Stingele Lab - Research

Cellular responses to DNA and RNA damage

Cells are constantly exposed to reactive substances that cause complex damage to cellular macromolecules. These damages stem from both endogenous reactive metabolites and a wide range of exogenous factors, including various forms of radiation, chemotherapeutic agents, and tobacco smoke. Almost all reactive substances act pleiotropically, meaning they cause diverse cellular lesions, particularly in DNA and RNA. If these damages are not detected and resolved, they can lead to premature aging, cancer, and other diseases. A key goal of our research is therefore to understand how damage to DNA and RNA is sensed and eventually resolved. By uncovering the underlying molecular mechanisms, we aim to lay the groundwork for new therapeutic strategies to prevent or treat cancer and degenerative diseases.

Research Highlights

A particularly relevant source of endogenous cellular damage are reactive aldehydes, which are byproducts of various metabolic processes. For example, acetaldehyde is released during alcohol breakdown in the liver and is the primary cause of ethanol toxicity. Formaldehyde arises during one-carbon metabolism and enzymatic demethylation reactions. These aldehydes induce covalent DNA-protein crosslinks (DPCs), which are highly toxic, because they block transcription and replication. Over the last years, we have discovered several pathways and regulatory mechanisms enabling the repair of DPCs.

The specialized DPC protease SPRTN degrades the protein component of DPCs, thereby promoting replication of DPC-containing DNA. The DPC protease SPRTN is highly promiscuous, which is useful, given that virtually every chromatin protein can become crosslinked to DNA. However, how cleavage is restricted to crosslinked proteins had remained unclear. We found that SPRTN achieves specificity by recognizing specific DNA structures which trigger activation of the protease (Reinking et al.). Additionally, we discovered that SPRTN cannot process folded protein adducts by itself, which requires in addition the activity of the FANCJ helicase. Using in vitro reconstitution, we showed that FANCJ binds next to the DPC and uses its ATPase activity to unfold the protein adduct, exposing the underlying DNA and enabling cleavage of the crosslinked protein by SPRTN (Yaneva et al.). Moreover, we discovered that the proteins CSB and CSA provide resistance to agents that induce DPCs. Mutations in CSB and CSA cause Cockayne syndrome, a severe growth and neurological disorder. We found that CSB and CSA respond if RNA polymerases stall at DPCs, promoting DPC repair and restart of transcription. Our findings suggest that defective transcription-coupled DPC repair contributes to the unique features of Cockayne syndrome (Carnie et al.).

In addition to damaging DNA, aldehydes also induce crosslinking between proteins and RNA. We therefore hypothesized that cells must harbor pathways to detect and eliminate such RNA lesions. However, the complexity of aldehyde-induced damage complicates the analysis of the responsible quality control mechanisms. To investigate how cells respond to RNA crosslinking damage, my group developed a protocol to specifically induce RNA damage, which led to the discovery of a cellular pathway that resolves RNA-protein crosslinks (Zhao et al.).

Most DNA-damaging agents also damage RNA, a fact overlooked by most researchers for the last decades. The central objective of our future research is therefore to develop a comprehensive understanding of how cells preserve the integrity of both, DNA and RNA. By identifying and characterizing the cellular mechanisms responsible for resolving DNA and RNA damage, we aim to uncover new biological principles and to provide a foundation for innovative therapeutic strategies in cancer treatment.