Immune cell monitoring is imperative for almost any clinical study. The problem: Current procedures require viable cells, a demand often torpedoed by sample logistics.
What do cancer, autoimmune diseases, and Covid-19 have in common? Hint: Think of immune cells.
In immuno-oncology, therapeutic approaches provoke a targeted immune response against the tumor. In autoimmune diseases, a dysregulated response of the immune system attacks the body’s cells. In Covid-19, severe complications are attributed to immune cell activity rather than to the toxicity of the virus.
Monitoring the immune cell status is, therefore, essential to study these conditions. In clinical trials, monitoring the activity of immune cells and the changing composition of various immune cell types helps researchers understand what is going on in each phase of the disease, develop new therapies, and evaluate drug efficacy.
Flow cytometry is the current standard method for immune cell monitoring. It analyzes whole cells based on surface protein biomarkers. However, these proteins are often fragile. If cells have been damaged during sample collection, transport, or storage, they are no longer amenable to analysis.
“Clinical samples have always been a logistical challenge. Cells losing their shape or viability during transport can greatly affect data quality, or even render the analysis of those cells impossible. In extreme cases, more than half of the cells can be destroyed, significantly affecting data quality,” explained Eva Raschke, Director of Scientific Affairs at Precision for Medicine, a global clinical research organization.
Epigenetics for immune cell monitoring
Acquired by Precision for Medicine in 2017, the Berlin-based lab Epiontis (now known as Precision for Medicine GmbH) has developed the Epiontis ID technology for monitoring immune cells. Epiontis ID does not require viable cells that may be damaged by logistical processes.
Instead, epigenetic features in the immune cell DNA are analyzed – in particular, the presence of methyl groups on cytosine bases. These modifications are characteristic of specific immune cell types so that methylation patterns can be directly linked to the immune cell composition in a sample.
In the fully automated and accredited Epiontis ID workflow, isolated DNA is treated with bisulfite reagents that convert all unmethylated cytosine bases to uracil, while methylated cytosines are not affected. The resulting changes in the DNA sequence are detected by quantitative PCR, making it possible to determine the numbers of specific immune cell types.
Standardized data for global collaborations – and stepping back in time
Precision for Medicine, which in addition to the Berlin lab, has six other specialty labs in Europe and the US, supports biomarker-driven, precision clinical research through specialized lab services and technologies developed in-house.
Today, customers can create a customized panel of immune cells from a selection of more than 30 pre-validated markers. Standardized reports list the percentage of individual cell types in a sample, as well as the absolute number of cells present per μl of blood. For large clinical studies, data can also be directly transferred to the client’s database.
Because DNA-based data are highly reproducible, they can be aligned between cohorts and study sites, allowing researchers to interact globally. On top of that, new results can be compared with data from previous studies for re-evaluation – like stepping back in time.
Blood, tissue, and beyond
Compared to surface proteins, DNA molecules are very stable, so the Epiontis ID technology is not limited to fresh blood samples. Independent of storage conditions, it also works with all kinds of tissue samples (fresh, frozen, or paraffin-embedded), dried blood spots, and saliva.
In response to the current pandemic, even throat swabs are analyzed to study the effect of the SARS-CoV-2 virus – which causes Covid-19 – directly at the site of infection.
“We are excited to have an ongoing internal research project that employs the Epiontis ID monitoring technology to try to provide a prognosis for the disease course of Covid-19 patients,” Raschke explained.
DNA-based immune monitoring overcomes the three major limitations of current cell-based methods: sample stability, sample type, and standardization. As of today, the Epiontis ID technology has been used in more than 100 clinical studies, with nearly 70,000 samples analyzed. And maybe the next groundbreaking therapy will be developed thanks to epigenetic immune cell monitoring – from a Berlin-based lab.
This article was originally published in September 2020 and has since been updated.
Header image via Shutterstock.com and article images via Precision for Medicine