A population-based study describing characteristics, survival and the effect of TKI treatment on patients with EGFR mutated stage IV NSCLC in the Netherlands

INTRODUCTION: Since 2011, treatment guidelines advise targeted therapy (tyrosine kinase inhibitor, TKI) for patients with activating epidermal growth factor receptor (EGFR) mutations (EGFR+) in non-small cell lung cancer (NSCLC). We describe characteristics, first line treatment and survival of patients diagnosed with EGFR+ NSCLC in a European population, focussing on age, gender and trends over time and compare to the whole group and EGFR-. METHODS: All patients with non-squamous NSCLC stage IV, diagnosed 2011-2018, were identified from the population-based Netherlands Cancer Registry (N = 31,291). RESULTS: Among all, 7.0% were registered to be EGFR+, with highest prevalence in females 65 years to 23.6 months in the EGFR+ group <50 years treated with TKI. Over time, OS for the whole group increased by 0.6 months, of which 33% due to TKI treatment in EGFR+. The increase was strongest in females <50 years, where median OS almost doubled to 12.4 months. In the EGFR+, multivariable hazard of death was most strongly associated with the use of TKI (HR 0.45(0.41-0.49)). Of the patients with EGFR+ this space need or not, 71% received TKI treatment. Being young reduced the hazard of death (HR 0.71(95%CI:0.59-0.85)) irrespective of treatment, while male gender increased the hazard of death (HR 1.22(95%CI:1.11-1.33)). CONCLUSION: At population level, TKI treatment in patients with non-squamous NSCLC stage IV EGFR+ has very strong beneficial effects on outcome. Of the improvement in OS that was made over the years for the whole group, about one third seems to be attributed to TKI treatment in EGFR+ patients

AGER expression and alternative splicing in bronchial biopsies of smokers and never smokers

Abstract Cigarette smoking is one of the major risk factors for the development of chronic obstructive pulmonary disease (COPD). Evidence is accumulating that Receptor for Advanced Glycation-End products (RAGE)-signaling is a key pathway in the pathophysiology of COPD. To date, it is unknown how smoking affects RAGE expression. In the current study, we investigated the effect of smoking on AGER, the gene encoding RAGE, expression and on alternative splicing of AGER. To this end, we conducted RNA-Seq on bronchial biopsies for asymptomatic smokers (n = 36) and never smokers (n = 40). Total AGER gene expression was accessed using DESeq2, while alternative splicing was investigated by measuring the number of specific split reads spanning exon-exon junctions and the total split reads. One of the major isoforms of RAGE is endogenous soluble (es) RAGE, an anti-inflammatory decoy receptor, making up for approximately 10% of the total amount of soluble (s)RAGE. We found that smokers show decreased total gene expression of AGER in bronchial biopsies, while the relative abundance of the esRAGE isoform is increased. Furthermore, no difference in the serum levels of total sRAGE were observed between smokers and non-smokers. Our data indicates that smoking initiates a protective anti-inflammatory mechanism with decreased expression of the pro-inflammatory gene AGER and increased relative abundance of the anti-inflammatory isoform esRAGE

The legacy effect of synthetic N fertiliser

Cumulative crop recovery of synthetic fertiliser nitrogen (N) over several cropping seasons (legacy effect) generally receives limited attention. The increment in crop N uptake after the first-season uptake from fertiliser can be expressed as a fraction (∆RE) of annual N application rate. This study aims to quantify ∆RE using data from nine long-term experiments (LTEs). As such, ∆RE is the difference between first season (RE1st) and long-term (RELT) recovery of synthetic fertiliser N. In this study, RE1st was assessed either by the 15N isotope method, or by a zero-N subplot freshly superimposed on a long-term fertilised LTE treatment plot. RELT was calculated by comparing N uptake in the total aboveground crop biomass between a long-term fertilised and long-term control (zero-N) treatment. Using a mixed linear effect model, the effects of climate, crop type, experiment duration, average N rate, and soil clay content on ∆RE were evaluated. Because the experimental setup required for calculation of ∆RE is relatively rare, only nine suitable LTEs were found. Across these nine LTEs in Europe and North America, mean ∆RE was 24.4% (±12.0%, 95% CI) of annual N application, with higher values for winter wheat than for maize. This result shows that fertiliser-N retained in the soil and stubble may contribute substantially to crop N uptake in subsequent years. Our results suggest that an initial recovery of 43.8% (±11%, 95% CI) of N application may increase to around 66.0% (±15%, 95% CI) on average over time. Furthermore, we found that ∆RE was not clearly related to long-term changes in topsoil total N stock. Our findings show that the - often used - first year recovery of synthetic fertiliser N application does not express the full effect of fertiliser application on crop nutrition. The fertiliser contribution to soil N supply should be accounted for when exploring future scenarios on N cycling, including crop N requirements and N balance schemes

