Research

Our research integrates principles from structural biology, protein engineering, and immunology to address fundamental questions in antigen presentation and T cell activation, with the ultimate goal of translating these insights into novel therapeutic modalities.

Structural mechanism of MHC-I immune repertoire processing

CryoEM structure of an MHC-I/TAPBPR peptide bound intermediate reveals the mechanism of antigen proofreading

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. Recently, a groundbreaking study from our lab provides unprecedented insight into how our immune system selects the right targets to fight disease. Using cutting-edge structural biology techniques, we visualized for the first time how TAPBPR scrutinizes potential threats. Like a molecular quality control inspector, TAPBPR examines fragments of proteins (peptides) to determine which ones should be displayed on cell surfaces to alert immune cells. The study reveals in exquisite detail how TAPBPR captures these peptides and tests their fit, only allowing the most secure ones to pass inspection. This selective process ensures our immune system focuses on legitimate threats while avoiding false alarms that could lead to autoimmune disorders. Beyond advancing our fundamental understanding of immunity, this work has important implications for vaccine design and cancer immunotherapy, potentially leading to more targeted and effective treatments that harness the power of our own immune defenses.

Identifying and targeting peptide:HLA tumor antigens for personalized cancer therapy

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

MHC class I proteins play a pivotal role in adaptive immunity, exhibiting remarkable polymorphism with over 15,000 known allotypes in humans. This extensive diversity ensures that each allotype presents a unique repertoire of peptide antigens, contributing to species-level adaptability against emerging pathogens. However, this polymorphism presents significant challenges in developing broadly applicable therapeutic approaches across diverse ethnic populations.

Our laboratory’s long-term research goal focuses on two primary areas:

1. Development of MHC-I reagent libraries: We’re engineering tools to generate extensive libraries of MHC-I reagents for: a) Screening and selecting antigenic peptides b) Monitoring antigen-specific T cells across various donors. We’ve developed two orthogonal approaches: i) Engineered molecular chaperones: We’ve modified TAPBPR (TAP-binding protein related), a key player in the MHC-I peptide-loading complex, to facilitate controlled peptide exchange. ii) Conformationally stabilized “open” MHC-I proteins: These modified MHC-I molecules maintain a peptide-receptive state, allowing for efficient in vitro peptide exchange. Both methods enable rapid and efficient peptide exchange in vitro, significantly advancing our ability to create diverse pMHC complexes for various applications.
2. Investigating MHC-I in pathological contexts: MHC-I molecules serve as a critical interface between intracellular protein metabolism and T cell immunosurveillance by presenting the intracellular peptidome on the cell surface. In the context of cancer, tumor cells can present fragments derived from oncoproteins, forming tumor-specific peptide/MHC-I complexes. We’re pursuing two parallel research directions: a) Tumor-reactive T cell screening: Utilizing our engineered TAPBPR, we’re generating libraries of pMHC tetramers to screen for tumor-reactive T cells. This approach allows for high-throughput identification of T cells specific for tumor-associated antigens. b) Novel immunotherapeutic strategies: We’re designing peptide-focused binding modules that specifically target tumor-associated pMHC-I antigens. These modules have potential applications in personalized immunotherapies, including:
   • CAR-T cells: By incorporating these binding modules into chimeric antigen receptors, we aim to enhance the specificity and efficacy of CAR-T cell therapies.
   • Bispecific T cell Engagers (BiTEs): These binding modules can be used to create BiTEs that bridge T cells with tumor cells expressing specific pMHC-I complexes.

These molecular tools and approaches are significantly advancing our understanding of MHC-I antigen repertoires in various disease settings, particularly in cancer. By elucidating the complexities of MHC-I-mediated antigen presentation and T cell recognition, we’re paving the way for more targeted and personalized immunotherapeutic strategies.

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