Nuclear Receptor Signaling Atlas Research Articles

A FAIR-Based Approach to Enhancing the Discovery and Re-Use of Transcriptomic Data Assets for Nuclear Receptor Signaling Pathways

Public transcriptomic assets in the nuclear receptor (NR) signaling field hold considerable collective potential for exposing underappreciated aspects of NR regulation of gene expression. This potential is undermined however by a series of enduring informatic pain points that retard the routine re-use of these datasets. Here we describe a coordinated biocuration and web development approach to redress this situation that is closely aligned with ideals articulated in the FAIR (findable, accessible, interoperable, re-usable) principles on data stewardship. To improve findability, biocurators engage authors of studies in collaborating journals to secure datasets for deposition in public archives. Annotated derivatives of the archived datasets are assigned digital object identifiers and regulatory molecule identifiers that support persistent linkages between datasets and their associated research articles, integration in relevant records in gene and small molecule knowledgebases, and indexing by dataset search engines. To enhance their accessibility and interoperability, datasets are visualizable in responsively designed web pages, retrievable in machine-readable spreadsheets, or through an application programming interface. Re-use of the datasets is supported by their interrogation as a universe of data points through the Transcriptomine search engine, highlighting transcriptional intersections between NR signaling pathways, physiological processes and disease states. We illustrate the value of our approach in connecting disparate research communities using a use case of persistent interoperability between the Nuclear Receptor Signaling Atlas and the Pharmacogenomics Knowledgebase. Our FAIR-aligned model demonstrates the enduring value of discovery-scale datasets that accrues from their systematic compilation, biocuration and distribution across the digital biomedical research enterprise.

Research Resource: A Reference Transcriptome for Constitutive Androstane Receptor and Pregnane X Receptor Xenobiotic Signaling.

The pregnane X receptor (PXR) (PXR/NR1I3) and constitutive androstane receptor (CAR) (CAR/NR1I2) members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors are well-characterized mediators of xenobiotic and endocrine-disrupting chemical signaling. The Nuclear Receptor Signaling Atlas maintains a growing library of transcriptomic datasets involving perturbations of NR signaling pathways, many of which involve perturbations relevant to PXR and CAR xenobiotic signaling. Here, we generated a reference transcriptome based on the frequency of differential expression of genes across 159 experiments compiled from 22 datasets involving perturbations of CAR and PXR signaling pathways. In addition to the anticipated overrepresentation in the reference transcriptome of genes encoding components of the xenobiotic stress response, the ranking of genes involved in carbohydrate metabolism and gonadotropin action sheds mechanistic light on the suspected role of xenobiotics in metabolic syndrome and reproductive disorders. Gene Set Enrichment Analysis showed that although acetaminophen, chlorpromazine, and phenobarbital impacted many similar gene sets, differences in direction of regulation were evident in a variety of processes. Strikingly, gene sets representing genes linked to Parkinson's, Huntington's, and Alzheimer's diseases were enriched in all 3 transcriptomes. The reference xenobiotic transcriptome will be supplemented with additional future datasets to provide the community with a continually updated reference transcriptomic dataset for CAR- and PXR-mediated xenobiotic signaling. Our study demonstrates how aggregating and annotating transcriptomic datasets, and making them available for routine data mining, facilitates research into the mechanisms by which xenobiotics and endocrine-disrupting chemicals subvert conventional NR signaling modalities.

Nuclear Receptor Signaling Atlas: Opening Access to the Biology of Nuclear Receptor Signaling Pathways.

Signaling pathways involving nuclear receptors (NRs), their ligands and coregulators, regulate tissue-specific transcriptomes in diverse processes, including development, metabolism, reproduction, the immune response and neuronal function, as well as in their associated pathologies. The Nuclear Receptor Signaling Atlas (NURSA) is a Consortium focused around a Hub website (www.nursa.org) that annotates and integrates diverse ‘omics datasets originating from the published literature and NURSA-funded Data Source Projects (NDSPs). These datasets are then exposed to the scientific community on an Open Access basis through user-friendly data browsing and search interfaces. Here, we describe the redesign of the Hub, version 3.0, to deploy “Web 2.0” technologies and add richer, more diverse content. The Molecule Pages, which aggregate information relevant to NR signaling pathways from myriad external databases, have been enhanced to include resources for basic scientists, such as post-translational modification sites and targeting miRNAs, and for clinicians, such as clinical trials. A portal to NURSA’s Open Access, PubMed-indexed journal Nuclear Receptor Signaling has been added to facilitate manuscript submissions. Datasets and information on reagents generated by NDSPs are available, as is information concerning periodic new NDSP funding solicitations. Finally, the new website integrates the Transcriptomine analysis tool, which allows for mining of millions of richly annotated public transcriptomic data points in the field, providing an environment for dataset re-use and citation, bench data validation and hypothesis generation. We anticipate that this new release of the NURSA database will have tangible, long term benefits for both basic and clinical research in this field.

