Nasal gene expression differentiates COPD from controls and overlaps bronchial gene expression

Background

Nasal gene expression profiling is a promising method to characterize COPD non-invasively. We aimed to identify a nasal gene expression profile to distinguish COPD patients from healthy controls. We investigated whether this COPD-associated gene expression profile in nasal epithelium is comparable with the profile observed in bronchial epithelium.

Methods

Genome wide gene expression analysis was performed on nasal epithelial brushes of 31 severe COPD patients and 22 controls, all current smokers, using Affymetrix Human Gene 1.0 ST Arrays. We repeated the gene expression analysis on bronchial epithelial brushes in 2 independent cohorts of mild-to-moderate COPD patients and controls.

Results

In nasal epithelium, 135 genes were significantly differentially expressed between severe COPD patients and controls, 21 being up- and 114 downregulated in COPD (false discovery rate?<?0.01). Gene Set Enrichment Analysis (GSEA) showed significant concordant enrichment of COPD-associated nasal and bronchial gene expression in both independent cohorts (FDR_GSEA <?0.001).

Conclusion

We identified a nasal gene expression profile that differentiates severe COPD patients from controls. Of interest, part of the nasal gene expression changes in COPD mimics differentially expressed genes in the bronchus. These findings indicate that nasal gene expression profiling is potentially useful as a non-invasive biomarker in COPD.

Trial registration

ClinicalTrials.gov registration number NCT01351792 (registration date May 10, 2011), ClinicalTrials.gov registration number NCT00848406 (registration date February 19, 2009), ClinicalTrials.gov registration number NCT00807469 (registration date December 11, 2008).

     

Deficiency in the organic cation transporters 1 and 2 (Oct1/Oct2 [Slc22a1/Slc22a2]) in mice abolishes renal secretion of organic cations

The polyspecific organic cation transporters 1 and 2 (Oct1 and -2) transport a broad range of substrates, including drugs, toxins, and endogenous compounds. Their strategic localization in the basolateral membrane of epithelial cells in the liver, intestine (Oct1), and kidney (Oct1 and Oct2) suggests that they play an essential role in removing noxious compounds from the body. We previously showed that in Oct1(-/-) mice, the hepatic uptake and intestinal excretion of organic cations are greatly reduced. Since Oct1 and Oct2 have extensively overlapping substrate specificities, they might be functionally redundant. To investigate the pharmacologic and physiologic roles of these proteins, we generated Oct2 single-knockout and Oct1/2 double-knockout mice. Oct2(-/-) and Oct1/2(-/-) mice are viable and fertile and display no obvious phenotypic abnormalities. Absence of Oct2 in itself had little effect on the pharmacokinetics of tetraethylammonium (TEA), but in Oct1/2(-/-) mice, renal secretion of this compound was completely abolished, leaving only glomerular filtration as a TEA clearance mechanism. As a consequence, levels of TEA were substantially increased in the plasma of Oct1/2(-/-) mice. This study shows that Oct1 and Oct2 together are essential for renal secretion of (small) organic cations. A deficiency in these proteins may thus result in increased drug sensitivity and toxicity.     

Bringing science and pragmatism together a tiered approach for modelling toxicological impacts in LCA

Goal, Scope and Background  The EU 5^th framework project OMNIITOX will develop models calculating characterisation factors for assessing the potential toxic impacts of chemicals within the framework of LCA. These models will become accessible through a web-based information system. The key objective of the OMNIITOX project is to increase the coverage of substances by such models. In order to reach this objective, simpler models which need less but available data, will have to be developed while maintaining scientific quality. Methods. Experience within the OMNIITOX project has taught that data availability and quality are crucial issues for calculating characterisation factors. Data availability determines whether calculating characterisation factors is possible at all, whereas data quality determines to what extent the resulting characterisation factors are reliable. Today, there is insufficient knowledge and/or resources to have high data availability as well as high data quality and high model quality at the same time. Results  The OMNIITOX project is developing two inter-related models in order to be able to provide LCA impact assessment characterisation factors for toxic releases for as broad a range of chemicals as possible: 1) A base model representing a state-of-the-art multimedia model and 2) a simple model derived from the base model using statistical tools. Discussion. A preliminary decision tree for using the OMNIITOX information system (IS) is presented. The decision tree aims to illustrate how the OMNIITOX IS can assist an LCA practitioner in finding or deriving characterisation factors for use in life cycle impact assessment of toxic releases. Conclusions and Outlook  Data availability and quality are crucial issues when calculating characterisation factors for the toxicity impact categories. The OMNIITOX project is developing a tiered model approach for this. It is foreseen that a first version of the base model will be ready in late summer of 2004, whereas a first version of the simple base model is expected a few months later.     

