ABC Discover
Researcher: Professor Paul Skipp
Additional Academic Staff Funded: Dr Andrew Shapanis, Dr Ben Nicholas and Luis Coy (PhD student)
Location: University of Southampton
Dates: July 2019 – March 2025 Status: Completed
Funding: £1,200,879
ABC’s Research Theme: Detection, Prevention
Summary
ABC Discover, led by Professor Paul Skipp at the University of Southampton, completed a highly successful 5-year period* in 2025 with multiple breakthroughs achieved across the three pillars of ABC research: prevention, earlier detection, and better treatments of secondary breast cancer.
ABC Discover gave rise to miONCO-Dx, the multiple early cancer detection test that can detect twelve of the most common and deadly cancers from only a few drops of blood (test could transform cancer diagnosis). Dr Andy Shapanis led the early development of miONCO-Dx through an Artificial Intelligence (AI) – based machine learning model that uses a panel of blood miRNAs (micro RNAs) to predict whether cancer is present with 99% sensitivity and the site of cancer with 96% accuracy.
During ABC Discover, the DietCompLyf Biobank was transferred to the University of Southampton from the previous custodians at University College London (UCL) and the University of Westminster (UoW). Created as part of the Against Breast Cancer-funded DietCompLyf study, the biobank is a unique resource of blood, serum and urine samples collected from 3390 breast cancer patients who also completed food-diaries and lifestyle questionnaires. The biobank will be central to ongoing studies during ABC Discover 2 (2025-2030) is investigating how diet and lifestyle affect the risk of secondary breast cancer.
Personalised vaccine development models for breast cancer were established by Dr Ben Nicholas using cutting-edge techniques to hunt for novel breast cancer vaccine targets. ABC Discover funded PhD student Luis Coy successfully defended his thesis entitled ‘Characterising a 3D Culture Model of Triple-Negative Breast Cancer Through Systems-Based Molecular Phenotyping’ in June 2024.
*including extension due to the Covid-19 pandemic
Background
Working closely with the Centre for Cancer Immunology, ABC Discover was the flagship research programme under the umbrella of the newly established Integrative Molecular Phenotyping Centre (IMPC) at the University of Southampton.
To understand why patients with seemingly similar breast cancers can experience very different outcomes, ABC Discover established a multi-omics approach to answer this and other breast cancer research questions. By combining clinical information with ‘molecular fingerprints’, proteomic (measures proteins), transcriptomic (measures genes) and metabolomic data (products of metabolism), is used alongside detailed diet and lifestyle information collected through the DietCompLyf study to create ‘molecular handprints’ of biological and behavioural factors that influence recurrence, metastasis and survival after a breast cancer diagnosis. This allows distinct patient groups to be uncovered and a route to develop more personalised approaches to treatment, prognosis, and prevention. Ultimately, the goal is to understand not only the biology of breast cancer, but also how lifestyle factors may improve outcomes and reduce the risk of recurrence. With the arrival of the biobank in Southampton, this work continues with expanded scope in ABC Discover 2.
miONCO-Dx Multiple Early Cancer Detection Test
miONCO-DX is a blood test under development that allows early detection of up to twelve cancers, including breast cancer, from only a few drops of blood. The test measures up to fifty different small gene fragments called micro RNAs (miRNAs) that are released by cancer cells into the bloodstream. The results allow researchers to determine if cancer is present and if so, what type of cancer. Originating from ABC funding in ABC Discover, miONCO-Dx has the potential to be a low-cost and widely available screening method to catch cancer in the early stages, when treatments are most effective. The founders, Dr Andy Shapanis and Professor Paul Skipp, have created a spin-out company called Xgenera to accelerate the development of the test. In 2025, Xgenera received a £2.4 million grant from the NIHR (National Institute of Health and Care Research) to continue miONCO-Dx development, including manufacture of the test and to perform clinical trials on patient samples. The potential of miONCO-Dx to detect the recurrence of breast cancer is being evaluated in ABC Discover 2.
