Targeting NR1D1 in organ injury: challenges and prospects

Zhang‑sunetal. Military Medical Research (2023) 10:62 https://doi.org/10.1186/s40779‑023‑00495‑3 REVIEW Open Access © The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecom‑ mons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Targeting NR1D1 inorgan injury: challenges andprospects Zi‑Yin Zhang‑sun1,2†, Xue‑Zeng Xu3†, Germaine Escames4,5†, Wang‑Rui Lei1,2, Lin Zhao3, Ya‑Zhe Zhou1,2, Ye Tian1,2, Ya‑Nan Ren1,2, Darío Acuña‑Castroviejo4,5,6* and Yang Yang1,2* Abstract Nuclear receptor subfamily 1, group D, member 1 (NR1D1, also known as REV‑ERBα) belongs to the nuclear recep‑ tor (NR) family, and is a heme‑binding component of the circadian clock that consolidates circadian oscillators. In addition to repressing the transcription of multiple clock genes associated with circadian rhythms, NR1D1 has a wide range of downstream target genes that are intimately involved in many physiopathological processes, includ‑ ing autophagy, immunity, inflammation, metabolism and aging in multiple organs. This review focuses on the pivotal role of NR1D1 as a key transcription factor in the gene regulatory network, with particular emphasis on the mile‑ stones of the latest discoveries of NR1D1 ligands. NR1D1 is considered as a promising drug target for treating diverse diseases and may contribute to research on innovative biomarkers and therapeutic targets for organ injury‑related diseases. Further research on NR1D1 ligands in prospective human trials may pave the way for their clinical applica‑ tion in many organ injury‑related disorders. Keywords NR1D1, REV‑ERBα, Circadian rhythms, Liver, Heart, Lung, Kidney Background Nuclear receptor subfamily 1, group D, member 1 (NR1D1, also known as REV-ERBα) was first discovered in 1989 and is an approximately 56 kD protein encoded by the ERBA (also known as THRA) oncogene’s reverse DNA strand [1]. In 1994, multiple labs successfully discovered a new orphan receptor with high homology to the rat REV-ERBα gene product (especially in the DNA binding domain and ligand binding domain) referred to as NR1D2 or REV-ERBβ [2–4]. NR1D1 and NR1D2 are key transcriptional repressors of regulatory networks with a circadian expression pattern and are widely expressed in many tissues [1, 5]. NR1D1 can bind to the promoters of many genes to mediate transcriptional repression of autophagy-associated proteins, inflammasome genes, T-cell differentiation cofactors, lipid-metabolizing enzymes, and other important players in the physiological and pathological processes of various organs. Molecularly, NR1D1 inhibits enhancer-derived RNA (eRNA) transcription and †Zi‑Yin Zhang‑sun, Xue‑Zeng Xu and Germaine Escames have contributed equally to this work. *Correspondence: Darío Acuña‑Castroviejo [email protected] Yang Yang [email protected] 1 Department of Cardiology, Northwest University First Hospital, Faculty of Life Sciences and Medicine, Northwest University, Xi’an 710069, China 2 Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine , Northwest University, Xi’an 710069, China 3 Department of Cardiovascular Surgery, Xijing Hospital, Air Force Medical University, Xi’an 710032, China 4 Biomedical Research Center, Department of Physiology, Faculty of Medicine, Institute of Biotechnology, Technological Park of Health Sciences, University of Granada, 18016 Granada, Spain 5 Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable (CIBERFES), Ibs.Granada, San Cecilio University Hospital, 18016 Granada, Spain 6 UGC of Clinical Laboratories, San Cecilio Clinical University Hospital, 18016 Granada, Spain Page 2 of 20 Zhang‑sunetal. Military Medical Research (2023) 10:62 reduces target gene mRNA expression by recruiting the nuclear receptor corepressor (NCOR)-histone deacetylase 3 (HDAC3) complex to the enhancers or promoters of target genes [6]. This review examined the milestones of the latest discoveries regarding NR1D1 in many physiopathological processes in multiple organs, including the liver [7], heart [8], lung [9], and kidney [10]. According to NR1D1 involvement in autophagy, immunity, inflammation, aging and metabolism, researchers have identified and designed diverse natural and synthetic NR1D1 ligands that are capable of stimulating or blocking inherent signal transduction. These agonists and antagonists are typically small synthetic compounds, and some have progressed to preclinical trials. Therefore, NR1D1 is considered a prospective pharmacological target of numerous diseases, and it may contribute to providing novel insights into therapeutic strategies for organ injury. The structure andaction forms ofNR1D1 NR1D1 and NR1D2 belong to the nuclear receptor (NR) subfamily, but their structures are slightly different from the classical nuclear receptors [11, 12]. There are four primary domains that distinguish typical nuclear hormone receptors in NRs: a variable amino N-terminal activation function 1 (AF-1), a highly conserved DNAbinding domain (DBD) consisting of two zinc finger motifs, a hinge region linking the DBD to the carboxyterminal ligand-binding domain (LBD), and a conserved LBD mediating coactivator interactions through the absence or presence of regulatory AF-2 region [13, 14]. DBD facilitates the precise recruitment of NRs monomers, homodimers, and heterodimers to their DNA response element after targeting the receptor to certain DNA sequences known as hormone response