Nuclear receptor atlas of female mouse liver parenchymal, endothelial, and Kupffer cells

The liver consists of different cell types that together synchronize crucial roles in liver homeostasis. Since nuclear receptors constitute an important class of drug targets that are involved in a wide variety of physiological processes, we have composed the hepatic cell type-specific expression profile of nuclear receptors to uncover the pharmacological potential of liver-enriched nuclear receptors. Parenchymal liver cells (hepatocytes) and liver endothelial and Kupffer cells were isolated from virgin female C57BL/6 wild-type mice using collagenase perfusion and counterflow centrifugal elutriation. The hepatic expression pattern of 49 nuclear receptors was generated by real-time quantitative PCR using the NUclear Receptor Signaling Atlas (NURSA) program resources. Thirty-six nuclear receptors were expressed in total liver. FXR-α, EAR2, LXR-α, HNF4-α, and CAR were the most abundantly expressed nuclear receptors in liver parenchymal cells. In contrast, NUR77, COUP-TFII, LXR-α/β, FXR-α, and EAR2 were the most highly expressed nuclear receptors in endothelial and Kupffer cells. Interestingly, members of orphan receptor COUP-TF family showed a distinct expression pattern. EAR2 was highly and exclusively expressed in parenchymal cells, while COUP-TFII was moderately and exclusively expressed in endothelial and Kupffer cells. Of interest, the orphan receptor TR4 showed a similar expression pattern as the established lipid sensor PPAR-γ. In conclusion, our study provides the most complete quantitative assessment of the nuclear receptor distribution in liver reported to date. Our gene expression catalog suggests that orphan nuclear receptors such as COUP-TFII, EAR2, and TR4 may be of significant importance as novel targets for pharmaceutical interventions in liver.

Research Resource: dkCOIN, the National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK) Consortium Interconnectivity Network: A Pilot Program to Aggregate Research Resources Generated by Multiple Research Consortia

The National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK) supports multiple basic science consortia that generate high-content datasets, reagent resources, and methodologies, in the fields of kidney, urology, hematology, digestive, and endocrine diseases, as well as metabolic diseases such as diabetes and obesity. These currently include the Beta Cell Biology Consortium, the Nuclear Receptor Signaling Atlas, the Diabetic Complications Consortium, and the Mouse Metabolic Phenotyping Centers. Recognizing the synergy that would accrue from aggregating information generated and curated by these initiatives in a contiguous informatics network, we created the NIDDK Consortium Interconnectivity Network (dkCOIN; www.dkcoin.org). The goal of this pilot project, organized by the NIDDK, was to establish a single point of access to a toolkit of interconnected resources (datasets, reagents, and protocols) generated from individual consortia that could be readily accessed by biologists of diverse backgrounds and research interests. During the pilot phase of this activity dkCOIN collected nearly 2000 consortium-curated resources, including datasets (functional genomics) and reagents (mouse strains, antibodies, and adenoviral constructs) and built nearly 3000 resource-to-resource connections, thereby demonstrating the feasibility of further extending this database in the future. Thus, dkCOIN promises to be a useful informatics solution for rapidly identifying useful resources generated by participating research consortia.

