Profiling protein-protein interactions of single cancer cells with in situ lysis and co-immunoprecipitation

Smart Droplet Microfluidic System for Single-Cell Selective Lysis and Real-Time Sorting Based on Microinjection and Image Recognition

Single-cell analysis has important implications for understanding the specificity of cells. To analyze the specificity of rare cells in complex blood and biopsy samples, selective lysis of target single cells is pivotal but difficult. Microfluidics, particularly droplet microfluidics, has emerged as a promising tool for single-cell analysis. In this paper, we present a smart droplet microfluidic system that allows for single-cell selective lysis and real-time sorting, aided by the techniques of microinjection and image recognition. A custom program evolved from Python is proposed for recognizing target droplets and single cells, which also coordinates the operation of various parts in a whole microfluidic system. We have systematically investigated the effects of voltage and injection pressure applied to the oil-water interface on droplet microinjection. An efficient and selective droplet injection scheme with image feedback has been demonstrated, with an efficiency increased dramatically from 2.5% to about 100%. Furthermore, we have proven that the cell lysis solution can be selectively injected into target single-cell droplets. Then these droplets are shifted into the sorting area, with an efficiency for single K562 cells reaching up to 73%. The system function is finally explored by introducing complex cell samples, namely, K562 cells and HUVECs, with a success rate of 75.2% in treating K562 cells as targets. This system enables automated single-cell selective lysis without the need for manual handling and sheds new light on the cooperation with other detection techniques for a broad range of single-cell analysis.

Cytotrap: An Innovative Approach for Protein-Protein Interaction Studies for Cytoplasmic Proteins

Protein-protein interaction mapping has gained immense importance in understanding protein functions in diverse biological pathways. There are various in vivo and in vitro techniques associated with the protein-protein interaction studies but generally, the focus is confined to understanding the protein interaction in the nucleus of the cell, and thus it limits the availability to explore protein interactions that are happening in the cytoplasm of the cell. Since posttranslational modification is a crucial step in signaling pathways and cellular protein interactions harnessing the cytoplasmic protein and evaluating the interaction in the cytoplasm, this protocol will provide more information about studying these types of protein interactions. Cytotrap is a type of yeast-two-hybrid system that differs in its ability to anchor along the membrane, thus directing the protein of interest to anchor along the membrane through the myristoylation signaling unit. The vector containing the target protein contains the myristoylation unit, called the prey, and the bait unit contains the protein of interest as a fusion with the hSos protein. In an event of interaction between the target and the protein of interest, the hSos protein unit will be localized to the membrane and the GDP/GTP exchange unit will trigger the activation of the Ras pathway that leads to the survival of the temperature-sensitive yeast strain at a higher temperature.

Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context

At the heart of the cellular machinery through the regulation of cellular functions, protein-protein interactions (PPIs) have a significant role. PPIs can be analyzed with network approaches. Construction of a PPI network requires prediction of the interactions. All PPIs form a network. Different biases such as lack of data, recurrence of information, and false interactions make the network unstable. Integrated strategies allow solving these different challenges. These approaches have shown encouraging results for the understanding of molecular mechanisms, drug action mechanisms, and identification of target genes. In order to give more importance to an interaction, it is evaluated by different confidence scores. These scores allow the filtration of the network and thus facilitate the representation of the network, essential steps to the identification and understanding of molecular mechanisms. In this review, we will discuss the main computational methods for predicting PPI, including ones confirming an interaction as well as the integration of PPIs into a network, and we will discuss visualization of these complex data.

Knockdown of KRAB domain-associated protein 1 suppresses the proliferation, migration and invasion of thyroid cancer cells by regulating P68/DEAD box protein 5

KRAB domain-associated protein 1 (KAP-1) has been reported to be an oncogene in diverse tumors. KAP-1 was found to have abundant existence in malignant thyroid tissues, but its role in thyroid cancer hasn’t been elucidated clearly. This study was carried out to explore the role of KAP-1 in thyroid cancer, and to clarify its molecular mechanism. The expressions of KAP-1 and P68/DEAD box protein 5 (DDX5) were assessed under the help of qRT-PCR and western blot. Then, we downregulated KAP-1 or upregulated DDX5 by cell transfection in TPC-1 cells. A series of cellular experiments on proliferation, apoptosis, migration and invasion were conducted with CCK-8, EdU, TUNEL, wound-healing and Transwell assays. Besides, the relationship between KAP-1 and DDX5 was verified by co-immunoprecipitation (Co-IP). The results showed that both of KAP-1 and DDX5 were upregulated in thyroid cancer cells. Loss-of-function experiments revealed that KAP-1 knockdown imparted suppressive effects on cell proliferation, migration and invasion, but promoted cell apoptosis. Additionally, KAP-1 was demonstrated to interact with DDX5 and positively regulate DDX5 expression. The following rescued experiments exhibited that the inhibitory effects of KAP-1 knockdown on cellular activities of thyroid cancer and Wnt/β-catenin signaling were also partly reversed by DDX5 overexpression. Moreover, activation of Wnt/β-catenin signaling retarded the anti-tumor activity of KAP-1 knockdown. In conclusion, the data in this study disclosed that KAP-1 silence helped to repress the cell proliferation, migration and invasion by degrading DDK5, so as to hinder the development of thyroid cancer.