elements. Along with the hinge region and the LBD, DBD also participates in the dimerization of NRs with their partner. Additionally, LBD promotes ligand-dependent interactions with transcriptional co-activators or co-repressors through conformational changes. After binding ligand, LBD allows the receptor to switch into a transcriptionally active state. It also has the crucial feature of hormone recognition and controls the selectivity and specificity of the physiologic response [15]. These half-sites are arranged either as a palindromic sequence or a direct repeat. Carboxyl terminal helix AF-2 segment identifies coactivators necessary for transcriptional activation, andis crucial for ligand-dependent recruitment of coactivators and NRs transcriptional activation. Notably, NR1D1 and NR1D2 lack AF-2 region, and are therefore considered to be incapable of activating transcription. Hence, they are indeed constitutive transcriptional inhibitors that control the transcription of genetic information by binding to specific DNAsequence. NR1D1 has two main action forms to suppress transcription, that is monomer and homodimer (Fig. 1). NR1D1 generally acts as a monomer to bind to the thyroid/retinoic acid receptor half-site AGG TCA , which is flanked 5’ by an A/T-rich sequence. This half-site is located in target genes promoter, and is referred to ROR/ REV-ERB-response element (RORE/RevRE) [2, 16]. In 1998, Zhao etal. [17] revealed the interaction between the A/T-rich 5’ extension of the AGG TCA half-site and the C-terminal extension of DBD enhances their high affinity. In addition, NR1D1 acts as a homodimer to bind to tandem repeat sequences of Rev monomer sites spaced by 2bp (“DR2”), while the A/T-rich sequences flanks on the 5’ half-site of DR2. Such that the sequence is called RevDR2 (Fig. 2). In comparison to NR1D1 monomer Fig. 1 Four transcriptional inhibitory modes of NR1D1. a NR1D1 can bind to a single RORE as a monomer but cannot recruit the co‑repressor NCOR1‑HDAC3; b NR1D1 can bind to a RORE as a homodimer and recruit the co‑repressor NCOR1‑HDAC3; c Two NR1D1 monomers can also recruit NCOR1‑HDAC3 to repress transcription when they bind independently to two ROREs; d NR1D1 can also coordinate transcriptional repression together with TFs. HDAC3 histone deacetylase 3, NCOR nuclear receptor corepressor, NR1D1 nuclear receptor subfamily 1, group D, member 1, RORE ROR response element, TF transcription factor Page 3 of 20 Zhang‑sunetal. Military Medical Research (2023) 10:62 binding to the Rev monomer site, this interaction is 5 to 10 times more stable [2, 16]. In some circumstances, two NR1D1 molecules can individually link to two nearby ROREs and recruit co-repressors (NCOR1-HDAC3) to repress gene transcription [16]. The role ofNR1D1 inthebiological clock Since the eighteenth century, research on the mechanism of the circadian clock has been underway. Konopka etal. [18] originally used Drosophila as a model system to investigate biological clock genes, and they discovered clock genes in Drosophila mutants. There is a central “master” clock located in the suprachiasmatic nucleus (SCN) of the mammalian hypothalamus that integrates information from light and synchronizes our physiology to the day/night cycle (Fig.3). In fact, many rhythmic activities are mediated by peripheral oscillators in various tissues and cells, and the central clock in the brain coordinates various rhythmic activities in different tissues [19]. Circadian rhythms are the biological clock-generated 24-h behavioral and physiological rhythms found in many species. In mammals, the biological clock is housed in the SCN. On the one hand, the master pacemaker in the SCN receives a principal entraining signal from the environmental light-dark cycle [20, 21]. On the other hand, it maintains the synchronized rhythms of behavior and physiology in cells and tissues by aligning circadian gene oscillations within extra-SCN neurons and peripheral tissues [19, 22, 23]. Nearly all physiology is regulated by the circadian clock, and disturbances have serious detrimental effects on health [24]. The most important mechanism by which circadian rhythms can be maintained on an approximately 24h cycle is the transcription-translation feedback loop (TTFL) of the biological clock. The internal clock consists of many genes and the proteins that they encode, such as brain and muscle ARNT-like 1 (BMAL1), circadian locomotor output cycles kaput (CLOCK), Period (PER), Cryptochrome (CRY), REVERBα and RAR-related orphan receptor α (RORα), all of which affect different physiological processes in the body via TTFLs. The central molecular circadian oscillator loop consists of the BMAL1/CLOCK heterodimer. CLOCK and BMAL1 interact with the E-box in the promoter regions of Per and Cry in mammals, triggering the transcription of these two genes in the nucleus [25]. These genes are subsequently translated into the target proteins PER1-3 and CRY1-2 in the cytoplasm. Conversely, PER1-3 and CRY1-2 can suppress the transcription of CLOCK and BMAL1, forming a negative feedback loop [26]. Importantly, numerous clock-controlled genes(CCGs) are located downstream of these four components and coordinate the oscillation of multiple physiological functions. The nuclear receptors REV-ERBs and RORs form the second feedback loop. Daily oscillations in Rev-erbs transcription are caused by CLOCK/BMAL binding to the E-box of the promoter [27]. REV-ERBα is a major repressor of Bmal1 transcription, and RORα is a transcriptional activator. The two factors compete to bind the RORE/RevRE site located in the Bmal1 promoter and then regulate the transcription of Bmal1 and RORE/RevRE-controlled genes (RCGs) [27]. Therefore, REV-ERBα and RORα engage in the regulatory circuit and are essential for the appropriate timing of the core clock mechanism and the occupancy of the Bmal1 promoter. In the third loop, PER2 (an output geneproduct from the main loop) and D-box controlled genes (DCGs) Fig. 2 NR1D1 action structure domain. Two NR1D1 respectively bind to the AGG TCA half‑site of the DNA sequence through DBD domain. CTE C‑terminal, DBD DNA‑binding domain Page 4 of 20 Zhang‑sunetal. Military Medical Research (2023) 10:62 are influenced by DBP and E4 promoter binding protein 4 (E4BP4) [28]. Although the patterns differ, all clock genes are expressed cyclically. Notably, numerous clock-controlled genes (CCGs), such as Bmal1 and E4bp4, are under the control of NR1D1 and exhibit distinctive patterns in contrast to NR1D1 [25]. Accordingly, NR1D1, which is a transcription repressor, is one of the crucial players that controls negative feedback mechanisms of the biological clock. NR1D1 inautophagy, immunity, inflammation, metabolism andaging In addition to the regulation in circadian rhythms, NR1D1 also performs as a transcriptional repressor in numerous crucial biological processes, including autophagy, immunity, inflammation, metabolism, and aging. NR1D1 inautophagy Autophagyisa highly conserved intracellular degradation system, and is essential for maintaining cellular homeostasis during stress conditions. NR1D1 participates in autophagy in various organelles, including mitochondria and lysosomes. Adipocytes, macrophages, and granulosa cells (GCs) are important cell types associated with NR1D1-regulated autophagy. NR1D1 deficiency reduces mitochondrial synthesis and accelerates the clearance of mitochondria in skeletal muscle by increasing mitochondrial autophagy, decreasing mitochondrial quantity, and impairing respiratory chain function [29]. Unc-51like kinase 1 (ULK1) is a beneficial partner of NR1D1 in Fig. 3 Transcription‑translation feedback network of the central circadian oscillator in mammals. Input of light signal and diet signal to the SCN of the mammalian hypothalamus produces transcriptional activation of Per, which regulates the PER concentration and subsequently affects biological clock phasing. Mechanically, the core clock proteins BMAL1 and CLOCK form BMAL1‑CLOCK heterodimer, translocating into the nucleus and binding to the E‑box containing DNA region upstream of the promoters of downstream genes. Then, the transcription of downstream genes is activated, including Per, Cry, Rev-erbs and DBPs and other CCGs. The products of these genes partially translocate back to the nucleus, which feedback regulates the transcription of other clock genes. For example, PER and CRY form a complex that is phosphorylated by CKIε/δ, and subsequently returns to the nucleus to inhibit the activation of the BMAL1/CLOCK complex; REV‑ERBs and RORs exert negative and positive regulation of Bmal1 transcription by competitively binding to the RORE in the promoter, respectively; DBP translocates to the nucleus and activates the transcription of Rors, Per, and CCGs. Subsequently, the activation of CCGs regulates the output of multiple circadian behaviors, such as biological rhythms and several physiological processes. BMAL1 brain and muscle ARNT‑like 1, CCGs clock control genes, CLOCK circadian locomotor output cycles kaput, CRY cryptochrome, CKIε/δ cyclin‑dependent kinase inhibitor protein ε/δ, DBP D site binding protein, PER period, ROR RAR‑related orphan receptor, E4bp4 E4 promoter binding protein 4, SCN suprachiasmatic nucleus Page 5 of 20 Zhang‑sunetal. Military Medical Research (2023) 10:62 mitochondrial autophagy, as determined by Ferder etal. [30]. NR1D1 upregulates ULK1 (essential for autophagy onset) expression in adipocytes by interacting with the Ulk1 promoter [30]. In addition to ULK1, NR1D1 also regulates autophagy rhythms via other autophagyassociated genes. Nr1d1 knockdown increases autophagy protein 5 (ATG5) expression in mouse GCs. In contrast, rapamycin-induced autophagy and ATG5 expression are partly inhibited by treatment with SR9009 (NR1D1 agonist), indicating that NR1D1 maintains autophagy homeostasis in mouse GCs [31]. Wu etal. [32] discovered that in GSK4112 (an NR1D1 agonist)-treated tilapia, the majority of autophagy-related genes were decreased and exhibited altered rhythmicity involving Atg4c, Bnip3la, Lc3a, Lc3b, and Lc3c mRNA levels. Moreover, Chandra etal. [33] demonstrated that NR1D1 activation by GSK4112 stimulated an increase in autophagic flux and lysosome formation in human macrophages via transcription factor EB (TFEB)-associated pathways. Molecularly, TFEB and transcription factor E3 (TFE3), which are the main drivers of autophagy and lysosomal biogenesis, directly bind to the Nr1d1 promoter without the formation of the BMAL1-CLOCK complex to regulate Nr1d1 expression. This indicates that TFEB and TFE3 collaborate with the fundamental components of the clock mechanism. Endogenous Nr1d1 knockdown triggers the overexpression of TFEB and TFE3, which leads to enhanced autophagic flux. Thus, the rival but interconnected forces controlled by NR1D1, TFEB and TFE3 determine the duration of