Characterization of persistent chromatin states in aging hematopoiesis

Abstract

Across homeostasis, development, and disease, hematopoietic stem cells (HSCs) orchestrate blood production by deploying cis‑regulatory programs that balance quiescence, self‑renewal, and differentiation. With aging, the hematopoietic system undergoes significant changes, characterized by expansion of phenotypic HSCs, reduced lymphoid potential and a dominant myeloid bias. While chronic low grade inflammation and somatic mutations are known drivers of this decline, the extent to which aging related immune dysfunction is encoded as a stable, cell intrinsic epigenetic memory remains an important question for immune rejuvenation. This thesis explores the hypothesis that aging installs persistent chromatin states in long lived HSCs that are inherited by downstream myeloid progeny, thereby driving systemic immune dysfunction. First, we used a combination of aging mouse models and multiomics to establish the stability of hematopoietic aging signatures. By utilizing an ex vivo expansion system to isolate HSCs from the aged bone marrow micro environment, we demonstrate that aging associated chromatin accessibility signatures are not only transient responses to extrinsic inflammatory cues but are cell intrinsic features that persist through expansion and differentiation. Second, we translated these findings to humans by generating a high resolution single cell multiomic atlas of CD34+ HSPCs from young and aged donors. Through ex vivo culture and expansion, we distinguished aging associated cell intrinsic mechanisms from the extrinsic, niche dependent signals, identifying persistent chromatin states that remain stable even after two weeks of culture. And to make direct measurements of these chromatin states from progenitors to effector cells such as CD14 monocytes, we leveraged mitochondrial somatic mutations for clonal tracing (Mito-SHARE-seq). This approach enables us to directly map HSC derived chromatin states to transcriptional phenotypes of CD14 monocytes with the same clonal lineage. Through this analysis, we identified a robust, age specific regulatory program anchored by RUNX and ETS transcription factors. This program facilitates increased accessibility at inflammatory and myeloid primed enhancers, which is clonally propagated to drive a proinflammatory, antigen presenting gene expression profile in CD14 monocytes. Our results reveal that the aged HSC epigenome serves as a stable reservoir of regulatory memory, ensuring the continuous production of primed myeloid cells that could potentially contribute to systemic inflammation. By defining the specific cis-reulatory module and transcription factors that maintain these aging programs, this works provides a mechanistic foundation for targeted rejuvenation strategies to reset the immune system to a more youthful state.