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Background: Chronic pulmonary inflammation strongly contributes to respiratory failure and mortality in patients with cystic fibrosis (pwCF). Effective anti-microbial immunity and maintaining lung homeostasis require continuous structural-immune cell communication. Whether and how this crosstalk is altered in CF remains poorly understood, obscuring potential new angles for therapy development to restore airway homeostasis in pwCF., Methods: We performed droplet-based single cell RNA-sequencing on bronchial biopsies from pwCF to investigate structural-immune cell crosstalk. Computational analyses were used to compare these data to samples obtained from healthy controls., Results: CF airway wall biopsies showed lower proportions and altered transcriptomes of basal cells, submucosal gland cells and endothelial cells, and a higher abundance of ciliated cells, monocytes, macrophages and T cells. Both B and T lymphocytes displayed aberrantly activated phenotypes with transcriptional changes linked to hypoxia and vascular endothelial growth factor signaling, indicative of crosstalk with endothelial cells. The CF lung displayed unique changes in intercellular communication potential involving ionocytes, macrophages, endothelial cells and lymphocytes. This included interactions between HLA-E on structural cells and the druggable CD94/NKG2A immune checkpoint on CD8 + T cells., Conclusions: We report the first single cell transcriptome atlas of the CF lung containing the full spectrum of structural and immune cells, providing a valuable resource for investigating changes to cellular composition, phenotypes and crosstalk linked to CF. Our analyses highlight dysregulated basal cell function and adaptive immunity in pwCF - despite favorable responses to CFTR modulator therapy. We identify novel aspects of CF pathophysiology and potential entry points for therapeutic strategies., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: JGJVA reports grants or consulting fees from Boehringer-Ingelheim, MSD, BMS, Astra-Zeneca, Eli-Lilly, Verastem, Nutricia, Amphera and CureVac, which are not related to this work. All other authors declare no potential competing interests., (Copyright © 2025 The Author(s). Published by Elsevier B.V. All rights reserved.)

Background: In patients with asthma, respiratory syncytial virus (RSV) infections can cause disease exacerbation by infecting the epithelial layer of the airways, inducing subsequent immune response. The type I interferon antiviral response of epithelial cells upon RSV infection is found to be reduced in asthma in most-but not all-studies. Moreover, the molecular mechanisms causing the differences in the asthmatic bronchial epithelium in response to viral infection are poorly understood., Methods: Here, we investigated the transcriptional response to RSV infection of primary bronchial epithelial cells (pBECs) from patients with asthma (n=8) and healthy donors (n=8). The pBECs obtained from bronchial brushes were differentiated in air-liquid interface conditions and infected with RSV. After 3 days, cells were processed for single-cell RNA sequencing., Results: A strong antiviral response to RSV was observed for all cell types, for all samples (p<1e-48). Most (1045) differentially regulated genes following RSV infection were found in cells transitioning to secretory cells. Goblet cells from patients with asthma showed lower expression of genes involved in the interferon response (false discovery rate <0.05), including OASL , ICAM1 and TNFAIP3 . In multiciliated cells, an impairment of the signalling pathways involved in the response to RSV in asthma was observed., Conclusion: Our results highlight that the response to RSV infection of the bronchial epithelium in asthma and healthy airways was largely similar. However, in asthma, the response of goblet and multiciliated cells is impaired, highlighting the need for studying airway epithelial cells at high resolution in the context of asthma exacerbation., Competing Interests: Competing interests: GHK, MCN and MvdB received project funding from GlaxoSmithKline. GHK and MvdB received funding from AstraZeneca. MvdB received funding from Novartis, Genentech and Roche., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Vitamin D (VD) suffers from low water solubility and strong degradation, which both decrease its bioavailability. This work aims at obtaining a silica-surfactant-VD hybrid material and verifying if this system can protect VD from degradation and enhance its solubility. This preliminary study aspires at tuning the mesostructure order of the hybrid system (by modifying the surfactant amount) with the scope of controlling, somewhat, its drug release capability. To this purpose, two silica-surfactant-VD systems with different long-range order were synthesized and characterized in terms of physico-chemical properties and release behavior in a model solution mimicking the topical environment. Results show that the hybrid materials are able to incorporate VD, protect it from degradation up to 17 months and release it in aqueous media. The mesostructure order and the interaction between VD, surfactant and silica seem to play a key role in tuning kinetics and the amount of released drug. While the less ordered structure incorporates less VD with faster and higher release percentage, the more ordered one incorporates more VD but, due to the stronger interactions with the carrier, requires a partial dissolution of the matrix to occur before releasing the drug, so inducing a lag-time and a smaller released quantity., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors. Published by Elsevier Ltd.)

