Artificial intelligence-driven automated lung sizing from chest radiographs.

Lung size measurements play an important role in transplantation, as optimal donor-recipient size matching is necessary to ensure the best possible outcome. Although several strategies for size matching are currently used, all have limitations, and none has proven superior. In this pilot study, we leveraged deep learning and computer vision to develop an automated system for generating standardized lung size measurements using portable chest radiographs to improve accuracy, reduce variability, and streamline donor/recipient matching. We developed a 2-step framework involving lung mask extraction from chest radiographs followed by feature point detection to generate 6 distinct lung height and width measurements, which we validated against measurements reported by 2 radiologists (M.K.I. and R.R.) for 50 lung transplant recipients. Our system demonstrated <2.5% error (<7.0 mm) with robust interrater and intrarater agreement compared with an expert radiologist review. This is especially promising given that the radiographs used in this study were purposely chosen to include images with technical challenges such as consolidations, effusions, and patient rotation. Although validation in a larger cohort is necessary, this study highlights artificial intelligence's potential to both provide reproducible lung size assessment in real patients and enable studies on the effect of lung size matching on transplant outcomes in large data sets.

In vivo and in vitro anti-inflammatory, antipyretic and ulcerogenic activities of pyridone and chromenopyridone derivatives, physicochemical and pharmacokinetic studies.

Throughout this study, we present the victorious synthesis of a novel class of 2(1H)-pyridone molecules, bearing a 4-hydroxyphenyl moiety through a one-pot reaction of 2-cyano-N-(4-hydroxyphenyl)acetamide with cyanoacetamide, acetylacetone or ethyl acetoacetate, and their corresponding aldehydes. In addition, the chromene moiety was introduced into the pyridine skeleton through the cyclization of the cyanoacetamide 2 with salicylaldehyde, followed by treatment with malononitrile, ethyl cyanoacetate, and cyanoacetamide, in order to improve their biological behaviour. Due to their anti-inflammatory, ulcerogenic, and antipyretic characters, the target molecules have undergone in-vitro and in-vivo examination, that display promising results. Moreover, in order to predict the physicochemical and ADME traits of all synthesized compounds and standard reference drugs, paracetamol and phenylbutazone, the in-silico prediction methodology was provided.

Fluorescent Probes for Monitoring Serine Ubiquitination.

In a radical departure from the classical E1-E2-E3 three-enzyme mediated ubiquitination of eukaryotes, the recently described bacterial enzymes of the SidE family of Legionella pneumophila effectors utilize NAD+ to ligate ubiquitin onto target substrate proteins. This outcome is achieved via a two-step mechanism involving (1) ADP ribosylation of ubiquitin followed by (2) phosphotransfer to a target serine residue. Here, using fluorescent NAD+ analogues as well as synthetic substrate mimics, we have developed continuous assays enabling real-time monitoring of both steps of this mechanism. These assays are amenable to biochemical studies and high-throughput screening of inhibitors of these effectors, and the discovery and characterization of putative enzymes similar to members of the SidE family in other organisms. We also show their utility in studying enzymes that can reverse and inhibit this post-translational modification.

Unveiling Hidden Disparities: Evaluating US Multiple Listing Practices in Lung Transplantation.

BACKGROUND: Multiple listing (ML) is a practice used to increase the potential for transplant but is controversial due to concerns that it disproportionately benefits patients with greater access to health care resources. RESEARCH QUESTION: Is there disparity in ML practices based on social deprivation in the United States and does ML lead to quicker time to transplant? STUDY DESIGN AND METHODS: A retrospective cohort study of adult (≥ 18 years of age) lung transplant candidates listed for transplant (2005-2018) was conducted. Exclusion criteria included heart only or heart and lung transplant and patients relisted during the observation period. Data were obtained from the United Network for Organ Sharing Standard Transplant Analysis and Research File. The first exposure of interest was the Social Deprivation Index with a primary outcome of ML status, to assess disparities between ML and single listing (SL) participants. The second exposure of interest was ML status with a primary outcome of time to transplant, to assess whether implementation of ML leads to quicker time to transplant. RESULTS: A total of 35,890 patients were included in the final analysis, of whom 791 (2.2%) were ML and 35,099 (97.8%) were SL. ML participants had lower median level of social deprivation (5 units, more often female: 60.0% vs 42.3%) and lower median lung allocation score (35.3 vs 37.3). ML patients were more likely to be transplanted than SL patients (OR, 1.42; 95% CI, 1.17-1.73), but there was a significantly quicker time to transplant only for those whom ML was early (within 6 months of initial listing) (subdistribution hazard ratio, 1.17; 95% CI, 1.04-1.32). INTERPRETATION: ML is an uncommon practice with disparities existing between ML and SL patients based on several factors including social deprivation. ML patients are more likely to be transplanted, but only if they have ML status early in their transplant candidacy. With changing allocation guidelines, it is yet to be seen how ML will change with the implementation of continuous distribution.

