Associating growth factor secretions and transcriptomes of single cells in nanovials using SEC-seq
Shreya Udani, Justin Langerman, Doyeon Koo, Sevana Baghdasarian, Brian Cheng, Simran Kang, Citradewi Soemardy, Joseph de Rutte, Kathrin Plath & Dino Di Carlo
Nature Nanotechnology, December 2023
Abstract
Cells secrete numerous bioactive molecules that are essential for the function of healthy organisms. However, scalable methods are needed to link individual cell secretions to their transcriptional state over time. Here, by developing and using secretion-encoded single-cell sequencing (SEC-seq), which exploits hydrogel particles with subnanolitre cavities (nanovials) to capture individual cells and their secretions, we simultaneously measured the secretion of vascular endothelial growth factor A (VEGF-A) and the transcriptome for thousands of individual mesenchymal stromal cells. Our data indicate that VEGF-A secretion is heterogeneous across the cell population and is poorly correlated with the VEGFA transcript level. The highest VEGF-A secretion occurs in a subpopulation of mesenchymal stromal cells characterized by a unique gene expression signature comprising a surface marker, interleukin-13 receptor subunit alpha 2 (IL13RA2), which allowed the enrichment of this subpopulation. SEC-seq enables the identification of gene signatures linked to specific secretory states, facilitating mechanistic studies, the isolation of secretory subpopulations and the development of means to modulate cellular secretion.
Workflow for SEC-seq. Cells are loaded, adhered and incubated in gelatin-coated nanovials functionalized with secretion capture antibodies. Secreted and captured proteins are labelled with oligo-barcoded detection antibodies. Nanovials loaded with single cells are then introduced into the 10x Chromium workflow for library preparation. Sequencing of the resulting libraries results in matched secretion and transcriptomics data for downstream analyses. Schematic partially created with BioRender.com.
Topics
SEC-seq
Cell Types
Mesenchymal Stromal Cells
Instruments
SONY SH800S, 10X Chromium, Illumina NovaSeq