"Unleashing the Power of Medusa's Petrifying Stare"

In a groundbreaking study published in Nature Chemical Biology, scientists have developed a new analytical method that can identify genetic determinants of cell death, offering promising implications for cancer research and drug discovery.

The study, led by researchers at the Icahn School of Medicine at Mount Sinai, presents a novel approach to chemogenetic profiling, a technique used to reveal genetic determinants that coordinate phenotypic responses to therapeutics. Traditional methods of chemogenetic profiling, however, primarily measure changes in cell proliferation and can conflate the biology that regulates proliferation and cell death outcomes.

To address this limitation, the researchers developed MEDUSA (Method for Evaluating Death Using a Simulation-assisted Approach), an analytical method that integrates experimental data with computational models to deconvolute drug-induced changes to both cell proliferation and cell death rates.

"MEDUSA allows us to infer a death rate from measured clonal abundance and calculated proliferation inhibition data," explains Jesse D. Gelles, co-author of the study. "By leveraging these data and experimentally-derived models, MEDUSA can specifically identify death-regulatory genes that underlie the drug response."

The researchers demonstrate that traditional chemogenetic profiles measuring relative viability are more sensitive towards detecting proliferation-regulatory genes while failing to identify death-regulatory genes. MEDUSA, on the other hand, accurately identifies death-regulatory genes using simulations of drug-induced population dynamics constructed from a plate-based assay for measuring and parameterizing live and dead cell populations over time.

As a proof of concept, the researchers studied DNA damage-induced death in the presence or absence of TP53, a commonly mutated tumor suppressor gene that induces both cell cycle arrest and pro-apoptotic signaling downstream of DNA damage. The study revealed that loss of TP53 led to increased rates of drug-induced death, in apparent contradiction with prior studies measuring viability or apoptosis.

"Experimental and genetic approaches, combined with MEDUSA analysis, revealed a unique dependency upon the electron transport chain and mitochondrial oxidative phosphorylation in p53-deficient cells treated with the conventional chemotherapeutic agent, etoposide," says Jerry Edward Chipuk, co-author of the study.

The researchers further determined that the DNA damage-induced cell death in p53-deficient cells is dependent on high NAD+ levels, and drug-induced lethality was rescued by genetic or pharmacological reduction of the NAD+ pool.

The study highlights the bias in chemogenetic profiles based on clonal abundance and demonstrates MEDUSA's capability to score the death-regulatory function of genes. The researchers suggest that MEDUSA can aid in characterizing forms of non-apoptotic cell death that remain poorly understood and contribute to broader human diseases and therapies.

"MEDUSA is a promising analytical method for chemogenetic profiling efforts, and its ability to determine death rates through extrapolation without requiring recovery of dead cells makes it particularly suitable for models that undergo non-apoptotic cell death," says Gelles.

The study's findings lay the groundwork for future investigations into the role of MEDUSA in various drug mechanisms and non-apoptotic cell death, providing valuable insights into the complex interplay between genes, drugs, and cell death regulation.

Source:

Gelles, J.D., Chipuk, J.E. The death gaze of MEDUSA. Nat Chem Biol (2024). <https://doi.org/10.1038/s41589-024-01594-5>