Profiling DNA Cargos in Single Extracellular Vesicles via Hydrogel-Based Droplet Digital Multiple Displacement Amplification

Due to the substantial heterogeneity among extracellular vesicle (EV) subpopulations, single-EV analysis has the potential to elucidate the mechanisms behind EV biogenesis and shed light on the myriad functions, leading to the development of novel diagnostics and therapeutics. While many studies have been devoted to reveal between-EV variations in surface proteins and RNAs, DNA cargos (EV-DNA) have received little attention. Here, we report a hydrogel-based droplet digital multiple displacement amplification approach for the comprehensive analysis of EV-DNA at the single-EV level. Single EVs are dispersed in thousands of hydrogel droplets and lysed for DNA amplification and identification. The droplet microfluidics strategy empowers the assay with single-molecule sensitivity and capability for absolute quantification of DNA-containing EVs. In particular, our findings indicate that 5–40% EVs are associated with DNA, depending on the cell of origin. Large EVs exhibit a higher proportion of DNA-containing EVs and a more substantial presence of intraluminal DNA, compared to small EVs. These DNA-containing EVs carry multiple DNA fragments on average. Furthermore, both double-stranded DNA and single-stranded DNA were able to be detected at the single-EV level. Utilizing this method, the abundance, distribution, and biophysical properties of EV-DNA in various EV populations are evaluated. The DNA level within EVs provides insight into the status of the originating cells and offers valuable information on the outcomes of anticancer treatments. The utilization of single-EV analysis for EV-DNA holds significant promise for early cancer detection and treatment response monitoring

Shear Stress-Enhanced Internalization of Cell Membrane Proteins Indicated by a Hairpin-Type DNA Probe

Shear stress is an important mechanical stimulus that plays a critical role in modulating cell functions. In this study, we investigated the regulating effects of shear stress on the internalization of cell membrane proteins in a microfluidic chip. A hairpin-type DNA probe was developed and indiscriminately anchored to the cell surface, acting as an indicator for the membrane proteins. When cells were exposed to shear stress generated from fluid cell medium containing external proteins, strong fluorescence was emanated from intracellular regions. With intensive investigation, results revealed that shear stress could enhance the specific cell endocytosis pathway and promote membrane protein internalization. This process was indicated by the enhanced intracellular fluorescence, generated from the internalized and mitochondria accumulated DNA probes. This study not only uncovered new cellular mechanotransduction mechanisms but also provided a versatile method that enabled in situ and dynamic indication of cell responses to mechanical stimuli

Shear Stress-Enhanced Internalization of Cell Membrane Proteins Indicated by a Hairpin-Type DNA Probe

Shear stress is an important mechanical stimulus that plays a critical role in modulating cell functions. In this study, we investigated the regulating effects of shear stress on the internalization of cell membrane proteins in a microfluidic chip. A hairpin-type DNA probe was developed and indiscriminately anchored to the cell surface, acting as an indicator for the membrane proteins. When cells were exposed to shear stress generated from fluid cell medium containing external proteins, strong fluorescence was emanated from intracellular regions. With intensive investigation, results revealed that shear stress could enhance the specific cell endocytosis pathway and promote membrane protein internalization. This process was indicated by the enhanced intracellular fluorescence, generated from the internalized and mitochondria accumulated DNA probes. This study not only uncovered new cellular mechanotransduction mechanisms but also provided a versatile method that enabled in situ and dynamic indication of cell responses to mechanical stimuli

Single-Cell Analysis Using Drop-on-Demand Inkjet Printing and Probe Electrospray Ionization Mass Spectrometry

This study describes a novel method for single-cell analysis and lipid profiling by combining drop-on-demand inkjet cell printing and probe electrospray ionization mass spectrometry (PESI-MS). Through inkjet sampling of a cell suspension, droplets with single cells were generated, precisely dripped onto a tungsten-made electrospray ionization needle, and immediately sprayed under a high-voltage electric field. Lipid fingerprints of single cells were obtained by a mass spectrometry (MS) detector. A homemade magnetic stirring device was applied to the cell suspension reservoir, which controlled the homogeneous distribution of cells in liquid and improved the single-cell-droplet percentage by 43.8%. Eight types of single cells were screened in our platform and further differentiated by principal component analysis based on cellular surface phospholipids. Thus, this study successfully provides a facile method for the direct MS profiling of single-cell lipids by PESI-MS