autophagy activation to some extent [34]. NR1D1 ininflammation NR1D1 plays essential roles in inflammation mediated by multiple cell types, among which macrophages are the primary effector cells of inflammation associated with NR1D1 and the circadian clock. NR1D1 modulates inflammation through various mechanisms, such as reducing the secretion of inflammatory cytokines, regulating gene transcriptionandthe NLRP3 inflammasome pathway, and inhibiting macrophage polarization. Gibbs etal. [35] demonstrated that administration of a synthetic NR1D1 ligand effectively modulated the generation and secretion of IL-6 (a proinflammatory cytokine), and decreased the mRNA expression of Tlr4, Cxcl11, Ccl2, Cxcl6, and Il19. GSK4112 or SR9011(the agonists of NR1D1) dose-dependently suppresses the expression of proinflammatory cytokines [such as interleukin-6 (IL6) and tumor necrosis factor-α (TNF-α)] through the nuclear factor kappa-B (NF-κB) pathway, thereby mitigating microglia-mediated neuroinflammation [36]. Pharmacological activation of NR1D1 by SR9009 attenuates the release of several inflammatory cytokines, including IL-1β, IL-6, IL-8, IL-18 and TNF-α, and suppresses Tolllike receptor 4 (TLR4)-regulated NF-κB activation and the inflammatory response in human endometrial stroma cells (hESCs) [37]. Lipopolysaccharides (LPS) is not only a typical proinflammatory mediator, but also promotes M1-like macrophage polarization [38]. LPS inhibits the expression of NR1D1 in macrophages, whereas SR9009 inhibits M1 polarization in differentiated macrophages induced by LPS via the phosphatidylinositol-3-kinase (PI3K) signaling pathway [38]. Likewise, NR1D1 activation reduces matrix metalloproteinase (MMP) and chondrocyte levels, and inhibits the polarization of M1 macrophages from fibroblast-like synoviocytes (FLSs) [39–41]. In particular, NR1D1 inhibits the transcription of eRNAs, which are short RNA strands generated from an enhancer site that support enhancer versatility, and inactivates the transcription of adjacent genes (including Mmp9 and the chemokine receptor Cx3cr1) in macrophages [6]. Additionally, Wang et al. [42] found that the NLRP3 inflammasome, which is a key platform that stimulates the maturation and production of proinflammatory cytokines, is inactivated by NR1D1 mainly during the priming stage in mouse primary macrophages. Mechanistically, NR1D1 not only directly inhibits Nlrp3 transcription by binding to its promoter, but also indirectly suppresses NLRP3 by blocking the NF-κB pathway. NR1D1 inimmunity NR1D1 functions as a clock output node, connecting cellular circadian clocks with innate immune responses. Innate immunity is accompanied by inflammation, and inflammatory cells secrete inflammation-related cytokines to participate in immune defense in response to foreign pathogens. After being activated, naïve CD4 T cells develop into various T helper (Th) subtypes that generate lineage-specific cytokines. Effector Th subtypes play essential roles in coordinating immune responses to a range of infections and are involved in the pathogenesis of numerous inflammatory illnesses, including autoimmunity, allergy, and asthma, by producing unique sets of cytokines. The principal transcription factor for Th2 cell differentiation is GATA binding protein 3 (GATA3) [43]. NR1D1 directly binds to the Gata3 promoter and interacts with its cellular companion NCOR-HDAC3 to create a durable repression complex, ultimately restricting Th2 cell production [44]. Retinoic acid-related orphan receptor γt (RORγt) is the master transcription factor for the differentiation of interleukin-17-producing CD4 Th17 cells, which are a class of proinflammatory immune cells that protect mucosal surfaces from bacterial and fungal infections [45, 46]. Yu etal. [47] found that E4BP4 Page 6 of 20 Zhang‑sunetal. Military Medical Research (2023) 10:62 inhibited Rorγt transcription by binding to GTT ACT TAA sequenceon the Rorγt promoter, thereby restricting Th17 cell differentiation. Moreover, NR1D1 is associated with the development and biological clock of Th17 cells by binding to the consensus sequence of the E4BP4 locus and directly repressing E4BP4 transcription. This guarantees that Th17 lineage specification preferentially emerges at a specific stage of the circadian cycle instead of at random times during the day-night cycle, thus preventing the excessive accumulation of Th17 cells. Of note, Zhuang et al. [48] highlighted an innovative role for NR1D1 in limiting RNA virus replication, which opens up promising therapeutic possibilities for treating infectious disorders. The Flaviviridae family of positive-strand RNA viruses is the major pathogen in several diseases with high morbidity and mortality and includes the human pathogens hepatitis C virus (HCV), dengue virus (DENV) and Zika virus (ZIKV). Pharmacological activation of NR1D1 prevents HCV entry and restricts the replication of HCV, DENV and ZIKV RNA by disrupting fatty acid metabolism and stearoyl-CoAdesaturase (SCD) activity [48]. However, a recent study revealed that NR1D1 could also impair the host defense response. In gastric epithelial cells (GECs) infected with Helicobacter pylori, NR1D1 not only directly suppresses the expression of antibacterial proteins (including Reg3b and β-defensin-1)to impaire bactericidal effects against Helicobacter pylori, but also directly limits production of the chemokine (C-C motif) ligand 21 (CCL21) as a consequence of the diminished bacterial clearance capacity of the Helicobacter pylori-specific Th1 cell response. NR1D1 inmetabolism Numerous studies have shown that NR1D1 is a crucial and novel physiological regulator of lipid metabolism, glucose metabolism and insulin resistance. Raspé etal. [49] found that apolipoprotein (apo)C-III expression was positively correlated with the risk of cardiovascular disease development and identified NR1D1 as a biological repressor of apoC-III gene transcription. The expression of rat apo A-I` [a crucial component of high-density lipoproteins (HDL)] and apoC-III (an apolipoprotein implicated in the metabolism of triglyceriderich lipoproteins) are suppressed by NR1D1 through binding to the AGG TCA half-site located in the apoA-I or apoC-III promoter [49, 50]. Notably, NR1D1 inhibits transcription of both apolipoproteins, whereas RORα activates apoA-I and apoC-III transcription after binding to the same response element, demonstrating the cross-talk between these nuclear receptors and common target genes. In addition, NR1D1 participates in the transcriptional regulation of various lipid metabolism-related enzymes. Elovl3, a gene that codes for an extremely long-chain fatty acid elongase, is suppressed by NR1D1 [51]. NR1D1 also modulates peroxisome proliferators-activated receptor α (PPARα)/retinoid X receptor α (RXRα)-dependent transactivation in a response element-specific manner and reduces the expression of enoyl CoA hydratase/3-hydroxyacyl CoA dehydrogenase, which participates in the peroxisomal β-oxidation pathway [52]. Cytochrome P450 (CYP450), which are a superfamily of enzymes containing heme as a cofactor, play important roles in the clearance of many substances (such as oxidized steroids, fatty acids, and xenobiotics) and the synthesis and catabolism of hormones in mammals. An alternative pathway for fatty acid metabolism is lipid ω-hydroxylation of mediumand long-chain fatty acids metabolized by the cytochrome CYP4A family. According to Yang etal. [53], NR1D1 inhibits the transcription of Cyp4a10 and Cyp4a14, and NR1D1 deficiency significantly increases the expression levels of both factors, which promotes lipid accumulation and oxidative stress. Additionally, NR1D1 enhances serum cholesterol levels and hepatic cholesterol accumulation by inhibiting the production of cholesterol 7α-hydroxylase expression (CYP7A1), an enzyme that converts cholesterol into bile acids. Various glucose metabolic pathways, including gluconeogenesis, the pentose phosphate pathway (PPP), glycolysis, and the tricarboxylic acid (TCA) cycle, are also directly and indirectly influenced by NR1D1. NR1D1 was identified as a putative apoA-IV-binding protein by Li etal. [54]. In 2013, researchers found that apoA-IV could bind to and activate NR1D1 to suppress the expression of phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase) in hepatocytes and decrease hepatic glucose production [54]. In 2015, they showed that apoA-IV and nuclear receptor subfamily 4, group A, member 1 (NR4A1) interacts at the RORα response element in the human G6Pase promoter, and both factors could mediate transcriptional repression of the G6Pase and Pepck genes by connecting with NR1D1 to reduce hepatic glucose output and lower blood glucose [55]. Increased NR4A1 expression induced by apoAIV in hepatocytes further inhibited gluconeogenesis, and NR1D1 and NR4A1 could serve similar or complementary roles in the apoA-IV-mediated regulation of gluconeogenesis. During gluconeogenesis, phosphoenolpyruvate carboxykinase 1 (PCK1) is the rate-limiting enzyme. SR9009 treatment of human HepG2 hepatoma cells significantly lowers PCK1 expression by directly binding to the − 325 to − 320bp region (a RevRE site) in Page 7 of 20 Zhang‑sunetal. Military Medical Research (2023) 10:62 the gene promoter to lower plasma glucose [56]. Similarly, the genes expression of hexokinase II, transketolase, and ribose-5-phosphate isomerase are elevated by NR1D1 deletion, thereby affecting glucose metabolism. Finally, NR1D1 is also involved in insulin resistance. Fibroblast growth factor-21 (FGF21) is a hepatic hormone that potently improves peripheral insulin sensitivity and lipid metabolism. NR1D1 binds to the RORE sites of FGF21 and negatively regulates FGF21 expression, thereby inhibiting EGF21 to improve insulin sensitivity [57]. NR1D1 inaging Aging is a key factor in the development of multiple diseases, and it has been reported that the circadian rhythms of many organs/cells are disrupted with age. Recently, many studies have also focused on the potential of NR1D1 as a therapeutic target for aging-related diseases. Retinal epithelial function declines with age, mainly due to the accumulation of oxidative stress. Huang etal. [58] performed pharmacological activation of NR1D1 and found that the monomer could directly bind to RORE/ RevRE (in a non-NCOR1/HDAC3-dependent manner) to modulate the transcription of nuclear factor erythroid 2-related factor 2 (NRF2) and its downstream antioxidant enzymes superoxide dismutase 1 (SOD1) and catalase, thereby attenuating retinal pigment epithelial and retinal damage and ameliorating oxidative stress in mice with age-related macular degeneration (AMD). Notably, NR1D1 levels were different in young and aged heartderived Sca-1+ CD31− cells, which are resident cardiac progenitor cells that can differentiate into cardiomyocytes. In young