The Alzheimer’s Disease Drug Development Landscape

Background: Alzheimer’s disease (AD) is a devastating neurodegenerative disease leading to dementia. The field has made significant progress over the last 15 years. AD diagnosis has shifted from syndromal, based on signs and symptoms, to a biomarker construct based on the pathological hallmarks of the disease: amyloid β deposition, pathologic tau, and neurodegeneration. Numerous genetic risk factors for sporadic AD have been identified, providing further insight into the molecular underpinnings of the disease. For the last two decades, however, drug development for AD has been proven to be particularly challenging. Here, we provide a unique overview of the drug development landscape for AD. By comparing preclinical and clinical drug development pipelines, we aim to describe trends and differences regarding target classes and therapeutic modalities in preclinical and clinical development. Methods: We analyzed proprietary and public databases and company websites for drugs in preclinical development for AD by the pharmaceutical industry and major clinical trial registries for drugs in clinical development for AD. Drugs were categorized by target class and treatment modality. Results: We found a higher proportion of preclinical interventions targeting molecular pathways associated with sporadic AD genetic risk variants, compared to clinical stage interventions. These include apolipoprotein E (ApoE) and lipids, lysosomal/endosomal targets, and proteostasis. Further, we observed a trend suggesting that more traditional therapeutic modalities are developed for these novel targets, while more novel treatment modalities such as gene therapies and enzyme treatments are in development for more traditional targets such as amyloid β and tau. Interestingly, the percentage of amyloid β targeting therapies in preclinical development (19.2%) is even higher than the percentage in clinical development (10.7%), indicating that diversification away from interventions targeting amyloid-beta has not materialized. Inflammation is the second most popular target class in both preclinical and clinical development. Conclusions: Our observations show that the AD drug development pipeline is diversifying in terms of targets and treatment modalities, while amyloid-targeting therapies remain a prominent avenue of development as well. To further advance AD drug development, novel companion diagnostics are needed that are directed at disease mechanisms related to genetic risk factors of AD, both for patient stratification and assessment of therapeutic efficacy in clinical trials

The influence of smoking status on exhaled breath profiles in asthma and COPD patients

Breath analysis using eNose technology can be used to discriminate between asthma and COPD patients, but it remains unclear whether results are influenced by smoking status. We aim to study whether eNose can discriminate between ever- vs. never-smokers and smoking <24 vs. >24 h before the exhaled breath, and if smoking can be considered a confounder that influences eNose results. We performed a cross-sectional analysis in adults with asthma or chronic obstructive pulmonary disease (COPD), and healthy controls. Ever-smokers were defined as patients with current or past smoking habits. eNose measurements were performed by using the SpiroNose. The principal component (PC) described the eNose signals, and linear discriminant analysis determined if PCs classified ever-smokers vs. never-smokers and smoking <24 vs. >24 h. The area under the receiver-operator characteristic curve (AUC) assessed the accuracy of the models. We selected 593 ever-smokers (167 smoked <24 h before measurement) and 303 never-smokers and measured the exhaled breath profiles of discriminated ever- and never-smokers (AUC: 0.74; 95% CI: 0.66-0.81), and no cigarette consumption <24h (AUC 0.54, 95% CI: 0.43-0.65). In healthy controls, the eNose did not discriminate between ever or never-smokers (AUC 0.54; 95% CI: 0.49-0.60) and recent cigarette consumption (AUC 0.60; 95% CI: 0.50-0.69). The eNose could distinguish between ever and neversmokers in asthma and COPD patients, but not recent smokers. Recent smoking is not a confounding factor of eNose breath profiles

Participation of Multifunctional RNA in Replication, Recombination and Regulation of Endogenous Plant Pararetroviruses (EPRVs)

