Umbilical cord subtotipotent-like stem cells reverse the ageing of thymic epithelial cells by inducing reprogramming of the whole-genome methylation and transcription profile

Abstract Background: A decrease in the number and activity of thymic epithelial cells (TECs) is an important factor in thymic degeneration, which can lead to dysfunction of T-cell differentiation, development and selection and a decrease in human immune function. Umbilical cord pluripotent-like stem cells (UCSSCs) can promote the structural and functional regeneration of the ageing thymus in vivo, but the mechanism of their action on TECs and molecules is not clear. Based on the discovery that UCSSCs promote thymus regeneration, we further analysed the changes in genome methylation modification profiles and their association with transcription profiles in ageing TECs cocultured with UCSSCs. Results: UCSSCs could promote thymus regeneration in ageing macaque monkeys, and an ageing model of TECs was established. Coculture of ageing TECs with UCSSCs for 48 hours significantly reduced the expression levels of ageing markers such as P16, P21 and p53 and increased the activity of ageing TECs. Genome-wide methylation and transcriptional sequencing analysis of TECs showed that methylation levels of 501 genes increased and 591 genes decreased in the promoter region. Twenty-three genes with increased methylation were enriched in the processes of negative regulation of cell growth, proliferation and apoptosis, and 37 genes with decreased methylation were enriched in the processes of promoting cell growth and proliferation and inhibiting apoptosis. Association analysis between promoter and transcription level revealed that there was a significant negative correlation between promoter methylation level and gene transcription in 66 genes, among which PDE5A, DUOX2, LAMP1 and SVIL, which inhibit growth and development, showed increased methylation and decreased transcription. Decreased methylation of POLR3G, PGF, CHTF18, KRT17, FOXJ1, NGF, DYRK3, LRP8, CDT1, PRELID1, F2R, KNTC1 and TRIM3, which promote cell growth, leads to an increase in transcription levels. Decreased promoter methylation of the transcription factor NGF gene, which leads to an increase in KRT17 and FOXJ1 transcription, plays a key role in reversing TEC senescence. Conclusion: UCSSC coculture ameliorates the age-associated hallmarks of ageing TECs. The methylation profile of senescent TEC genes was significantly changed after treatment with umbilical cord pluripotent stem cells. It was found that decreasing the methylation level of the transcription factor NGF and increasing the expression level of KRT17 and FOXJ1 play a key role in promoting the proliferation of TECs.