Extracellular matrix protein composition dynamically changes during murine forelimb development.

The extracellular matrix (ECM) is an integral part of multicellular organisms, connecting different cell layers and tissue types. During morphogenesis and growth, tissues undergo substantial reorganization. While it is intuitive that the ECM remodels in concert, little is known regarding how matrix composition and organization change during development. Here, we quantified ECM protein dynamics in the murine forelimb during appendicular musculoskeletal morphogenesis (embryonic days 11.5-14.5) using tissue fractionation, bioorthogonal non-canonical amino acid tagging, and mass spectrometry. Our analyses indicated that ECM protein (matrisome) composition in the embryonic forelimb changed as a function of development and growth, was distinct from other developing organs (brain), and was altered in a model of disease (osteogenesis imperfecta murine). Additionally, the tissue distribution for select matrisome was assessed via immunohistochemistry in the wild-type embryonic and postnatal musculoskeletal system. This resource will guide future research investigating the role of the matrisome during complex tissue development.

An Integrative Biology Approach to Quantify the Biodistribution of Azidohomoalanine In Vivo.

Background: Identification and quantitation of newly synthesized proteins (NSPs) are critical to understanding protein dynamics in development and disease. Probing the nascent proteome can be achieved using non-canonical amino acids (ncAAs) to selectively label the NSPs utilizing endogenous translation machinery, which can then be quantitated with mass spectrometry. We have previously demonstrated that labeling the in vivo murine proteome is feasible via injection of azidohomoalanine (Aha), an ncAA and methionine (Met) analog, without the need for Met depletion. Aha labeling can address biological questions wherein temporal protein dynamics are significant. However, accessing this temporal resolution requires a more complete understanding of Aha distribution kinetics in tissues. Results: To address these gaps, we created a deterministic, compartmental model of the kinetic transport and incorporation of Aha in mice. Model results demonstrate the ability to predict Aha distribution and protein labeling in a variety of tissues and dosing paradigms. To establish the suitability of the method for in vivo studies, we investigated the impact of Aha administration on normal physiology by analyzing plasma and liver metabolomes following various Aha dosing regimens. We show that Aha administration induces minimal metabolic alterations in mice. Conclusions: Our results demonstrate that we can reproducibly predict protein labeling and that the administration of this analog does not significantly alter in vivo physiology over the course of our experimental study. We expect this model to be a useful tool to guide future experiments utilizing this technique to study proteomic responses to stimuli. Supplementary Information: The online version contains supplementary material available at 10.1007/s12195-023-00760-4.

Transplanting candidates with stacked risks negatively affects outcomes.

BACKGROUND: Lung transplant (LT) centers are increasingly evaluating patients with multiple risk factors for adverse outcomes. The effects of these stacked risks remains unclear. Our aim was to determine the relationship between the number of comorbidities and post-transplant outcomes. METHODS: We performed a retrospective cohort study using the National Inpatient Sample (NIS) and UNOS Starfile (USF). We applied a probabilistic matching algorithm using 7 variables (transplant: month, year, and type; recipient: age, sex, race, payer). We matched recipients in the USF to transplant patients in the NIS between 2016 and 2019. The Elixhauser methodology was used to identify comorbidities present on admission. We determined the associations between mortality, length of stay (LOS), total charges, and disposition with comorbidity numbers using penalized cubic splines, Kaplan-Meier, and linear and logistic regression methods. RESULTS: From 28,484,087 NIS admissions, we identified 1,821 LT recipients. Matches were exact in 76.8% of the cohort. While the remaining cohort had a probability match of ≥0.94. Penalized splines of Elixhauser comorbidity number identified 3 knots defining 3 groups of stacked risk: low (<3), medium (3-6), and high risk (>6). Inpatient mortality increased from low to medium to high-risk categories: (1.6%, 3.9%, and 7.0%; p < 0.001), as did LOS (16, 21, 29 days, p < 0.001), total charges ($553,057, $666,791, $821,641.5; p = 0.004) and discharge to a skilled nursing facility (15%, 20%, 31%; p < 0.001). CONCLUSIONS: Stacked risks adversely affect post-LT mortality, LOS, charges, and discharge disposition. Further study to understand the details of specific stacked risks is warranted.

