Single-cell intracellular epitope and transcript detection reveals signal transduction dynamics

Area of Science:

• Cellular and Molecular Biology
• Biochemistry
• Immunology

Background:

• Understanding cellular responses to external stimuli requires methods that track both signaling pathways and gene expression.
• Existing single-cell methods often lack the ability to concurrently measure protein and RNA levels.

Purpose of the Study:

• To introduce QuRIE-seq, a new droplet-based platform for single-cell multi-omics analysis.
• To investigate dynamic changes in signaling (phospho)proteins and gene expression in response to B cell receptor pathway stimulation.
• To assess the impact of ibrutinib on cellular signaling and transcriptomic landscapes.

Main Methods:

• Development of QuRIE-seq for simultaneous quantification of single-cell RNA and intra-/extracellular (phospho)proteins via sequencing.
• Application of QuRIE-seq to Burkitt lymphoma cells stimulated via the B cell receptor pathway over various time points (2-180 minutes).
• Utilized the multi-omics factor analysis (MOFA+) framework to analyze multi-timescale changes in protein and gene expression data.

Main Results:

• QuRIE-seq successfully quantified dynamic changes in (phospho)protein and RNA levels at the single-cell level.
• Analysis revealed distinct temporal patterns in signaling and gene expression following B cell receptor stimulation.
• The study identified the effects of ibrutinib on both signaling pathways and gene expression profiles.

Conclusions:

• QuRIE-seq is a powerful tool for dissecting complex cellular responses at single-cell resolution.
• The method provides insights into the interplay between signaling networks and gene expression dynamics.
• QuRIE-seq facilitates the study of drug mechanisms and cellular perturbations.