Lipid-activated Transcription Factors Research Articles

Development of a Robust Read-Across Model for the Prediction of Biological Potency of Novel Peroxisome Proliferator-Activated Receptor Delta Agonists.

A robust predictive model was developed using 136 novel peroxisome proliferator-activated receptor delta (PPARδ) agonists, a distinct subtype of lipid-activated transcription factors of the nuclear receptor superfamily that regulate target genes by binding to characteristic sequences of DNA bases. The model employs various structural descriptors and docking calculations and provides predictions of the biological activity of PPARδ agonists, following the criteria of the Organization for Economic Co-operation and Development (OECD) for the development and validation of quantitative structure-activity relationship (QSAR) models. Specifically focused on small molecules, the model facilitates the identification of highly potent and selective PPARδ agonists and offers a read-across concept by providing the chemical neighbours of the compound under study. The model development process was conducted on Isalos Analytics Software (v. 0.1.17) which provides an intuitive environment for machine-learning applications. The final model was released as a user-friendly web tool and can be accessed through the Enalos Cloud platform's graphical user interface (GUI).

Signaling mechanisms in renal compensatory hypertrophy revealed by multi-omics

Loss of a kidney results in compensatory growth of the remaining kidney, a phenomenon of considerable clinical importance. However, the mechanisms involved are largely unknown. Here, we use a multi-omic approach in a unilateral nephrectomy model in male mice to identify signaling processes associated with renal compensatory hypertrophy, demonstrating that the lipid-activated transcription factor peroxisome proliferator-activated receptor alpha (PPARα) is an important determinant of proximal tubule cell size and is a likely mediator of compensatory proximal tubule hypertrophy.

Epigenomic regulation of macrophage polarization: Where do the nuclear receptors belong?

Our laboratory has a long-standing research interest in understanding how lipid-activated transcription factors, nuclear hormone receptors, contribute to dendritic cell and macrophage gene expression regulation, subtype specification, and responses to a changing extra and intracellular milieu. This journey in the last more than two decades took us from identifying target genes for various RXR heterodimers to systematically mapping nuclear receptor-mediated pathways in dendritic cells to identifying hierarchies of transcription factors in alternative polarization in macrophages to broaden the role of nuclear receptors beyond strictly ligand-regulated gene expression. We detail here the milestones of the road traveled and draw conclusions regarding the unexpectedly broad role of nuclear hormone receptors as epigenomic components of dendritic cell and macrophage gene regulation as we are getting ready for the next challenges.

Loss of the Nuclear Receptor Pparγ Primes T Effector (TEFF) Differentiation of Antigen-Specific CD8+ T Cells

