Understanding the molecular pathways that underpin production, sensing and protection against aldehydes

Short chain aldehydes (most importantly formaldehyde) are highly reactive molecules used routinely in manufacturing, and are commonplace as fixative agents in biological laboratories. Worryingly, these factors are also produced endogenously, including as by-products of metabolic pathways (e.g., alcohol metabolism) and cell differentiation events. Formaldehyde is a potent source of DNA damage, most understood as a DNA cross-linking agent, distorting the structure and preventing the separation of DNA. This leads to mutagenic breaks, prevents accurate reading and replication of our DNA. Fortunately, cells possess a "two-tiered" protection mechanism that limits the damaging effects of these molecules. The first tier represents metabolic enzymes that actively detoxify formaldehyde. The second is made up of DNA damage repair proteins that fix the damage after it has happened. While this redundancy means individuals with a single mutation can remain protected, mutations in multiple enzymes can result in: anaemia, progeria (accelerated ageing), bone marrow failure, neurodegeneration, cancer, developmental abnormalities, liver and kidney failure, and severe weight loss.
Where the overall physiological consequences of formaldehyde in the absence of two-tier protection have been heavily studied, we still know very little about the specific cellular process formaldehyde disrupts, nor of its origins. This project will look into the fundamental questions of how does the cell respond to formaldehyde and where is it produced? There are two current lines of evidence we can use to access this problem. Firstly, there are specific pathways sensitive to formaldehyde stress that are signalled to the transcriptional network and drive changes in gene expression. Secondly, there are signs of localised formaldehyde production in different transcriptional states.
This project will expand on both of these phenomena to build a picture of the sources of and responses to formaldehyde in cells. I will employ advanced gene editing and sequencing technologies to perform a CRISPR knock out screen, with the aim of identifying pathways sensitive to formaldehyde, and potentially new tier 1 protection enzymes. Downstream validation of the results of this will be performed first in in vitro systems, progressing into the generation of in vivo mouse models to determine their physiological importance. Secondly, I will use advanced microscopy and chemical probe tools to localise specific sites of formaldehyde catabolism in cells.
By understanding the molecular pathways and sites that render cells sensitive to formaldehyde, we can more broadly understand the mechanisms that underline formaldehyde induced morbidities. Expanding this knowledge of known genetic factors that drive formaldehyde stress, is an essential part in prevention and early detection of associated diseases, as well as opening avenues for precision medicine.