Modulation of proteolysis counteracts oxidative stress but impairs base excision repair in ATM-depleted cells

Ataxia-telangiectasia (A-T), also known as Louis-Bar syndrome, is a neurodegenerative autosomal recessive disease caused by bi-allelic mutations in the ataxia-telangiectasia mutated (ATM) gene. The product of the ATM gene is a serine/threonine kinase that acts as primary mediator of cellular signalling pathways in response to various genotoxic stresses, such as DNA damage and reactive oxygen species (ROS). It has been proposed that accumulation of oxidative stress due to loss of functional ATM contributes significantly to the pathogenesis and features of A-T, including neurodegeneration and immunodeficiency. However, despite the severity of the symptoms linked to A-T, lack of functional ATM protein is still compatible with life. We postulated that early adaptive mechanisms must be in place to allow cells to survive in the absence of ATM. Crucially, comprehension of these mechanisms would allow us to elucidate some of the molecular features of A-T, including genomic instability and predisposition to cancer. To this aim, we adopted a quantitative proteomics approach to study changes occurring early on in normal fibroblasts upon depletion of ATM. We observed that ATM-depleted cells display progressive accumulation of oxidised proteins in the nuclear compartment. Furthermore, our study showed that ATM-depleted cells modulate proteolysis to counteract oxidative stress, which contributes to the survival at early stages after ATM loss. On the other hand, increased proteolysis in ATM-depleted fibroblasts had a negative impact on the frontline DNA repair system counteracting oxidative DNA damage: the DNA base excision repair (BER) pathway. ATM-depleted cells showed lower BER protein levels and severely impaired BER capacity. We propose that DNA repair deficiency caused by BER impairment could be one of the early mechanisms leading to accumulation of genomic instability in ATM-depleted cells. These previously overlooked adaptation mechanisms give useful insight into the changes occurring very early on upon loss of ATM and provide a molecular explanation for some of the severe features of A-T.