Quantifying breast cancer adaption: platforms for studying transcriptional changes in single cells
File(s)
Author(s)
Saha, Debjani
Type
Thesis
Abstract
Hormone-dependent breast cancer (HDBC) is the most commonly diagnosed female malignancy. Patients are administered adjuvant endocrine therapies (ET) which induces temporary remission. However, up to 40% of patients relapse. Recent studies indicate that ET drives cells into a bottleneck where surviving micro-disseminated cells enter a reversible cell-cycle arrest – dormancy – from which, with time, they can asynchronously and spontaneously awaken via non-genetic cell state transitions. However, the exact mechanisms by which dormant cells awaken and re-enter the cell cycle remain poorly understood. Recent advances in single-cell technologies have enabled detailed cancer studies at unprecedented cellular scales. Unfortunately, traditional sequencing methods, are limited by their need to lyse cells and in doing so, provide only snapshots, preventing the tracking of dynamic transcriptional changes in the same cell over time. This limitation hinders our understanding of how cancer cells adapt and survive treatment, especially in HDBC, where dormancy and eventual recurrence are common.
This project bridges a key technological gap, presenting the development of multiple techniques that can ultimately be used to probe cells at a sub-cellular level; introducing two minimally invasive platforms using nanotweezers and nanopipettes, enabling the sequential single-cell sampling of cytoplasmic RNA without resultant cell death. These techniques rely on dielectrophoresis to trap highly expressed RNA and cytosolic volume, respectively. By facilitating continuous monitoring, these approaches capture dynamic transcriptional changes, crucial for understanding dormancy and adaptation in HDBC. Additionally, given the challenges experienced in dynamic technology development, alternative static approaches that yield insight into these states and variations in hormone-receptor expression with age, with spatial resolution, have also been optimised and presented. With further work, these techniques should enable the generation of a dynamic, longitudinal model of gene expression and the processes that underlie adaptation in HDBC, ultimately offering new perspectives on cancer progression and resistance.
This project bridges a key technological gap, presenting the development of multiple techniques that can ultimately be used to probe cells at a sub-cellular level; introducing two minimally invasive platforms using nanotweezers and nanopipettes, enabling the sequential single-cell sampling of cytoplasmic RNA without resultant cell death. These techniques rely on dielectrophoresis to trap highly expressed RNA and cytosolic volume, respectively. By facilitating continuous monitoring, these approaches capture dynamic transcriptional changes, crucial for understanding dormancy and adaptation in HDBC. Additionally, given the challenges experienced in dynamic technology development, alternative static approaches that yield insight into these states and variations in hormone-receptor expression with age, with spatial resolution, have also been optimised and presented. With further work, these techniques should enable the generation of a dynamic, longitudinal model of gene expression and the processes that underlie adaptation in HDBC, ultimately offering new perspectives on cancer progression and resistance.
Version
Open Access
Date Issued
2024-11-01
Date Awarded
01/10/2025
License URL
Advisor
Magnani, Luca
Edel, Joshua
Ivanov, Aleksandar
Publisher Department
Department of Surgery & Cancer
Department of Chemistry
Publisher Institution
Imperial College London
Qualification Level
Doctoral
Qualification Name
Doctor of Philosophy (PhD)