Single-cell Analysis with Microfluidic Devices

Bioinformatics data combined with single-cell analysis reveals patterns of immunoinflammatory infiltration and cell death in melanoma

BACKGRUOND

Melanoma is a common cancer in dermatology, but its molecular mechanisms remain poorly explained.

AIM

Utilizing single-cell analytics and bioinformatics, the work sought to discover the immunological infiltration and cellular molecular mechanisms of melanoma.

METHODS

Melanoma genes databases were downloaded from GeneCards, and gene expression profiles were chosen from the Gene Expression Omnibus (GSE244889). Establishing and analyzing protein-protein interaction networks for functional enrichment made use of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases. The process assesses the immunological cell infiltration variations between normal and malignant samples by Immune Cell AI software program. Different cell type differences were clarified by cell quality control, filtration, removal of batch effects and cell clustering analysis using single cell analysis techniques.

RESULTS

Using a variety of machine learning techniques, 20 differentially expressed hub genes were found; among these, TP53, HSP90AB1, HSPA4, RHOA, CCND1, CYCS, PPARG, NFKBIA, CAV1, ANXA5, ENO1, ITGAM, YWHAZ, RELA, SOD1, and VDAC1 were found to be significantly significant. The results of enrichment analysis demonstrated that immune response and inflammatory response were strongly associated with melanoma. Animal mitophagy, ferroptosis, the PI3K-Akt signaling pathway, and the HIF-1 signaling pathway were the primary signaling pathways implicated. Cells of immunity, T-cells, lymphocytes, B-cells, NK-cells, monocytes, and macrophages were shown to be significantly infiltrated in melanoma patients, according to analysis. Single cell analysis also demonstrated that ferroptosis is a significant mechanism of cell death that contributes to the advancement of melanoma and that macrophages are important in the disease.

CONCLUSION

In summary, different immune cell infiltrations-particularly macrophages-have a significant impact on the onset and course of melanoma, and our findings may help direct future investigations into melanoma macrophages.

Pollution-Free and Highly Sensitive Lactate Detection in Cell Culture Based on a Microfluidic Chip

Cell metabolite detection is important for cell analysis. As a cellular metabolite, lactate and its detection play an important role in disease diagnosis, drug screening and clinical therapeutics. This paper reports a microfluidic chip integrated with a backflow prevention channel for cell culture and lactate detection. It can effectively realize the upstream and downstream separation of the culture chamber and the detection zone, and prevent the pollution of cells caused by the potential backflow of reagent and buffer solutions. Due to such a separation, it is possible to analyze the lactate concentration in the flow process without contamination of cells. With the information of residence time distribution of the microchannel networks and the detected time signal in the detection chamber, it is possible to calculate the lactate concentration as a function of time using the de-convolution method. We have further demonstrated the suitability of this detection method by measuring lactate production in human umbilical vein endothelial cells (HUVEC). The microfluidic chip presented here shows good stability in metabolite quick detection and can work continuously for more than a few days. It sheds new insights into pollution-free and high-sensitivity cell metabolism detection, showing broad application prospects in cell analysis, drug screening and disease diagnosis.

A single-cell surgery microfluidic device for transplanting tumor cytoplasm into dendritic cells without nuclei mixing

This study aimed to demonstrate the feasibility of generating tumor cell vaccine models by single-cell surgery in a microfluidic device that integrates one-to-one electrofusion, shear flow reseparation, and on-device culture. The device was microfabricated from polydimethylsiloxane (PDMS) and consisted of microorifices (aperture size: ∼3 μm) for one-to-one fusion, and microcages for on-device culture. Using the device, we could achieve one-to-one electrofusion of leukemic plasmacytoid dendritic cells (DC-like cells) and Jurkat cells with a fusion efficiency of ∼ 80%. Fusion via the narrow microorifices allowed DC-like cells to acquire cytoplasmic contents of the Jurkat cells while preventing nuclei mixing. After fusion, the DC-like cells were selectively reseparated from the Jurkat cells by shear flow application to generate tumor nuclei-free antigen-recipient DC-like (tarDC-like) cells. When cultured as single cells on the device, these cells could survive under gentle medium perfusion with a median survival time of 11.5 h, although a few cells could survive longer than 36 h. Overall, this study demonstrates single-cell surgery in a microfluidic device for potential generation of dendritic cell vaccines which are uncontaminated with tumor nucleic materials. We believe that this study will inspire the generation of safer tumor cell vaccines for cancer immunotherapy.

A Dual-Channel Microfluidic Chip for Single Tobacco Protoplast Isolation and Dynamic Capture

Protoplasts are widely used in gene function verification, subcellular localization, and single-cell sequencing because of their complete physiological activities. The traditional methods based on tissues and organs cannot satisfy the requirement. Therefore, the isolation and capture of a single protoplast are most important to these studies. In this study, a dual-channel microfluidic chip based on PDMS with multi-capture cavities was designed. The design theory of the dual-channel microfluidic chip's geometry was discussed. The capture mechanism of the single cell in a dual-channel microfluidic chip was studied by simulation analysis. Our results showed that a single polystyrene microsphere or tobacco protoplast was successfully isolated and trapped in this chip. The capture efficiency of the chip was 83.33% for the single tobacco protoplast when the inlet flow rate was 0.75 μL/min. In addition, the dynamic capture of the polystyrene microsphere and tobacco protoplasts was also presented. Overall, our study not only provided a new strategy for the subsequent high throughput single protoplast research, but also laid a theoretical foundation for the capture mechanism of the single cell.

A Microfluidic Device for Modulation of Organellar Heterogeneity in Live Single Cells

The quantitatively controlled organellar transfer between living single cells provides a unique experimental platform to analyze the contribution of organellar heterogeneity on cellular phenotypes. We previously developed a microfluidic device which can perform quantitatively controlled mitochondrial transfer between live single cells by promoting strictured cytoplasmic connections between live single cells, but its application to other organelles is unclear. In this study, we investigated the quantitative properties of peroxisome transfer in our microfluidic device. When cells were fused through a 10 or 4 μm long microtunnel by a Sendai virus envelope-based method, a strictured cytoplasmic connection was achieved with a length corresponding to that of the microtunnel, and a subsequent recovery culture disconnected the fused cells. The peroxisome number being transferred through a 10 μm length of the microtunnel was smaller than that of 4 μm. These data suggest that our microfuidic device can perform a quantitative control of peroxisome transfer.

Spatially Resolved Analytical Chemistry in Intact, Living Tissues

Tissues are an exciting frontier for bioanalytical chemistry, one in which spatial distribution is just as important as total content. Intact tissue preserves the native cellular and molecular organization and the cell-cell contacts found in vivo. Live tissue, in particular, offers the potential to analyze dynamic events in a spatially resolved manner, leading to fundamental biological insights and translational discoveries. In this Perspective, we provide a tutorial on the four fundamental challenges for the bioanalytical chemist working in living tissue samples as well as best practices for mitigating them. The challenges include (i) the complexity of the sample matrix, which contributes myriad interfering species and causes nonspecific binding of reagents; (ii) hindered delivery and mixing; (iii) the need to maintain physiological conditions; and (iv) tissue reactivity. This framework is relevant to a variety of methods for spatially resolved chemical analysis, including optical imaging, inserted sensors and probes such as electrodes, and surface analyses such as sensing arrays. The discussion focuses primarily on ex vivo tissues, though many considerations are relevant in vivo as well. Our goal is to convey the exciting potential of analytical chemistry to contribute to understanding the functions of live, intact tissues.