Research Resource: Comparative Nuclear Receptor Atlas: Basal and Activated Peritoneal B-1 and B-2 Cells

Naïve murine B cells are typically divided into three subsets based on functional and phenotypic characteristics: innate-like B-1 and marginal zone B cells vs. adaptive B-2 cells, also known as follicular or conventional B cells. B-1 cells, the innate-immune-like component of the B cell lineage are the primary source of natural antibodies and have been shown to modulate autoimmune diseases, human B-cell leukemias, and inflammatory disorders such as atherosclerosis. On the other hand, B-2 cells are the principal mediators of the adaptive humoral immune response and represent an important pharmacological target for various conditions including rheumatoid arthritis, lupus erythematosus, and lymphomas. Using the resources of the Nuclear Receptor Signaling Atlas program, we used quantitative real-time PCR to assess the complement of the 49 murine nuclear receptor superfamily expressed in quiescent and toll-like receptor (TLR)-stimulated peritoneal B-1 and B-2 cells. We report the expression of 24 nuclear receptors in basal B-1 cells and 25 nuclear receptors in basal B-2 cells, with, in some cases, dramatic changes in response to TLR 4 or TLR 2/1 stimulation. Comparative nuclear receptor profiling between B-1 and peritoneal B-2 cells reveals a highly concordant expression pattern, albeit at quantitatively dissimilar levels. We also found that splenic B cells express 23 nuclear receptors. This catalog of nuclear receptor expression in B-1 and B-2 cells provides data to be used to better understand the specific roles of nuclear receptors in B cell function, chronic inflammation, and autoimmune disease.

Research Resource: Tissue-Specific Transcriptomics and Cistromics of Nuclear Receptor Signaling: A Web Research Resource

Nuclear receptors (NRs) are ligand-regulated transcription factors that recruit coregulators and other transcription factors to gene promoters to effect regulation of tissue-specific transcriptomes. The prodigious rate at which the NR signaling field has generated high content gene expression and, more recently, genome-wide location analysis datasets has not been matched by a committed effort to archiving this information for routine access by bench and clinical scientists. As a first step towards this goal, we searched the MEDLINE database for studies, which referenced either expression microarray and/or genome-wide location analysis datasets in which a NR or NR ligand was an experimental variable. A total of 1122 studies encompassing 325 unique organs, tissues, primary cells, and cell lines, 35 NRs, and 91 NR ligands were retrieved and annotated. The data were incorporated into a new section of the Nuclear Receptor Signaling Atlas Molecule Pages, Transcriptomics and Cistromics, for which we designed an intuitive, freely accessible user interface to browse the studies. Each study links to an abstract, the MEDLINE record, and, where available, Gene Expression Omnibus and ArrayExpress records. The resource will be updated on a regular basis to provide a current and comprehensive entrez into the sum of transcriptomic and cistromic research in this field.

WebWatch

WebWatch

Signals from NURSA

By distilling the process of building a web site down to theclickofabutton,weblogs,orblogs,removemany of the technological impediments of the Internet, empowering scientists to both inform peers and educate students in their respective fields in a highly accessible and distributable format. Molecular Endocrinology is engaged in an ongoing partnership with Nuclear Receptor Signaling Atlas (NURSA) web resource, one of whose missions is to act as a communications hub for the nuclear receptor and coregulator research communities. For example, Molecular Endocrinology articles of particular interest to the nuclear receptor and coregulator fields are often highlighted on the NURSA web site. Furthermore, links to generic resources such as NCBI’s Entrez Gene and PubMed are also provided where appropriate. Commensurate with its goal of disseminating important, late-breaking research to the scientific community, NURSA’s bioinformatics group earlier this year launched a new blog, Signals, with features to enable researchers to keepuptodatewithcurrenteventsandconferences.With busy schedules and finite financial resources, it’s impossible to attend all the meetings we would like to, but in this age of enhanced communication, there’s little reason thisshouldbeanobstacletokeepingscientistsapprisedof the concepts and themes emerging from major conferences. Consistent with journal policies on prepublication ofdetailedresearchfindings,thisseemsaperfectnichefor a blog to fill. Earlier this year, the second Jensen Symposium on Nuclear Receptors at the University of Cincinnati recognized the trailblazing achievements of Elwood Jensen in nuclear receptor biology nearly 50 yr ago. While this is a small conference,itisneverthelessoneofgreatsignificance,and this year’s gathering again attracted many notable names, both established and upcoming, in nuclear receptor and coregulator biology. At the invitation of the meeting organizers, Sohaib Khan and Jorge Muscat, Signals provided short, high-level summaries of keynote and plenary session talks, giving readers an insight into current research and thinking in some of the leading laboratories in the field. Leveraging existing features of the NURSA web site, these summaries link to the NURSA Molecule Pages where possible, to provide readers with rapid, convenient access to contextual links. To view Signals’ report on the Jensen Symposium, please visit www. nursa.org/jensen2009.

