Abstract PR017: Properties of somatic methylation changes in human hematopoietic stem cells in health and disease
Authors: Kregar Lori D. , Williams Nicholas , Lee Joe , Nangalia Jyoti , Campbell Peter 
Published: February 2024

Cancer is the proliferation of a genetic clone at the expense of its neighbours and normal tissue function. Studies have shown that with ageing, normal tissues become colonised by expanding clones, which acquired fitness-enhancing mutations that allow them to over-proliferate relative to their neighbours. However, whether the clones’ founding cell also carries an epigenome that is inherited by the expanding clone is incompletely understood. In the following study, we performed multi-omic profiling of human hematopoietic stem cells (HSCs) to establish the role of epigenetic heritability through time in health and disease. We sequenced whole genomes and methylomes of single human HSCs from three healthy individuals and several individuals diagnosed with myeloproliferative neoplasm or chronic myeloid leukaemia. Based on the patterns of shared and sample-specific somatic mutations, we built phylogenies of HSCs for each individual. To establish whether loss or gain of methylation, both partial and complete, was heritable, we developed a method which analyses read counts at a CpG site across cells together with their phylogeny. Our model assumes CpG sites are in one of three states (i.e. they are 0%, 50% or 100% methylated, as measured by the number of methylated reads divided by number of total reads at a site), methylation states are inherited during cell division and a cell’s state can spontaneously transition to any of the other two. Our method finds sites, which follow these assumptions, and proposes the most likely zygotic starting state and identifies phylogeny’s branches, which underwent a change, to produce the observed methylation profile of cells at a CpG site. We analysed approximately 25 million CpG sites per individual, and we find that the majority of sites exhibit heritability of methylation states with the aforementioned properties. The method allows us to accurately time when methylation changes occurred as the branches of a phylogeny can be linked to a developmental period, thus disentangling their evolutionary history. Applying the method across millions of CpG sites and thousands of single cells from these individuals, we found the rates of methylation change is several folds higher than the rate of somatic mutations and that methylation changes are stochastic and allele-specific. Moreover, we observe that these changes are remarkably stable as we found that hundreds of such changes are acquired between the time of X-chromosome inactivation and germ layer formation and are stably inherited until old age. In addition, 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 are able to unravel the process of normal ageing from disease development.

Citation Format: Lori D. Kregar, Nicholas Williams, Joe Lee, Jyoti Nangalia, Peter Campbell. Properties of somatic methylation changes in human hematopoietic stem cells in health and disease [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr PR017.