Reprogramming Plasticity 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, over 90% 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 chemosensitive whereas revCSC are both chemorefractory and radioresistant. Moreover, cancer associated fibroblasts (CAFs) from the CRC tumour microenvironment (TME) can polarise chemosensitive rectal proCSC to chemorefractory revCSC [3]. As chemo-radiotherapy can only target mitotic proCSC cells, drug tolerant persister cells that survive treatment are all in the revCSC state [4]. As a result, we must find a way to eliminate revCSC cells to improve the treatment of CRC patients [5].

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 both genetic, epigenetic, and microenvironmental cues. However, irrespective of upstream stimulus, the proCSC to revCSC transition is always mediated through a change in intracellular signalling. Despite this revolution in our understanding of CRC biology, several questions remain unanswered:

Question 1: What are the essential signalling regulators of the proCSC to revCSC transition and how do they vary across CRC patients

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

Question 3: How can we reprogramme revCSC signalling 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 knock out 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 x30 CRC patients.

Aim 3: Finally, we will validate the heterocellular effects of stem cell reprogramming using subcellular spatial transcriptomics (Xenium) analysis of patient-derived assembloids (PDAs). This combinatorial signal rewiring will provide a novel therapeutic approach to treat advanced chemorefractory CRC.

By combining CRC patient-derived organoid cohorts, genome-wide CRISPR screening, custom single-cell perturbation analysis, and spatial transcriptomics 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 Research Placements

1. Graeme Hewitt, Comprehensive Cancer Centre, King’s College London
2. Bart Vanhaesebroeck, Cancer Institute, UCL
3. Julian Downward, The 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. 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.
4. Opzoomer, J.W., et al., SIGNAL-seq: Multimodal Single-cell Inter- and Intra-cellular Signalling Analysis. bioRxiv, 2024: p. 2024.02.23.581433.
5. Tape, C.J., Plastic persisters: revival stem cells in colorectal cancer. Trends Cancer, 2024. 10(3): p. 185-195.