A team led by CRG Barcelona deploys EPI-Clone, a targeted single-cell DNA methylation profiling method, to reconstruct clonal trajectories and quantify how blood stem cell diversity erodes with age, uncovering myeloid-biased clone expansion and its role in inflammaging.
Key points
EPI-Clone integrates targeted single-cell CpG methylation profiling on the Tapestri platform to capture clonal barcodes across 230,358 cells.
Aged mice and human donors exhibit up to 70% dominance of a few HSC clones, with a shift toward myeloid-biased hematopoiesis linked to inflammaging.
Distinct CpG subsets reflect both differentiation stage and stochastic epimutations, enabling simultaneous lineage mapping and clonal barcode generation.
Why it matters:
This approach enables precise tracking of HSC clonal dynamics, offering insights into inflammaging mechanisms and potential early biomarkers of age-related hematologic risk.
Q&A
What is EPI-Clone?
How does DNA methylation barcoding work?
What causes inflammaging?
Why use single-cell sequencing?
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Academy
Blood Stem Cell Aging and Epigenetic Clonal Tracing
Overview: The human blood system relies on hematopoietic stem cells (HSCs) in the bone marrow to generate red blood cells, white blood cells, and platelets throughout life. With aging, the diversity of HSCs diminishes, leading to dominant stem cell clones that can skew blood production and contribute to chronic inflammation, known as inflammaging.
Hematopoietic Stem Cells (HSCs)
HSCs are multipotent cells capable of both self-renewal and differentiation into all blood lineages. In youth, tens of thousands of HSCs cooperate to maintain a balanced production of cell types. They respond to infection, injury, and daily turnover by generating billions of new cells each day. As people age, some stem cells outcompete others, reducing overall diversity and making the system more vulnerable to stress and disease.
Epigenetic Marks and DNA Methylation
DNA methylation is an epigenetic modification where methyl groups attach to cytosine bases in CpG dinucleotides. Two patterns emerge: regulated methylation changes that drive lineage commitment during differentiation, and random, stochastic methylation errors that accumulate over time. These random epimutations can serve as unique identifiers for each cell’s lineage history.
Principles of Clonal Tracing
- Select CpG sites that show stable differentiation patterns to infer cell type and maturation stage.
- Identify stochastic CpG epimutations that occur randomly and uniquely in each cell over its lifetime.
- Combine both datasets to reconstruct clonal lineages: differentiation marks assign cell type, while random epimutations barcode clonal identity.
The EPI-Clone Method
EPI-Clone is built by adapting Mission Bio’s Tapestri single-cell sequencing platform. It targets hundreds of CpG positions in each cell, reads both differentiation-associated and stochastic methylation states, and then uses computational algorithms to extract digital barcodes. Researchers applied EPI-Clone to mouse and human blood samples, capturing over 230,000 single-cell methylation profiles and mapping how individual stem cell clones contribute to blood production over time.
Implications for Longevity Science
Age-related loss of HSC diversity and expansion of myeloid-biased clones underlie inflammaging and increase risks of cardiovascular disease, stroke, and blood cancers. By precisely tracking clonal dynamics, EPI-Clone offers a tool to monitor blood aging, evaluate interventions, and develop targeted therapies that restore healthy stem cell diversity, ultimately improving immune resilience and longevity.