heart-derived Sca-1 CD31 cells, higher levels of NR1D1 inhibit cell proliferation and promote apoptosis. Conversely, downregulation of NR1D1 in the latter promotes cell proliferation and inhibits apoptosis by blocking the G0/G1 phase of the cell cycle. Furthermore, Pu etal. [59] demonstrated thatNR1D1 inhibits the expression of NR3A4 by binding to its promoter, which allows NR3A4 to further interact with the promoter of serine protease inhibitory factor 3 (Serpina3, a gene associated with apoptosis inhibition), ultimately attenuating the transcriptional repression of Serpina3 and exerting an antiapoptotic effect. Interestingly, NR1D1 is sex-differentiated during liver aging, and its expression is higher in the aging livers of male rats than in those of female rats, while the opposite is true for the expression of many its downstream circadian genes [60]. Physiological andpathological roles ofNR1D1 invarious organs NR1D1 is widely expressed in numerous tissues or organs and exerts many biological effects on heart, liver, lung, kidney and many other organ injuries (Table1; Fig.4). NR1D1 intheheart The heart provides sufficient blood flow, oxygen, and various nutrients to organs and tissues and removes the end products of metabolism to maintain normal cellular metabolism and function. Myocardial infarction (MI) is the blockage of the coronary arteries of the heart, resulting in massive ischemic necrosis in myocardial cells and serious complications. Reperfusion may trigger cardiac inflammation, infarct expansion, and heart failure (HF) after MI. Reitz etal. [61] identified cardiac fibroblasts as the target cells of SR9009 and showed that SR9009 inhibited the production of the NLRP3 inflammasome and the recruitment of immune cells to the heart, thereby healing vulnerable infarcts, improving adverse cardiac remodeling and facilitating long-term cardiac repair and reperfusion in MI mice [61, 62]. Furthermore, Zhang etal. [8] demonstrated that SR9009 enhanced several metabolic molecules and pathways that were downregulated in HF mice, especially pyruvate dehydrogenase kinase 4 (PDK4), which is an important regulator of fatty acid oxidation. The researchers observed that PDK4 expression increased when NR1D1 was linked to the Pdk4 enhancer, suggesting that PDK4 was one of the principal targets of NR1D1 during cardiac metabolic remodeling [8]. NR1D1 ameliorates thrombosis-based cardiovascular disorders associated with day/night cycles in animal models. The major cause of acute cardiovascular events is thrombosis, which can result from vulnerable plaque rupture. NR1D1 plays a protective role in the vasculature by modulating inflammation and oxidative stress to stabilize fragile plaques. According to Wu etal. [63], NR1D1 deficiency increased macrophage infiltration, inflammation, and oxidative stress, which enhanced the fragility of the plaque and could cause it to spontaneously rupture with intraluminal thrombosis. In mouse bone marrowderived macrophages (BMDMs), NR1D1 activation reduces macrophage pyroptosis via the NF-κB/NLRP3 inflammasome pathway, and decreases plaque susceptibility and rupture [63]. Notably, NR1D1 is expressed in platelets and functions as a positive thrombosis regulator, potentiating platelet activation and aggregation via oligophrenin-1-mediated OPHN-1/RhoA/ERM signaling [64]. Moreover, NR1D1 decreases ferric chloride-induced carotid artery occlusive thrombosis and protects against Page 8 of 20 Zhang‑sunetal. Military Medical Research (2023) 10:62 Table 1 Pathophysiological effects of NR1D1 in different organs AAI aristolochic acid I, AKI acute kidney injury, Atg5 Autophagy protein 5, BMDMs bone marrow‑derived macrophages, ERM ezrin/radixin/moesin, HF heart failure, HO1 heme oxygenase, LAD left anterior descending coronary artery, LPS lipopolysaccharide, MI myocardial infarction, mPGES-2 microsomal prostaglandin E synthase‑2, NLRP3 NOD‑like receptor thermal protein domain associated protein 3, NF-κB nuclear factor kappa‑B, NR1D1 nuclear receptor subfamily 1, group D, member 1, OPHN-1 oligophrenin 1, PDK4 pyruvate dehydrogenase kinase 4, PKA protein kinase A, RhoA Ras homolog gene family, member A, SCLC small‑cell lung cancer, Slc7a11 solute carrier family 7 member 11, SHP small heterodimer partner Organ Disease Models/Materials Effects References Heart MI Nr1d1−/− mice SR9009 lowers NLRP3 inflammasome level in myocardial fibroblasts and immu‑ nocyte recruitment to heal the vulnerable infarct [61] HF MI mouse model induced by the permanent ligation of the left LAD SR9009 reduces adverse cardiac remodeling through alleviating inflammation [62] Pressure overload mouse model caused by the constriction of aortic arch between the right and the left carotid arteries NR1D1 represses the transcription of numerous genes involved in cardiomyo‑ cyte hypertrophy in vitro. SR9009 enhances fatty acid oxidation via increasing PDK4 expression, and blocks the cellular remodeling induced by pressure overload in vivo [8] Thrombus BMDMs and NR1D1−/− mouse model of rupture‑prone vulnerable plaques induced by partly ligating the left renal artery and the left internal and the exter‑ nal carotid arteries NR1D1 activation inhibits macrophage pyroptosis in a NF‑κB/NLRP3 inflamma‑ some‑dependent manner in BMDMs, and mitigates macrophage infiltration, inflammation, and oxidative stress to stabilize rupture‑prone vulnerable plaques [63] Acute MI mouse model induced by ligation