What traits of a cancer cell are identified by the immune system? Understanding potential target structures for immune cells is crucial for creating personalized cancer treatments. Researchers from the German Cancer Research Center (DKFZ) and NCT Heidelberg have introduced a highly sensitive mass spectroscopy method to pinpoint tumor-specific “neoepitopes”. This technique is tailored to detect these rare protein fragments using minimal sample sizes.
Personalized immunotherapies are increasingly seen as an effective way to combat cancer. These therapies may involve tailored cancer vaccines or T cell therapies where the T cell receptors are customized to target the individual’s specific tumor. A key requirement for developing any personalized immunotherapy is to identify the proteins altered by cancer that the patient’s immune system can recognize.
Researchers call the mutated protein fragments that the immune system identifies “neoepitopes.” To discover these, the tumor’s genome must be sequenced first. Advanced bioinformatics techniques then analyze the DNA and RNA sequencing results to find mutations that result in altered proteins potentially recognized as “foreign” by the immune system.
For the immune system to be activated, these modified protein fragments need to be displayed on the surface of the cancer cells. “Only neoepitopes shown by HLA proteins on cancer cell membranes can activate T cells,” notes immunologist Angelika Riemer from DKFZ.
Mass spectrometry (MS) is the method used for identifying these neoepitopes. This technique determines the mass of charged protein fragments. “Mass spectrometry provides definitive proof of a neoepitope’s presentation. However, traditional MS methods often miss low-abundance peptides like tumor neoepitopes,” explains the researcher.
Now, Angelika Riemer and her team from DKFZ and NCT Heidelberg have published a new analytical approach aimed at identifying patient-specific cancer neoepitopes more swiftly and accurately.
Using sequences from tumor DNA and RNA, researchers pinpoint the relevant protein fragments. Knowledge about the binding properties of HLA molecules further aids in predicting which neoepitopes are most likely presented on the tumor surface.
The innovative part of this method is that the peptides are first synthesized in the lab, which helps tailor the mass spectrometer’s settings for analyzing each specific peptide. Only after optimizing the settings do they analyze actual tumor tissue samples, ensuring the best conditions for detecting neoepitopes.
“As a result, our new protocol allows for much smaller tumor tissue samples to be analyzed,” Riemer explains. Her team successfully identified a neoepitope using only a sample from two and a half million cancer cells. “That’s even less than the size of a grain of sand,” notes the immunologist.
They managed to detect five distinct neoepitopes from small tumor samples taken from three patients, and in some instances, confirmed them through the interaction of the patients’ T cells.
“The future importance of personalized cancer immunotherapies is undeniable,” states senior author Riemer. “In this context, MS offers the ultimate proof that a neoepitope exists on cancer cell surfaces, making it a valuable target for therapy. Our optiPRM protocol will facilitate this validation using minimal tissue samples and help point clinicians toward tailored cancer treatments.”
Currently, mRNA-based tumor vaccines in clinical trials often involve roughly 30 various predicted cancer neoepitopes. Riemer is optimistic: “We believe a focused strategy using validated neoepitopes could deliver the same effectiveness with fewer epitopes.” The experts also stress the importance of validating target epitopes for developing therapeutic T cells tailored to specifically attack cancer cells.