DietCompLyf Biobank Transfer
The biobank was created during the DietCompLyf study, a UCL-sponsored, Against Breast Cancer-funded, multi-centre observational study designed to investigate associations between diet and lifestyle factors and the risk of secondary breast cancer. Over 3,300 breast cancer patients were recruited between 1996 and 2014 at fifty-six UK NHS hospitals and provided biological samples for up to five years, along with clinical and diet and lifestyle information. The Biobank provides a valuable resource which is now available on which to apply the latest cutting-edge techniques and data analysis methods during ABC Discover 2. This will enable the discovery of new biomarkers and associated risk factors that can be used to improve patient outcomes both in terms of disease progression and reducing recurrence.
The transfer of the DietCompLyf was a lengthy process involving numerous regulatory and ethical steps that are required when patient samples are transferred between institutions. Professor Skipp gained approval for submissions to the Data Security and Protection Toolkit (NHS Digital), Integration Research Application System (IRAS), Confidentiality Advisory Group (CAG) and made a Hospital Episodes Statistics (HES) application to NHS Digital to obtain the 10-year follow-up data for patients included in the DietCompLyf study. Professor Skipp has established a dedicated, secure, and temperature-controlled laboratory that houses the biobank in six specialised freezers that maintain the samples at minus-80oC.
Potential benefit for patients
With the number of people living after a primary breast cancer diagnosis predicted to increase dramatically over the coming years, the need to detect secondary cancer earlier has never been greater. Identifying biomarkers that predict the risk of developing secondary cancer or early detection by tests like miONCO-Dx will revolutionise treatment intervention and improve patient outcomes. ABC Discover and ongoing work in ABC Discover 2 is helping identify which patients will benefit from further monitoring or treatment as well as determining which people do not require follow-up. Understanding cancer behaviour in response to diet and lifestyle factors may also provide evidence-based advice that patients can adopt to help reduce the risk of secondary cancer.
ABC Discover support of PhD student researcher
ABC Discover funded PhD student Luis Coy was awarded his doctorate for his research thesis ‘Characterising a 3D Culture Model of Triple-Negative Breast Cancer Through Systems-Based Molecular Phenotyping’ in June 2024. The now Dr Coy, presented his research at the BSPR-EUPA 2023 conference (British Society and European Proteomics Associations) and had a paper published in the journal Advances in Proteomics in Cancer. An additional paper is in preparation focusing on gene expression analyses of these 3D models of triple negative breast cancer. Dr Coy is now part of the team at Xgenera, the spin-out company created to continue development of the miONCO-Dx multiple early cancer detection test.
Publications
WDHD1 is essential for the survival of PTEN-inactive triple negative breast cancer. Cell Death and Disease. Ertay, A., Liu, H., Liu, D., Peng, P., Hill, C., Xiong, H., Hancock, D., Yuan, X., Przewloka, M., Coldwell, M., Howell, M., Skipp, P., Ewing, R., Downward, J., & Wang, Y. (2020). , 11:1001.
Identification of proteins associated with development of metastasis from cutaneous squamous cell carcinomas (cSCCs) via proteomic analysis of primary cSCCs. Shapanis, A., Lai, C., Smith, S., Coltart, G., Sommerlad, M., Schofield, J., Skipp P. J., Healy, E. (2020). British Journal of Dermatology. DOI: 10.1111/bjd.19485
Comparative analysis of protein expression between oesophageal adenocarcinoma and normal adjacent tissue Nicholas B, Bailey A, McCann KJ, Walker RC, Johnson P, Elliott T, Underwood TJ, Skipp P. PLoS One. 2025;20(3):e0318572.
Characterising a 3D culture model of triple-negative breast cancer through systems-based molecular phenotyping. Luis Coy, (2024) University of Southampton, Doctoral Thesis, 282pp