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Charting the single-cell landscape of colorectal cancer stem cell polarisation

Cardoso Rodriguez, Ferran; (2023) Charting the single-cell landscape of colorectal cancer stem cell polarisation. Doctoral thesis (Ph.D), UCL (University College London). Green open access

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Abstract

Colonic epithelia is regulated by cell-intrinsic and cell-extrinsic cues, both in homeostatic tissues and colorectal cancer (CRC), where the tumour microenvironment closely interacts with mutated epithelia. Our understanding on how these cues polarise colonic stem cell (CSC) states remains incomplete. Indeed, charting the interaction between intrinsic and stromal cues requires a systematic study yet to be found in the literature. In this work I present my efforts towards computationally studying colonic stem cell polarisation at single-cell resolution. Leveraging the scalability of organoid models, my colleagues and I dissected the heterocellular CRC organoid system presented in Qin & Cardoso Rodriguez et al. using single-cell omic analyses, resolving complex interaction and polarisation processes. First, I identified bottlenecks in common mass cytometry (MC) analysis workflows benefiting from either increased accessibility or automation; designing the CyGNAL pipeline and developing a cell-state classifier to tackle these points respectively. I then used single-cell RNA sequencing (scRNA-seq) data to reveal a shared landscape of CSC polarisation; wherein stromal cues polarise the epithelia towards slow-cycling revival CSC (revCSC) and oncogenic mutations trap cells in a hyper-proliferative CSC (proCSC) state. I then developed a method to visualise single-cell differentation using a novel valley-ridge (VR) score, which can generate data-driven Waddington-like landscapes that recapitulate differentiation dynamics of the colonic epithelia. Finally, I explored an approach for holistic inter- and intra-cellular communication analysis by incorporating literature information as a directed knowledge graph (KG), showing that low-dimensional representations of the graph retain biological information and that projected cellular profiles recapitulate their transcriptomes. These results reveal a polarisation landscape where CRC epithelia is trapped in a proCSC state refractory to stromal cues, and broadly show the importance of joint collaborative wet- and dry-lab work; central towards targeting gaps in the method space and generating a comprehensive analysis of heterocellular signalling in cancer.

Type: Thesis (Doctoral)
Qualification: Ph.D
Title: Charting the single-cell landscape of colorectal cancer stem cell polarisation
Open access status: An open access version is available from UCL Discovery
Language: English
Additional information: Copyright © The Author 2023. Original content in this thesis is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) Licence (https://creativecommons.org/licenses/by-nc/4.0/). Any third-party copyright material present remains the property of its respective owner(s) and is licensed under its existing terms. Access may initially be restricted at the author’s request.
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute
URI: https://discovery.ucl.ac.uk/id/eprint/10177700
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