Resolving Fates and Single-Cell Transcriptomes of Hematopoietic Stem Cell Clones by PolyloxExpress Barcoding

Area of Science:

• Hematopoiesis research
• Stem cell biology
• Molecular genetics

Background:

• Hematopoietic stem cells (HSCs) are crucial for blood cell production.
• Understanding HSC fate and transcriptional states is vital for regenerative medicine.
• Current methods analyze HSC fate or transcriptome separately, not simultaneously.

Purpose of the Study:

• To develop a method linking HSC fate and transcriptome within the same cell.
• To identify transcriptional signatures associated with distinct HSC fates.
• To explore the transcriptional landscape of hematopoietic stem cell clones.

Main Methods:

• Development of the PolyloxExpress allele for in situ RNA barcoding.
• Cre-recombinase-dependent barcoding to track cell lineage.
• Simultaneous analysis of HSC fate and single-cell transcriptome.

Main Results:

• Identified transcriptional signatures specific to HSC fates, not visible with separate analyses.
• Demonstrated that differentiation-inactive, multilineage, and lineage-restricted HSC clones occupy distinct transcriptional regions.
• Differentiation-inactive HSC clones are transcriptionally close to the origin but lack a quiescent gene signature.
• Fate-specific gene signatures suggest coherent clonal HSC fates and stable HSC output over time.

Conclusions:

• The developed method enables combined analysis of HSC fate and transcriptome.
• Distinct transcriptional landscapes correlate with specific HSC clonal behaviors.
• This approach may help identify molecular drivers of HSC fate decisions.