The aging process is manifested by a multitude of interlinked biological processes. These processes contribute to genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient-sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and altered intercellular communication. Together these are recognized as of the main risk factors of the world’s most prevalent diseases, such as neurodegenerative disorders, cancer, cardiovascular disease, and metabolic disease. The mammalian ortholog of the yeast silent information regulator (Sir2) SIRT1 is a NAD + -dependent class III histone deacetylase and has been recognized to be involved in many of the forementioned processes. Therefore, its activity is connected to aging via the regulation of apoptosis, cell differentiation, development, stress response, metabolism, and tumorigenesis. Furthermore, the physiological activity of several sirtuin family members has been connected to the regulation of life span of lower organisms (Caenorhabditis elegans and Drosophila melanogaster) as well as mammals. Aging in somatic cells of mammals is accompanied by mutations and other forms of DNA damage. These might manifest in transient cell cycle arrest associated with DNA repair, apoptosis, senescence, or cell differentiation. The activity of SIRT1 has previously been reported to be regulated by the DNA damage response pathway. On the one hand, SIRT1 is recruited from ATM to DBS and is required for DNA damage repair, but on the other hand, SIRT1 activity was also found to be negatively regulated by genotoxic stress via the interaction of ATM with Deleted in Breast Cancer 1 (DBC1). Increased levels of DBS are associated with downregulation of ATM and lower phosphorylation levels of AKT and GSK3ß, with significant implications for mesenchymal stem cell (MSC) maintenance and differentiation. In this proposed “stem cell checkpoint,” the ATM signalling pathway initiated by DBS maintains MSCs and blocks their differentiation. Based on this, it has already been established that in senescent mesenchymal stem cells, SIRT1 expression is decreased, while its overexpression delays the onset of senescence and loss of differentiation capacity/ability. In the present study, we provide evidence that SIX2-positive urine derived renal progenitor cells-UdRPCs isolated directly from human urine show typical hallmarks of aging when obtained from elderly donors. This includes the transcriptional downregulation of SIRT1 and its downstream targets AKT and GSK3ß. This transcriptional downregulation is accompanied by an increase in DNA damage and transcriptional levels several cell cycle inhibitors such as P16, reflecting possibly the ATM induced “stemness checkpoint” to maintain UdRPC stemness and differentiation capacity. We provide evidence that the renal progenitor transcription factor SIX2 binds to the coding sequence of SIRT1 and both factors mutually influence the transcription of each other. Furthermore, we show that the SIRT1 promoter region is methylation sensitive and becomes subsequently methylated in UdRPCs derived from aged donors, dividing them into SIRT1 high and low expressing UdRPCs. This downregulation might render the cells more vulnerable to endogenous noxae accelerating the accumulation of DNA damage and ultimately the accumulation of aging associated hallmarks.