The tipping point for cancer

Primary supervisor: Nicholas McGranahan, UCL

Secondary supervisor: Charles Swanton, Francis Crick Institute

Project

Recent work has demonstrated that healthy human tissues contain a patchwork of somatic alterations and driver mutations [1]. Yet, if all cells contain a myriad of somatic mutations, are these cells poised for malignant transformation? And, if so, why is cancer not more prevalent?

Work from the Swanton group, using an EGFR mutant mouse model, has demonstrated that air pollution, particularly PM2.5 (particular-matter <2.5 micrometres in diameter), can promote cancer transformation of EGFR mutant AT2 lung cells [2]. This work emphasizes the importance of considering not only the putative pre-cancerous cell, but also its environment and the role of promoters during tumorigenesis.

A key feature of cancer cells which has not been fully evaluated in the context of normal tissue is chromosomal instability (CIN), an elevated rate of gain or loss of chromosomes or parts of chromosomes [3]. Work in the context of pre-invasive lung carcinoma in situ suggests chromosomal instability and the immune microenvironment are key rate-limiting steps in the transformation to cancer [4].

However, existing approaches to interrogate somatic evolution in normal tissue have necessarily focussed on point mutations due to both sampling and sequencing limitations.

Here we propose to dissect the route from normal cell to cancer, by evaluating the interplay between promoters, chromosomal instability and selection at a single cell level in a unique cohort of normal lung tissue.

Aim 1. An atlas of lung normal tissue karyotypes and transcriptomes.

We have built a resource of normal lung samples from patients with and without cancer, and from a range of ages and ethnicities. We have recently developed an approach to simultaneously evaluate genomic instability and the transcriptome through long-read RNA nuclear single-cell sequencing. We will apply this approach to our cohort of normal lung tissue to obtain an atlas of normal tissue karyotypes and transcriptomes (n>100,000 cells).

Aim 2: Quantifying the rate of instability in normal tissue

We will quantify CIN and infer the rate of instability in normal lung tissue. We will measure fundamental copy number features previously shown to encode patterns of CIN. We will then compare this to copy number data available for lung cancers (bulk and single cell).

Aim 3: Exploring the immune environment and cell state in normal tissue

We will harness our transcriptomic single-cell data to explore cell-states and the microenvironment in the context of normal tissue. Long-read sequencing will enable exploration of both cell-state, gene-expression, different isoforms and splicing. We will compare this to data available from lung cancers.

Aim 4: Quantifying somatic selection in normal tissue in the context of the environment

Finally, we will integrate existing data from duplex sequencing (enabling point mutations, mutational signatures and selection to be inferred), with novel long-read single cell sequencing to evaluate how the immune microenvironment influences selection and CIN in normal tissue and how this differs from cancers[5].

Together this project will provide a detailed understanding of somatic evolution in normal tissue, shedding light on the importance of promoters and CIN in cancer initiation.

Candidate background

This project would suit candidates with a biological background, strong computational experience, and a desire to pursue a computational project. This project will involve integrating multiple data modalities and set-up computational pipelines.

Potential Research Placements

1. Charles Swanton, Francis Crick Institute
2. James Reading, Cancer Institute, UCL
3. Simone Zaccaria, Cancer Institute, UCL

References

1. Acha-Sagredo A, Ganguli P, Ciccarelli FD. Somatic variation in normal tissues: friend or foe of cancer early detection? Ann Oncol. 2022 Dec;33(12):1239-1249. doi:0.1016/j.annonc.2022.09.156. Epub 2022 Sep 23. PMID: 36162751.
2. Hill W, Lim EL, Weeden CE,…, Swanton C., Lung adenocarcinoma promotion by air pollutants. Nature. 2023 Apr;616(7955):159-167. doi: 10.1038/s41586-023-05874-3. Epub 2023 Apr 5. PMID: 37020004; PMCID: PMC7614604.
3. Watkins TBK, Lim EL,…, McGranahan, N, Swanton C Pervasive chromosomal instability and karyotype order in tumour evolution. Nature. 2020 Nov;587(7832):126-132. doi: 10.1038/s41586-020-2698-6. Epub 2020 Sep 2. PMID: 32879494; PMCID: PMC7611706.
4. Pennycuick A, Teixeira VH,…,McGranahan N., Janes, S Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer. Cancer Discov. 2020 Oct;10(10):1489-1499. doi: 10.1158/2159-8290.CD-19-1366. Epub 2020 Jul 20. PMID: 32690541; PMCID: PMC7611527.
5. Rosenthal R, …, McGranahan N, Swanton C; TRACERx consortium. Neoantigen-directed immune escape in lung cancer evolution. Nature. 2019 Mar;567(7749):479-485. doi: 10.1038/s41586-019- 1032-7. Epub 2019 Mar 20. PMID: 30894752; PMCID: PMC6954100.