Extracellular vesicles (EVs) are nanoscale lipid bilayer particles secreted by cells. EVs may carry markers of the tissue of origin and its disease state, which makes them incredibly promising for disease diagnosis and surveillance. While the armamentarium of EV analysis technologies is rapidly expanding, there remains a strong need for multiparametric analysis with single EV resolution. Nanoprojectile (NP) secondary ion mass spectrometry (NP-SIMS) relies on bombarding a substrate of interest with individual gold NPs resolved in time and space. Each projectile creates an impact crater of 10-20 nm in diameter while molecules emitted from each impact are mass analyzed and recorded as individual mass spectra. We demonstrate the utility of NP-SIMS for analysis of single EVs derived from normal liver cells (hepatocytes) and liver cancer cells. EVs were captured on antibody (Ab)-functionalized gold substrate and then labeled with Abs carrying lanthanide (Ln) MS tags (Ab@Ln). These tags targeted four markers selected for identifying all EVs, and specific to hepatocytes or liver cancer. NP-SIMS was used to detect Ab@Ln-tags colocalized on the same EV and to construct scatter plots of surface marker expression for thousands of EVs with the capability of categorizing individual EVs. Additionally, NP-SIMS revealed information about the chemical nanoenvironment where targeted moieties colocalized. Our approach allowed analysis of population heterogeneity with single EV resolution and distinguishing between hepatocyte and liver cancer EVs based on surface marker expression. NP-SIMS holds considerable promise for multiplexed analysis of single EVs and may become a valuable tool for identifying and validating EV biomarkers of cancer and other diseases.
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http://dx.doi.org/10.1021/acsnano.3c06604 | DOI Listing |
Brief Bioinform
November 2024
Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
Regulatory genes are critical determinants of cellular responses in development and disease, but standard RNA sequencing (RNA-seq) analysis workflows, such as differential expression analysis, have significant limitations in revealing the regulatory basis of cell identity and function. To address this challenge, we present the TRIAGE R package, a toolkit specifically designed to analyze regulatory elements in both bulk and single-cell RNA-seq datasets. The package is built upon TRIAGE methods, which leverage consortium-level H3K27me3 data to enrich for cell-type-specific regulatory regions.
View Article and Find Full Text PDFBrief Bioinform
November 2024
College of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, China.
The role of cell-cell communications (CCCs) is increasingly recognized as being important to differentiation, invasion, metastasis, and drug resistance in tumoral tissues. Developing CCC inference methods using traditional experimental methods are time-consuming, labor-intensive, cannot handle large amounts of data. To facilitate inference of CCCs, we proposed a computational framework, called CellMsg, which involves two primary steps: identifying ligand-receptor interactions (LRIs) and measuring the strength of LRIs-mediated CCCs.
View Article and Find Full Text PDFJ Paediatr Child Health
January 2025
Department of Neonatology, University of Health Sciences, Ankara Bilkent City Hospital, Ankara, Turkey.
Objective: To evaluate the incidence of thin catheter surfactant administration (TCA) failure and compare short and long-term neonatal outcomes who failed TCA or did not.
Design: Single-center retrospective cohort study. Infants between 25 and 30 weeks of gestational age with respiratory distress syndrome and receiving 200 mg/kg poractant alfa via thin catheter administration were included.
Ann Surg Oncol
January 2025
Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA.
Background: Nearly 25% of opioid-related deaths are from prescribed opioids, and the exacerbation of the opioid epidemic by the coronavirus disease 2019 (COVID-19) pandemic underscores the urgent need to address superfluous prescribing. Therefore, we sought to align local opioid prescribing practices with national guidelines in postoperative non-metastatic breast cancer patients.
Methods: A single-institution analysis included non-metastatic breast surgery patients treated between April 2020 and July 2021.
Influenza Other Respir Viruses
January 2025
Department of Pediatrics, Fukushima Medical University, Fukushima, Japan.
Background: Nonpharmaceutical interventions for coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2, during the pandemic altered the epidemiology of respiratory viruses. This study aimed to determine the changes in respiratory viruses among children hospitalized from 2018 to 2023.
Methods: Nasopharyngeal specimens were collected from children aged under 15 years with fever and/or respiratory symptoms admitted to a medical institution in Fukushima Prefecture between January 2018 and December 2023.
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