Abstract PR002: Characteristics of methylation heritability in human somatic cells

Ageing is the decline in an organism's function over time, driven by internal and external stresses. Key features of ageing include genomic instability, telomere shortening, epigenetic changes, and loss of proteostasis, and they tend to worsen and compound with age. However, how do these molecular changes manifest in the observed systemic changes seen in ageing is unclear. Somatic mutations contribute to cancer but are thought to have a limited role in ageing, as the genome tolerates rare random errors. Yet, some mutations confer a fitness advantage to the cell, allowing it to overproliferate relative to other cells. To what extent does a clone's founding cell also confer a phenotype, which is inherited by the expanding clone is incompletely understood. It would be interesting to see if constant mutation rates coupled with slow but exponential clonal expansion leads to a sizable proportion of cells that also carry a stable phenotype, which could result in tissue ageing at a systemic level. We sequenced whole genomes and methylomes of single human hematopoietic stem cells (HSCs) from several healthy individuals of different ages and patients with hematologic malignancies. Based on the patterns of shared and cell-specific somatic mutations, we built phylogenies of HSCs for each individual. To establish whether loss or gain of methylation, both mono and bi-allelic, was heritable across cell division, we developed a method that recapitulates this process in a population of related cells. We analysed approximately 25 million CpG sites per individual, and find that methylation is highly heritable at the majority of sites. Moreover, the method allows us to accurately time when methylation changes occurred as methylation changes are assigned to a branch, which represents a common ancestor of the descendant cells, and the branches of a phylogeny can be linked to a developmental period, thus disentangling their evolutionary history. We observe that methylation changes are remarkably stable as we found that thousands of such changes are acquired before germ layer formation and are stably inherited until old age. Interestingly, the same regions across individuals acquire these pre-gastrulation changes that are maintained indefinitely. Moreover, we found the rates of methylation change are several folds higher than the rates of somatic mutations and that methylation changes are stochastic and allele-specific. Lastly, we find that some of these changes precede the neoplasm’s clone, which suggests they might play a role in function. By comparing normal healthy individuals of different ages with cancer patients, we have been able to unravel the process of normal ageing from disease development at an unprecedented scale and granularity.

Citation Format: Lori D Kregar, Nicholas Williams, Joe Lee, Emily Mitchell, Elisa Laurenti, Jyoti Nangalia, Peter Campbell. Characteristics of methylation heritability in human somatic cells [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Methylation, Clonal Hematopoiesis, and Cancer; 2025 Feb 1-4; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2025;85(3 Suppl):Abstract nr PR002.