Identification of a novel regulatory mechanism for the disease associated protein, uPAR

Expression quantitative trait loci (eQTLs), as determined through a series of statistical association studies collectively known as genome-wide association (GWA) studies, have provided us with a hypothesis free approach for the investigation into regulatory loci for disease and disease-associated proteins. This has led to the identification of multiple novel gene-disease interactions, especially in the field of respiratory medicine. This review describes the case study of a GWA approach in order to identify eQTLs for the soluble form of the urokinase plasminogen activator receptor (uPAR), a protein associated with obstructive respiratory disease. Molecular and cellular investigations based on the eQTLs identified for this GWA study has led to the identification of a novel regulatory mechanism with implications in the disease processes with which this protein is associated. This highlights the potential of eQTLs defined associations in the identification of novel mechanisms, with implications in disease.peer-reviewe

The Pion-Photon Transition Form Factor and New Physics in the Tau Sector

Recent measurement of the $\gamma\gamma^\ast$ form factor of the neutral pion in the high $Q^2$ region disagrees with {\em a priori} predictions of QCD-based calculations. We comment on existing explanations, and analyze a possibility that this discrepancy is not due to poorly understood QCD effects, but is a result of some new physics beyond the standard model (SM). We show that such physics would necessarily involve a new neutral light state with mass close to the mass of $\pi^0$, and with stronger than $\pi^0$ couplings to heavier SM flavors such as $c$, $\tau$, and $b$. It is found that only the coupling to the $\tau$ lepton can survive the existing constraints and lead to the observed rise of the pion form factor relative to $Q^{-2}$ at high $Q^2$. We perform numerical fits to data and determine the allowed range of masses and couplings for such new particles. This range of masses and couplings could also reduce or eliminate the tension between the $e^+e^-$ and $\tau$ decay determinations of the hadronic vacuum polarization. Dedicated experimental analysis of $\tau$ pair production in association with such new states should provide a conclusive test of the new physics hypothesis as an explanation to the pion form factor rise. We also comment on the calculations of the pion form factor in the chiral quark model, and point out a possible dynamical origin of the quark mass scale inferred from the form factor measurement.Comment: 13 pages, 6 figures, revtex4-1; v2: additional references, improved discussion of pion mixing case, published versio

Targeting chemokines : new drugs for old diseases

Chemokine receptor antagonists are set to become novel important pharmacological tools within the current therapeutic repertoire available for the management of various inflammatory conditions.peer-reviewe

Genetic risk factors for the development of allergic disease identified by genome-wide association

An increasing proportion of the worldwide population is affected by allergic diseases such as allergic rhinitis (AR), atopic dermatitis (AD) and allergic asthma and improved treatment options are needed particularly for severe, refractory disease. Allergic diseases are complex and development involves both environmental and genetic factors. Although the existence of a genetic component for allergy was first described almost 100 years ago, progress in gene identification has been hindered by lack of high throughput technologies to investigate genetic variation in large numbers of subjects. The development of Genome-Wide Association Studies (GWAS), a hypothesis-free method of interrogating large numbers of common variants spanning the entire genome in disease and non-disease subjects has revolutionised our understanding of the genetics of allergic disease. Susceptibility genes for asthma, AR and AD have now been identified with confidence, suggesting there are common and distinct genetic loci associated with these diseases, providing novel insights into potential disease pathways and mechanisms. Genes involved in both adaptive and innate immune mechanisms have been identified, notably including multiple genes involved in epithelial function/secretion, suggesting that the airway epithelium may be particularly important in asthma. Interestingly, concordance/discordance between the genetic factors driving allergic traits such as IgE levels and disease states such as asthma have further supported the accumulating evidence for heterogeneity in these diseases. While GWAS have been useful and continue to identify novel genes for allergic diseases through increased sample sizes and phenotype refinement, future approaches will integrate analyses of rare variants, epigenetic mechanisms and eQTL approaches, leading to greater insight into the genetic basis of these diseases. Gene identification will improve our understanding of disease mechanisms and generate potential therapeutic opportunities