of LAD NR1D1 potentiate platelet aggregation and activation via the OPHN‑1/RhoA/ ERM signaling mediated by oligophrenin‑1 [64] Liver FH Naïve peritoneal macrophages and primary BMDMs from Nr1d1−/− mice and Nr1d1+/+ littermates NR1D1 inhibits the NLRP3 inflammasome signaling, reduces inflammatory cytokines and CCL2‑mediated hepatic infiltration of innate immune cells [7] ALD Shp−/− mice fed modified ethanol‑binge NR1D1 reduces lipid accumulation and oxidative stress via SHP / REV‑ERBα / CYP4A axis [53] NAFLD Whole‑body or hepatocyte‑specific mPGES‑2‑deficient mice fed a high‑fat or methionine‑choline‑deficient diet NR1D1 decreases CYP4A14 and increases acyl‑CoA thioesterase 4 levels to potentiate lipid metabolism [65] NAFLD Nr1d1 Δex3/4 mice fed high fat diet The deletion of exons 3 and 4 in the mouse Nr1d1 gene worsens HFD‑induced hepatic steatosis [66] Apoptotic liver injury Acute hepatic damage mouse model induced by Fas GSK4112 decreases the level of Fas and the activity of caspase‑3 and caspase‑8, suppressing hepatocyte apoptosis [67] Lung ALI ALI mouse model made by intraperitoneal injection of LPS NR1D1 reduces lung vascular permeability and inflammatory cells infiltration via inhibiting the NF‑κB /NLRP3 pathway [9] Cigarette smoke ‑induced lung inflam‑ mation Lung inflammation mouse model induced by cigarette smoke GSK4112 decreases the release of inflammatory cytokines [68] Lung adenocarcinoma Lung adenocarcinoma cell line A549 Downregulation of NR1D1 stimulates the invasion and promotes the prolifera‑ tion of lung adenocarcinoma cell line A549 [69] Lung adenocarcinoma Nontumorigenic mouse hepatocyte cell line AML12 NR1D1 is targeted and destabilized by PKA, resulting in increased glucose production [70] SCLC Chemosensitive SCLC cells (H69 and H446) and the corresponding chemoresist‑ ant SCLC cells (H69AR and H446DDP) SR9009 directly represses the autophagy gene Atg5 to suppress SCLC cell autophagy activity [71] Kidney AKI NR1D1−/− mice and AKI mouse model induced by folic acid and AAI NR1D1 represses the transcription of Slc7a11 and HO1 to promote ferroptosis, and loss of NR1D1 reduces the sensitivity of mice to AKI and eliminates the cir‑ cadian time dependency in disease severity [72, 73] Colon Colitis BMDMs and colitis mouse model induced by dextran sulfate sodium salt NR1D1 plays an anti‑inflammatory role and affects the circadian rhythm of colitis through direct activation by berberine [74] Page 9 of 20 Zhang‑sunetal. Military Medical Research (2023) 10:62 microvascular microthrombi blockade and infarct growth in an acute MI model [64]. Taken together, these studies may deepen our comprehension of NR1D1 in many physiological processes and emphasize the importance of circadian clock mechanisms in platelet physiology and MI, paving the way for further studies on NR1D1-targeted therapeutics. NR1D1 intheliver The liver is referred to as the center of substance metabolism, and is crucial to all bodily functions, including digestion, absorption, excretion, biotransformation, and metabolism. Acute liver injury caused by hemorrhagic necrosis, extensive hepatocyte apoptosis and inflammation is known as fulminant hepatitis (FH). LPS/D-galactosamine (GalN)-induced FH mice with NR1D1 activation exhibits reduced CCL2-mediated hepatic infiltration of innate immune cells and inhibits activation of the NLRP3 inflammasome pathway, and these mice have higher survival rates [7]. On the one hand, SR9009 inhibits the recruitment of infiltrating monocytes, macrophages and neutrophils by preventing the increase in hepatic F4/80 and CCL2 expression. On the other hand, treatment with SR9009 lowers the expression of NLRP3, IL-1β and IL-18 in macrophages and subsequently attenuates NLRP3-driven inflammation [7]. One of the liver’s early detoxifying reactions to excessive alcohol consumption is hepatocyte lipid production, which ultimately results in alcoholic liver disease (ALD). Hepatocytes undergo steatosis when lipid ω-hydroxylation is inhibited. NR1D1 is a potential circadian transcriptional repressor of murine Cyp4a10 and Cyp4a14, which are extensively expressed in the liver and are similar to human CYP4A22 and CYP4A11 respectively [53]. Mechanistically, the DNA-binding structural domain of NR1D1 binds to the Cyp4a10 and Cyp4a14 promoters in the mouse liver, inhibiting their activation Fig. 4 Regulation of multiple physiological processes by NR1D1 in various organs. An overview of the effects of NR1D1 on autophagy, inflammation, metabolism, oxidative stress, apoptosis and other physiological processes in various organs. NR1D1 nuclear receptor subfamily 1, group D, member 1 Page 16 of 20 Zhang‑sunetal. Military Medical Research (2023) 10:62 (NREM) sleep duration in male mice [126]. In addition, even cells originating from the same individual produce different rhythms over generations of inheritance. Kim etal. [127] demonstrated that skin fibroblasts from diversity outbred (DO) mice underwent increased variations in circadian phenotypes over the course of inheritance. However, the mechanism by which NR1D1 regulates circadian rhythms in different species has not yet been clearly explored. More research is still needed to determine the specific regulatory role of NR1D1 in other species. Conclusions This review comprehensively summarizes the roles of NR1D1 in several vital organs, such as the heart, liver, lung, and kidney, by regulating key physiopathological