Pararetroviruses, taxon Caulimoviridae, are typical of retroelements with reverse transcriptase and share a common origin with retroviruses and LTR retrotransposons, presumably dating back 1.6 billion years and illustrating the transition from an RNA to a DNA world. After transcription of the viral genome in the host nucleus, viral DNA synthesis occurs in the cytoplasm on the generated terminally redundant RNA including inter- and intra-molecule recombination steps rather than relying on nuclear DNA replication. RNA recombination events between an ancestral genomic retroelement with exogenous RNA viruses were seminal in pararetrovirus evolution resulting in horizontal transmission and episomal replication. Instead of active integration, pararetroviruses use the host DNA repair machinery to prevail in genomes of angiosperms, gymnosperms and ferns. Pararetrovirus integration – leading to Endogenous ParaRetroViruses, EPRVs – by illegitimate recombination can happen if their sequences instead of homologous host genomic sequences on the sister chromatid (during mitosis) or homologous chromosome (during meiosis) are used as template. Multiple layers of RNA interference exist regulating episomal and chromosomal forms of the pararetrovirus. Pararetroviruses have evolved suppressors against this plant defense in the arms race during co-evolution which can result in deregulation of plant genes. Small RNAs serve as signaling molecules for Transcriptional and Post-Transcriptional Gene Silencing (TGS, PTGS) pathways. Different populations of small RNAs comprising 21–24 nt and 18–30 nt in length have been reported for Citrus, Fritillaria, Musa, Petunia, Solanum and Beta. Recombination and RNA interference are driving forces for evolution and regulation of EPRVs

Exhaled metabolite patterns to identify recent asthma exacerbations

Asthma is a chronic respiratory disease that can lead to exacerbations, defined as acute episodes of worsening respiratory symptoms and lung function. Predicting the occurrence of these exacerbations is an important goal in asthma management. The measurement of exhaled breath by electronic nose (eNose) may allow for the monitoring of clinically unstable asthma and exacerbations. However, data on its ability to perform this is lacking. We aimed to evaluate whether eNose could identify patients that recently had asthma exacerbations. We performed a cross-sectional study, measuring exhaled breath using the SpiroNose in adults with a physician-reported diagnosis of asthma. Patients were randomly divided into a training (n = 252) and validation (n = 109) set. For the analysis of eNose signals, principal component (PC) and linear discriminant analysis (LDA) were performed. LDA, based on PC1-4, reliably discriminated between patients who had a recent exacerbation from those who had not (training receiver operating characteristic (ROC)–area under the curve (AUC) = 0.76,95% CI 0.69–0.82), (validation AUC = 0.76, 95% CI 0.64–0.87). Our study showed that, exhaled breath analysis using eNose could accurately identify asthma patients who recently had an exacerbation, and could indicate that asthma exacerbations have a specific exhaled breath pattern detectable by eNose

Draft genome of a novel methanotrophic Methylobacter sp. from the volcanic soils of Pantelleria Island

The genus Methylobacter is considered an important and often dominant group of aerobic methane-oxidizing bacteria in many oxic ecosystems, where members of this genus contribute to the reduction of CH4 emissions. Metagenomic studies of the upper oxic layers of geothermal soils of the Favara Grande, Pantelleria, Italy, revealed the presence of various methane-oxidizing bacteria, and resulted in a near complete metagenome assembled genome (MAG) of an aerobic methanotroph, which was classified as a Methylobacter species. In this study, the Methylobacter sp. B2 MAG was used to investigate its metabolic potential and phylogenetic affiliation. The MAG has a size of 4,086,539 bp, consists of 134 contigs and 3955 genes were found, of which 3902 were protein coding genes. All genes for CH4 oxidation to CO2 were detected, including pmoCAB encoding particulate methane monooxygenase (pMMO) and xoxF encoding a methanol dehydrogenase. No gene encoding a formaldehyde dehydrogenase was present and the formaldehyde to formate conversion follows the tetrahydromethanopterin (H4MPT) pathway. “Ca. Methylobacter favarea” B2 uses the Ribulose-Mono-Phosphate (RuMP) pathway for carbon fixation. Analysis of the MAG indicates that Na+/H+ antiporters and the urease system might be important in the maintenance of pH homeostasis of this strain to cope with acidic conditions. So far, thermoacidophilic Methylobacter species have not been isolated, however this study indicates that members of the genus Methylobacter can be found in distinct ecosystems and their presence is not restricted to freshwater or marine sediments

Early life antibiotic exposure is associated with an increased risk of atopic eczema and hay fever

