Peroxisome Proliferator-Activated Receptors (PPARs) are a family of conserved ligand activated nuclear receptor transcription factors heterogeneously expressed in mammalian tissues. PPARγ is recognized as a master regulator of adipogenesis, fatty acid metabolism, and glucose homeostasis, but genetic evidence also supports the concept that PPARγ regulates the cardiovascular system, particularly vascular function and blood pressure. There is now compelling evidence that the beneficial blood pressure lowering effects of PPARγ activation are due to its activity in vascular smooth muscle and endothelium, through its modulation of nitric oxide-dependent vasomotor function. Endothelial PPARγ regulates the production and bioavailability of nitric oxide, while PPARγ in the smooth muscle regulates the vasomotor response to nitric oxide. We recently identified retinol binding protein 7 (RBP7) as a PPARγ target gene that is specifically and selectively expressed in the endothelium. We will discuss the evidence that RBP7 is required to mediate the antioxidant effects of PPARγand mediate PPARγ target gene selectivity in the endothelium, as well as the work so far in determining the mechanism of RBP7:PPARγ interaction. (56)

The aim of the work presented in this thesis was to establish chromatin immunoprecipitation method in our laboratory as a tool to study target genes of the nuclear receptor NHR-25 in C. elegans. Once the method is established, it will be also useful for studies of other DNA binding proteins. ChIP was performed in transiently transfected cells HEK293 and analyzed using PCR and qPCR. Although ChIP is typically used to find authentic target genes in the cell or in organisms, testing protein-DNA interactions by ChIP in transient transfection system (by transfecting both the expression vector of the protein of interest and a vector containing potential binding sequence/promoter of the protein) can be useful as it serves as a relatively quick tool to confirm the direct binding. Since the detection is by PCR, this method is sensitive yet less costly non radioactive method to analyze protein-DNA interaction. For the first step towards ChIP in C. elegans; pulling down tagged protein directly from the worm was also performed as a preparation for in vivo analysis of NHR-25 regulated genes.

The renin angiotensin system (RAS) is critical for the regulation of blood pressure, electrolyte/fluid, and metabolic homeostasis. Regulation of the RAS is important in the development and treatment of hypertension. As part of the rate-limiting step in a cascade of events ending in the production of angiotensin II, renin is a major regulator of the RAS. Its expression is localized to the juxtaglomerular (JG) cells of the JG apparatus where it is exquisitely located to respond to various physiological cues. Understanding the regulation of renin expression and development of the juxtaglomerular cells is critical. Two regulatory elements, the enhancer and proximal promoter, have been found to be important in controlling cell- and tissue- specific baseline expression of the renin gene. Within the enhancer is a hormone response element (HRE) which confers a high level of activity to the enhancer. Nuclear receptors that bind this element have been found to bind the HRE and regulate renin promoter transcriptional activity. We have previously characterized the role of the orphan nuclear receptor Nr2f6 as a negative regulator of renin expression that mediates its effects through the HRE. However, gel shift assays indicate that there are other transcription factors binding this element. We have identified other orphan nuclear receptors that regulate renin expression. The first, Nr2f2 acts as a negative regulator of renin promoter activity but does not appear to affect baseline expression of the endogenous renin gene. The other, Nr4a1, is a positive regulator of renin expression, but it does not appear to mediate its effects through the HRE. The transcriptional regulation of gene expression is controlled by regulatory elements separated by large distances from promoters. We and others have found that short transgenes of the human renin (hREN) locus are not sufficient to protect them from positional effects that can be exerted upon them by neighboring regulatory elements. We discovered a random truncation in a large genomic construct of the hREN gene that resulted in ubiquitous expression of renin not seen with the intact form. By locating the genomic insertion site of that transgene in the Zbtb20 gene, we found that the hREN promoter had come under control of that gene's regulatory elements. The gene downstream of renin however maintained its tissue-specific expression. We found that CCCTC-binding factor (CTCF) bound to chromatin in and around the renin locus. The presence of CTCF suggests that insulator elements are present in the renin locus, and their loss likely explains the results above. Finally, we assessed the role of microRNAs in the development of renin expressing cells in the mouse kidneys by cell-specific deletion of the processing enzyme Dicer. This resulted in reduction of renin expression and a decrease in the number of renin expressing cells in the kidney. Mice were hypotensive and had several kidney abnormalities including a hypertrophied vasculature and striped fibrosis. These results indicate that Dicer and the miRNAs it processes are critical for the development and maintenance of renin expressing cells that contribute to normal kidney development.

