Researchers at Children’s Hospital of Philadelphia (CHOP) have identified variants of a chaperone molecule known as TAPBPR that optimizes the binding and presentation of foreign antigens across the human population. The findings, they suggested, could unlock new applications in areas such as cell therapy and immunization, where robust presentation to the immune system is important.

“The knowledge gained by our studies can guide the design of engineered TAPBPR variants with tailored HLA specificity and catalytic efficiency for peptide exchange applications both in vitro and in vivo,” said Nikolaos G. Sgourakis, PhD, associate professor in the Center for Computational and Genomic Medicine at CHOP. Sgourakis is corresponding author of the team’s published paper in Science Advances, which is titled, “Xeno interactions between MHC-I proteins and molecular chaperones enable ligand exchange on a broad repertoire of HLA allotypes.”

Class I major histocompatibility complex (MHC-I) proteins are found on the surface of cells in all jawed vertebrates and play an essential role in the immune system. The MHC-I displays peptide fragments of proteins from within the cell on the cell surface, effectively “presenting” them to the immune system, which is constantly scanning the body for foreign or toxic antigens. When foreign peptides are identified, they trigger a cascade that allows cytotoxic T cells to eliminate intruders.

For a peptide to be presented to the immune system, it needs to be loaded on a folded MHC-I protein. Several molecules facilitate this process, including proteins known as molecular chaperones, which assist with MHC-I folding. And as the authors noted, “MHC-I folding and peptide loading are subject to intricate cellular quality control.”

Tapasin and a similar molecule known as TAPBPR are both molecular chaperones that facilitate MHC-I folding and peptide loading. “Immunological chaperones tapasin and TAP binding protein, related (TAPBPR) play key roles in antigenic peptide optimization and quality control of nascent class I major histocompatibility complex (MHC-I) molecules,” the team explained. Because TAPBPR functions independently outside of the peptide-loading complex (PLC), it is well-suited for clinical applications that involve peptide exchange, such as loading immunogenic peptides on MHC-I molecules and generating libraries to detect T cells that recognize peptides or antigens from infected or cancerous cells. “TAPBPR, a homolog of tapasin, which functions outside the PLC, plays a complementary role in pMHC-I optimization and quality control,” the team continued.

However, to date, TAPBPR-mediated peptide exchange has only worked for a limited set of common allotypes of human MHC-I, known as human leukocyte antigen (HLA), which has limited wider utility, the authors pointed out. “TAPBPR-mediated peptide exchange has only been demonstrated for a limited set of common HLA allotypes, mainly from the A02 and A24 supertypes, limiting a wide adoption of these technologies in biomedical applications.”

Over time, HLA subtypes, which include HLA-A, HLA-B, and HLA-C, have evolved such that not all alleles interact equally well with TAPBPR. This has been a roadblock in developing and enhancing novel therapies with the help of molecular chaperones, as some HLA allotypes do not interact with these molecules.

To solve this problem, the CHOP researchers analyzed three different TAPBPR proteins: one from humans, one from chickens, and one from mice. “Although predicted structures of TAPBPR from different species are remarkably similar, whether different orthologs can mediate peptide exchange on human MHC-I proteins has not been addressed,” they noted. Their studies showed that, unlike human TAPBPR, chicken TAPBPR co-evolved with its class I genes, so that it maintains high affinity across MHC-I allotypes. In their analysis, the researchers found that chicken TAPBPR was able to react with multiple HLA allotypes, many of which were not able to bind to human TAPBPR. They also demonstrated that TAPBPR stabilizes the empty MHC-I groove in an “open” conformation, boosting its affinity for peptide loading.

Simultaneously, in close collaboration with researchers at the University of Illinois led by Erik Procko, PhD, the research team used deep mutational scanning to characterize the effects from 100s of point mutations on human TAPBPR and found a variant that mimics the chicken sequence. Like the chicken TAPBPR, this variant enhanced peptide exchange across a broad range of HLA types.

“Although the highly polymorphic nature of MHC-I molecules makes it challenging to engineer ‘universal’ chaperones, our research team demonstrated that both a chicken ortholog of TAPBPR and a human variant with minor adjustments could enhance peptide exchange across multiple disease-relevant HLAs,” said Sgourakis. “These TAPBPR orthologs could be utilized in various cancer immunotherapeutic settings to narrow the peptide repertoire and increase immunogenicity.”

In their paper, the authors concluded, “Although the highly polymorphic nature of MHC-I molecules challenges the engineering of ‘universal’ chaperones, we demonstrated a relatively conserved TAPBPR-binding epitope on MHC-I and the possibility of designing and engineering off-the-shelf TAPBPR variants with minimal adjustments to enable peptide exchange on HLA allotypes of choice.” Moreover, they suggested, “TAPBPR orthologs can also be used in various cancer immunotherapeutic settings to narrow the peptide repertoire, thereby increasing neoepitope immunogenicity.”

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