Genome-Wide CRISPR and Single-Cell Phenoscaping to Identify Universal Plasticity Regulators in Colorectal Cancer

Primary supervisor: Chris Tape, UCL

Secondary supervisor: Graeme Hewitt, King’s College London

Project

Colorectal cancer (CRC) is the 2^nd most common cause of cancer death, with an alarming, rising incidence in young adults [1]. While targeted therapy and chemotherapy have improved survival, ~85% of patients with metastatic CRC still die within 5-years of diagnosis and new therapeutic options are desperately needed.

Through high-dimensional single-cell phenoscaping of thousands of colorectal organoids we recently discovered that colonic stem cells reside on a continuous transdetermination trajectory, spanning from a highly proliferative colonic stem cell (proCSC) through to a slow-cycling revival stem cell (revCSC) [2]. We then found that proCSC are extremely chemo-radiosensitive whereas revCSC are both chemorefractory and radioresistant [3]. Moreover, cancer associated fibroblasts (CAFs) from the CRC tumour microenvironment (TME) can polarise chemosensitive proCSC to chemo-radiorefractory revCSC [4, 5]. As chemo-radiotherapy can only target proCSC cells, drug tolerant persister cells that survive treatment are all in the revCSC state. As a result, we must find a way to eliminate revCSC cells to improve the treatment of CRC patients.

Stem cell admixture is found in all CRC patients and plays an essential role in metastasis and therapy failure. Current evidence suggests that stem cell plasticity can be regulated by genetic, epigenetic, and microenvironmental cues. However, irrespective of upstream stimulus, the proCSC to revCSC transition is always mediated through a change in intracellular signalling in all patients. This phenotypic convergence suggests that common signalling pathways drive the proCSC to revCSC transition in CRC across all patients. However, the common signalling nodes that transduce plasticity across patients are unknown.

This CRUK City of London Centre PhD project will address this by answering the following questions:

Question 1: What are the essential signalling regulators of the proCSC to revCSC transition and what are the common nodes across CRC patients?

Question 2: How does the combinatorial stimulation and inhibition of multiple signalling nodes regulate drug resistant revCSC cells across patients?

Question 3: How can we reprogramme universal revCSC signalling nodes to develop new therapies for CRC?

This CRUK City of London Centre PhD project will address these questions over the following aims:

Aim 1: We will use pooled genome-wide CRISPR knockout screening in a cohort of CRC patient-derived organoids (PDOs) to identify the essential intracellular signalling regulators of the proCSC-revCSC transition.

Aim 2: Using high-throughput single-cell PDO perturbation analysis we will then identify the combinatorial relationship between key signalling nodes across a cohort of 30 CRC patients.

Aim 3: Finally, we will combinatorially perturb essential cell signalling nodes in CRC PDOs to reprogramme stem cell transdetermination. This signal rewiring will provide a novel therapeutic approach to treat advanced chemorefractory CRC.

By combining CRC patient-derived organoid cohorts, genome-wide CRISPR screening, and custom single-cell perturbation analysis this PhD project will reveal how stem cell plasticity can be reprogrammed to treat advanced CRC.

Candidate background

This PhD project would suit candidates with a background in cell signalling and/or cancer biology, ideally with laboratory experience in 3D organoid culture, CRISPR screening, and/or single-cell analysis.

Potential placements

1. Graeme Hewitt, Comprehensive Cancer Centre, King’s College London
2. Bart Vanhaesebroeck, Cancer Institute, UCL
3. Julian Downward, Francis Crick Institute

References

1. Morgan, E., et al., Global burden of colorectal cancer in 2020 and 2040: incidence and mortality estimates from GLOBOCAN. Gut, 2023. 72(2): p. 338–344.
2. Qin, X., et al., An oncogenic phenoscape of colonic stem cell polarization. Cell, 2023. 186(25): p. 5554–5568 e18.
3. Li, N., et al., Epithelial Stem Cell Fate Determines Chemoradiotherapy Response in Rectal Cancer. bioRxiv, 2026: p. 2026.07.15.736775.
4. Ramos Zapatero, M., et al., Trellis tree-based analysis reveals stromal regulation of patient-derived organoid drug responses. Cell, 2023. 186(25): p. 5606–5619 e24.
5. Molyneux, C., et al., Stromal Prostaglandin is a Dominant Spatial Regulator of Cell-fate Plasticity in Colorectal Cancer. bioRxiv, 2026: p. 2026.06.14.732116.