Peroxisome proliferator activated receptors (PPARs) are transcription factors that belong to the nuclear hormone superfamily, with three distinct types identified: PPARalpha (PPARα), PPARgamma (PPARγ), and PPARbeta/delta (PPARβ/δ). PPARs possess a critical role in the regulation of lipid metabolism, and thus dictate the differentiation and fate of immune cells. PPARγ is a lipid-activated transcription factor mainly known to mediate anti-inflammatory effects on both innate and adaptive immune system. Synthetic ligands for activating PPARγ ameliorate disease outcomes in various models of inflammation and autoimmunity. The role of PPARγ in the immune system has been mainly studied in macrophages, where it is known to mediate M2 polarization. In the present study we investigated how PPARγ affects the differentiation and function of antigen-specific effector (TEFF) and memory (TM) CD8+ T cells using OTI TCR transgenic mice and OTI mice with T cell-specific PPARγ deletion (OTI/PPARγf/f-CD4-cre; thereafter named OTI/PPARγ-KO). Antigen-specific TEFF were generated in vitro by stimulation of OTI and OTI/PPARγ-KO T cells with Ova257-264 followed by culture with IL-2, whereas TM were generated by stimulation with Ova257-264 followed by culture with IL-15. Under both TEFF and TM conditions in vitro, antigen-specific stimulation of OTI/PPARγ-KO cells resulted in significantly greater proliferation and expansion relative to OTI control. Additionally, OTI/PPARγ-KO TM cells cultured with IL-15 co-expressed significantly higher CD44+/CD62L+ fractions indicating a greater expansion of central memory cells. Consistent with these, metabolomics analysis showed that under both culture conditions, PPARγ-deficient OTI cells had increased levels of glycolysis intermediates but also TCA metabolites consistent with a program of metabolically active cells with high levels of glycolysis and OXPHOS. RNA-sequencing studies showed that upon TEFF differentiation in vitro, OTI/PPARγ-KO T cells displayed a differential gene expression program compared to OTI controls. Pathway enrichment analysis revealed that PPARγ-deficient OTI cells were significantly enriched for genes related to T cell activation and proliferation, integrin activation, cytokine production, ribosomal function and biogenesis, RNA processing and protein translation. During antigen-specific stimulation in vivo performed after adoptive transfer of OTI/PPARγ-KO and OTI cells into syngeneic recipients followed by immunization with Ova-expressing Listeria monocytogenes (Lm-OVA), PPARγ deletion resulted in a rapid and enhanced TEFF cell activation and expansion as determined by the higher mitotic index, higher enrichment of Dextramer-positive antigen-specific T cells, and the higher expression of activation markers including KLRG1, CD44 and CD69, but also CTLA-4, PD-1, Lag-3 and Tim-3. These cells also developed higher numbers of TNF-α and IFN-γ-producing T cells, as well as ROR-γt expressing T cells consistent with Tc17 differentiation. In vivo stimulated antigen-specific PPARγ-deficient and control OTI T cells showed no numerical differences in TM differentiation or expansion. However, upon rechallenge in vitro, PPARγ-deficient TM cells exhibited improved capacity for TEFF differentiation with higher release of inflammatory cytokines and expression of CD69, PD-1 and CTLA-4. Our findings uncover a new role of PPARγ ablation in programming CD8+ T responses by regulating metabolism-mediated cues, which imprint T cell differentiation and long-term effector capacity.

Activity Screening of Fatty Acid Mimetic Drugs Identified Nuclear Receptor Agonists.

Fatty acid mimetics (FAM) are bioactive molecules acting through the binding sites of endogenous fatty acid metabolites on enzymes, transporters, and receptors. Due to the special characteristics of these binding sites, FAMs share common chemical features. Pharmacological modulation of fatty acid signaling has therapeutic potential in multiple pathologies, and several FAMs have been developed as drugs. We aimed to elucidate the promiscuity of FAM drugs on lipid-activated transcription factors and tested 64 approved compounds for activation of RAR, PPARs, VDR, LXR, FXR, and RXR. The activity screening revealed nuclear receptor agonism of several FAM drugs and considerable promiscuity of NSAIDs, while other compound classes evolved as selective. These screening results were not anticipated by three well-established target prediction tools, suggesting that FAMs are underrepresented in bioactivity data for model development. The screening dataset may therefore valuably contribute to such tools. Oxaprozin (RXR), tianeptine (PPARδ), mycophenolic acid (RAR), and bortezomib (RAR) exhibited selective agonism on one nuclear receptor and emerged as attractive leads for the selective optimization of side activities. Additionally, their nuclear receptor agonism may contribute relevant and valuable polypharmacology.

Disrupted Lipid Metabolism in Multiple Sclerosis: A Role for Liver X Receptors?

Multiple sclerosis (MS) is a chronic neurological disease driven by autoimmune, inflammatory and neurodegenerative processes leading to neuronal demyelination and subsequent degeneration. Systemic lipid metabolism is disturbed in people with MS, and lipid metabolic pathways are crucial to the protective process of remyelination. The lipid-activated transcription factors liver X receptors (LXRs) are important integrators of lipid metabolism and immunity. Consequently, there is a strong interest in targeting these receptors in a number of metabolic and inflammatory diseases, including MS. We have reviewed the evidence for involvement of LXR-driven lipid metabolism in the dysfunction of peripheral and brain-resident immune cells in MS, focusing on human studies, both the relapsing remitting and progressive phases of the disease are discussed. Finally, we discuss the therapeutic potential of modulating the activity of these receptors with existing pharmacological agents and highlight important areas of future research.

Peroxisome Proliferator Activated Receptor Gamma Sensitizes Non-small Cell Lung Carcinoma to Gamma Irradiation Induced Apoptosis.