Gene expression profiling of bronchial brushes is associated with the level of emphysema measured by computed tomography-based parametric response mapping

Parametric response mapping (PRM) is a computed tomography (CT)-based method to phenotype patients with chronic obstructive pulmonary disease (COPD). It is capable of differentiating emphysema-related air trapping with nonemphysematous air trapping (small airway disease), which helps to identify the extent and localization of the disease. Most studies evaluating the gene expression in smokers and COPD patients related this to spirometric measurements, but none have investigated the relationship with CT-based measurements of lung structure. The current study aimed to examine gene expression profiles of brushed bronchial epithelial cells in association with the PRM-defined CT-based measurements of emphysema (PRM(Emph)) and small airway disease (PRM(fSAD)). Using the Top Institute Pharma (TIP) study cohort (COPD = 12 and asymptomatic smokers = 32), we identified a gene expression signature of bronchial brushings, which was associated with PRM(Emph) in the lungs. One hundred thirty-three genes were identified to be associated with PRM(Emph). Among the most significantly associated genes, CXCL11 is a potent chemokine involved with CD8(+) T cell activation during inflammation in COPD, indicating that it may play an essential role in the development of emphysema. The PRM(Emph) signature was then replicated in two independent data sets. Pathway analysis showed that the PRM(Emph) signature is associated with proinflammatory and notch signaling pathways. Together these findings indicate that airway epithelium may play a role in the development of emphysema and/or may act as a biomarker for the presence of emphysema. In contrast, its role in relation to functional small airways disease is less clear

Use of organic inputs by arable farmers in six agro-ecological zones across Europe: Drivers and barriers

Soil organic matter (SOM) in agricultural soils builds up via – among others - the use of organic inputs such as straw, compost, farmyard manure or the cultivation of green manures or cover crops. SOM has benefits for long-term soil fertility and can provide ecosystem services. Farmer behaviour is however known to be motivated by a larger number of factors. Using the theory of planned behaviour, we aimed to disentangle these factors. We addressed the following research question: What are currently the main drivers and barriers for arable farmers in Europe to use organic inputs? Our study focuses on six agro-ecological zones in four European countries (Austria, Flanders [Belgium], Italy and the Netherlands) and four practices (straw incorporation, green manure or cover crops, compost and farmyard manure). In a first step, relevant factors were identified for each practice with farmers using 5 to ten semi-structured interviews per agro-ecological zone. In a second step, the relevance of these factors was quantified and they were classified as either drivers or barriers in a large scale farm survey with 1263 farmers. In the semi-structured interviews, 110 factors that influenced farmer decisions to use an organic input were identified. In the larger farm survey, 60% of the factors included were evaluated as drivers, while 40% were evaluated as barriers for the use of organic inputs. Major drivers to use organic inputs were related to the perceived effects on soil quality (such as improved soil structure or reduced erosion) and the positive influence from social referents (such as fellow farmers or agricultural advisors). Major barriers to use organic inputs were financial (increased costs or foregone income) and perceived effects on crop protection (such as increased weeds, pests and diseases, or increased pesticide use). Our study shows that motivating farmers to use organic inputs requires specific guidance on how to adapt cultivation practices to reduce weeds, pests and diseases for specific soil types, weather conditions, and crops. In addition, more research is needed on the long-term financial consequences of using organic inputs

Nitrogen fertiliser replacement values for organic amendments appear to increase with N application rates

Nitrogen (N) supply from organic amendments [such as farmyard manure (FYM), slurries or crop residues] to crops is commonly expressed in the amendment’s Nitrogen Fertiliser Replacement Value (NFRV). Values for NFRV can be determined by comparison of crop yield or N uptake in amended plots against mineral fertiliser-only plots. NFRV is then defined as the amount of mineral fertiliser N saved when using organic amendment-N (kg/kg), while attaining the same crop yield. Factors known to affect NFRV are crop type cultivated, soil type, manuring history and method or time of application. We investigated whether long-term NFRV depends on N application rates. Using data from eight long term experiments in Europe, values of NFRV at low total N supply were compared with values of NFRV at high total N supply. Our findings show that FYM has a significant higher NFRV value at high total N supply than at low total N supply (1.12 vs. 0.53, p = 0.04). For the other amendment types investigated, NFRV was also higher at high total N supply than at low total N supply, but sample sizes were too small or variations too large to detect significant differences. Farmers in Europe usually operate at high rates of total N applied. If fertiliser supplements are based on NFRV of the manure estimated at low total N supply, N fertiliser requirements might be overestimated. This might lead to overuse of N, lower N use efficiency and larger losses of N to the environment

