# Defining and targeting the proteome to kill quiescent cells

> **NIH NIH R01** · NEW YORK UNIVERSITY · 2022 · $377,079

## Abstract

Project Summary/Abstract
In organisms spanning microbes to humans, the vast majority of cells have exited the cell division cycle and
exist in a non-proliferative state. For many of these cells this is a reversible state of cell growth and cell cycle
arrest known as quiescence. Quiescent cells are characterized by low metabolic, gene expression, and cellular
activity. Quiescent cells are found in diverse clinical scenarios ranging from pathogenic microbes to human
tumors. As these cells are not actively cycling, many drugs that target cellular processes such as DNA
replication and protein synthesis are ineffective. The central hypothesis of our research proposal is that large-
scale remodeling of protein expression in quiescent cells is mediated by signaling networks that respond to
distinct signals to establish a common gene expression state. We postulate that this process leads to
fundamental changes in the cytoplasm of the cell resulting in distinct biophysical properties that can benefit the
long term survival of quiescent cells, and which can be exploited for therapeutic targeting of quiescent cells.
The goal of this proposal is to test this hypothesis using the model eukaryotic cell, Saccharomyces cerevisiae.
Our first aim is to define the dynamics with which the proteome is remodeled in response to distinct signals that
initiate quiescence. Using stable isotope labeling with amino acids in cell culture (SILAC) and mass
spectrometry, we will quantify the dynamics of protein expression changes in response to three different
starvation signals that result in the initiation of quiescence: nitrogen, carbon and phosphorus. To test the role of
specific signaling pathways in regulating remodeling of the proteome we will quantify expression dynamics in
strains impaired for the TORC1, AMPK, PKA and PHO85 pathways as well as the signal integrators, RIM15
and SCH9. In aim 2 we will define the biophysical properties of quiescent cells. Using genetically encoded
multimeric nanoparticles (GEMS) and imaging in microfluidics we will study cells as they enter quiescence and
quantify changes in cytoplasmic diffusion to quantify cytoplasmic crowding. To identify factors that contribute to
the altered biophysical properties of the cell we will quantify changes in organelle size and the abundance of
macromolecular complexes such as the ribosome. We will use genetic and chemical perturbations to test their
role in modulating the properties of quiescent cells and test the hypothesis that increased molecular crowding
confers increased stress resistance. To identify effective therapeutic strategies for quiescent cells we will test
the effectiveness of existing antifungal drugs in killing quiescent cells, identify genetic liabilities that enhance
the efficacy of antifungals in quiescent cells and test the use of adjuvants that mimic genetic effects. To
determine the clinical relevance of these findings, we will test newly identified therapeutic strategies in the
pat...

## Key facts

- **NIH application ID:** 10441479
- **Project number:** 5R01GM107466-09
- **Recipient organization:** NEW YORK UNIVERSITY
- **Principal Investigator:** David Gresham
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $377,079
- **Award type:** 5
- **Project period:** 2013-09-01 → 2024-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10441479

## Citation

> US National Institutes of Health, RePORTER application 10441479, Defining and targeting the proteome to kill quiescent cells (5R01GM107466-09). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10441479. Licensed CC0.

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