Humans are ubiquitously exposed to mixtures of per- and polyfluoroalkyl substances (PFAS). Exposure to well-studied PFAS including perfluorooctanoic acid (PFOA) is associated with multiple adverse health effects in humans including dysregulated lipid homeostasis. Evidence from epidemiological studies consistently shows a positive association between PFOA exposure and circulating total and low-density lipoprotein cholesterol levels with emerging evidence suggesting PFOA disrupts liver lipid homeostasis as well. Animal toxicity studies show that PFOA decreases, has no effect on, or increases circulating cholesterol levels in rodents and induces liver lipid accumulation. Mechanisms through which PFOA and other PFAS disrupt liver and whole body lipid homeostasis, and an explanation for the differences between species are poorly understood. The overarching hypothesis of this dissertation is that PFOA disrupts serum and liver lipid homeostasis through interactions with multiple hepatic nuclear receptors including peroxisome proliferator activated receptor α (PPARα). This hypothesis was tested with a focus on human-relevant experimental designs. In the first research aim, an in vivo exposure was used to test the hypothesis that the effects of PFOA on liver and serum triacylglyceride and cholesterol concentrations differ by PPARα genotype. Female mice expressing mouse PPARα, human PPARα (hPPARα), or no PPARα were exposed to PFOA (1.2, 3.4, or 14.8 μM) for 14 weeks via drinking water to achieve steady state exposure with co-exposure to a diet containing fat and cholesterol based on “What we eat in America.” PFOA increased liver and serum cholesterol content through PPARα-dependent mechanisms. Analysis of hepatic mRNA expression showed that the PPARα-dependent increase in serum and liver cholesterol was accompanied by a PPARα-dependent decrease in the mRNA expression of the rate-limiting enzyme that converts cholesterol to bile acids and represents an important source of cholesterol turnover in humans. In the second research aim, an in vivo exposure was used to test the hypothesis that PFOA disrupts liver lipid homeostasis by modulating multiple hepatic nuclear receptor pathways. Male and female hPPARα and PPARα null mice were exposed to PFOA (8 μM) for 6 weeks via drinking water in the context of a fat and cholesterol rich diet based on “What we eat in America.” PFOA exposure changed the abundance of multiple lipid classes in the liver with some changes depending on PPARα expression while others occurred via mechanisms independent of PPARα. Less than 60% of PFOA-induced transcriptomic changes depended on hPPARα. Signaling pathways for other nuclear receptors including CAR and PXR may account for the non- PPARα-dependent transcriptomic and lipidomic changes. Because the effects of PFOA on liver and whole-body lipid homeostasis are partially mediated by PPARα, the third research aim tested the hypothesis that hPPARα activation by PFAS mixtures can be predicted with the mathematical model Generalized Concentration Addition (GCA). Data generated using a full-length hPPARα-driven reporter assay showed that, in addition to differences in potency, PFAS differ in the efficacy with which they activate hPPARα. Perfluorinated carboxylic acids (PFCAs) tended to act as full hPPARα agonists while perfluorinated sulfonic acids (PFSAs) tended to act as partial hPPARα agonists. Because of these differences in efficacy, GCA more accurately predicted hPPARα activation by human-relevant PFAS mixtures than traditional mixtures modeling approaches that do not take into account differences in efficacy. Taken together, the research presented in this dissertation shows that hPPARα activation is one of several important molecular initiating events underlying PFOA-induced lipid dysregulation, including increased liver and serum cholesterol levels. Results from these studies support a causal association between PFOA exposure and increased serum cholesterol in humans. The data define important distinctions between PFCAs and PFSAs, which warrant consideration for regulatory agencies acting on the joint toxicity of PFAS mixtures. / 2026-01-03T00:00:00Z