Both cyclodextrin (CD) and porous silica possess interesting properties of adsorption and release. A silica-CD hybrid, therefore, could synergically merge the properties of the two components, giving rise to a material with appealing properties for both environmental and pharmaceutical applications. With this aim, in the present study, a first hybrid is obtained through one-pot sol-gel synthesis starting from CD and tetramethyl orthosilicate (TMOS) as a silica precursor. In particular, methyl-β-cyclodextrin (bMCD) is selected for this purpose. The obtained bMCD-silica hybrid is a dense material containing a considerable amount of bMCD (45 wt.%) in amorphous form and therefore represents a promising support. However, since a high specific surface area is desirable to increase the release/adsorption properties, an attempt is made to produce the hybrid material in the form of an aerogel. Both the synthesis of the gel and its drying in supercritical CO 2 are optimized in order to reach this goal. All the obtained samples are characterized in terms of their physico-chemical properties (infra-red spectroscopy, thermogravimetry) and structure (X-ray diffraction, electron microscopy) in order to investigate their composition and the interaction between the organic component (bMCD) and the inorganic one (silica).

Cell type-specific differential gene expression analyses based on single-cell transcriptome datasets are sensitive to the presence of cell-free mRNA in the droplets containing single cells. This so-called ambient RNA contamination may differ between samples obtained from patients and healthy controls. Current ambient RNA correction methods were not developed specifically for single-cell differential gene expression (sc-DGE) analyses and might therefore not sufficiently correct for ambient RNA-derived signals. Here, we show that ambient RNA levels are highly sample-specific. We found that without ambient RNA correction, sc-DGE analyses erroneously identify transcripts originating from ambient RNA as cell type-specific disease-associated genes. We therefore developed a computationally lean and intuitive correction method, Fast Correction for Ambient RNA (FastCAR), optimized for sc-DGE analysis of scRNA-Seq datasets generated by droplet-based methods including the 10XGenomics Chromium platform. FastCAR uses the profile of transcripts observed in libraries that likely represent empty droplets to determine the level of ambient RNA in each individual sample, and then corrects for these ambient RNA gene expression values. FastCAR can be applied as part of the data pre-processing and QC in sc-DGE workflows comparing scRNA-Seq data in a health versus disease experimental design. We compared FastCAR with two methods previously developed to remove ambient RNA, SoupX and CellBender. All three methods identified additional genes in sc-DGE analyses that were not identified in the absence of ambient RNA correction. However, we show that FastCAR performs better at correcting gene expression values attributed to ambient RNA, resulting in a lower frequency of false-positive observations. Moreover, the use of FastCAR in a sc-DGE workflow increases the cell-type specificity of sc-DGE analyses across disease conditions., (© 2023. The Author(s).)

Abnormal deposition of extracellular matrix (ECM) in lung tissue is a characteristic of idiopathic pulmonary fibrosis (IPF). Increased collagen deposition is also accompanied by altered collagen organization. Collagen type XIV, a fibril-associated collagen, supports collagen fibril organization. Its status in IPF has not been described at the protein level yet. In this study, we utilized publicly available datasets for single-cell RNA-sequencing for characterizing collagen type XIV expression at the gene level. For protein level comparison, we applied immunohistochemical staining for collagen type XIV on lung tissue sections from IPF patients and compared it to lung tissue sections from never smoking and ex-smoking donors. Analyzing the relative amounts of collagen type XIV at the whole tissue level, as well as in parenchyma, airway wall and bronchial epithelium, we found consistently lower proportions of collagen type XIV in all lung tissue compartments across IPF samples. Our study suggests proportionally lower collagen type XIV in IPF lung tissues may have implications for the assembly of the ECM fibers potentially contributing to progression of fibrosis., (© 2023. The Author(s).)

Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1 + profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas., (© 2023. The Author(s).)

