High-throughput mechanical phenotyping and transcriptomics of single cells

• Published in: Nature communications Vol. 15; no. 1; pp. 3812 - 13
• Main Authors: Shiomi, Akifumi, Kaneko, Taikopaul, Nishikawa, Kaori, Tsuchida, Arata, Isoshima, Takashi, Sato, Mayuko, Toyooka, Kiminori, Doi, Kentaro, Nishikii, Hidekazu, Shintaku, Hirofumi
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 17.05.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 147/3; 38/39; 38/62; 49/91; 631/1647/514/1949; 631/337/2019; 631/57/2271; 631/61/350/1058; Animals; Cell differentiation; Cell Line, Tumor; Cell Membrane - metabolism; Cell surface; Cells (biology); Cellular Senescence - genetics; Electroporation; Electroporation - methods; Gene Expression Profiling - methods; Gene regulation; Humanities and Social Sciences; Humans; Lipids; Malignancy; Mechanical properties; Mechanics; Mechanics (physics); Mice; multidisciplinary; Oligonucleotides; Phenotype; Phenotypes; Phenotyping; Progenitor cells; Science; Science (multidisciplinary); Senescence; Single-Cell Analysis - methods; Surface Tension; Transcriptome; Transcriptomics; Tumor cell lines
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-48088-5

The molecular system regulating cellular mechanical properties remains unexplored at single-cell resolution mainly due to a limited ability to combine mechanophenotyping with unbiased transcriptional screening. Here, we describe an electroporation-based lipid-bilayer assay for cell surface tension and transcriptomics (ELASTomics), a method in which oligonucleotide-labelled macromolecules are imported into cells via nanopore electroporation to assess the mechanical state of the cell surface and are enumerated by sequencing. ELASTomics can be readily integrated with existing single-cell sequencing approaches and enables the joint study of cell surface mechanics and underlying transcriptional regulation at an unprecedented resolution. We validate ELASTomics via analysis of cancer cell lines from various malignancies and show that the method can accurately identify cell types and assess cell surface tension. ELASTomics enables exploration of the relationships between cell surface tension, surface proteins, and transcripts along cell lineages differentiating from the haematopoietic progenitor cells of mice. We study the surface mechanics of cellular senescence and demonstrate that RRAD regulates cell surface tension in senescent TIG-1 cells. ELASTomics provides a unique opportunity to profile the mechanical and molecular phenotypes of single cells and can dissect the interplay among these in a range of biological contexts. The molecular system regulating cell surface mechanics remains largely unexplored at single-cell resolution. Here, the authors report a high-throughput single-cell assay, ELASTomics, which integrates mechanical phenotyping with unbiased transcriptomics.