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Research & Innovation

Ciccarelli Laboratory | Cancer Systems Biology Laboratory

We study the drivers of cancer evolution from early transformation to response to therapy through the integration of computational and wet-lab approaches.

Our research builds upon the idea that cancer results from systemic cell and gene perturbations and, although faulty genes driving cancer (cancer drivers) differ functionally, they share intrinsic properties that are not detectable when studying each gene individually. We use systems biology to characterise these distinctive properties in the context of genome and network evolution. We then use these properties to predict new drivers at cancer and patient-level resolution.

We also aim to understand the functional consequences of driver alterations within tumours through the integration of genomic and transcriptomic data from bulk tissues with high-resolution tissue imaging and single-cell data.

Our work is revealing a deeper understanding of how driver alterations occurring in individual cancer cells fuel the evolution of the whole tumour and surrounding microenvironment, pointing us toward potential targets for the development of new, more effective cancer therapies.

Our group is seconded to the Francis Crick Institute, which you can read about here.

Software

The Ciccarelli Laboratory has developed a number of tools and software for use with computational biology pipelines.

MEGA-V

MEGA-V (Mutation Enrichment Gene set Analysis of Variants) is an open-source R application to identify over-represented pathways of variant genes across cohorts to map mutation information to perturbed biological processes.

NCG

Network of Cancer Genes (NCG) is a publicly available and manually curated repository of cancer and healthy drivers from cancer and healthy tissue mutational screens.

sysSVM

sysSVM is an open-source algorithm to identify cancer driver genes at patient resolution using machine learning.

SIMPLI

SIMPLI (Single-cell Identification from MultiPLexed Images) is an end-to-end software for the analysis of high-dimensional tissue images. It is a flexible and technology-agnostic and unifies all steps of multiplexed imaging data analysis.

Members

Francesca Ciccarelli

Professor of Cancer Genomics

Chloé Woodman

PhD Student

Publications

Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas
Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Dec 2022, In: Communications Biology. 5, 1, 335. Research output: Contribution to journal › Article › peer-review. DOIs: https://doi.org/10.1038/s42003-022-03238-7
Reflected stemness as a potential driver of the tumour microenvironment
Rodrigues, F. S., Ciccarelli, F. D. & Malanchi, I., Dec 2022, In: Trends in cell biology. 32, 12, p. 979-987 9 p. Research output: Contribution to journal › Review article › peer-review. DOIs: https://doi.org/10.1016/j.tcb.2022.04.007
Somatic variation in normal tissues: friend or foe of cancer early detection?
Acha-Sagredo, A., Ganguli, P. & Ciccarelli, F. D., Dec 2022, In: Annals of Oncology. 33, 12, p. 1239-1249 11 p. Research output: Contribution to journal › Review article › peer-review. DOIs: https://doi.org/10.1016/j.annonc.2022.09.156
Topoisomerase I poison-triggered immune gene activation is markedly reduced in human small-cell lung cancers by impairment of the cGAS/STING pathway
Marinello, J., Arleo, A., Russo, M., Delcuratolo, M., Ciccarelli, F., Pommier, Y. & Capranico, G., 19 Oct 2022, In: British journal of cancer. 127, 7, p. 1214-1225 12 p. Research output: Contribution to journal › Article › peer-review. DOIs: https://doi.org/10.1038/s41416-022-01894-4
Genome-Protective Topoisomerase 2a-Dependent G2 Arrest Requires p53 in hTERT-Positive Cancer Cells
Lockwood, N., Martini, S., López-Pardo, A., Deiss, K., Segeren, H. A., Semple, R. K., Collins, I., Repana, D., Cobbaut, M., Soliman, T. N., Ciccarelli, F. & Parker, P. J., 3 May 2022, In: Cancer Research. 82, 9, p. 1762-1773 12 p. Research output: Contribution to journal › Article › peer-review. DOIs: https://doi.org/10.1158/0008-5472.CAN-21-1785
A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially-resolved tissue phenotyping at single-cell resolution
Bortolomeazzi, M., Montorsi, L., Temelkovski, D., Keddar, M. R., Acha-Sagredo, A., Pitcher, M. J., Basso, G., Laghi, L., Rodriguez-Justo, M., Spencer, J. & Ciccarelli, F. D., 9 Feb 2022, In: Nature Communications. 13, 1, 1 p., 781. Research output: Contribution to journal › Article › peer-review. DOIs: https://doi.org/10.1038/s41467-022-28470-x
Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource
Dressler, L., Bortolomeazzi, M., Keddar, M., Misetic, H., Sartini, G., Acha-Sagredo, A., Montorsi, L., Wijewardhane, N., Repana, D., Nulsen, J., Goldman, J., Pollit, M., Davis, P., Strange, A., Ambrose, K. & Ciccarelli, F., 26 Jan 2022, In: Genome Biology. 23, 1, 35. Research output: Contribution to journal › Article › peer-review. DOIs: https://doi.org/10.1186/s13059-022-02607-z
Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers: A pilot study
Gunady, E. F., Ware, K. E., Hoskinson Plumlee, S., Devos, N., Corcoran, D., Prinz, J., Misetic, H., Ciccarelli, F. D., Harrison, T. M., Thorne, J. L., Schopler, R., Everitt, J. I., Eward, W. C. & Somarelli, J. A., 2022, In: Evolution, medicine, and public health. 10, 1, p. 221-230 10 p. Research output: Contribution to journal › Article › peer-review. DOIs: https://doi.org/10.1093/emph/eoac016
Clone competition as a mechanism to reduce tumor formation
Acha-Sagredo, A., Malanchi, I. & Ciccarelli, F. D., 20 Dec 2021, In: Developmental Cell. 56, 24, p. 3307-3308 2 p. Research output: Contribution to journal › Article › peer-review. DOIs: https://doi.org/10.1016/j.devcel.2021.12.003
Serial Circulating Tumor DNA Detection Using a Personalized, Tumor-Informed Assay in Esophageal Adenocarcinoma Patients Following Resection
OCCAMS Consortium, Nov 2021, In: Gastroenterology. 161, 5, p. 1705-1708.e2 Research output: Contribution to journal › Short survey › peer-review. DOIs: https://doi.org/10.1053/j.gastro.2021.07.011

View all publications

Staff members:

PhD students:

Hrvoje Misetic
Chloe Woodman

Our partners

Cancer Research UK

European Commission Horizon 2020

Cancer Research UK King's Health Partners Centre

Cancer Research UK City of London (CoL) Centre

Group lead

Professor Francesca Ciccarelli

Professor of Cancer Genomics

Contact us

Professor Francesca Ciccarelli - Group Leader

francesca.ciccarelli@kcl.ac.uk