Boehringer Ingelheim (Germany)

Current ICH guidelines, e.g.ICH E6 (R3), advocate a risk-based statistical review of clinical trial data to identify anomalies. The open-source R package, clinical trial anomaly spotter (CTAS) has been developed by Bayer and the Intercompany Quality Analytics (IMPALA) consortium, helps detect inconsistencies in subject time series data at both site and subject levels, facilitating timely intervention. CTAS analyzes time series of equal length. Each subject-level time series is summarized as six optional scalars: mean, standard deviation, range, relative unique value count, autocorrelation and local outlier factor. To detect site-level anomalies, sites can be scored using 3 different scoring methods. The performance of the CTAS algorithm was tested using simulations, artificially introducing site anomalies of various types and degrees into clinical trial data sets. We found that CTAS can reliably detect site anomalies depending on the degree of the anomaly introduced. Less complex anomalies such as mean were easier to detect than complex outlier such as local outlier factor. The three scoring methods differed in their ability to detect anomalous sites with a small number of patients and their false positive rates. CTAS is a valuable tool for timely detection of outliers in clinical data, suitable for integration into risk-based strategies. Choosing the appropriate site anomaly scoring method is crucial for handling sites with fewer subjects effectively.

Idiopathic pulmonary fibrosis (IPF) is characterised by progressive scarring primarily of the distal regions of the lung in a distinctive histological pattern. Consequently, drug discovery has focused on the activity of scar-forming fibroblasts, with some success shown by the pharmaceutical agents nintedanib and pirfenidone, and more recently nerandomilast. Yet an unmet medical need remains, pointing toward pathobiology not addressed by standard-of-care therapies. In recent years, single-cell sequencing of patient lung tissue has revealed several novel disease-associated epithelial populations. In addition, we are now beginning to understand, through functional co-culture studies, the importance of cellular crosstalk in both lung homeostasis and disease. Here, we review the advances made in “omic” technologies, the approaching spatial profiling revolution, current and future functional cell systems, novel in vivo models, how we assign disease-relevance to test systems via computational gene set enrichment analysis, and link all these elements to clinically relevant biomarkers. We show how epithelial populations, identified and validated through cutting-edge technologies, may provide targets for the next wave of therapeutics for patients with IPF.

Borderline personality disorder (BPD) is a significant cause of morbidity with no approved pharmacological treatment. We assessed treatment trajectories of patients with BPD in real-world clinical practice to help identify treatment gaps. This retrospective, observational, cohort study used de-identified MindLinc electronic health records data from the Holmusk NeuroBlu database (Version 21R2) to analyse the treatment journey of patients with BPD (aged ≥ 12 years with ≥1 diagnosis of BPD) that were prescribed pharmacological treatment within 14 days of diagnosis (baseline) and had treatment data for ≥12 months. Of those prescribed pharmacological treatment at baseline, 1461 patients (16.1%) had 12 months of follow-up data. Antidepressants were the most frequently prescribed medication at baseline (80.4%) either alone or in combination with other medication classes, followed by second-generation antipsychotics (SGAs), anxiolytics and mood stabilisers. In the 12 months post-baseline, the most frequently recorded treatment pathway was a switch from 1 antidepressant to another. Sertraline (5.5%), fluoxetine (5%), and citalopram (5%) were the most-prescribed antidepressants; lamotrigine (24.9%), gabapentin (15.4%), and valproate (7.1%) were the most prescribed mood stabilisers; and quetiapine (22.1%) and aripiprazole (19.0%) were the most prescribed SGAs. Polypharmacy (defined as the prescription of ≥ 1 psychotropic medication) was observed in 83.1% of patients at baseline and increased with follow-up time and age. The high rates of polypharmacy observed suggest that current clinical practices may not fully align with treatment guidelines for BPD, and that patients with BPD experience a considerable treatment burden. Limitations of this study include the absence of psychotherapy data and the use of prescription records without information on treatment adherence. Nonetheless, the diversity of treatment patterns observed reflects the complex symptomatology of BPD and highlights the need to deepen our understanding of its neurobiology to improve pharmacological treatment strategies and translate to meaningful patient outcomes. Not applicable.

NUT carcinoma (NC) is a rare, yet aggressive disease (median survival of 6.5 months) of the young defined by a translocation of the nuclear protein in testis gene 1 (NUTM1). Neither surgery nor radiochemotherapy or targeted therapies provide effective disease control, thereby creating a need for innovative therapeutic strategies. Recently, the recombinant oncolytic virus (OV) VSV-GP entered phase I clinical testing (NCT05155332). We (1) visualized VSV-GPs' replication cycle in transmission electron microscopy; (2) analyzed VSV-GP's oncolytic efficacy and replication kinetics using viability assays, xCELLigence analyses, RT-qPCR, TCID50 assays, and FACS analysis; as well as (3) explored potential resistance mechanisms in seven human NC cell lines. Upon infection with VSV-GP, we noticed profound oncolysis, apoptosis, and high replication kinetics in five out of seven NC cell lines. Investigations of molecular determinants of resistance showed that VSV-GPs' entry receptor α-dystroglycan was equally expressed by VSV-GP-permissive and -resistant cell lines. While synthesis of intrinsic interferon (IFN)-β was found to be suppressed in VSV-GP-infected NC cell lines, intracellular IFN-β signaling was functional. Since VSV-GP is a promising compound for virotherapy of NC patients, exploration of virus-induced immunogenicity and identification of resistance mechanisms could pave the way for additional combination treatment regimes in NC.