Molecular Endocrinology: A Portal for Enhanced Access and Utility of the Nuclear Receptor Signaling Atlas (NURSA) Web Resource

This issue of Molecular Endocrinology features a minireview that describes the evolution and status of The Nuclear Receptor Signaling Atlas (NURSA). This National Institutes of Health-sponsored consortium was launched in 2002 to generate high-content, discovery-driven research datasets as a platform for developing an understanding of the role of nuclear receptors and coregulators in normal metabolic processes and pathologies. It was charged with integrating its research output of these component projects into an informatics framework and a supporting website for distributing the datasets and their analyses to the wider research community. A second, equally important challenge was to leverage legacy knowledge in the nuclear receptor and coregulator field and integrate it with Consortium datasets to create a unique resource that would be accessible to the entire scientific community. In addition to the support of the community, NURSA’s success relies on forging partnerships with the existing publishing infrastructure in the field. To this end, the NURSA consortium and Molecular Endocrinology have entered a partnership that is unique in scientific publishing. Specifically, in 2006, an agreement was made in which the NURSA curation team would annotate relevant Molecular Endocrinology articles back to 2002. These annotations would then be used to create direct links to NURSA Molecule Pages from the web versions of the articles, providing readers with a wealth of contextual information on a molecule relevant to that article. The NURSA Molecule Page is designed to integrate in a condensed, easily navigated form the essential elements of the mechanism, biology, and pathology of nuclear receptors, their coregulators, and their ligands. Recognizing that retrieving nuclear receptor- and coregulator-specific information in monolithic biological databases like NCBI and UniProt can be a daunting prospect, NURSA curators sifted these resources, gleaned the most important and essential descriptors (GeneID, UniProt ID, RefSeqs), and spliced them together in a single menu-driven interface. In addition, the Molecule Pages tie in relevant content from smaller specialist databases such as those curating crystal structures (PDB), splicing events (FastDB), expression (MousePAT, Allen Brain Atlas), and posttranslational modifications (Phosphosite). The collaboration between Molecular Endocrinology and NURSA also includes features designed to aid basic researchers in identifying translational aspects of their work. Specifically, the Molecule Page contains a distillation of databases documenting the key pathological associations of nuclear receptors and coregulators (HPRD, GAD, OMIM, in addition to NURSA’s own in-house curation) and the physiological consequences of their disruption in animal models. Finally, a new Google-powered search engine on the Molecule Page accommodates search strategies based on a specific disease or phenotype. The goals of the Molecule Page require the support of the research community, the National Institutes of Health, and The Endocrine Society. Accordingly, NURSA is developing features in the Molecule Pages that will afford motivated researchers to add to the NURSA knowledge base. Any of the components of the Molecule Pages that are based around literature citations will soon have built into them an interface in which a researcher can contribute articles for annotation. NURSA also welcomes the opportunity to host more extensive curational efforts. We urge all of our readers to visit and exploit the wealth of information available on the NURSA web site (www.nursa.org). Molecular Endocrinology is pleased to have been a part of this unique effort to enhance the accessibility and utility of comprehensive datasets to the field of endocrinology, and we look forward to new developments and resources provided by NURSA. In that regard, please look for a semiannual “What’s New in NURSA” editorial feature that will highlight new datasets and research tools provided by NURSA. We also hope to expand our journal’s role as a portal to other scientific collaborations and consortia that provide novel web-based datasets, informatics tools, and tutorials for the continued benefit of endocrinology research.