The nuclear receptors known as peroxisome proliferator activated receptor gamma (PPARG) are lipid-activated transcription factors that have emerged as key regulators of inflammation. PPARG ligands have been shown to have an anti-proliferative effect on a variety of cancers. These ligands can induce apoptosis via TP53 (Tumor protein p53) or ERK1/2 (Extracellular signal-regulated kinases 1/2) (EPHB2) pathways. However, the exact mechanism is not known. PPAR, a type II nuclear hormone receptor deserves attention as a selective target for radiotherapy. Our study examines the potential of selective agonism of PPARG for radiation therapy in non-small cell lung carcinoma (NSCLC). We found that the overexpression of PPARG protein as well as its induction using the agonist, rosiglitazone was able to stimulate radiation-induced cell death in otherwise radio resistant NSCLC A549 cell line. This cell death was apoptotic and was found to be BAX (BCL2 associated X) mediated. The treatment also inhibited radiation-induced AKT (Protein Kinase B) phosphorylation. Interestingly, the ionising radiation (IR) induced apoptosis was found to be inversely related to TP53 levels. A relatively significant increase in the levels of radiation induced apoptosis was observed in H1299 cells (TP53 null) under PPARG overexpression condition further supporting the inverse relationship between apoptosis and TP53 levels. The combination of PPARG agonist and radiation was able to induce apoptosis at a radiation dose at which A549 and H1299 are radioresistant, thus confirming the potential of the combinatorial strategy. Taken together, PPARG agonism was found to invigorate the radiosensitising effect and hence its use in combination with radiotherapy is expected to enhance sensitivity in otherwise resistant cancer types.

PPAR-α acutely inhibits functional activity of ASICs in rat dorsal root ganglion neurons.

Peroxisome proliferator-activated receptor-α (PPAR-α), a lipid activated transcription factor of nuclear hormone receptor superfamily, can relieve pain through a rapid-response mechanism. However, little is known about the underlying mechanism. Herein, we report that PPAR-α activation acutely inhibits the functional activity of acid-sensing ion channels (ASICs), key sensors for extracellular protons, in rat dorsal root ganglion (DRG) neurons. Pre-application of PPAR-α agonist GW7647 for 2 min decreased the amplitude of proton-gated currents mediated by ASICs in a concentration-dependent manner. GW7647 shifted the concentration-response curve for proton downwards, with a decrease of 36.9 ± 2.3% in the maximal current response to proton. GW7647 inhibition of proton-gated currents can be blocked by GW6471, a selective PPAR-α antagonist. Moreover, PPAR-α activation decreased the number of acidosis-evoked action potentials in rat DRG neurons. Finally, peripheral administration of GW7647 dose-dependently relieved nociceptive responses to injection of acetic acid in rats. These results indicated that activation of peripheral PPAR-α acutely inhibited functional activity of ASICs in a non-genomic manner, which revealed a novel mechanism underlying rapid analgesia through peripheral PPAR-α.

Macrophage PPARγ, a Lipid Activated Transcription Factor Controls the Growth Factor GDF3 and Skeletal Muscle Regeneration

Tissue regeneration requires inflammatory and reparatory activity of macrophages. Macrophages detect and eliminate the damaged tissue and subsequently promote regeneration. This dichotomy requires the switch of effector functions of macrophages coordinated with other cell types inside the injured tissue. The gene regulatory events supporting the sensory and effector functions of macrophages involved in tissue repair are not well understood. Here we show that the lipid activated transcription factor, PPARγ, is required for proper skeletal muscle regeneration, acting in repair macrophages. PPARγ controls the expression of the transforming growth factor-β (TGF-β) family member, GDF3, which in turn regulates the restoration of skeletal muscle integrity by promoting muscle progenitor cell fusion. This work establishes PPARγ as a required metabolic sensor and transcriptional regulator of repair macrophages. Moreover, this work also establishes GDF3 as a secreted extrinsic effector protein acting on myoblasts and serving as an exclusively macrophage-derived regeneration factor in tissue repair.

Decreased peroxisome proliferator-activated receptor γ level and signalling in sebaceous glands of patients with acne vulgaris.

