Research

The Sgourakis laboratory blends structural approaches, protein engineering, functional studies using patient samples, and computational biology to elucidate the mechanisms by which tumors process intracellular antigens and present a panel of cell-surface biomarkers that can be targeted for personalized cancer therapy.

Our research centers on understanding the structure and function of the human Major Histocompatibility Complex (MHC), with a goal of facilitating cancer immunotherapy and tuning immune responses to address a variety of diseases. The MHC includes a concentrated group of diverse genes that affect vulnerability to numerous health conditions such as autoimmune disorders, infections, and varied illnesses ranging from Cancer, Narcolepsy to Schizophrenia. The MHC’s primary components are Class I and Class II molecules. These molecules are crucial in triggering immune responses by presenting antigenic peptide fragments to T cell receptors, thus signaling an aberrant cellular state. A significant portion of our work focuses on understanding how these molecules are assembled intracellularly, and what functions they serve on the cell surface. We concentrate on two main research direction

Structural mechanism of MHC-I immune repertoire processing

MHC-I presents a repertoire of peptide antigens on the cell surface. Optimized high-affinity peptide-loaded MHC-I can be recognized by T cell receptors (TCRs) and Natural Killer (NK) cells. Dedicated molecular chaperones tapasin and TAPBPR are involved in the process of selecting and optimizing the MHC-I peptide repertoire. We are focused on understanding this molecular mechanism of antigen processing and presentation.

Tapasin and TAPBPR are essential in stabilizing empty MHC-I molecules, optimizing the repertoire of their peptide cargos, and mediating quality control of peptide-loaded MHC-I. We have demonstrated that TAPBPR emerges as a critical component for small-molecule metabolite presentation on MHC-related 1 (MR1) molecules. Our lab also focuses on characterizing the transient state of peptide-bound MHC-I/TAPBPR. More recently, we captured this conformation and visualized an MHC-I/TAPBPR complex bound to a peptide decoy by cryoEM. Our work has important ramifications for the creation of modified proteins used for therapeutic development and the selection of immunogenic epitopes for vaccine design applications.

Personalized cancer therapeutics

Structural principles of peptide-centric chimeric antigen receptor recognition guide therapeutic expansion

MHC-I proteins are extremely polymorphic (>15,000 known allotypes) in the human population. Each allotype displays a unique repertoire of peptide antigens, ensuring species adaptability to emerging pathogens. However, this complexity challenges the development of robust therapeutic approaches that can cover patients of diverse ethnic backgrounds. A long-term research goal of our laboratory is to develop tools for generating libraries of MHC-I reagents that can be used to screen and select antigenic peptides and monitor antigen-specific T cells across donors. We have developed two orthogonal approaches employing i) Engineered molecular chaperones or ii) conformationally stabilized “open” MHC-I proteins, that can be readily applied to enable peptide exchange in vitro. The molecular tools generated by the new approaches are significantly advancing our understanding of MHC-I antigen repertoires in different disease settings.

MHC-I molecules display the intracellular peptidome on the cell surface, serving as a window for T cell immunosurveillance by sampling a large pool of peptide fragments. Tumor cells can present fragments derived from oncoproteins on the cell surface, in the form of peptide/MHC-I complexes. In one research direction, we are using our engineered version of the MHC-I chaperone TAPBPR to generate libraries of pMHC tetramers that can be used to screen for tumor-reactive T cells.

In a parallel direction, we are designing novel, peptide-focused binding modules targeting tumor-associated pMHC-I antigens for enabling personalized therapeutics using CAR-Ts or Bispecific T cell Engagers (BiTEs).

Our computational tools

T-CREGs: https://github.com/titaniumsg/find_tcreg

  • Prediction of MHC-I restriction of T cell receptors

HLA3DB: https://hla3db.research.chop.edu/

  • An automated, curated database of peptide/MHC-I structures

RepPred: https://zenodo.org/record/8372876

  • Structure prediction of peptide/HLA complexes

MAUS: https://maus.research.chop.edu/

  • Automated methyl assignment of NOESY data