Enhancing cytotoxic T-lymphocyte tumour-fighting capacity through the modulation of metabolic pathways regulated by ZFP36/ZFP36L1 RNA-binding proteins

Project Information

EnhancemenT

Grant agreement ID: 101022265

DOI

10.3030/101022265

Project closed

EC signature date 11 October 2021

Start date 1 March 2023

End date 28 February 2025

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 212 933,76

EU contribution

€ 212 933,76

Coordinated by

THE BABRAHAM INSTITUTE
United Kingdom

Periodic Reporting for period 1 - EnhancemenT (Enhancing cytotoxic T-lymphocyte tumour-fighting capacity through the modulation of metabolic pathways regulated by ZFP36/ZFP36L1 RNA-binding proteins)

Reporting period: 2023-03-01 to 2025-02-28

Summary of the context and overall objectives of the project

Cytotoxic CD8+ T-lymphocytes (CTLs) are a type of immune cell specialised in recognising and killing infected and tumour cells. This ability to kill cancer cells is also exploited in T-lymphocyte-based immunotherapies using chimeric antigen receptor (CAR) T-cells, where these cells are genetically engineered and transferred into the patient to potentiate their anti-tumour immune response.
CTLs are generated upon a process in which naïve T-lymphocytes recognise a specific “foreign” protein from a tumour or a virus, start proliferating, and differentiate into a cohort of effector T-lymphocytes which maintain specificity for the same foreign protein. However, CTLs are often limited upon long-term exposure to viral or cancer molecules and eventually fail in defeating the disease. Therefore, there is need to discover new strategies to potentiate CTL survival and effector functions in chronic infections and cancer, also to improve T-lymphocyte-based immunotherapies.
My project aimed at identifying new molecular pathways that control T-lymphocyte activation and effector functions. I focused on the role of specific RNA-binding proteins belonging to the ZFP36-family. I discovered that beyond regulating the production of specific effector molecules in T-lymphocytes, ZFP36-family proteins also regulate RNAs encoding epigenetic and metabolic factors, ultimately affecting T-lymphocyte epigenetics. By epigenetics we refer to all those processes that regulate the activation or repression of a gene at the DNA level, without changing the DNA sequence.
Therefore, my work laid the basis for the identification of new molecular pathways that may be targeted to improve success of cancer immunotherapy and develop innovative treatments for chronic infections, both very urgently needed.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

During my project I discovered new effects of the ZFP36-family proteins on the regulation of the epigenetic landscape of CD8+ T-lymphocytes. Particularly I found that when we deplete ZFP36-family proteins from mouse T-lymphocytes, there are profound effects on one aspect of T-lymphocyte epigenetics, which is the physical accessibility of DNA sequences throughout the genome. This affects the possibility of proteins that activate or repress a gene to bind the DNA and exert their regulatory function. In fact, we found that these changes in DNA accessibility result in changes of gene expression in T-lymphocytes.
We hypothesise that ZFP36-family RNA-binding proteins affect this aspect of T-lymphocyte epigenetics both directly, by regulating epigenetic factors, and indirectly, by modulating cell metabolism (which can ultimately affect epigenetics). In fact, I found that among the mRNA molecules bound by the ZFP36-family proteins there are many that encode epigenetic proteins and metabolic enzymes.
Moreover, during my project I generated two genetically modified mouse models that will allow us to better understand, from a molecular point of view, how ZFP36-family proteins regulate T-lymphocyte activation.
During the project, my research work was disseminated through an oral presentation at an Immunology Departmental meeting (Babraham Institute) and poster presentations at the RNA UK 2024 meeting and the UK Ageing Research Funders’ Forum Early Career Researchers’ Event. The audience of the two external conferences was not restricted to immunologists, as the first event brought together scientists working with different biological systems with a common interest in RNA research, and the second one also included researchers with non-biological or non-scientific backgrounds. In May 2025 I will present a poster which will include the work I did during my fellowship at the EMBL Conference “Chromatin and epigenetics” in Germany. Once published in a peer-reviewed journal, the results of my research will be open-access, and this will be preceded by submission of the manuscript to a pre-print server. Data and metadata will be available through public repositories. In the future, the results of my work will be exploited also by other scientists and will open new research avenues.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

During my fellowship I identified new pathways through which ZFP36-family proteins regulate T-lymphocytes activation. My results and data will be available to other immunologists and molecular biologists, and this will encourage further exploration of the complex relationship between RNA-binding proteins, epigenetics and metabolism in immune cells. All this will contribute to find new ways to improve success of cancer immunotherapy to help more and more patients in the future.

ZFP36-family proteins regulate mRNAs encoding epigenetic factors and metabolic enzymes in T-cells