Little is known about the altered lipid metabolism-related transcriptional events occuring in sebaceous glands of patients with acne vulgaris. Peroxisome proliferator-activated receptor (PPAR)γ, a lipid-activated transcription factor, is implicated in differentiation and lipid metabolism of sebocytes. We have observed that PPARγ and its target genes, ADRP (adipose differentiation related protein) and PGAR (PPARγ angioprotein related protein) are expressed at lower levels in sebocytes from patients with acne than in those from healthy controls (HCs) Furthermore, endogenous PPARγ activator lipids such as arachidonic acid-derived keto-metabolites (e.g. 5KETE, 12KETE) are increased in acne-involved and nonacne-involved skin of patients with acne, compared with skin from healthy individuals. Our findings highlight the possible anti-inflammatory role of endogenous ligand-activated PPARγ signaling in human sebocyte biology, and suggest that modulating PPARγ- expression and thereby signaling might be a promising strategy for the clinical management of acne vulgaris.

PPARγ-Mediated and Arachidonic Acid–Dependent Signaling Is Involved in Differentiation and Lipid Production of Human Sebocytes

The transcriptional basis of sebocyte differentiation and lipid production is mostly unclear. Peroxisome proliferator-activated receptor gamma (PPARγ), a lipid-activated transcription factor, has been implicated in differentiation and lipid metabolism of various cell types. Here, we show that PPARγ is differentially expressed in normal and pathological human sebocytes and appears to have roles in their differentiation and lipid production. We used laser-microdissected normal and pathological human sebaceous glands (SGs) and SZ95 cells (immortalized sebocyte cell line) analyzed by real-time quantitative PCR and immunohistochemistry. Lipids were analyzed by quantitative fluorimetry- and mass spectrometry-based approaches. We have observed that PPARγ and its target genes, ADRP (adipose differentiation-related protein) and PGAR (PPARγ angiopoietin-related protein), are expressed in sebocytes and show association with their level of differentiation. Also, PPARγ is present in normal and hyperplastic SG, whereas its expression levels are decreased in SG adenoma and SG carcinoma cells, reflecting a maturation-linked expression pattern. Furthermore, in SZ95 sebocytes, naturally occurring lipids, including arachidonic acid and arachidonic acid keto-metabolites (e.g., 5-KETE (5-oxo-6E,8Z,11Z,14Z-eicosatetraenoic acid), 12-KETE (12-oxo-5Z,8Z,10E,14Z-eicosatetraenoic acid)), appear to regulate PPARγ signaling pathways, which in turn modulate phospholipid biosynthesis and induce neutral lipid synthesis. Collectively, our findings highlight the importance of endogenous ligand-activated PPARγ signaling in human sebocyte biology and suggest that PPARγ might be a promising candidate for the clinical management of SG disorders.

Pro-inflammatory cytokines negatively regulate PPARγ mediated gene expression in both human and murine macrophages via multiple mechanisms

PPARγ is a lipid activated transcription factor that connects lipid metabolism and immune function. It is known that anti-inflammatory cytokines, such as IL-4 that mediates the differentiation of alternatively activated macrophages, positively modulate PPARγ at three levels: by (1) increasing its expression (2), initiating a complex formation with STAT6 enhances its transcriptional activity and (3) increasing endogenous ligand production. On the other hand, PPARγ is known to inhibit inflammatory processes via transrepression. However, the impact of a pro-inflammatory cytokine milieu on PPARγ transcriptional activity in macrophages is less understood.We hypothesized that pro-inflammatory cytokines, such as IFNγ and TNFα negatively regulate PPARγ activity and sought to test this within human and murine macrophage models using both global and single target gene expression analysis. We found that IFNγ/TNFα inhibited PPARγ expression in human CD14+ monocytes derived macrophages and mouse bone marrow derived macrophages, but not in macrophages originating from CD34+ stem cells or Thp-1 monocytic cells. Irrespective of the model system, the ability of PPARγ to regulate gene expression was inhibited. Moreover, we demonstrated that in Thp-1 cells PPARγ in vitro DNA binding remained unchanged following IFNγ/TNFα pre-treatment.Taken together, our data suggest that pro-inflammatory conditions inhibit PPARγ activity at the gene expression level and propose two, mutually not exclusive models as mechanisms: (1) the level of PPARγ itself is down-regulated by the cytokines leading to loss of function, while (2) PPARγ itself remains associated with the DNA though unable to initiate gene expression. These findings support that inflammatory conditions skew the lipid sensing function of macrophages, further contributing to the vicious circle of metabolic disorders.