Os PPARs são fatores de transcrição ativados por ligantes, pertencentes à superfamília dos receptores nucleares, que são considerados sensores de lipídeos capazes de transformar alterações nos padrões de lipídeos/ácidos graxos dos organismos em atividade metabólica. Com isto, os 3 isotipos (α, δ e γ) estão associados a diferentes desordens metabólicas como doenças vasculares, diabetes, obesidade, câncer e certas doenças mentais que constituem um grave problema de saúde pública mundial, o que torna esta classe de proteínas, um valioso alvo para a indústria farmacêutica. Embora a importância do hPPARδ na regulação da transcrição de genes relacionados a uma série de processos metabólicos seja conhecida, não há ainda nenhum fármaco no mercado cujo alvo seja este receptor. O maior conhecimento a respeito da estrutura deste receptor pode trazer esclarecimentos capazes de auxiliar o desenvolvimento racional de fármacos. Desta forma, no presente trabalho, buscou-se encontrar características estruturais importantes para a seletividade e especificidade dos ligantes pelo isotipo δ. Para tal, determinou-se as condições de expressão e purificação da proteína hPPARδ LBD, bem como as condições apropriadas de manutenção da mesma por meio da técnica de dicroísmo circular. O estado oligomérico deste receptor foi determinado em solução através das técnicas de cromatografia por exclusão de tamanho e por espalhamento dinâmico de luz, onde se concluiu que a proteína é monomérica nas condições testadas. Além disto, através de uma estrutura de alta resolução da proteína hPPARδ LBD com o ligante GW 0742, propôs-se a construção de dois mutantes, V312M e I328M, através dos quais concluiu-se que estes dois resíduos são potencialmente importantes para interação de ligantes estruturalmente relacionados com GW 0742, ao isotipo δ, indicando dois determinantes relacionados à seletividade de ligantes por este isotipo. Como existem poucos relatos sobre a estrutura completa deste receptor, e consequentemente da influência que os domínios N-terminal e DBD apresentam sobre o domínio LBD, um breve estudo da interação diferencial entre o receptor nuclear hPPARδ Full e três diferentes cofatores, em presença de ligante agonista e antagonista foi realizado. Para isto, determinou-se as condições de expressão e purificação da proteína hPPARδ Full, e prosseguiu-se com ensaios de anisotropia de fluorescência, através dos quais ficou claro que cada cofator apresenta um padrão diferente de interação com a proteína que pode ser dependente de outras regiões da proteína além daquelas já classicamente descritas. Isto é um forte indicativo de que diferentes regiões do hPPARδ podem ser chave no processo de regulação por intermédio de cofatores. / PPARs are transcription factors activated by ligands, belonging to the superfamily of nuclear receptors, which are considered to be lipid sensors capable of making changes in patterns of lipid/fatty acid metabolic activity of organisms. The three isotypes (α, δ and γ) are associated with different metabolic disorders and vascular diseases as diabetes, obesity, cancer and certain mental illnesses which comprise a serious worldwide public health problem, making this class of proteins a valuable target for the pharmaceutical industry. Although it is known the importance of hPPARδ in regulating transcription of genes related to a series of metabolic processes, there is still no drug on the market directed to this receptor. Knowledge about the structure of this receptor can bring clarification able to assist the rational development of drugs. Therefore, in the present study, we sought to find structural features important for selectivity and specificity of ligand binding by the isotype δ. To this end, we determined the conditions of expression and purification of the protein hPPARδ LBD, as well as the appropriate conditions for maintaining it through the technique of circular dichroism. The oligomeric state of this receptor in solution was determined through the techniques of size exclusion chromatography and dynamic light scattering, which concluded that the protein is monomeric under the conditions tested. In addition, through a high-resolution structure of the protein hPPARδ LBD with the ligand GW 0742, we proposed the construction of two mutants, V312M and I328M, through which it was concluded that these two residues are potentially important for interaction of ligands structurally related to GW 0742 with the δ isotype. As there are few reports based on the complete structure of this receptor, and consequently about the influence of the N-terminal and DBD domains with the LBD domain, a brief study of the interaction between the nuclear receptor differential hPPARδ Full and three different cofactors in the presence of agonist and antagonist ligands were performed. For this, we determined the conditions of expression and purification of the protein hPPARδ Full, and using fluorescence anisotropy, it became clear that each cofactor has a different pattern of interaction with the protein which may be dependent on other regions of the protein in addition to those already described classically. This is a strong indication that different regions of hPPARδ can be key points in the regulatory process through cofactors.

Pluripotent stem cells have the capacity to develop into different cell lineages and can be manipulated into certain cell types through the use of small molecule inducers. Retinoic acid (RA) signaling through retinoic acid receptors (RAR) and retinoid X receptors (RXR) has the ability to direct lineage determination but has yielded disappointing results in promoting skeletal myogenesis in embryonic stem (ES) cells. RXR is crucial in embryonic development although it is generally considered to act as a silent partner for other nuclear receptors such as RAR. Our findings demonstrate that rexinoid specific signaling enhances skeletal myogenesis and requires β-catenin but not RAR. Moreover, RXR signalling in mouse ES cells can efficiently enhance skeletal myogenesis and closely recapitulates sequential events observed in vivo. Since ES cells closely represent the properties of the developing embryo, efficiently generating skeletal muscle provides a means to further scrutinize signaling pathways in myogenic development in view of developing therapies for muscle related diseases.