Recent progress of microfluidic technology for pharmaceutical analysis

In recent years, the progress of microfluidic technology has provided new tools for pharmaceutical analysis and the proposal of pharm-lab-on-a-chip is appealing for its great potential to integrate pharmaceutical test and pharmacological test in a single chip system. Here, we summarize and highlight recent advances of chip-based principles, techniques and devices for pharmaceutical test and pharmacological/toxicological test focusing on the separation and analysis of drug molecules on a chip and the construction of pharmacological models on a chip as well as their demonstrative applications in quality control, drug screening and precision medicine. The trend and challenge of microfluidic technology for pharmaceutical analysis are also discussed and prospected. We hope this review would update the insight and development of pharm-lab-on-a-chip.

Subcellular Dynamic Immunopatterning of Cytosolic Protein Complexes on Microstructured Polymer Substrates

Analysis of protein–protein interactions in living cells by protein micropatterning is currently limited to the spatial arrangement of transmembrane proteins and their corresponding downstream molecules. Here, we present a robust and straightforward method for dynamic immunopatterning of cytosolic protein complexes by use of an artificial transmembrane bait construct in combination with microstructured antibody arrays on cyclic olefin polymer substrates. As a proof, the method was used to characterize Grb2-mediated signaling pathways downstream of the epidermal growth factor receptor (EGFR). Ternary protein complexes (Shc1:Grb2:SOS1 and Grb2:Gab1:PI3K) were identified, and we found that EGFR downstream signaling is based on constitutively bound (Grb2:SOS1 and Grb2:Gab1) as well as on agonist-dependent protein associations with transient interaction properties (Grb2:Shc1 and Grb2:PI3K). Spatiotemporal analysis further revealed significant differences in stability and exchange kinetics of protein interactions. Furthermore, we could show that this approach is well suited to study the efficacy and specificity of SH2 and SH3 protein domain inhibitors in a live cell context. Altogether, this method represents a significant enhancement of quantitative subcellular micropatterning approaches as an alternative to standard biochemical analyses.

An Approach for the Real-Time Quantification of Cytosolic Protein-Protein Interactions in Living Cells

In recent years, cell-based assays have been frequently used in molecular interaction analysis. Cell-based assays complement traditional biochemical and biophysical methods, as they allow for molecular interaction analysis, mode of action studies, and even drug screening processes to be performed under physiologically relevant conditions. In most cellular assays, biomolecules are usually labeled to achieve specificity. In order to overcome some of the drawbacks associated with label-based assays, we have recently introduced "cell-based molography" as a biosensor for the analysis of specific molecular interactions involving native membrane receptors in living cells. Here, we expand this assay to cytosolic protein-protein interactions. First, we created a biomimetic membrane receptor by tethering one cytosolic interaction partner to the plasma membrane. The artificial construct is then coherently arranged into a two-dimensional pattern within the cytosol of living cells. Thanks to the molographic sensor, the specific interactions between the coherently arranged protein and its endogenous interaction partners become visible in real time without the use of a fluorescent label. This method turns out to be an important extension of cell-based molography because it expands the range of interactions that can be analyzed by molography to those in the cytosol of living cells.

Listening to the Whispers in Neuroimmune Crosstalk: A Comprehensive Workflow to Investigate Neurotrophin Receptor p75NTR Under Endogenous, Low Abundance Conditions

Inflammatory conditions are critically influenced by neuroimmune crosstalk. Cytokines and neurotrophic factors shape the responses of both nervous and immune systems. Although much progress has been made, most findings to date are based on expression of recombinant (tagged) proteins. The examination of receptor interactions by immunoprecipitation (IP) at endogenous levels provides further insight into the more subtle regulations of immune responses. Here, we present a comprehensive workflow and an optimized IP protocol that provide step-by-step instructions to investigate neurotrophin receptor p75NTR at endogenous, low abundance levels: from lysate preparation and confirmation of receptor expression to antibody validation and successful detection of protein-protein interactions. We employ human melanoma cell line A375 to validate specific antibodies and IP conditions, and apply these methods to explore p75NTR interactions in human leukemic plasmacytoid dendritic cell line PMDC05 detecting 14-3-3ϵ:p75NTR interaction in this cell type. With p75NTR as an exemplary protein, our approach provides a strategy to detect specific interaction partners even under endogenous, low abundance expression conditions.

Microfluidics-Based Sensing of Biospecies

Over the past decades, microfluidic devices based on many advanced techniques have aroused widespread attention in the fields of chemical, biological, and analytical applications. Integration of microdevices with a variety of chip designs will facilitate promising functionality. Notably, the combination of microfluidics with functional nanomaterials may provide creative ideas to achieve rapid and sensitive detection of various biospecies. In this review, focused on the microfluids and microdevices in terms of their fabrication, integration, and functions, we summarize the up-to-date developments in microfluidics-based analysis of biospecies, where biomarkers, small molecules, cells, and pathogens as representative biospecies have been explored in-depth. The promising applications of microfluidic biosensors including clinical diagnosis, food safety control, and environmental monitoring are also discussed. This review aims to highlight the importance of microfluidics-based biosensors in achieving high throughput, highly sensitive, and low-cost analysis and to promote microfluidics toward a wider range of applications.