The mechanisms governing ageing, which is a multifactorial process, have not been resolved and constitute a fundamental open question in cell and organismal biology research worldwide. Exceptionally, in rare genetic diseases like the Cockayne syndrome (CS), the ageing phenotype is greatly accelerated1. Understanding the molecular defects responsible for these premature ageing diseases is critical to develop treatments, which are dramatically missing to date, and also elucidate physiological ageing in general. We recently identified a completely hitherto undiscovered pathway that is altered in cells from CS patients2 (Partner1-Ricchetti). This pathway is uncoupled from the well-documented DNA repair defect and rather involves mitochondrial and metabolic impairments. Although mitochondrial defects have been described in CS cells (mutated in the DNA repair factor CSA or CSB)1, they have been essentially considered consequences of impaired DNA repair in the nucleus and in the organelle. Conversely, our findings show that in CS cells oxidative and nitrosative stress (ROS/RNS) promotes overexpression of the HTRA3 protease, which results in the degradation of the key mitochondrial DNA polymerase POLG1 responsible for replication of the organelle genome, and triggers mitochondrial dysfunction. Importantly, we rescued defects in CS patient cells by scavenging oxidative/nitrosative molecules (with MnTBAP), paving the path to therapeutic approaches for CS that are missing to date. These findings led to an international patent application (WO2012123588), and the designation by the EMA (European Medicines Agency) of MnTBAP as Orphan Drug for CS (P1-Ricchetti and Partner2-Laugel). Our findings represent a paradigm shift to understand and possibly challenge the causes of precocious ageing in CS, and perhaps in normal ageing. It urges now to identify the underlying mechanisms and evaluate the impact of these cellular alterations on progeroid dysfunction. Importantly, our (unpublished) results reveal genome-wide epigenetic changes that are correlated with the severity of disease, making possible the identification of novel key effectors in the establishment of CS. Based on a consortium that has the largest collection of research and clinical paradigms to study CS, and a robust set of preliminary data, we launch a research program to elucidate how CSA/B deficiency alters the HTRA3/POLG1/mitochondrial pathway and the epigenetic landscape in the presence of nitroso-redox imbalance. This study has also implications for the clinical treatment of CS and possible interventions for physiological ageing. The present study has four aims: 1) assess the mechanism by which HTRA3 overexpression results in POLG1 depletion and in turn mitochondrial dysfunction; 2) link epigenetic modifications specific to CS fibroblasts (manuscript, ms1, in preparation) to transcriptome changes, and to iPSC-derived neuronal cells/structures, for the identification of novel effectors of CS defects, and assess whether they are reverted upon MnTBAP treatment; 3) correlate CS cell alterations with clinical phenotypes for diagnostic and therapeutic purposes, taking also advantage from iPSC-derived neuronal organoids (to date produced only by our consortium) for personalized rescue strategies with MnTBAP (bench-to-bedside developments); and 4) investigate CS-specific alterations during regular ageing, by assessing the mechanism responsible for their occurrence in the senescence of normal cells (a process linked to ageing), that we have identified (ms2 to submit), and validating common epigenetic changes in CS and during normal ageing.