Updated revision on “alcohol-aging-TE” manuscript in bioRXIV

— We just updated our bioRxiv preprint manuscript titled “Chronic alcohol exposure drives inflammaging and transposon derepression in hematopoietic stem and progenitor cells” (Yuda et al., 2025). This revision updates the initial manuscript submitted to bioRxiv in December 2025. The revised manuscript contains several key updates, as follows:

1. Added LPS inflammatory challenge and EdU incorporation assays to demonstrate the impact of prior ethanol exposure on HSPC reactivation in response to inflammatory stimuli, presented in Figure 2.
2. Added additional data points to strengthen the robustness of the Ki67 and γH2AX measurements in Figure 1.
3. Re-analyzed the scRNA-seq data from human xenotransplanted HSPCs to incorporate differences between cohort 1 and cohort 2, presented in Figure 6.
4. Added transposable element analysis from bulk RNA-seq data of in vitro cultured human CD34+ cells exposed to ethanol, presented in Figure 7.
5. Added analysis of transposable elements in human HSCs and MPPs from cohorts 1 and 2, presented in Figure 7.
6. Added GO (gene ontology) term analysis of total and TE-overlapping OCRs (open chromatin regions) found in scATAC-seq data, presented in Figure 7 and Supplemental Figure 7.
7. Added motif analysis of total and TE-overlapping OCRs found in scATAC-seq data, presented in Figure 7.
8. Added RT-qPCR data for IFNA1, IFNB1, and IFNG from alcohol-exposed human CD34+ cell cultures, presented in Figure 7.
9. Refined the Discussion section to focus more strongly on transposable elements and inflammaging, and incorporated recent literature describing TE upregulation during stress hematopoiesis.

Together, these updates strengthen the overall conclusion that chronic alcohol exposure induces transposable element upregulation in both mouse and human hematopoietic systems in an age-dependent manner, and position this study as a novel observation linking alcohol exposure, inflammaging, and TE derepression in HSPCs.

The updated version 2 of Yuda et al (2025) manuscript can be found here. The original December 2025’s version of the manuscript can be found here.