Tet2 Deficiency Mitigates Epigenetic Aging in Clonal Hematopoiesis
Authors: Li Sheng Shirley , Karmakar Shilpita , Motakis Efthymios , Liu Yang , Sengupta Kaustav , Naddaf Lamis , Roeder Travis , Vu Brandon , Mujica Kristina D. , Pietras Eric M. , DeGregori James V , Trowbridge Jennifer J. , Oguro Hideyuki 
Published: December 2024

Aging is a process of systemic deterioration and the most significant risk factor for cancers. Clonal hematopoiesis (CH) commonly occurs with aging and links to higher mortality, leukemia risk, and cardiovascular diseases. Age-related CH involves the abnormal clonal expansion of hematopoietic stem cells (HSCs) bearing somatic mutations in genes frequently mutated in leukemia, including genes encoding epigenetic regulators, such as the DNA demethylase TET2. While such mutations are known to alter the HSC epigenome, the mechanisms through which these mutations drive HSC self-renewal, myeloid transformation, and inflammatory response remain elusive.

In this study, we hypothesize that aging and CH mutations cooperatively reshape the HSC transcriptomic landscape and enhancing HSC competitive advantage that facilitates clonal expansion. Recently, aging has been closely associated with Tet2 mutation impact. Using single-cell multi-omic analyses and flow-cytometric phenotyping, we demonstrated, for the first time, that HSC aging processes at transcriptomic, epigenomic, and cellular levels are mitigated by Tet2 deficiency in mice, in an age-dependent manner. at ages greater than or equal to 16 months, but not at a young age, based on gene expression and chromatin accessibility at a single-cell resolution. This age mitigation was further validated by differential analysis of gene expression, open chromatin accessibility and DNA methylation that are elevated with aging but lowered with Tet2 deficiency in HSCs from old mice. Moreover, we found that Tet2 deficiency , a cellular hallmark of HSC aging, in an age-dependent manner. We observed increased gene expression with aging, such as for Eya4 and Lars2, which are downregulated by Tet2∆/∆ in HSCs from older mice, suggesting that Tet2 deficiency mitigates the process of aging. Also, the increased expression of Cdk6, Msi2, and Sox4 in Tet2∆/∆ HSCs, normally reduced in old HSC, promote the HSC self-renewal as shown in earlier. These gene expression changes were confirmed by single-nuclear open chromatin accessibility analysis, suggesting that Tet2 deficiency mitigates epigenome reprograming during HSC aging, as shown by increased differential single-nuclear chromatin accessibility of their motifs via ChromVar analysis. These TFs' target genes play critical roles in HSC commitment to progenitors, hemostasis, and proliferation. The methylation status of these TF binding motifs is linked to the regulation for the targets' gene expression.

In conclusion, our findings reveal that Tet2 deficiency significantly contributes to the mitigation of HSC aging and hijacks the HSC expansion strategy during HSC aging via epigenetic reprogramming, which contributes to age-related clonal hematopoiesis. By elucidating the transcriptomic and epigenomic alterations in Tet2-deficient HSCs, our study provides novel insights into how age and somatic mutations interact to promote the pathogenesis of age-related hematological diseases. These discoveries not only enhance our understanding of HSC aging mechanisms but also offer potential biomarkers for early detection and targets for therapeutic intervention in age-associated clonal disorders.