Background: Several studies suggested that early life exposure to antibiotics is associated with an increased risk of developing allergies later in life, but results are inconsistent. In this study we aimed to systematically review and quantify the relationship between early life exposure to antibiotics and the risk of atopic eczema (dermatitis) or hay fever (allergic rhinitis). Method: PubMed and Web of Science databases were searched for observational studies published from January 1966 through November 11, 2015. Studies were included that assessed the association between antibiotic consumption during the first 2 years of life and the risk of eczema or hay fever later in life. Separate metaanalyses were performed to assess the risk estimates for cohort studies, cross sectional studies and case control studies. Furthermore, in subgroup analyses the effect of child's age at the time of antibiotic use/diagnosis of allergies, and the number of courses of antibiotic treatments have been analyzed. Overall pooled estimates of the odds ratios (ORs) were obtained using fixed or random-effects models. Results: Twenty-two studies (including 394 517 patients) were selected to study the risk of eczema and 23 studies (including 256 609 patients) to study the risk of hay fever. In all separate meta-analyses of the distinct study designs, those who were exposed to antibiotics early in life were found to have a statistically significantly increased risk of eczema and hay fever. The summary OR for risk of eczema were 1.24 (95% CI, 1.09-1.41; I2: 60.0%) in the meta-analyses of the cohort studies (n = 50 824); 1.41 (95% CI, 1.33-1.49; I2: 0.0%) in the cross sectional studies (n = 217 752), and 1.15 (95% CI, 1.01- 1.42; I2: 79.5%) in the case control studies (n = 125 941). The summary OR for risk of hay fever were 1.18 (95% CI, 1.01-1.37; I2: 74.3%) in the cohort studies (n = 46 540); 1.56 (95% CI, 1.29-1.90; I2: 63.6%) in cross sectional studies (n = 27 608), and 1.14 (95% CI, 1.04-1.26; I2: 64.8%) in the case control studies (n = 182 461). In subgroup analyses, there was no statistically significant effect of the child's age at time of antibiotic use as well as the time of allergy diagnosis on these associations. The association was stronger if patients had been treated with ≥2 courses compared with one course of antibiotics both for eczema and for hay fever. Conclusion: Early life exposure to antibiotics is related to an increased risk of both atopic eczema and hay fever later in life

The role of grass volatiles on oviposition site selection by Anopheles arabiensis and Anopheles coluzzii

Background: The reproductive success and population dynamics, of Anopheles malaria mosquitoes is strongly influenced by the oviposition site selection of gravid females. Mosquitoes select oviposition sites at different spatial scales, starting with selecting a habitat in which to search. This study utilizes the association of larval abundance in the field with natural breeding habitats, dominated by various types of wild grasses, as a proxy for oviposition site selection by gravid mosquitoes. Moreover, the role of olfactory cues emanating from these habitats in the attraction and oviposition stimulation of females was analysed. Methods: The density of Anopheles larvae in breeding sites associated with Echinochloa pyramidalis, Echinochloa stagnina, Typha latifolia and Cyperus papyrus, was sampled and the larvae identified to species level. Headspace volatile extracts of the grasses were collected and used to assess behavioural attraction and oviposition stimulation of gravid Anopheles arabiensis and Anopheles coluzzii mosquitoes in wind tunnel and two-choice oviposition assays, respectively. The ability of the mosquitoes to differentiate among the grass volatile extracts was tested in multi-choice tent assays. Results: Anopheles arabiensis larvae were the most abundant species found in the various grass-associated habitats. The larval densities described a hierarchical distribution, with Poaceae (Echinochloa pyramidalis and Echinochloa stagnina)-associated habitat sites demonstrating higher densities than that of Typha-associated sites, and where larvae were absent from Cyperus-associated sites. This hierarchy was maintained by gravid An. arabiensis and An. coluzzii mosquitoes in attraction, oviposition and multi-choice assays to grass volatile extracts. Conclusions: The demonstrated hierarchical preference of gravid An. coluzzii and An. arabiensis for grass volatiles indicates that vegetation cues associated with larval habitats are instrumental in the oviposition site choice of the malaria mosquitoes. Identifying volatile cues from grasses that modulate gravid malaria mosquito behaviours has distinct potential for the development of tools to be used in future monitoring and control methods

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The current assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n=14) containing 32,928 and 36,697 protein-coding genes, respectively. The Petunia lineage has experienced at least two rounds of paleohexaploidization, the older gamma hexaploidy event, which is shared with other Eudicots, and the more recent Solanaceae paleohexaploidy event that is shared with tomato and other Solanaceae species. Transcription factors that were targets of selection during the shift from bee- to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral color patterns and pollination systems. The high quality genome sequences will enhance the value of Petunia as a model system for basic and applied research on a variety of unique biological phenomena