Nuclear receptors (NR’s) comprise a large, ancient, superfamily of eukaryotic transcription factors that govern a wide range of metabolic, homeostatic, and developmental pathways, and which have been implicated in disease states including cancer, inflammation, and diabetes. The ability of NRs to activate or repress gene transcription is modulated through direct binding of small lipophilic ligands which induce conformational changes in their cognate receptor. These changes are structural in nature and lead to the recruitment of coactivator or corepressor complexes, ultimately regulating the expression of target genes to whose response elements NRs are bound. In Drosophila 18 NRs have been identified which have representative members belonging to each of the six major NR subfamilies, and which show a high degree of homology to their vertebrate counterparts. This fact, in addition to the power and ease of genetic manipulation, make Drosophila an excellent model system in which to study NR function. When I began my project, 17 of the 18 NRs in Drosophila were ‘orphan’ receptors for which no cognate ligand had been identified. As a first step in an effort to identify potential ligands for these 17 receptors I first set out to determine how, where and when nuclear receptors are regulated by small chemical ligands and/or their protein partners. In order to do so I contributed to developing a ‘ligand sensor’ system to visualize spatial activity patterns for each of the 18 Drosophila nuclear receptors in live, developing animals. This system is based upon transgenic lines that express the ligand binding domain of each Drosophila NR fused to the DNA-binding domain of yeast GAL4. When combined with a GAL4-responsive reporter gene, these fusion proteins show tissue- and stage-specific patterns of activation. Analysis using this system has revealed the stage and tissue specificity of NR activation for each of the fly NRs. The amnioserosa, yolk, midgut and fat body, which play major roles in lipid storage, metabolism and developmental timing, were identified as frequent sites of nuclear receptor activity. Dynamic changes in activation that are indicative of sweeping changes in ligand and/or co-factor production are also a prominent feature that has been revealed using this approach. In addition, I went on to characterize the ligand regulated function of a single Drosophila nuclear receptor, Ecdysone inducible protein 75 (E75). Previous work from our lab has demonstrated that E75 binds to heme, and that its function as a transcriptional repressor is regulated in vitro by binding of the small diatomic gases nitric oxide (NO) and carbon monoxide (CO) to its heme moiety. In an effort to validate and to further understand the in vivo relevance of E75 regulation by NO I used gain and loss of function transgenes, as well as tissues manipulated in culture to show that NO acts directly on the Drosophila nuclear receptor E75, reversing its ability to block the activity of its heterodimer partner Drosophila Hormone Receptor 3 (DHR3). By specifically focusing on the Drosophila larval ring gland, the principal endocrine organ responsible for the production of the metamorphosis-inducing hormone, ecdysone, I have shown that failure to produce NO and to inactivate E75 results in failure to recognize the signals that normally trigger metamorphosis.

The orphan nuclear receptor EAR-2 (NR2F6) is a gene that I previously found to be expressed at a higher level in clonogenic leukemia single cells than in leukemia cells that can not divide. For this thesis I undertook to perform the first investigations of the roles EAR-2 may play in normal haematopoiesis and in the pathogenesis of acute myelogenous leukaemia. Here, I show that EAR-2 is overexpressed in the bone marrow of patients with MDS, AML and CMML compared to healthy controls and that EAR-2 is a gatekeeper to hematopoietic differentiation. Over-expression of EAR-2 prevents the differentiation of cell lines, while knock down induces their spontaneous differentiation. In vitro, primary bone marrow cells that over-express EAR-2 do not differentiate into granulocytes in suspension culture, but have greatly extended replating capacity in colony assays. In vivo, overexpression of EAR-2 in a chimeric mouse model leads to a condition that resembles myelodysplastic syndrome characterised by hypercellular bone marrow, an increase in blasts, abnormal localization of immature progenitors, morphological dysplasia of the erythroid lineage and a competitive advantage over wild-type cells, that eventually leads to AML in a subset of the mice. Furthermore, animals that are transplanted with grafts of sorted bone marrow develop a rapidly fatal leukemia that is characterized by pancytopenia, enlargement of the spleen, infiltration of blasts into the spleen, liver and peripheral blood. Interestingly, development of leukemia is preceded by expansion of the stem cell compartment. Overexpression of EAR-2 increases the maintenance of KSL primitive bone marrow cells in ex vivo suspension culture, while knockdown of EAR-2 induces rapid differentiation of KSL cells into granulocytes. These data establish that EAR-2 is a novel oncogene that regulates hematopoietic cell differentiation. Furthermore, I show that EAR-2 is also a novel negative regulator of T-cell lymphopoiesis, and demonstrate that down-regulation of EAR-2 is important for the survival, proliferation and differentiation of T-cell progenitors. Overall, this work establishes that expression of EAR-2 is an important determinant of cell fate decisions in the hematopoietic system.