In the context of the development of carriers for amino acids delivery, Spherical Mesoporous Silica Particles (SMSP), characterized by particles size ranging from 0.15 µm to 0.80 µm and average pore diameter of 2.4 nm, were synthesised and loaded with L-arginine (ARG), a basic amino acid involved in several physiological processes. The loading was performed using water as a solvent through the wet impregnation method (with a final arginine content of 9.1% w / w ). The material was characterized before and after impregnation by means of X-Ray Diffraction (XRD), nitrogen sorption analysis, Field Emission Scanning Electron Microscopy (FESEM) and Fourier Transform Infrared (FT-IR) spectroscopy. SMSP are shown to suffer degradation upon impregnation, which dramatically affects their porosity. To elucidate the role of the pH of the ARG impregnating solution (originally set at pH ≈ 11) on SMSP degradation, the loading was performed under different pH conditions (5 and 9) keeping constant the ARG concentration. The impregnation performed with acidic solution did not modify the carrier. All samples displayed ARG in amorphous form: zwitterionic species were present in SMSP impregnated at basic pH whereas positive protonated species in that impregnated at acidic pH.

Cyclodextrins are widely used in pharmaceutics to enhance the bioavailability of many drugs. Conventional drug/cyclodextrin complexation techniques suffer from many drawbacks, such as a high residual content of toxic solvents in the formulations, the degradation of heat labile drugs and the difficulty in controlling the size and morphology of the product particles. These can be overcome by supercritical fluid technology thanks to the outstanding properties of supercritical CO 2 (scCO 2 ) such as its mild critical point, its tunable solvent power, and the absence of solvent residue after depressurization. In this work the use of scCO 2 as an unconventional medium to achieve the complexation with native and substituted cyclodextrins of over 50 drugs, which belong to different classes, are reviewed. This can be achieved with different approaches such as the "supercritical solvent impregnation" and "particle-formation" techniques. The different techniques are discussed to point out how they affect the complexation mechanism and efficiency, the physical state of the drug as well as the particle size distribution and morphology, which finally condition the release kinetics and drug bioavailability. When applicable, the results obtained for the same drug with various cyclodextrins, or different complexation techniques are compared with those obtained with conventional approaches.

Piroxicam (PRX) is a commonly prescribed nonsteroidal anti-inflammatory drug. Its efficacy, however, is partially limited by its low water solubility. In recent years, different studies have tackled this problem and have suggested delivering PRX through solid dispersions. All these strategies, however, involve the use of potentially harmful solvents for the loading procedure. Since piroxicam is soluble in supercritical CO 2 (scCO 2 ), the present study aims, for the first time, to adsorb PRX onto mesoporous silica using scCO 2 , which is known to be a safer and greener technique compared to the organic solvent-based ones. For comparison, PRX is also loaded by adsorption from solution and incipient wetness impregnation using ethanol as solvent. Two different commercial mesoporous silicas are used (SBA-15 and Grace Syloid ® XDP), which differ in porosity order and surface silanol population. Physico-chemical analyses show that the most promising results are obtained through scCO 2 , which yields the amorphization of PRX, whereas some crystallization occurs in the case of adsorption from solution and IWI. The highest loading of PRX by scCO 2 is obtained in SBA-15 (15 wt.%), where molecule distribution appears homogeneous, with very limited pore blocking.

Supercritical solvent impregnation (SSI) is a green unconventional technique for preparing amorphous drug formulations. A mesoporous nanostructured ZnO (mesoNsZnO) carrier with 8-nm pores, spherical-nanoparticle morphology, and an SSA of 75 m 2 /g has been synthesized and, for the first time, subjected to SSI with poorly water-soluble drugs. Ibuprofen (IBU), clotrimazole (CTZ), and hydrocortisone (HC) were selected as highly, moderately, and poorly CO 2 -soluble drugs. Powder X-ray diffraction, Fourier transform infrared spectroscopy, field emission scanning electron microscopy, nitrogen adsorption analysis, and ethanol extraction coupled with ultraviolet spectroscopy were employed to characterize the samples and quantify drug loading. Successful results were obtained with IBU and CTZ while HC loading was negligible, which could be related to different solubilities in CO 2 , drug size, and polarity. Successful SSI resulted in amorphous multilayer confinement of the drug. The mesoNsZnO-IBU system showed double drug loading than the mesoNsZnO-CTZ one, with a maximum uptake of 0.24 g/g. Variation of contact time during SSI of the mesoNsZnO-IBU system showed that drug loading triplicated between 3 and 8 h with an additional 30% increment between 8 h and 24 h. SSI did not affect the mesoNsZnO structure, and the presence of the adsorbed drug reduced the chemisorption of CO 2 on the carrier surface., Competing Interests: The authors declare no conflict of interest.