The role and regulation of the urokinase receptor in asthma and COPD

The urokinase plasminogen activator receptor (PLAUR) is a membrane anchored receptor that has been associated with a number of disease states. In these diseases, elevated receptor levels were associated with increased disease aggressiveness and higher mortality rates. Through genetic studies PLAUR has been identified as an asthma susceptibility gene. In these studies, coding and untranslated region single nucleotide polymorphisms showed association with asthma diagnosis and decline in lung function. In addition, association with baseline lung function in smokers and PLAUR SNPs was identified. This suggests that PLAUR plays a role in respiratory disease. Work presented in this thesis aimed to i) identify whether serum levels of PLAUR are associated with obstructive lung disease and lung function parameters, ii) identify novel regulatory mechanisms determining PLAUR levels, both at the genetic level in primary bronchial epithelial cells and at the protein level for serum PLAUR, iii) explore a role for the different isoforms in asthma and COPD and iv) determine novel variation in the PLAUR gene and 5` and 3` distal regions through next generation sequencing. Levels of the soluble cleaved form of PLAUR in serum were determined to be significantly elevated in COPD and asthma subjects compared to a control population. This identified an association between the soluble cleaved receptor and disease per se. However, PLAUR levels in serum could not be related to lung function parameters. With regards to receptor regulation, a genome-wide association study identified a novel post-translational PLAUR regulatory mechanism. This involved key SNPs in the human plasma kallikrein gene promoter that directed human plasma kallikrein enzymatic activity to cleave PLAUR in a post-translational mechanism. PLAUR gene regulation was also investigated via molecular biology, identifying that in primary bronchial epithelial cells, PLAUR regulation involves the gene’s 5 prime and 3 prime untranslated regions. Investigation of regulation under multiple stimulations pertinent to respiratory disease identified that cigarette smoke extract selectively elevated the soluble spliced variant of the receptor through a three prime untranslated region mechanism. This suggests that bronchial epithelial damage driven by cigarette smoke may be at least partially mediated by the soluble spliced form of PLAUR. Overexpression of PLAUR identified that the receptor has an important role in regulating primary bronchial epithelial cell function, including migration and rate of mitochondrial activity. Interestingly, results identified isoform specific roles for the different forms of the receptor suggesting that variant-specific over-expression of PLAUR could have diverse effects on cell function. Importantly this study was also the first to define a role for the soluble spliced form of PLAUR. Investigation into variation in the PLAUR gene and surrounding regions through next generation sequencing in asthma (n=200) and control (n=200) populations identified a number of novel variants including 4 variants unique to asthma population. In summary, the work described in this thesis has identified a novel association between serum soluble cleaved PLAUR and obstructive lung disease, as well defining novel genetic and post-translational regulatory mechanisms for PLAUR, importantly defining isoform specific PLAUR regulation for the first time. This work has also identified novel isoform specific roles for PLAUR, which have significant modulatory effects on bronchial epithelial cell function, and has through next generation sequencing furthered knowledge on universal and asthma specific PLAUR variation

Response

We thank Dr. Rasmussen and colleagues for their comments on our work outlined in “Genome-wide protein QTL mapping identifies human plasma kallikrein as a post-translational regulator of serum uPAR levels” (FASEB J. 28, 923–934) and the opportunity to respond to key points

Urokinase plasminogen activator receptor polymorphisms and airway remodelling in asthma

PLAUR polymorphisms and levels are associated with markers of airway remodelling in lung biopsies of asthma patients http://ow.ly/X5Sr

Genome-wide protein QTL mapping identifies human plasma kallikrein as a post-translational regulator of serum uPAR levels

The soluble cleaved urokinase plasminogen activator receptor (scuPAR) is a circulating protein detected in multiple diseases, including various cancers, cardiovascular disease, and kidney disease, where elevated levels of scuPAR have been associated with worsening prognosis and increased disease aggressiveness. We aimed to identify novel genetic and biomolecular mechanisms regulating scuPAR levels. Elevated serum scuPAR levels were identified in asthma (n=514) and chronic obstructive pulmonary disease (COPD; n=219) cohorts when compared to controls (n=96). In these cohorts, a genome-wide association study of serum scuPAR levels identified a human plasma kallikrein gene (KLKB1) promoter polymorphism (rs4253238) associated with serum scuPAR levels in a control/asthma population (P=1.17×10−7), which was also observed in a COPD population (combined P=5.04×10−12). Using a fluorescent assay, we demonstrated that serum KLKB1 enzymatic activity was driven by rs4253238 and is inverse to scuPAR levels. Biochemical analysis identified that KLKB1 cleaves scuPAR and negates scuPAR's effects on primary human bronchial epithelial cells (HBECs) in vitro. Chymotrypsin was used as a proproteolytic control, while basal HBECs were used as a control to define scuPAR-driven effects. In summary, we reveal a novel post-translational regulatory mechanism for scuPAR using a hypothesis-free approach with implications for multiple human diseases

Physics Opportunities with the 12 GeV Upgrade at Jefferson Lab

This white paper summarizes the scientific opportunities for utilization of the upgraded 12 GeV Continuous Electron Beam Accelerator Facility (CEBAF) and associated experimental equipment at Jefferson Lab. It is based on the 52 proposals recommended for approval by the Jefferson Lab Program Advisory Committee.The upgraded facility will enable a new experimental program with substantial discovery potential to address important topics in nuclear, hadronic, and electroweak physics.Comment: 64 page