Additional file 5 of Three tyrosine kinase inhibitors cause cardiotoxicity by inducing endoplasmic reticulum stress and inflammation in cardiomyocytes

Additional file 5. Original western blot gel images, related to Fig. 4

Additional file 4 of Three tyrosine kinase inhibitors cause cardiotoxicity by inducing endoplasmic reticulum stress and inflammation in cardiomyocytes

Additional file 4. Supplementary research methods and details on the reagent or resource used in the experiment

Additional file 2 of Three tyrosine kinase inhibitors cause cardiotoxicity by inducing endoplasmic reticulum stress and inflammation in cardiomyocytes

Additional file 2: Figure S1. EC50s of response calculated based on a four-parameter log-logistic model in the ATP fold change, related to Fig. 1. Figure S2. Seahorse experiment on acute effects of TKIs on mitochondrial oxygen consumption and extracellular acidification, related to Fig. 1. Figure S3. Mitochondrial membrane potential changes in response to TKIs observed by TMRE staining and its fold change, related to Fig. 1. Figure S4. Clustering of TKI-induced transcriptome data based on tSNE analysis, related to Fig. 2. Figure S5. Cluster 0, 2, 3, 4, 6 contained over 10 significant DEGs found by log2-based fold changes, related to Fig. 2. Figure S6. Expression of genes related to tRNA aminoacylation for protein translation in different clusters or in response to different drugs, related to Fig. 2. Figure S7. Good quality and consistency of 3’DGE-UMI RNA-seq, related to Fig. 2. Figure S8. The Jackstraw plot of the top 15 principal components in the tSNE analysis, related to Fig. 2. Figure S9. The number of unique genes, total counts, and proportion of mitochondrial DNA present in the 3'DGE-UMI RNA-seq data, related to Fig. 2. Figure S10. Correlation analysis between mitochondrial DNA and total counts or between unique genes and total counts in 3’DGE-UMI RNA-seq data, related to Fig. 2. Figure S11. Comparison of differentially expressed genes detected by 3'DGE-UMI and bulk RNA-seq for sorafenib and sunitinib treatments, related to Fig. 2

Additional file 1 of Three tyrosine kinase inhibitors cause cardiotoxicity by inducing endoplasmic reticulum stress and inflammation in cardiomyocytes

Additional file 1: Table S1. An introduction to the pharmacology and toxicology of TKI drugs of different cardiotoxicity levels. Table S2. Endoplasmic reticulum stress gene markers under different conditions of sorafenib. Table S3. The ARRIVE checklist

Additional file 3 of Three tyrosine kinase inhibitors cause cardiotoxicity by inducing endoplasmic reticulum stress and inflammation in cardiomyocytes

Additional file 3: Figure S12. Cell viability of NRCMs in response to afatinib, sorafenib, and ponatinib, related to Fig. 4. Figure S13. Low dose of TKIs induce ER stress over time in NRCMs, measured by mRNA fold changes, related to Fig. 4. Figure S14. Effects of ponatinib and sorafenib on heart weight, body weight, heart-to-body weight ratio, and Ddit3 expression in rat hearts, related to Fig. 4. Figure S15. Lipid peroxidation levels in NRCMs treated with cumene hydroperoxide and ethanol, related to Fig. 5. Figure S16. The effect of trolox on lipid peroxidation and ER stress induced by TKIs, related to Fig. 5. Figure S17. ISRIB and 4μ8c affected gene targets of Atf4 and Xbp1s induced by TKIs in NRCMs, related to Fig. 6. Figure S18. ISRIB and 4μ8c did not rescue NRCMs from cell death induced by the 3 TKIs, related to Fig. 6. Figure S19. The effects of ISRIB and 4μ8c on TKI-induced cell death examined using fluorescence imaging and quantification, related to Fig. 6. Figure S20. Persistent eIF2α phosphorylation up-regulated Nfkb1 and Il6 expression induced by 3 TKIs in H9C2 cells, but not Il1b or Tnf, related to Fig. 6

Table S9_The total_Information of SSH-G

Table S9_The total_Information of SSH-