The physico⁻chemical and biological properties of nanostructured ZnO are combined with the non-toxic and eco-friendly features of the scCO₂-mediated drug loading technique to develop a multifunctional antimicrobial drug delivery system for potential applications in wound healing. Two nanostructured ZnO (NsZnO) with different morphologies were prepared through wet organic-solvent-free processes and characterized by means of powder X-ray diffraction, field emission scanning electron microscopy (FESEM), and nitrogen adsorption analysis. The antimicrobial activity of the two samples against different microbial strains was investigated together with the in vitro Zn 2+ release. The results indicated that the two ZnO nanostructures exhibited the following activity: S. aureus > C. albicans > K. pneumoniae . A correlation between the antimicrobial activity, the physico⁻chemical properties (specific surface area and crystal size) and the Zn 2+ ion release was found. Ibuprofen was, for the first time, loaded on the NsZnO carriers with a supercritical CO₂-mediated drug impregnation process and in vitro dissolution studies of the loaded drug were performed. A successful loading up to 14% w / w of ibuprofen in its amorphous form was obtained. A preliminary drug release test showed that up to 68% of the loaded ibuprofen could be delivered to a biological medium, confirming the feasibility of using NsZnO as a multifunctional antimicrobial drug carrier.

Critical properties and acentric factor are widely used in phase equilibrium calculations but are difficult to evaluate with high accuracy for many organic compounds. Quantitative Structure-Property Relationship (QSPR) models are a powerful tool to establish accurate correlation between molecular properties and chemical structure. QSPR multi-linear (MLR) and radial basis-function-neural-network (RBFNN) models have been developed to predict the critical temperature, critical pressure and acentric factor of a database of 306 organic compounds. RBFNN models provided better data correlation and higher predictive capability (an AAD% of 0.92⁻2.0% for training and 1.7⁻4.8% for validation sets) than MLR models (an AAD% of 3.2⁻8.7% for training and 6.2⁻12.2% for validation sets). The RMSE of the RBFNN models was 20⁻30% of the MLR ones. The correlation and predictive performances of the models for critical temperature were higher than those for critical pressure and acentric factor, which was the most difficult property to predict. However, the RBFNN model for the acentric factor resulted in the lowest RMSE with respect to previous literature. The close relationship between the three properties resulted from the selected molecular descriptors, which are mostly related to molecular electronic charge distribution or polar interactions between molecules. QSPR correlations were compared with the most frequently used group-contribution methods over the same database of compounds: although the MLR models provided comparable results, the RBFNN ones resulted in significantly higher performance.

The objective of this study was to develop a high-fidelity prototype for delivering multi-gene sequencing panel (GS) reports to clinicians that simulates the user experience of a final application. The delivery and use of GS reports can occur within complex and high-paced healthcare environments. We employ a user-centered software design approach in a focus group setting in order to facilitate gathering rich contextual information from a diverse group of stakeholders potentially impacted by the delivery of GS reports relevant to two precision medicine programs at the University of Maryland Medical Center. Responses from focus group sessions were transcribed, coded and analyzed by two team members. Notification mechanisms and information resources preferred by participants from our first phase of focus groups were incorporated into scenarios and the design of a software prototype for delivering GS reports. The goal of our second phase of focus group, to gain input on the prototype software design, was accomplished through conducting task walkthroughs with GS reporting scenarios. Preferences for notification, content and consultation from genetics specialists appeared to depend upon familiarity with scenarios for ordering and delivering GS reports. Despite familiarity with some aspects of the scenarios we proposed, many of our participants agreed that they would likely seek consultation from a genetics specialist after viewing the test reports. In addition, participants offered design and content recommendations. Findings illustrated a need to support customized notification approaches, user-specific information, and access to genetics specialists with GS reports. These design principles can be incorporated into software applications that deliver GS reports. Our user-centered approach to conduct this assessment and the specific input we received from clinicians may also be relevant to others working on similar projects., Competing Interests: The authors declare that there are no conflicts of interest., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Delivering genetic test results to clinicians is a complex process. It involves many actors and multiple steps, requiring all of these to work together in order to create an optimal course of treatment for the patient. We used information gained from focus groups in order to illustrate the current process of delivering genetic test results to clinicians. We propose a business process model and notation (BPMN) representation of this process for a Translational Pharmacogenomics Project being implemented at the University of Maryland Medical Center, so that personalized medicine program implementers can identify areas to improve genetic testing processes. We found that the current process could be improved to reduce input errors, better inform and notify clinicians about the implications of certain genetic tests, and make results more easily understood. We demonstrate our use of BPMN to improve this important clinical process for CYP2C19 genetic testing in patients undergoing invasive treatment of coronary heart disease.