Uncoupling of cell size from DNA content and its implications for genome function and cell senescence
Description: Cell size is tightly controlled in all cells, suggesting that having a specific size is critical for cell function. Indeed, changes in size correlate with altered function during development, differentiation or in response to altered environmental conditions. In addition, deviation from normal size is associated with loss of cell function during cell senescence. Interestingly, there is a strong correlation between cell size and DNA content both, within and between species, suggesting that maintaining a constant DNA:cytoplasm ratio is critical for cell function. How the coupling of cell size and DNA content is established and why it is important is unclear. Our previous studies showed that continued cell growth during prolonged cell cycle arrest results in a breakdown of multiple cell functions in both, yeast and human cells. Importantly, excessive cell growth causes a loss of proliferative potential and drives cultured human cells into senescence. Most of the growth induced dysfunctions in oversized cells are caused by a decrease in the ratio of DNA to cytoplasm. In budding yeast, DNA becomes limiting for mRNA and protein production if cells grow too large, but changing the DNA:cytoplasm ratio also directly affects genome function and maintenance. An excessive increase in cell size changes gene expression and causes severe genome homeostasis defects in both, yeast and human cells. Our preliminary findings indicate that increased cell size makes DNA more fragile and impairs the DNA damage response. Mutations that decrease cell size or an acute increase in cellular ploidy on the other hand cause replication stress. How these changes in cell size or DNA content affect genome biology is unclear. Here we will determine how alterations in the DNA:cytoplasm ratio affect cell- and nuclear function. In addition, we will determine how cell growth contributes to chemotherapy induced senescence. In Aim 1 we will determine how increased cell size affects nuclear organization and function in yeast and human cells. We will use DNA break sequencing and ATAC-Seq to determine where DNA damage occurs in oversized cells and characterize how size associated changes such as increased nuclear volume and higher transcription rates affect genome homeostasis.In Aim 2 we will investigate how cells respond do an increase in DNA content in yeast and how the coupling of cell size to DNA content is established. For this purpose, we developed a genetic tool to induce large changes in the cellular DNA content without affecting gene dosage. We will determine how additional DNA affects genome replication and cell cycle progression and perform genetic screens to identify mutations that uncouple cell size from DNA content.In Aim 3 we will determine the broader significance of cell growth-induced senescence. Specifically, we will use organoid systems to determine how a complex tissue environment influences this process and determine whether continued cell growth contributes to the cytotoxicity of approved cancer drugs. The experiments described above will give insight into how changes in the DNA:cytoplasm ratio affect cell and nuclear function. This fundamental knowledge will lay the foundation to understand how changes in cell size that occur naturally during development contribute to altered gene expression and DNA replication. Furthermore, our studies will shed light on the fitness cost of maintaining DNA, which will give insight on the evolutionary pressures against the presence of non-coding DNA in the genome. In addition, this knowledge will help to identify vulnerabilities of cells that carry additional DNA burden such as aneuploid cells or cells infected with a DNA virus. Finally, understanding how cell growth influences the response to different cancer drugs in a tissue environment could ultimately help making treatment decisions in the clinic. If borne out, the results from our experiments would lay the basis for more patient-oriented studies.
Amount: CHF 800,000
Funding type: research
Funder scheme: Project funding
Start date: 2025-07-01
End date: 2029-06-30
Investigator: Neurohr, Gabriel
Institution: ETH Zurich – ETHZ
Funded outputs count: 0
Funder award ID: 10003562
OpenAlex ID: G7819944496