Disrupting cellular memory to overcome drug resistance

Author:

Harmange GuillaumeORCID,Hueros Raúl A. Reyes,Schaff Dylan L.,Emert Benjamin,Saint-Antoine Michael,Kim Laura C.ORCID,Niu Zijian,Nellore Shivani,Fane Mitchell E.ORCID,Alicea Gretchen M.,Weeraratna Ashani T.,Simon M. CelesteORCID,Singh AbhyudaiORCID,Shaffer Sydney M.ORCID

Abstract

AbstractGene expression states persist for varying lengths of time at the single-cell level, a phenomenon known as gene expression memory. When cells switch states, losing memory of their prior state, this transition can occur in the absence of genetic changes. However, we lack robust methods to find regulators of memory or track state switching. Here, we develop a lineage tracing-based technique to quantify memory and identify cells that switch states. Applied to melanoma cells without therapy, we quantify long-lived fluctuations in gene expression that are predictive of later resistance to targeted therapy. We also identify the PI3K and TGF-β pathways as state switching modulators. We propose a pretreatment model, first applying a PI3K inhibitor to modulate gene expression states, then applying targeted therapy, which leads to less resistance than targeted therapy alone. Together, we present a method for finding modulators of gene expression memory and their associated cell fates.

Funder

U.S. Department of Health & Human Services | National Institutes of Health

U.S. Department of Health & Human Services | NIH | National Cancer Institute

National Science Foundation

U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences

Publisher

Springer Science and Business Media LLC

Subject

General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry,Multidisciplinary

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