Altered respiratory barrier integrity and impaired lung regeneration are hallmarks of chronic obstructive pulmonary disease (COPD). To investigate the molecular mechanisms driving the impaired regeneration of alveolar epithelial progenitors in COPD, we generated whole-genome DNA methylation and transcriptome maps of sorted human primary alveolar type 2 cells (AT2) at different disease stages. Our analysis revealed aberrant DNA methylation at specific gene promoters in AT2 during COPD, which was anticorrelated with gene expression changes. Interferon signaling was the top-upregulated pathway in COPD, associated with a concomitant loss of promoter-proximal DNA methylation. Integrated pathway analysis revealed transcription factor IRF9 as the master regulator of interferon signaling in COPD. Epigenetic regulation of the interferon pathway was validated by targeted DNA demethylation of the IRF9 gene, mimicking the effects observed in COPD-derived AT2. Our findings suggest that COPD-associated DNA methylation alterations in AT2 cells may impair internal regeneration programs in lung parenchyma.

Cigarette smoke contains over 5000 compounds, including polycyclic aromatic hydrocarbons, which induce cytochrome P450 (CYP) enzymes, particularly CYP1A1 and CYP1A2. Therefore, smoking significantly alters drug metabolism and can reduce therapeutic efficacy. To investigate tissue-specific CYP enzyme induction by cigarette smoke extract (CSE), a previously established hepatic in vitro smoke induction model was expanded to include human intestinal organoids and lung cell models. CYP1A1, CYP1A2, and CYP3A4 mRNA expression and CYP1A1 and CYP1A enzyme activity were quantified following CSE exposure. CYP1A1 mRNA expression and enzyme activity were robustly induced in all tissues and donors (up to 77-fold and 212-fold respectively). CYP1A2 mRNA and CYP1A enzyme activity were induced in liver and intestine (up to 13-fold) but were only weakly detectable in lung. CYP3A4 induction was exclusively observed in liver (up to 16-fold). Comparison of F2- and Emax-values of concentration-dependent induction across all models revealed that intestinal cells showed significantly lower values of CYP1A1 induction than liver cells. Other comparisons were non-significant. Inter-donor variability was visible across all cell models, CYP enzymes and tissue types (57-82% CV). This reflects physiological inter-individual variability, supporting the conclusion that these single-cell models capture donor-specific differences. Conclusively, it was shown that extrahepatic metabolism is altered by CSE and that considering tissue-specific CYP enzyme induction may be beneficial in clinical pharmacology to optimize drug efficacy and safety in smoking populations.

This study examines the effect of combining quantum mechanical (QM) descriptors with traditional structural descriptors in predicting ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties for molecular drug candidates. We focus on four end points: HLM (human liver microsomes) stability, permeability, solubility, and hERG (human ether-a-go-go-related gene) inhibition. First, we studied the prediction of molecules in the same chemical space as the training data. Our results show that incorporating QM descriptors enhances prediction accuracy across all end points. We find that the most significant improvement in permeability is achieved, with the QM dispersion energy proving to be the second most important feature. In general, feature importance analysis revealed that QM descriptors are ranked among the top five features, providing more comprehensive insights than structural descriptors alone. Next, we studied predicting molecules in chemical spaces distinct from the training data. Here, QM descriptors exhibited superior extrapolation capabilities, particularly for permeability and hERG data sets. In an extrapolation scenario where the training data set size was systematically reduced, QM descriptors maintained higher stability than structural descriptors in prediction. A hybrid approach combining all QM descriptors with key structural descriptors improved predictive accuracy, reduced variation in results, and yielded greater robustness in small data sets. This work highlights the value of QM descriptors for ADMET predictions, especially in challenging extrapolation tasks and scenarios with limited training data.

Introduction Idiopathic pulmonary fibrosis (IPF) is a lethal lung disease involving injury and a dysregulated repair response of an ageing epithelium. Here we investigate the contribution of senescence and telomere shortening to bleomycin-induced injury in alveolar epithelial cells (EpCs) derived from lung parenchymal tissue of patients with pulmonary fibrosis (PF), predominantly IPF, in vitro . Methods Injury responses of EpCs in air liquid interface (ALI) culture were assessed by ELISA, qPCR and/or immunofluorescence at 48 and 96 h post-bleomycin (30 μg·mL −1 ) treatment. Telomere length was evaluated by qPCR and corroborated by fluorescence in situ hybridisation (FISH). Results Bleomycin treatment increased markers of inflammation ( i.e. interleukin-6 and −36γ) and senescence ( i.e. p16 and p21) in EpCs from PF patients (PF-EpCs) ( p <0.05); responses markedly higher than control EpCs (Ctrl-EpCs). Conversely, the effects of bleomycin on the expression of type I and type II alveolar EpC markers were supressed or down-regulated in cultures of PF-EpCs (when compared to Ctrl-EpCs), whereas the percentage of keratin 17 positive type I and II intermediate EpCs were increased ( p <0.05). Telomere length was also significantly shorter in PF- than Ctrl-EpCs at baseline and further reduced post-bleomycin treatment ( p <0.05). Induction of telomere shortening by cell passaging augmented bleomycin-induced PF-EpC injury, whereas pharmacological telomerase activation and selected senotherapeutics were protective. Conclusion This study provides evidence that senescence-associated telomere shortening increases the susceptibility of IPF-lung EpCs to injury. Our cell-based lung epithelial injury model has utility as a pre-clinical tool for drug discovery and the evaluation of potential senotherapeutics for IPF treatment.

A seven-step enantioselective route for the synthesis of benzyl (R)-10-oxo-2-oxa-7-azaspiro[4.5]decane-7-carboxylate (1) with >99% ee is reported on a multi-hundred-gram scale in 42% overall yield. The synthesis features an asymmetric allylic alkylation to establish the quaternary stereocenter on a piperidine ring, followed by an oxidation/reduction and Mitsunobu conditions sequence to construct the tetrahydrofuran ring within the chiral oxa-azaspirocycle.