Management, regulation and environmental impacts of nitrogen fertilization in northwestern Europe under the Nitrates Directive; a benchmark study

Implementation of the Nitrates Directive (NiD) and its environmental impacts were compared for member states in the northwest of the European Union (Ireland, United Kingdom, Denmark, the Netherlands, Belgium, Northern France and Germany). The main sources of data were national reports for the third reporting period for the NiD (2004–2007) and results of the MITERRA-EUROPE model. Implementation of the NiD in the considered member states is fairly comparable regarding restrictions for where and when to apply fertilizer and manure, but very different regarding application limits for N fertilization. Issues of concern and improvement of the implementation of the NiD are accounting for the fertilizer value of nitrogen in manure, and relating application limits for total nitrogen (N) to potential crop yield and N removal. The most significant environmental effect of the implementation of the NiD since 1995 is a major contribution to the decrease of the soil N balance (N surplus), particularly in Belgium, Denmark, Ireland, the Netherlands and the United Kingdom. This decrease is accompanied by a modest decrease of nitrate concentrations since 2000 in fresh surface waters in most countries. This decrease is less prominent for groundwater in view of delayed response of nitrate in deep aquifers. In spite of improved fertilization practices, the southeast of the Netherlands, the Flemish Region and Brittany remain to be regions of major concern in view of a combination of a high nitrogen surplus, high leaching fractions to groundwater and tenacious exceedance of the water quality standards. On average the gross N balance in 2008 for the seven member states in EUROSTAT and in national reports was about 20 kg N ha&lt;sup&gt;−1&lt;/sup&gt; yr&lt;sup&gt;−1&lt;/sup&gt; lower than by MITERRA. The major cause is higher estimates of N removal in national reports which can amount to more than 50 kg N ha&lt;sup&gt;−1&lt;/sup&gt; yr&lt;sup&gt;−1&lt;/sup&gt;. Differences between procedures in member states to assess nitrogen balances and water quality and a lack of cross-boundary policy evaluations are handicaps when benchmarking the effectiveness of the NiD. This provides a challenge for the European Commission and its member states, as the NiD remains an important piece of legislation for protecting drinking water quality in regions with many private or small public production facilities and controlling aquatic eutrophication from agricultural sources

Neutrophilic Asthma Is Associated With Smoking, High Numbers of IRF5+, and Low Numbers of IL10+ Macrophages

Asthma is a heterogenous disease with different inflammatory subgroups that differ in disease severity. This disease variation is hampering treatment and development of new treatment strategies. Macrophages may contribute to asthma phenotypes by their ability to activate in different ways, i.e., T helper cell 1 (Th1)-associated, Th2-associated, or anti-inflammatory activation. It is currently unknown if these different types of activation correspond with specific inflammatory subgroups of asthma. We hypothesized that eosinophilic asthma would be characterized by having Th2-associated macrophages, whereas neutrophilic asthma would have Th1-associated macrophages and both having few anti-inflammatory macrophages. We quantified macrophage subsets in bronchial biopsies of asthma patients using interferon regulatory factor 5 (IRF5)/CD68 for Th1-associated macrophages, CD206/CD68 for Th2-associated macrophages and interleukin 10 (IL10)/CD68 for anti-inflammatory macrophages. Macrophage subset percentages were investigated in subgroups of asthma as defined by unsupervised clustering using neutrophil/eosinophil counts in sputum and tissue and forced expiratory volume in 1 s (FEV1). Asthma patients clustered into four subgroups: mixed-eosinophilic/neutrophilic, paucigranulocytic, neutrophilic with normal FEV1, and neutrophilic with low FEV1, the latter group consisting mainly of smokers. No differences were found for CD206+ macrophages within asthma subgroups. In contrast, IRF5+ macrophages were significantly higher and IL10+ macrophages lower in neutrophilic asthmatics with low FEV1 as compared to those with neutrophilic asthma and normal FEV1 or mixed-eosinophilic asthma. This study shows that neutrophilic asthma with low FEV1 is associated with high numbers of IRF5+, and low numbers of IL10+ macrophages, which may be the result of combined effects of smoking and having asthma.</p