Profiling and perturbing the inheritance of drug-induced metabolic states in cancer with Inheritance-Seq

Non-genetic acquired resistance has been implicated in the therapy failure of multiple cancer types. Therefore,
there have been significant efforts to uncover the mechanisms regulating such drug-resistant cellular states
and how these states may be perturbed to promote cancer cell death and curb disease progression. While
there has been much progress in understanding and characterizing drug-induced cellular states, little is known
about what controls the inheritance of these states by daughter cells. Understanding the heritability of
drug-induced states is not only useful to determine dosing frequency but also is critical in designing effective
combination treatment regimens. Existing approaches to characterize cell state inheritance fall short of this
goal because the features needed to define cell states are inaccessible, the temporal windows needed to
observe state transitions are exceedingly long, and the cellular throughput needed to robustly read out effects
of systematic perturbation is prohibitively high. Here, we propose inheritance-Seq, a new method that enables
quantification of cell state heritability to meet the need for an approach to understand the heritability of
drug-induced states. Inheritance-Seq combines CRISPR-based genetic lineage tracing and phenotyping with
microscopy and in situ sequencing (ISS) to enable scalable measurement of phenotype inheritance with
systematic pooled genetic perturbations to explore the mechanisms of phenotypic trait inheritance in cells. In
the proposed work, we will design and implement a general framework to quantify the heritability of cell states
and validate the performance of inheritance-Seq by identifying known factors regulating the inheritance of
drug-induced metabolic state changes in OVCAR8 cells following carboplatin treatment.

Grant Number: 5R61CA278536-03
NIH Institute/Center: NIH
Principal Investigator: Paul Blainey