RIP140, a Janus metabolic switch involved in defense functions

RIP140, a Janus metabolic switch involved in defense functions

Liver X receptor and peroxisome proliferator‐activated receptor as integrators of lipid homeostasis and immunity

Lipid metabolism has emerged as an important modulator of innate and adaptive immune cell fate and function. The lipid-activated transcription factors peroxisome proliferator-activated receptor (PPAR) α, β/δ, γ and liver X receptor (LXR) are members of the nuclear receptor superfamily that have a well-defined role in regulating lipid homeostasis and metabolic diseases. Accumulated evidence over the last decade indicates that PPAR and LXR signaling also influence multiple facets of inflammation and immunity, thereby providing important crosstalk between metabolism and immune system. Herein, we provide a brief introduction to LXR and PPAR biology and review recent discoveries highlighting the importance of PPAR and LXR signaling in the modulation of normal and pathologic states of immunity. We also examine advances in our mechanistic understanding of how nuclear receptors impact immune system function and homeostasis. Finally, we discuss whether LXRs and PPARs could be pharmacologically manipulated to provide novel therapeutic approaches for modulation of the immune system under pathologic inflammation or in the context of allergic and autoimmune disease.

Peroxisome Proliferator-Activated Receptor γ-Regulated Cathepsin D Is Required for Lipid Antigen Presentation by Dendritic Cells

It is well established that dendritic cells (DCs) take up, process, and present lipid Ags in complex with CD1d molecules to invariant NKT cells. The lipid-activated transcription factor, peroxisome proliferator-activated receptor γ (PPARγ), has previously been shown to regulate CD1d expression in human monocyte-derived DCs, providing a link between lipid metabolism and lipid Ag presentation. We report that PPARγ regulates the expression of a lysosomal protease, cathepsin D (CatD), in human monocyte-derived DCs. Inhibition of CatD specifically reduced the expansion of invariant NKT cells and furthermore resulted in decreased maturation of saposins, a group of lipid transfer proteins required for lysosomal lipid Ag processing and loading. These results reveal a novel mechanism of lipid Ag presentation and identify CatD as a key component of this machinery and firmly place PPARγ as the transcriptional regulator linking lipid metabolism and lipid Ag processing.

STAT6 transcription factor is a facilitator of the nuclear receptor PPARγ-regulated gene expression in macrophages and dendritic cells.

SummaryPeroxisome proliferator-activated receptor γ (PPARγ) is a lipid-activated transcription factor regulating lipid metabolism and inflammatory response in macrophages and dendritic cells (DCs). These immune cells exposed to distinct inflammatory milieu show cell type specification as a result of altered gene expression. We demonstrate here a mechanism how inflammatory molecules modulate PPARγ signaling in distinct subsets of cells. Proinflammatory molecules inhibited whereas interleukin-4 (IL-4) stimulated PPARγ activity in macrophages and DCs. Furthermore, IL-4 signaling augmented PPARγ activity through an interaction between PPARγ and signal transducer and activators of transcription 6 (STAT6) on promoters of PPARγ target genes, including FABP4. Thus, STAT6 acts as a facilitating factor for PPARγ by promoting DNA binding and consequently increasing the number of regulated genes and the magnitude of responses. This interaction, underpinning cell type-specific responses, represents a unique way of controlling nuclear receptor signaling by inflammatory molecules in immune cells.

Lipid-activated transcription factors control bile acid glucuronidation

Bile acids subserve important physiological functions in the control of cholesterol homeostasis. Indeed, hepatic bile acid synthesis and biliary excretion constitute the main route for cholesterol removal from the human body. On the other hand, bile acids serve as natural detergents for the intestinal absorption of dietary cholesterol. However, due to their detergent properties, bile acids are inherently cytotoxic, and their cellular level may be tightly controlled to avoid pathological situations such as cholestasis. Recent investigations have illustrated the crucial roles that a series of ligand-activated transcription factors has in the control of hepatic bile acids synthesis, transport and metabolism. Thus, the lipid-activated nuclear receptors, farnesoid X-receptor (FXR), liver X-receptor (LXR), pregnane X-receptor (PXR) and peroxisome proliferator-activated receptor alpha (PPAR alpha), modulate the expression and activity of genes controlling bile acid homeostasis in the liver. Several members of the UDP-glucuronosyltransferase (UGT) enzymes family are among the bile acid metabolizing enzymes regulated by these receptors. UGTs catalyze glucuronidation, a major phase II metabolic reaction, which converts hydrophobic bile acids into polar and urinary excretable metabolites. This article summarizes our recent observations on the regulation of bile acid conjugating UGTs upon pharmacological activation of lipid-activated receptors, with a particular interest for the role of PPAR alpha and LXRalpha in controlling human UGT1A3 expression.