Nuclear receptors (NR’s) comprise a large, ancient, superfamily of eukaryotic transcription factors that govern a wide range of metabolic, homeostatic, and developmental pathways, and which have been implicated in disease states including cancer, inflammation, and diabetes. The ability of NRs to activate or repress gene transcription is modulated through direct binding of small lipophilic ligands which induce conformational changes in their cognate receptor. These changes are structural in nature and lead to the recruitment of coactivator or corepressor complexes, ultimately regulating the expression of target genes to whose response elements NRs are bound. In Drosophila 18 NRs have been identified which have representative members belonging to each of the six major NR subfamilies, and which show a high degree of homology to their vertebrate counterparts. This fact, in addition to the power and ease of genetic manipulation, make Drosophila an excellent model system in which to study NR function. When I began my project, 17 of the 18 NRs in Drosophila were ‘orphan’ receptors for which no cognate ligand had been identified. As a first step in an effort to identify potential ligands for these 17 receptors I first set out to determine how, where and when nuclear receptors are regulated by small chemical ligands and/or their protein partners. In order to do so I contributed to developing a ‘ligand sensor’ system to visualize spatial activity patterns for each of the 18 Drosophila nuclear receptors in live, developing animals. This system is based upon transgenic lines that express the ligand binding domain of each Drosophila NR fused to the DNA-binding domain of yeast GAL4. When combined with a GAL4-responsive reporter gene, these fusion proteins show tissue- and stage-specific patterns of activation. Analysis using this system has revealed the stage and tissue specificity of NR activation for each of the fly NRs. The amnioserosa, yolk, midgut and fat body, which play major roles in lipid storage, metabolism and developmental timing, were identified as frequent sites of nuclear receptor activity. Dynamic changes in activation that are indicative of sweeping changes in ligand and/or co-factor production are also a prominent feature that has been revealed using this approach. In addition, I went on to characterize the ligand regulated function of a single Drosophila nuclear receptor, Ecdysone inducible protein 75 (E75). Previous work from our lab has demonstrated that E75 binds to heme, and that its function as a transcriptional repressor is regulated in vitro by binding of the small diatomic gases nitric oxide (NO) and carbon monoxide (CO) to its heme moiety. In an effort to validate and to further understand the in vivo relevance of E75 regulation by NO I used gain and loss of function transgenes, as well as tissues manipulated in culture to show that NO acts directly on the Drosophila nuclear receptor E75, reversing its ability to block the activity of its heterodimer partner Drosophila Hormone Receptor 3 (DHR3). By specifically focusing on the Drosophila larval ring gland, the principal endocrine organ responsible for the production of the metamorphosis-inducing hormone, ecdysone, I have shown that failure to produce NO and to inactivate E75 results in failure to recognize the signals that normally trigger metamorphosis.

Pluripotent stem cells have the capacity to develop into different cell lineages and can be manipulated into certain cell types through the use of small molecule inducers. Retinoic acid (RA) signaling through retinoic acid receptors (RAR) and retinoid X receptors (RXR) has the ability to direct lineage determination but has yielded disappointing results in promoting skeletal myogenesis in embryonic stem (ES) cells. RXR is crucial in embryonic development although it is generally considered to act as a silent partner for other nuclear receptors such as RAR. Our findings demonstrate that rexinoid specific signaling enhances skeletal myogenesis and requires β-catenin but not RAR. Moreover, RXR signalling in mouse ES cells can efficiently enhance skeletal myogenesis and closely recapitulates sequential events observed in vivo. Since ES cells closely represent the properties of the developing embryo, efficiently generating skeletal muscle provides a means to further scrutinize signaling pathways in myogenic development in view of developing therapies for muscle related diseases.