Minireview: Evolution of NURSA, the Nuclear Receptor Signaling Atlas

Nuclear receptors and coregulators are multifaceted players in normal metabolic and homeostatic processes in addition to a variety of disease states including cancer, inflammation, diabetes, obesity, and atherosclerosis. Over the past 7 yr, the Nuclear Receptor Signaling Atlas (NURSA) research consortium has worked toward establishing a discovery-driven platform designed to address key questions concerning the expression, organization, and function of these molecules in a variety of experimental model systems. By applying powerful technologies such as quantitative PCR, high-throughput mass spectrometry, and embryonic stem cell manipulation, we are pursuing these questions in a series of transcriptomics-, proteomics-, and metabolomics-based research projects and resources. The consortium's web site (www.nursa.org) integrates NURSA datasets and existing public datasets with the ultimate goal of furnishing the bench scientist with a comprehensive framework for hypothesis generation, modeling, and testing. We place a strong emphasis on community input into the development of this resource and to this end have published datasets from academic and industrial laboratories, established strategic alliances with Endocrine Society journals, and are developing tools to allow web site users to act as data curators. With the ongoing support of the nuclear receptor and coregulator signaling communities, we believe that NURSA can make a lasting contribution to research in this dynamic field.

Identification and Characterization of a Novel Nuclear Protein Complex Involved in Nuclear Hormone Receptor-mediated Gene Regulation

NRC/NCoA6 plays an important role in mediating the effects of ligand-bound nuclear hormone receptors as well as other transcription factors. NRC interacting factor 1 (NIF-1) was cloned as a novel factor that interacts in vivo with NRC. Although NIF-1 does not directly interact with nuclear hormone receptors, it enhances activation by nuclear hormone receptors presumably through its interaction with NRC. To further understand the cellular and biological function of NIF-1, we identified NIF-1-associated proteins by in-solution proteolysis followed by mass spectrometry. The identified components revealed factors involved in histone methylation and cell cycle control and include Ash2L, RbBP5, WDR5, HCF-1, DBC-1, and EMSY. Although the NIF-1 complex contains Ash2L, RbBP5, and WDR5, suggesting that the complex might methylate histone H3-Lys-4, we found that the complex contains a H3 methyltransferase activity that modifies a residue other than H3-Lys-4. The identified components form at least two distinctly sized NIF-1 complexes. DBC-1 and EMSY were identified as integral components of an NIF-1 complex of approximately 1.5 MDa and were found to play an important role in the regulation of nuclear receptor-mediated transcription. Stimulation of the Sox9 and HoxA1 genes by retinoic acid receptor-alpha was found to require both DBC-1 and EMSY in addition to NIF-1 for maximal transcriptional activation. Interestingly, NRC was not identified as a component of the NIF-1 complex, suggesting that NIF-1 and NRC do not exist as stable in vitro purified complexes, although the separate NIF-1 and NRC complexes appear to functionally interact in the cell.

Endocrine-Related Resources from the National Institutes of Health

Endocrine-Related Resources from the National Institutes of Health

Endocrine-Related Resources from the National Institutes of Health

Endocrine-Related Resources from the National Institutes of Health

Endocrine-Related Resources from the National Institutes of Health

Endocrine-Related Resources from the National Institutes of Health

Endocrine-Related Resources from the National Institutes of Health

Endocrine-Related Resources from the National Institutes of Health

Endocrine-Related Resources from the National Institutes of Health

Endocrine-Related Resources from the National Institutes of Health

Endocrine-Related Resources from the National Institutes of Health

Endocrine-Related Resources from the National Institutes of Health

Endocrine-Related Resources from the National Institutes of Health

Endocrine-Related Resources from the National Institutes of Health

The Nuclear Receptor Signaling Atlas: Catalyzing Understanding of Thyroid Hormone Signaling and Metabolic Control

The Nuclear Receptor Signaling Atlas (NURSA) was established as a trans-National Institutes of Health resource to develop, accrue, and communicate information about the nuclear receptor (NR) superfamily of ligand-dependent and -independent transcription factors. NRs have broad involvement in the regulation of development, reproduction, and metabolism. Receptors for thyroid hormones represent important members of the NR superfamily with key roles in development and homeostasis. NURSA has attempted to create a resource for information on NRs, associated coregulators, and ligands. The Web portal (www.NURSA.org) creates a window through which the general research community can gain access to data generated by NURSA investigators and linked from other sources. The molecule pages provide detailed curated information about the NR superfamily and allow the user to search for information useful to their own specific research problems. With the application of bioinformatics solutions, analyses of large amounts of data can be utilized to validate and/or create hypotheses that will ultimately lead to translational opportunities to take information about NRs, in general, and thyroid receptors, in particular to potential clinical applications.