Epitope Megapools – Application of T Cell Epitope Identification for Deriving Novel Immunological Insights


Alessandro Sette, Dr.Biol.Sci.
La Jolla Institute for Immunology

Daniela Weiskopf, Ph.D.
La Jolla Institute for Immunology

Cecilia Lindestam-Arleham, Ph.D.
La Jolla Institute for Immunology

Alba Grifoni, Ph.D.
La Jolla Institute for Immunology

T Cell Epitopes

Harnessing Epitope Megadata to Create Reagents and Quantitate Antigen Specific Responses

Epitopes, in the context of T cell recognition, are short peptides typically derived by antigen processing, and presented on the cell surface bound to MHC molecules (HLA molecules in humans) for T cell repertoire (TCR) scrutiny. By identifying epitopes on viruses and bacteria, scientists can assess the immune system’s ability to fight infection and the potential for vaccines and therapies to protect the population.

A team of scientists in the Sette and Peters labs at La Jolla Institute for Immunology have identified epitope “megapools” that can be used to extract and isolate antigen-specific T cells for a variety of indications, including SARS-CoV-2, pertussis, dengue, Zika, and other bacterial and viral infections. Characterizing these T cells and the overall immune signature is key for understanding how vaccines or therapies can enhance a protective T cell response. Studying antigen-specific T cells also opens the door to new diagnostics and research tools.

This megapool approach has also been validated for a variety of different targets, including tetanus toxoid [148], Zika virus [57], and various allergens [78149150]. In the case of dengue virus, CD4 and CD8 megapools have been produced and utilized to quantitate responses in endemic areas and in response to vaccination.