Scientists have created a new, highly effective method of tracing blood cells’ lineage. This can improve our understanding of clonal hematopoiesis and its impact on an aging organism [1].
Hostile takeover
In the human body, a relatively small pool of hematopoietic stem cells (HSCs) sustains a system that produces 100-200 billion mature blood cells each day. Tracing descendant cells back to their ancestral stem cells is key to understanding aging and some diseases. With age, some stem cells acquire traits, through mutations or other mechanisms, that give them a reproductive edge. Their progeny multiply faster and gradually take over the blood system.
Many of these dominant clones skew toward producing pro-inflammatory cells, which are often less immunocompetent. This process, called clonal hematopoiesis, may be an important contributor to chronic age-related inflammation (inflammaging) [2]. It has been linked to cancer, cardiovascular diseases, and increased mortality [3].
“Our blood stem cells compete for survival,” explained Dr. Lars Velten, Group Leader at the Center for Genomic Regulation (CRG) in Barcelona and co-corresponding author of this new study published in Nature. “In youth, this competition produces a rich, diverse ecosystem, while in old age, some drop out entirely. A few stem cells take over, and these work extra hard to compensate. This reduces diversity, which is bad for the blood system’s resilience. Diverse stem cells can respond to different stresses, so the dominance of a handful of clones makes the whole system more fragile.”
The new method
Current lineage-tracing methods, such as introducing artificial mutations that are inherited by cellular descendants, are time-consuming and have key limitations. They cannot be used in humans because they require genetic engineering, and they often fail to provide information about the cell’s functional state, such as when it has terminally differentiated. In model organisms, most clonal hematopoiesis experiments are done using transplantation, in which the animal’s blood system is wiped out by irradiation and artificially rebuilt so that researchers can observe clonal dynamics “from scratch.”
This creates the need for methods that rely on endogenous markers, such as naturally occurring mutations or epigenetic changes, and can perform high-throughput, single-cell analysis across large cell populations. The authors of this study propose using epigenetic changes, specifically somatic methylation patterns, as such a marker.
DNA methylation is the addition of a methyl group to a nucleotide in a DNA molecule. Multitudes of those markers create a unique epigenetic landscape that is inherited by the cell’s progeny. Crucially, the researchers showed that different methylation sites carry different types of information: some reflect a cell’s differentiation state, since methylation controls gene expression at various stages, while more static sites preserve inherited patterns that act as molecular tracers of clonal identity.
“Our cells carry genetic alterations which collectively make us unique individuals,” said Dr. Alejo Rodriguez-Fraticelli, co-corresponding author of the study and Group Leader at IRB Barcelona. “But we’re also a mosaic of epigenetic alterations. Groups of cells, even if they end up doing different jobs, carry shared methylation marks which tie them back to a common ancestor stem cell. We’ve been finally able to construct the epigenetic family tree by reading information written directly into the DNA of each cell.”
For this purpose, the researchers developed EPI-Clone, a high-throughput single-cell methylation analysis method. Their first test utilized HSCs that were labeled with traditional genetic barcodes and transplanted into irradiated mice. After five months, they profiled these cells with EPI-Clone. This method successfully reconstructed the known clonal structures, confirming that methylation patterns alone could trace lineages.
“DNA methylation works like a kind of binary code. At each position in the genome, a site is either methylated or not, like a 1 or a 0,” explained Dr. Michael Scherer, bioinformatician and co-first author of the study. “This simple on-off information can be transformed into a natural barcode. Five years ago, I wouldn’t have thought this possible at single-cell resolution, across tens of thousands of cells. It’s been a huge leap forward in technology.”
“After 60, it becomes almost inevitable”
Having validated the tool, the scientists turned to native, unmanipulated mouse hematopoiesis; this is a key step, since transplantation experiments impose artificial stress and regenerative demands that do not reflect normal aging. Analyzing young and old mice, they found that young bone marrow maintained a diverse clonal structure, with many small clones contributing to blood production. In contrast, old mice showed a shift toward oligoclonality, with a few expanded clones dominating the system.
Strikingly, some of the largest aged clones were filled with undifferentiated HSCs that appeared stuck in a self-renewing state, producing few mature progeny. The team transplanted aged bone marrow into new recipients and found that these dominant old clones engrafted poorly while smaller, non-expanded clones drove successful regeneration. This suggests a tradeoff: some clones gain a replicative edge at the price of reduced functional output, consistent with current understanding of clonal hematopoiesis and its harmful effects.
The researchers next applied EPI-Clone to human bone marrow samples from donors of different ages and observed a similar pattern: with age, larger clones begin to take over. “The change from diversity to dominance isn’t random but clock-like,” said Indranil Singh, co-first author of the study and a final-year PhD student at IRB Barcelona. “By age 50, you can already see it starting, and after 60, it becomes almost inevitable.”
While scientists have already identified several mutations that induce clonal hematopoiesis, EPI-Clone was able to detect both these known driver-driven expansions and large driver-negative clones, which are clonal expansions with no known genetic trigger. These novel clones shared features with known ones, such as a bias toward myeloid over lymphoid progeny. The findings suggest that age-driven clonal expansion is not just about known driver mutations in genes like DNMT3A or TET2 but is part of a broader, clock-like process of clonal selection and drift involving both genetic and non-genetic mechanisms.
“If we want to move beyond generic anti-aging treatments and into real precision medicine for aging, this is exactly the kind of tool we need,” says Dr. Velten. “We can’t fix what we can’t see and for the first time, EPI-Clone can facilitate this for humans.”
Literature
[1] Scherer, M., Singh, I., Braun, M. M., Szu-Tu, C., Sanchez Sanchez, P., Lindenhofer, D., … & Velten, L. (2025). Clonal tracing with somatic epimutations reveals dynamics of blood ageing. Nature, 1-10.
[2] Winter, S., Götze, K. S., Hecker, J. S., Metzeler, K. H., Guezguez, B., Woods, K., … & Platzbecker, U. (2024). Clonal hematopoiesis and its impact on the aging osteo-hematopoietic niche. Leukemia, 38(5), 936-946.
[3] Zink, F., Stacey, S. N., Norddahl, G. L., Frigge, M. L., Magnusson, O. T., Jonsdottir, I., … & Stefansson, K. (2017). Clonal hematopoiesis, with and without candidate driver mutations, is common in the elderly. Blood, The Journal of the American Society of Hematology, 130(6), 742-752.