Nuclear receptors, transcription factors linking lipid metabolism and immunity: the case of peroxisome proliferator‐activated receptor gamma

Exposure to lipids has a major effect on mammalian cells. Naturally, it has a profound impact on their metabolism, but it can also significantly alter their cellular and molecular phenotypes and responses. This latter is via specific signalling pathways leading to alterations in the expression of genes and gene networks. Multicellular organisms utilize a specialized group of proteins to detect and transduce lipid signals to the level of the expression of the genome. These proteins, termed nuclear hormone receptors, are lipid-activated transcription factors regulating gene expression upon binding of small fatty ligands. In this review, we discuss the role and contribution of peroxisome proliferator-activated receptor gamma (PPAR gamma) to macrophage and dendritic cell biology and also to gut epithelial cell function. We discuss how using different experimental systems and approaches the pathways activating the receptor and its target genes can be identified and complex biological processes unravelled. It appears that PPAR gamma is part of the macrophage's response to pathogenic lipoproteins and it coordinately regulates lipid uptake and efflux. Intriguingly, in another cell type of the immune system, dendritic cells, the receptor has overlapping, but distinct functions. In these cells, activation of PPAR gamma leads to altered immune phenotype characterized by increased phagocytic capacity, antigen processing and lipid antigen presenting capacity. This nuclear hormone receptor links lipid metabolism and immune cell function and these links provide unique insights into the regulatory logic of normal physiological responses and certain pathologies, such as atherosclerosis, chronic inflammatory diseases and autoimmunity.

Integration of metabolism and inflammation by lipid-activated nuclear receptors

The nuclear receptors known as PPARs and LXRs are lipid-activated transcription factors that have emerged as key regulators of lipid metabolism and inflammation. PPARs and LXRs are activated by non-esterified fatty acids and cholesterol metabolites, respectively, and both exert positive and negative control over the expression of a range of metabolic and inflammatory genes. The ability of these nuclear receptors to integrate metabolic and inflammatory signalling makes them attractive targets for intervention in human metabolic diseases, such as atherosclerosis and type 2 diabetes, as well as for the modulation of inflammation and immune responses.

PPARγ controls CD1d expression by turning on retinoic acid synthesis in developing human dendritic cells

Dendritic cells (DCs) expressing CD1d, a molecule responsible for lipid antigen presentation, are capable of enhancing natural killer T (iNKT) cell proliferation. The signals controlling CD1 expression and lipid antigen presentation are poorly defined. We have shown previously that stimulation of the lipid-activated transcription factor, peroxisome proliferator-activated receptor (PPAR)γ, indirectly regulates CD1d expression. Here we demonstrate that PPARγ, turns on retinoic acid synthesis by inducing the expression of retinol and retinal metabolizing enzymes such as retinol dehydrogenase 10 and retinaldehyde dehydrogenase type 2 (RALDH2). PPARγ-regulated expression of these enzymes leads to an increase in the intracellular generation of all-trans retinoic acid (ATRA) from retinol. ATRA regulates gene expression via the activation of the retinoic acid receptor (RAR)α in human DCs, and RARα acutely regulates CD1d expression. The retinoic acid–induced elevated expression of CD1d is coupled to enhanced iNKT cell activation. Furthermore, in vivo relevant lipids such as oxidized low-density lipoprotein can also elicit retinoid signaling leading to CD1d up-regulation. These data show that regulation of retinoid metabolism and signaling is part of the PPARγ-controlled transcriptional events in DCs. The uncovered mechanisms allow the DCs to respond to altered lipid homeostasis by changing CD1 gene expression.