processes, including autophagy, immunity, inflammation, metabolism, and aging. Given the pivotal biological functions of NR1D1, it is imperative to explore novel ligands targeting NR1D1 for the development of chemical probes and targeted drugs. Many NR1D1 ligands have been shown to improve inflammation, inhibit apoptosis, regulate metabolism and exert other biological effects in preclinical studies. However, there has been little clinical progress on NR1D1 ligands, and challenges include drug safety concerns, poor bioavailability and pharmacokinetic properties, and differences in circadian mechanisms between humans and rodents. Moreover, considering the intimate association between NR1D1 and the central circadian clock, NR1D1 also holds great promise for therapeutic strategies addressing rhythmic disorders. Abbreviations AAA Abdominal aortic aneurysm AAI Aristolochic acid I AF‑1 Activation function‑1 AF‑2 Activation function‑2 AKI Acute renal injury ALD Alcoholic liver disease ALI Acute lung injury AMD Age‑related macular degeneration Apo Apolipoprotein ATG5 Autophagy protein 5 Bmal1 Brain and muscle ARNT‑like 1 BMDM Bone marrow‑derived macrophage CCG Clock‑controlled gene CLOCK Circadian locomotor output cycles kaput CRY Cryptochrome COPD Chronic obstructive pulmonary disease CS Cigarette smoke CYP Cytochrome CYP7A1 Cholesterol 7α‑hydroxylase DBD DNA‑binding domain Dcg D‑box controlled gene DENV Dengue virus dMφ Decidual macrophage EMT Epithelial‑mesenchymal transition eRNA Enhancer‑derived RNA ETC Electron transport chain E4BP4 E4 promoter binding protein 4 E75 Ecdysone‑induced protein 75 FGF21 Fibroblast growth factor 21 FH Fulminant hepatitis FLS Fibroblast‑like synoviocyte GATA3 GATA binding protein 3 GC Granulosa cell GEC Gastric epithelial cell GalN Galactosamine HCV Hepatitis C virus HDAC3 Histone deacetylase 3 HDL High‑density lipoprotein hESC Human endometrial stroma cell HF Heart failure HFL‑1 Human fetal lung fibroblast‑1 HK1 Hexokinase 1 I/R Ischemia/reperfusion IMQ Imiquimod LBD Ligand‑binding domain MD Molecular dynamics Mmp Matrix metalloproteinase MI Myocardial infarction MLF Mouse lung fibroblast mtDNA Mitochondrial deoxyribonucleic acid mPGES‑2 Microsomal prostaglandin E synthase‑2 NAFLD Non‑alcoholic fatty liver disease NCOR Nuclear receptor corepressor NO Nitric oxide NR Nuclear receptor NR4A1 Nuclear receptor subfamily 4, group A, member 1 Nrf2 Nuclear factor erythroid 2‑related factor 2 NR1D1 Nuclear receptor subfamily 1, group D, member 1 PARP Poly‑ADP‑ribose polymerase PCK1 Phosphoenolpyruvate carboxykinase 1 PDK4 Pyruvate dehydrogenase kinase 4 PER Period PPP Pentose phosphate pathway PKM2 Pyruvate kinase M2 PKA Protein kinase A RANKL Receptor activator of nuclear factor‑κB ligand RCG RORE/RevRE‑controlled gene RCC Renal cell carcinoma Stra8 Stimulated by retinoic acid gene 8 RORα RAR related orphan receptor α RORE/RevRE ROR/REV‑ERB‑response element SCD Stearoyl‑CoA‑desaturase SCN Suprachiasmatic nucleus SHP Small heterodimer partner Sod1 Superoxide dismutase 1 Serpina3 Serine protease inhibitory factor 3 SAEC Small airway epithelial cell SCLC Small‑cell lung cancer TCA Tricarboxylic acid Th T helper THIQ Tetrahydroisoquinoline TF Transcription factor TFEB Transcription factor EB TFE3 Transcription factor E3 TTFL Transcription‑translation feedback loop VSMC Vascular smooth muscle cell ULK1 Unc‑51‑like kinase 1 ZIKV Zika virus Acknowledgements Thanks to all authors who contributed to this work. In particular, we truly thank Dr. Qiong Liu and Ms. Xiao‑Ru Li for creating Fig. 2. Author contributions ZYZS, XZX, and GE collected relevant literature and drafted manuscripts. WRL, LZ, YZZ, YNR, and YT reviewed and made significant revisions to the manuscript. ZYZS, XZX, YZZ, and WRL prepared figures and tables. YY and Page 17 of 20 Zhang‑sunetal. Military Medical Research (2023) 10:62 DAC guided the preparation of this manuscript. All authors have read and approved the final manuscript. Funding This work was supported by the National Natural Science Foundation of China (82070422, 82200330), the China Postdoctoral Science Foundation (2023T160526 and 2022M722571), the Research Plan Project of Shaanxi Institute of Basic Science (22JHQ053), the High‑end Foreign Expert Introduc‑ tion Program of National Science and Technology (G2022040014L), and the Qinchuangyuan Traditional Chinese Medicine Innovation Research and Development Transformation Project (2022‑QCYZH‑036). Availability of data and materials Data sharing is not applicable to this article as no new data were created or analyzed in this study. Declarations Ethical approval and consent to participate Not applicable. Consent for publication All authors contributed to the article and approved the submitted version. Competing interests The authors declare that they have no competing interests. Received: 8 June 2023 Accepted: 13 November 2023 References 1. Lazar MA, Hodin RA, Darling DS, Chin WW. A novel member of the thyroid/steroid hormone receptor family is encoded by the oppo‑ site strand of the rat c‑erbA alpha transcriptional unit. Mol Cell Biol. 1989;9(3):1128–36. 2. Dumas B, Harding HP, Choi HS, Lehmann KA, Chung M, Lazar MA, et al. A new orphan member of the nuclear hormone receptor superfamily closely related to rev‑erb. Mol Endocrinol. 1994;8(8):996–1005. 3. Forman BM, Chen J, Blumberg B, Kliewer SA, Henshaw R, Ong ES, et al. 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