Model and test in a fungus of the probability that beneficial mutations survive drift

Determining the probability of fixation of beneficial mutations is critically important for building predictive models of adaptive evolution. Despite considerable theoretical work, models of fixation probability have stood untested for nearly a century. However, recent advances in experimental and theoretical techniques permit the development of models with testable predictions. We developed a new model for the probability of surviving genetic drift, a major component of fixation probability, for novel beneficial mutations in the fungus Aspergillus nidulans, based on the life-history characteristics of its colony growth on a solid surface. We tested the model by measuring the probability of surviving drift in 11 adapted strains introduced into wild-type populations of different densities. We found that the probability of surviving drift increased with mutant invasion fitness, and decreased with wild-type density, as expected. The model accurately predicted the survival probability for the majority of mutants, yielding one of the first direct tests of the extinction probability of beneficial mutations.     

Smad gene expression in pulmonary fibroblasts: indications for defective ECM repair in COPD

Background

Endothelial dysfunction is a major complication of pulmonary endarterectomy (PTE) that can lead to pulmonary edema and persistent pulmonary hypertension. We hypothesized that endothelial dysfunction is related to increased endothelial-cell (EC) death.

Methods

In piglets, the left pulmonary artery (PA) was ligated to induce lung ischemia then reimplanted into the main PA to reperfuse the lung. Animals sacrificed 5 weeks after ligation (n = 5), 2 days after reperfusion (n = 5), or 5 weeks after reperfusion (n = 5) were compared to a sham-operated group (n = 5). PA vasoreactivity was studied and eNOS assayed. EC apoptosis was assessed by TUNEL in the proximal and distal PA and by caspase-3 activity assay in the proximal PA. Gene expression of pro-apoptotic factors (thrombospondin-1 (Thsp-1) and plasminogen activator inhibitor 1 (PAI-1)) and anti-apoptotic factors vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF) was investigated by QRT-PCR.

Results

Endothelium-dependent relaxation was altered 5 weeks after ligation (p = 0.04). The alterations were exacerbated 2 days after reperfusion (p = 0.002) but recovered within 5 weeks after reperfusion. EC apoptosis was increased 5 weeks after PA ligation (p = 0.02), increased further within 2 days after reperfusion (p < 0.0001), and returned to normal within 5 weeks after reperfusion. Whereas VEGF and bFGF expressions remained unchanged, TSP and PAI-1 expressions peaked 5 weeks after ligation (p = 0.001) and returned to normal within 2 days after reperfusion.

Conclusion

Chronic lung ischemia induces over-expression of pro-apoptotic factors. Lung reperfusion is followed by a dramatic transient increase in EC death that may explain the development of endothelial dysfunction after PE. Anti-apoptotic agents may hold considerable potential for preventing postoperative complications.     

Integrated stratigraphy of the Early Miocene lacustrine deposits of Pag Island (SW Croatia): Palaeovegetation and environmental changes in the Dinaride Lake System

An integrated stratigraphic study of a Neogene lacustrine succession on the Pag Island (Croatia), combining quantitative pollen analysis, magnetostratigraphy, cyclostratigraphy, biostratigraphy and gamma-ray measurements, provides new insights into orbitally controlled variations in palaeo-vegetation and depositional patterns in the Dinaride Lake System. The quantitative palynological record shows a cyclical pattern of vegetation changes that closely corresponds to sedimentological patterns. The intervals with a high abundance of thermophilous and xeric indicators, suggesting a warm and dry climate, generally coincide with intervals of frequent lignite deposition and shallow lake facies. This suggests that both records are dominantly controlled by variations in past climatic conditions and lake level. Our data show two large-scale warming and shallowing-upward cycles, which are interpreted to be forced by the ~ 100 kyr eccentricity cycle of the Earth's orbit. Magnetostratigraphic data of the examined section reveal a long (113 m) reversed polarity interval, followed by a 7 m thick interval of normal polarity at the top. The inferred depositional rate of ~ 0.3 mm/yr, combined with biostratigraphic constraints by mollusks, suggests that the most logical correlation of the reversed interval is to chron C5Cr. This indicates that the Pag succession was deposited between 17.1 and 16.7 Ma and that it corresponds to the Burdigalian Stage of the Early Miocene, and the regional Karpatian Stage of the Central Paratethys. The high relative percentage of thermophilous pollen taxa, Engelhardia and Taxodium-type being the most prominent, generally indicates a subtropical humid climate for the SW Croatian part of the Dinaride Lake System. The observed warming trend is possibly related to the onset of the Miocene Climatic Optimum.