Metabolic labeling of secreted matrix to investigate cell-material interactions in tissue engineering and mechanobiology.

Re-creating features of the native extracellular matrix (ECM) with engineered biomaterials has become a valuable tool to probe the influence of ECM properties on cellular functions (e.g., differentiation) and toward the engineering of tissues. However, characterization of newly secreted (nascent) matrix and turnover, which are important in the context of cells interacting with these biomaterials, has been limited by a lack of tools. We developed a protocol to visualize and quantify the spatiotemporal evolution of newly synthesized and deposited matrix by cells that are either cultured atop (2D) or embedded within (3D) biomaterial systems (e.g., hydrogels, fibrous matrices). This technique relies on the incorporation of a noncanonical amino acid (azidohomoalanine) into proteins as they are synthesized. Deposited nascent ECM components are then visualized with fluorescent cyclooctynes via copper-free cycloaddition for spatiotemporal analysis or modified with cleavable biotin probes for identification. Here we describe the preparation of hyaluronic acid hydrogels through ultraviolet or visible light induced cross-linking for 2D and 3D cell culture, as well as the fluorescent labeling of nascent ECM deposited by cells during culture. We also provide protocols for secondary immunofluorescence of specific ECM components and ImageJ-based ECM quantification methods. Hyaluronic acid polymer synthesis takes 2 weeks to complete, and hydrogel formation for 2D or 3D cell culture is performed in 2-3 h. Lastly, we detail the identification of nascent proteins, including enrichment, preparation and analysis with mass spectrometry, which can be completed in 10 d.

Mutated p53 in HGSC-From a Common Mutation to a Target for Therapy.

Mutations in tumor suppressor gene TP53, encoding for the p53 protein, are the most ubiquitous genetic variation in human ovarian HGSC, the most prevalent and lethal histologic subtype of epithelial ovarian cancer (EOC). The majority of TP53 mutations are missense mutations, leading to loss of tumor suppressive function of p53 and gain of new oncogenic functions. This review presents the clinical relevance of TP53 mutations in HGSC, elaborating on several recently identified upstream regulators of mutant p53 that control its expression and downstream target genes that mediate its roles in the disease. TP53 mutations are the earliest genetic alterations during HGSC pathogenesis, and we summarize current information related to p53 function in the pathogenesis of HGSC. The role of p53 is cell autonomous, and in the interaction between cancer cells and its microenvironment. We discuss the reduction in p53 expression levels in tumor associated fibroblasts that promotes cancer progression, and the role of mutated p53 in the interaction between the tumor and its microenvironment. Lastly, we discuss the potential of TP53 mutations to serve as diagnostic biomarkers and detail some more advanced efforts to use mutated p53 as a therapeutic target in HGSC.

Biocontrol Activity of Bacillus megaterium BM344-1 against Toxigenic Fungi.

Mycotoxins are secondary metabolites of some fungal species and represent important contaminants of food and feed. This study aimed to explore the biological control activity of Bacillus megaterium BM344-1 volatile organic compounds (VOCs) on the growth and mycotoxin production of single representatives of the toxigenic species Aspergillus flavus, Aspergillus carbonarius, Penicillium verrucosum, and Fusarium verticillioides. In vitro co-incubation experiments indicated the P. verrucosum isolate as the most sensitive one, with a growth inhibition ratio of 66.7%, followed by A. flavus (29.4%) and F. verticillioides (18.2%). Exposure of A. flavus, P. verrucosum, and F. verticillioides to BM344-1 VOCs resulted in complete inhibition of aflatoxins (AFB1, AFG1, and AFG2), ochratoxin A, and fumonisin B1 (FB1) synthesis on artificial media, respectively. In vivo experiments on maize kernels showed 51% inhibition of fungal growth on ears simultaneously infected with A. flavus spores and exposed to BM344-1 volatiles. Likewise, AF synthesis by A. flavus was significantly (p < 0.05) inhibited (25.34 ± 6.72 µg/kg) by bacterial volatiles as compared to that in control maize ears (91.81 ± 29.10 µg/kg). Gas chromatography-tandem mass spectrometry-based analysis of headspace volatiles revealed hexadecanoic acid methyl ester (palmitic acid) and tetracosane as bioactive compounds in the BM344-1 volatilome. Bacterial volatiles have promising potential to control the growth and mycotoxin synthesis of toxigenic fungi and may present valuable aid in the efforts to warrant food and feed safety.

