While intratumour heterogeneity in colorectal cancer has been extensively studied in terms of genetic alterations, only recently has single-cell transcriptomics studies started to reveal the diversity of phenotypic states. Growing evidence suggests that metastatic colonization relies on intrinsic cancer cell plasticity that allows cancer cells to switch between cellular states and reversibly adapt to microenvironmental challenges in absence of genetic evolution.

We aim to study cancer cell plasticity and the combination of intrinsic and extrinsic factors promoting this plastic cell behaviour in colorectal cancer metastasis, using a combination of single cell multi-omics and bulk genomics data derived from primary and metastatic patient tumours. Understanding the underlying mechanisms of cancer cell plasticity could motivate therapeutic targeting of plasticity.

To phenotypically understand the tumour microenvironment (TME), we must be able to accurately measure multiple cell-types and cell-states. This CRUK City of London Centre project will develop a new multimodal single-cell technology to accurately identify cell-types (via mRNA) and cell-states (via intracellular proteins, PTMs, and nucleotide probes) in TME organoids.

We will develop a multimodal SPLiT-Seq technology to measure cell-types (mRNA) and cell-states (proteins/PTMs) in single-organoid cells. In addition to intracellular antibody probes, we will also develop a novel oligo-tagged EdU click chemistry probe to accurately measure S-phase in scRNA-Seq experiments. We will apply multimodal SPLiT-Seq to simultaneously measure differentiated cell-types and cell-states in TME organoids across all sites of the CRUK City of London Centre (CRC = Tape Lab (UCL), PDAC = Hodivala-Dilke Lab (BCI), Breast Cancer = Kong Lab (KCL), and NSCLC = Charles Swanton & Krijn Dijkstra (Crick)).

Pancreatic cancer has a very poor outcome due to late diagnosis and poor response to therapy. Immunotherapy approaches, which have made significant impact on other difficult to treat cancers, are particularly ineffective in pancreatic cancer. This has been attributed to the dense fibrotic and immunosuppressive tumour microenvironment. We have found that preventing the activation of fibroblasts in the pancreatic stroma can modulate the immune infiltrate in pancreatic tumours. Interestingly, we have been able to induce tertiary lymphoid structures in tumours. This is exciting because tertiary lymphoid structures are associated with better outcome in pancreatic cancer and are known to promote anti-tumour immune responses in other cancers.

In the current project we are going to examine whether increased tertiary lymphoid structure content is associated with an enhanced anti-tumour immune response in pancreatic cancer. We are collaborating with Dr Sophie Acton at UCL who is a leading expert on lymphoid tissue function. Together we hope to identify a new therapeutic opportunity to enhance anti-tumour immunity with the potential to impact on immunotherapy approaches in pancreatic cancer.

Immunotherapy is changing the way cancer patients are treated. However, only a minority of patients respond to these therapies and metastatic disease remains largely incurable. Therefore, a better understanding of the role of the immune cells in metastasis is urgently needed.

Immunometabolism is emerging as a key area in cancer research, as metabolic changes in the immune cells are essential to shape their functions and define the way they support tumour growth. However, how knowledge in the field is currently limited, particularly in human. Here, we want to focus on colorectal cancer, a main cause of death worldwide, with up to 30% of patients developing liver metastasis during the course of the disease, associated with poor prognosis.

This CRUK City of London Centre Project Fund will allow to perform spatially-resolved transcriptomics of the immune niche in human colorectal cancer liver metastases samples and analyse changes in metabolic pathways within both the cancer cells and immune cells. This study will be a collaboration between the labs of Dr. Luigi Ombrato and Dr. Trevor Graham at QMUL, and Dr. Mariia Yuneva at the Crick. The results obtained will help developing a 3D platform to perturb metabolic pathways in order to impair cancer cell growth.