Integrative Single-Cell Analysis Reveals the Regulation of Transposable Elements in HSPCs during the Aging Process
Authors: Rivera Logan , Hong Tingting , Rathod Kunjal , Guzman Anna , Wohlan Katharina , Zhou Yubin , Goodell Margaret , Huang Yun Nancy 
Published: December 2024

Clonal hematopoiesis (CH) shows strong prevalence during aging (Jaiswal and Ebert, 2019; Jaiswal et al., 2014). CH is defined as a disproportionate distribution of a small portion of mutant hematopoietic stem and progenitor cells (HSPCs) in the mature peripheral blood (Busque et al., 2012), exhibiting increased risk of malignant transformation and other age-related diseases, e.g., cardiovascular diseases (Jaiswal et al., 2017; Fuster et al., 2017). Genetic mutations and epigenetic alterations are frequently observed in CH and drive clonal expansion of mutant HSPCs. Furthermore, accumulating evidence suggests an intimate connection between inflammation and CH. For example, an inflammatory environment, such as elevated IL6 and IFN signaling, promotes the clonal expansion of TET2 or DNMT3A mutant HSPCs, respectively (Meisel et al., 2018; Hormaechea-Agulla et al., 2021). In our recent study, we reported that age-related heterochromatin dysregulation mediates the upregulation of retrotransposable elements (TEs) and promotes the expression of interferon-stimulated genes (ISGs). This contributes to the functional decline of normal HSPCs during aging, thereby causing them to lose their competitive capability against TET2 mutant HSPCs (Hong et al., 2023). Our findings further indicate that, in addition to the external inflammatory environment, age-related upregulation of TEs might induce an intracellular innate immune response and suppress normal HSPC self-renewal and lineage specification in aged HSPCs. To further delineate the transcriptional and epigenetic regulation of TEs during HSPC aging, we collected single-cell RNA-seq (scRNA-seq) and single-cell ATAC-seq (scATAC-seq) data in Lineage-negative (Lin-) HSPCs from C57BL/6 mice at 12-week-old, 12-, 24-, and 30-month old mice. Capitalizing on a deep learning-based model, we examined the expression of different subsets of TEs in various cell populations of Lin- HSPCs. Significant changes in gene expression and chromatin accessibility profiles were observed during HSPC aging. Notable differences in TE profiles among cell populations at different ages were observed, suggesting the accumulation of transposable elements as one of the molecular features of HSPC aging and might contribute to CH pathogenesis. In parallel, we identified dynamic TE expression changes in HSPCs during the aging process. By comparing the scRNA-seq and scATAC-seq data, we also identified age-related signature TEs and the most affected genomic regions at the single-cell level. Overall, these integrative bioinformatic analyses have revealed that, in addition to the coding genes, the expression of TEs is cell-type specific and undergoes dynamic changes during the aging. This high-resolution multi-omics approach of TE analysis, coupled with sophisticated cluster labeling and extensive analysis, proves to be beneficial for investigating complex cellular processes to accelerate the mechanistic dissection of hematopoiesis and aging.