optimization of lead compounds for clinical applications.

In vivo imaging techniques like positron emission tomography (PET) and magnetic resonance imaging (MRI) are increasingly used to study nuclear receptor (NR) activity in living organisms. These methods allow real-time tracking of NR signaling and the effects of ligands or drugs on receptor function in tissues. Live-cell imaging with fluorescent biosensors also reveals dynamic interactions between NRs and their co-regulatory proteins at the cellular level.⁴⁸² This approach offers a quantitative, in vivo equivalent to classic radioligand binding assays.⁴⁸³ In vivo imaging helps identify when and where NRs are active during development, aging, and disease, providing insights into how ligands or receptor modulators influence these processes.⁴⁸⁴ Other technologies, such as organoids, 3D cell cultures, nanotechnology, and systems biology, have also advanced NR research. Notably, PROTACs (proteolysis-targeting chimeras), which degrade target proteins via the 26S proteasome, offer new possibilities for targeting challenging NRs, including orphan receptors or those without enzymatic activity. In cases of drug resistance due to NR mutations (e.g., in hormone-dependent cancers), PROTACs can bypass resistance by degrading the mutated receptors instead of inhibiting their activity.

Emerging technologies are significantly enhancing the field of nuclear receptor research by providing deeper insights into their structure, function, and regulation. The combination of high-resolution imaging, gene editing tools, and advanced computational techniques has opened new avenues for understanding how NRs control physiological processes and contribute to disease. As these technologies continue to evolve, they hold promise for the development of more precise and effective therapeutic strategies targeting nuclear receptors in a variety of disorders.

Concluding remarks

Nuclear receptors are a crucial class of transcription factors that regulate gene expression in response to various ligands, such as hormones, vitamins and metabolic products. They play pivotal roles in processes such as metabolism, immune responses and development, making them key targets for therapeutic intervention in cardiovascular disease, cancer, metabolic disorders and inflammatory conditions. In recent years, targeted therapies aimed at NRs, such as ERs, ARs and VDRs, have shown significant promise in clinical applications, particularly in oncology and metabolic regulation. Newer nuclear receptors, such as LXR and PXR, are being investigated for their therapeutic potential, revealing novel pathways for drug development.

Despite recent advances, several challenges remain in targeting NRs for therapeutic purposes. One key difficulty is the extensive crosstalk between NRs and their signaling pathways, which can lead to synergistic or antagonistic effects, limiting the effectiveness of targeting a single receptor and causing off-target effects. Additionally, NRs exhibit tissue-specific expression and functional outcomes, making designing drugs that selectively modulate receptor activity in specific tissues or cell types challenging. The specificity of ligand-receptor interactions is another hurdle, as NRs can be activated by various small molecules, and ligand promiscuity or cross-reactivity can lead to unwanted side effects. Moreover, long-term NR modulation may result in side effects or even toxicity, such as liver damage or increased cardiovascular risk. Finally, many NRs are regulated by complex feedback mechanisms, complicating predictions about how receptor activity changes in response to treatment. These dynamic regulatory loops require careful consideration to avoid unintended consequences and therapeutic resistance.

Future research will likely focus on understanding the complex interactions of nuclear receptors in various physiological contexts, developing more selective modulators, and exploring novel strategies for more precise and selective targeting of NRs to minimize off-target effects and enhance therapeutic efficacy. Integration of data from transcriptomics, proteomics, and metabolomics will help model NR signaling networks and predict the effects of targeting a specific NR in the context of broader cellular networks. Structure-based drug design employing leverage X-ray crystallography, cryo-EM, and computational modeling will facilitate the identification or design of small molecules that specifically interact with a target NR’s ligand-binding domain, minimizing cross-reactivity. Cutting-edge technologies such as gene editing CRISPR/Cas9 technology and advanced drug delivery systems achieve tissue- or cell-specific targeting of NRs to minimize off-target effects and enhance therapeutic efficacy. Noninvasive techniques to monitor the activity of NRs via specifically binding imaging agents to activated nuclear receptors or linking reporter genes (e.g., luciferase, GFP) to NR-responsive promoters will allow real-time visualization and quantification of receptor activity in preclinical models. In addition, the fact that NRs are key host sensors of microbial signals offers a promising avenue for gut microbiota-targeted drug discovery by leveraging NR-mediated environmental adaptations.^485,486,487 For example, FXR plays a pivotal role in modulating the gut microbiota and is thereby involved in various biological processes, including the metformin response,⁴⁸⁸ bile acid homeostasis,⁴⁸⁹ and core metabolic functions.⁴⁹⁰ Overall, with the advancement of these technologies, new breakthroughs will be made in the discovery of novel drugs that target NRs.