This release was adapted from an article by CHOP. 

Researchers from Stanford University and Children’s Hospital of Philadelphia (CHOP) published this week about new immunotherapy platforms to help immune systems target diseased cells, such as those involved in viral infection, cancer, or autoimmune diseases. The platforms, called TRACeR, are presented in two papers – one about TRACeR-I and one about TRACeR-II – published in Nature Biotechnology. 

Immunotherapy presents a promising strategy for treating cancer, autoimmune diseases, and viral infections, but its effectiveness depends on its ability to target diseases cells. Monoclonal antibodies are widely used because they can target antigens – proteins generated by cancer cells that trigger an immune response – on the surface of diseased cells, but uniquely expressed antigens found on the surface are sparse.

Another potentially powerful target involves peptide fragments of these proteins that major histocompatibility complex (MHC) molecules attach to and present on the tumor cell surface for identification by immune cells. There are tens of thousands of different versions of MHC proteins in humans, which makes it incredibly challenging to develop treatments that can recognize the peptides they present across large groups of patients and diseases. MHC’s also fall into two broad classes: MHC-I molecules exist in almost every cell membrane and MHC-II molecules exist in macrophages and lymphocytes, which are immune cells. 

To take advantage of MHC peptides for immunotherapy, researchers at Stanford, led by Possu Huang, an assistant professor of bioengineering in the schools of Engineering and Medicine, have developed TRACeRs. The TRACeR platform acts like a “master key” that can fit a variety of peptide-MHCs to unlock their potential as targets for the treatment of diseased cells while sparing healthy cells. 

“Our TRACeR-I and TRACeR-II platforms unlock the potential for targeting disease-associated class I and class II MHC antigens through novel binding mechanisms that overcomes many of the hurdles that have historically limited the broader development of MHC-targeting molecules,” said Huang, who is senior author of the study. “Our platforms have high peptide-focused specificity, broad compatibility with a variety of antigens, and simpler development that significantly expand the accessibility of targetable MHC biomarkers.” 

As part of the TRACeR-I work, CHOP revealed the molecular structure to help optimize designs for the platform. TRACeR-I has the potential to be used to develop cancer treatments by either directly modifying immune cells or by creating proteins that help immune cells locate cancer cells. The Stanford researchers hope to apply TRACeR-II to treatments for diseases related to autoimmune inflammation. 

Novel potential 

To better understand the potential of the TRACeR-I platform, researchers from CHOP used X-ray crystallography to show exactly how the platform attaches to parts of the MHC-I complex that stay the same across different versions while continuing to recognize the peptides that indicate cancer cells or other dangerous material being displayed on the surface. 

“We revealed TRACeR-I’s novel binding mechanism and how the structure of this platform is able to help it recognize surface proteins that indicate cancer cells,” said Nikolaos Sgourakis, PhD, associate professor in the Center for Computational and Genomic Medicine at CHOP. “With this collaborative work, we were able to take the Huang lab’s designs and help realizing their exciting therapeutic potential.” 

Huang and his lab developed TRACeR-II to address class-II MHCs because they are prevalent in all diseases. An added challenge, however, is that the peptides in MHC-II have fewer structural features, which make them harder to bind to than their class-I counterparts. 

“We uncovered a biologically inspired strategy to achieve highly-specific MHC-II peptide recognition using a single loop on a protein, which can be mutated to adapt to different targets,” said Huang. “This single loop-medicated interface enabled us to vastly simplify the process for creating MHC-II binders, to an extent that we could directly design binding sequences on a computer. This unprecedented capability to create MHC-II targeting binders will offer new tools for research and therapeutics.” This work was carried out in collaboration with Stanford Medicine faculty K. Christopher Garcia, the Younger Family Professor and professor of structural biology and of molecular and cellular physiology, and Elizabeth Mellins, who was a professor of pediatrics. Sadly, Mellins passed away in March 2024. 

A tool and a treatment 

The researchers have their sights set on clinical applications for TRACeR-I. Huang’s lab and CHOP are looking into oncology targets, and Huang is additionally interested in whether TRACeR-I can eradicate virally infected cells hidden from the immune system. “We are in collaboration with Nadia Roan of UCSF and Gladstone Institutes and Peter Bruno of UCSF on HIV cure strategies, and with Tobias Lanz at Stanford on intervention with EBV infected B cells,” said Huang. 

TRACeR-II can be a tool to study many diseases aggravated by autoimmune inflammation. One example the Stanford researchers are pursuing in collaboration with Xiaobo Mao of Johns Hopkins University is using TRACeR-II to understand the spread of the alpha-synuclein protein within the gut-brain pathway, which is linked to the development of Parkinson’s disease.