A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages

Area of Science:

• Single-cell biology
• Molecular immunology
• Genomics

Background:

• Understanding cellular heterogeneity is crucial in immunology, cancer, and developmental biology.
• Existing methods often struggle to link multi-generational cell behavior with individual cell transcriptomes.

Purpose of the Study:

• To develop and validate a microfluidic platform for simultaneous lineage tracking and single-cell RNA sequencing.
• To investigate transcriptional similarity within and between cell lineages.
• To explore the relationship between cell cycle progression and gene expression in distinct cell types.

Main Methods:

• Development of a microfluidic device for controlled cell culture and lineage tracking.
• Off-chip single-cell RNA sequencing (scRNA-seq) for whole-transcriptome profiling.
• Computational analysis of gene expression similarity and covariance with cell cycle data.

Main Results:

• Both primary murine CD8+ T-cells and a leukemia cell line exhibit greater intra-lineage transcriptional similarity than inter-lineage similarity.
• Genes related to lymphocyte function, such as Granzyme B, show higher expression similarity within CD8+ T-cell lineages.
• Cell type-specific transcriptional signatures correlating with cell cycle progression were identified.

Conclusions:

• The developed microfluidic platform effectively links multi-generational lineage history with single-cell transcriptomes.
• Transcriptional similarity is largely conserved within cell lineages, with lineage-specific genes showing strong intra-lineage coherence.
• This technology provides a powerful tool for studying cellular heterogeneity and clonal dynamics in various biological fields.