The Dynamic Relationship of Breast Cancer Cells and Fibroblasts in Fibronectin Accumulation at Primary and Metastatic Tumor Sites.

In breast cancer (BC), tissue stiffening via fibronectin (FN) and collagen accumulation is associated with advanced disease progression at both the primary tumor and metastatic sites. Here, we evaluate FN production in 15 BC cell lines, representing a variety of subtypes, phenotypes, metastatic potentials, and chemotherapeutic sensitivities. We demonstrate that intracellular and soluble FN is initially lost during tumorigenic transformation but is rescued in all lines with epithelial-mesenchymal plasticity (EMP). Importantly, we establish that no BC cell line was able to independently organize a robust FN matrix. Non-transformed mammary epithelial cells were also unable to deposit FN matrices unless transglutaminase 2, a FN crosslinking enzyme, was overexpressed. Instead, BC cells manipulated the FN matrix production of fibroblasts in a phenotypic-dependent manner. In addition, varied accumulation levels were seen depending if the fibroblasts were conditioned to model paracrine signaling or endocrine signaling of the metastatic niche. In the former, fibroblasts conditioned by BC cultures with high EMP resulted in the largest FN matrix accumulation. In contrast, mesenchymal BC cells produced extracellular vesicles (EV) that resulted in the highest levels of matrix formation by conditioned fibroblasts. Overall, we demonstrate a dynamic relationship between tumor and stromal cells within the tumor microenvironment, in which the levels and fibrillarization of FN in the extracellular matrix are modulated during the particular stages of disease progression.

Dynamics of Non-Canonical Amino Acid-Labeled Intra- and Extracellular Proteins in the Developing Mouse.

INTRODUCTION: Mapping protein synthesis and turnover during development will provide insight into functional tissue assembly; however, quantitative in vivo characterization has been hindered by a lack of tools. To address this gap, we previously demonstrated murine embryos can be labeled with the non-canonical amino acid azidohomoalanine (Aha), which enables the enrichment and identification of newly synthesized proteins. Using this technique, we now show how protein turnover varies as a function of both time and cellular compartment during murine development. METHODS: Pregnant C57BL/6 mice were injected with Aha or PBS (control) at different embryonic time points. Aha-labeled proteins from homogenized E12.5 and E15.5 embryos were conjugated with diazo biotin-alkyne, bound to NeutrAvidin beads, selectively released, then processed for either SDS-PAGE or LC-MS/MS. For turnover studies, embryos were harvested 0-48 h after Aha injection at E12.5, separated into different cellular fractions based on solubility, and analyzed via western blotting. RESULTS: We developed an enhanced method for isolating Aha-labeled proteins from embryos that minimizes background signal from unlabeled proteins and avidin contamination. Approximately 50% of all identified proteins were found only in Aha samples. Comparing proteins present in both Aha and PBS samples, 90% were > 2-fold enriched in Aha-treated embryos. Furthermore, this method could resolve differences in the Aha-labeled proteome between developmental time points. Newly synthesized Aha-labeled proteins were observed by 3 h and peak labeling was around 6 h. Notably, extracellular matrix and cytoskeletal turnover appeared lower than the cytosolic fraction. CONCLUSIONS: The methods developed in this work enable the identification and quantification of protein synthesis and turnover in different tissue fractions during development. This will provide insight into functional tissue assembly and ultimately inform the design of regenerative therapies that seek to promote growth and repair.

Non-canonical amino acid labeling in proteomics and biotechnology.

Metabolic labeling of proteins with non-canonical amino acids (ncAAs) provides unique bioorthogonal chemical groups during de novo synthesis by taking advantage of both endogenous and heterologous protein synthesis machineries. Labeled proteins can then be selectively conjugated to fluorophores, affinity reagents, peptides, polymers, nanoparticles or surfaces for a wide variety of downstream applications in proteomics and biotechnology. In this review, we focus on techniques in which proteins are residue- and site-specifically labeled with ncAAs containing bioorthogonal handles. These ncAA-labeled proteins are: readily enriched from cells and tissues for identification via mass spectrometry-based proteomic analysis; selectively purified for downstream biotechnology applications; or labeled with fluorophores for in situ analysis. To facilitate the wider use of these techniques, we provide decision trees to help guide the design of future experiments. It is expected that the use of ncAA labeling will continue to expand into new application areas where spatial and temporal analysis of proteome dynamics and engineering new chemistries and new function into proteins are desired.