Marta Grzelak is the Production Lead at Omniscope and serves as Omniscope’s Technical Coordinator for the EPIVINF project. She leads the implementation of Omniscope’s work plan, overseeing the TCR/BCR repertoire profiling and single-cell transcriptomics workstreams. She also works closely with consortium partners to coordinate technical activities, ensuring high-resolution multi-omics data are shared efficiently and integrated seamlessly across the project.
1. Could you share the most recent findings or outputs from Omniscope’s work in the EPIVINF project?
Our recent work at Omniscope highlights the potential of our osT technology to better understand how the immune system responds to HIV infection by studying T cell receptors (TCRs). Using blood samples collected from five individuals before and after they acquired HIV, we found that infection triggers two key responses: it generates new HIV-specific T cell receptors and causes existing HIV-specific T cell receptors to expand. When we examined samples collected after antiretroviral therapy (ART) began, these expanded T cell populations had largely contracted, consistent with the virus being brought under control and the immune stimulus being reduced.
Our next step is to combine these T cell receptor findings with single-cell analyses and extend the study to a larger group of participants. This will help us better understand how a person’s immune system before infection influences their response to chronic viral diseases.
At the same time, our multi-omics analysis of samples from the therapeutic vaccine trial is making strong progress. We have now received the complete transcriptomic and DNA methylation datasets, providing a comprehensive view of how the vaccine affects the immune system. Since the vaccine has already shown strong immunogenicity, we are now analyzing these data to identify molecular and epigenetic biomarkers that could predict treatment responses and guide the development of more effective therapeutic vaccines in the future.
2. Why is it important to study both HIV and SARS-CoV2 viruses in the same research project?
Studying both HIV and SARS-CoV-2 within the same research project is important for several strategic and scientific reasons. Although these viruses are fundamentally different, they share key biological and clinical features that need comparative investigation. These include clinical similarities, such as long-term neurological complications, marked disruption of immune homeostasis during acute infection, profound lymphopenia, and impaired immune responses to unrelated co-pathogens.
In addition, preliminary analyses have identified partially overlapping host genome methylation patterns in response to both viruses. This finding suggests that HIV and SARS-CoV-2 may trigger shared early epigenetic pathways, potentially revealing common therapeutic targets for the development of broadly applicable antiviral interventions.
3. How do sequencing technologies allow us to analyse the immune system?
Modern sequencing technologies allow researchers to study the immune system in unprecedented detail, revealing how individual immune cells respond to infection or vaccination.
Using high-throughput single-cell sequencing and next-generation sequencing (NGS), scientists can analyse millions of T-cell and B-cell receptors (TCRs and BCRs) at the same time. This enables them to track how immune cell populations grow, change, and mature over the course of an immune response, providing insights into how protective immunity develops.
Multiplexed 10x single-cell transcriptomics adds another layer of information by examining gene activity in individual immune cells. This allows researchers to identify different immune cell types and determine their functional state, such as whether they are activated, developing into specialised cells, carrying out immune functions, or becoming exhausted.
Together, these technologies provide a comprehensive picture of the immune response at the single-cell level, helping researchers understand not only which immune cells are involved, but also how they behave and interact over time.
Genomic technologies can also measure epigenetic changes across the genome by analysing hundreds of thousands of DNA methylation (CpG) sites simultaneously. These measurements reveal how viral infections influence gene regulation, showing how important host defence genes are switched on or off during an immune response.
4. What impact could your findings have in the future?
This project will deliver important scientific, clinical, economic, and societal benefits. It will improve our understanding of how viral infections alter immune and neurological function through epigenetic mechanisms, helping to identify individual risk factors, discover biomarkers for severe disease and long-term complications such as Long COVID and neuro-HIV, and predict vaccine responses.
These findings will support more personalised disease management through earlier diagnosis, improved risk stratification, and targeted treatments, while increasing the cost-effectiveness of long-term care. By validating biomarkers and therapeutic targets, the project will facilitate translation into clinical applications through collaboration with biotechnology and pharmaceutical companies, strengthening Europe’s research and innovation ecosystem.
In the longer term, the project will support the development of personalised therapies and preventive strategies, including epigenetic therapies (“epidrugs”), with the aim of improving health outcomes and quality of life for people affected by persistent viral diseases.
