SARS-CoV-2–specific T cells are rapidly expanded for therapeutic use and target conserved regions of the membrane protein

Abstract

T-cell responses to SARS-CoV-2 have been described in recovered patients, and may be important for immunity following infection and vaccination as well as for the development of an adoptive immunotherapy for the treatment of immunocompromised individuals. In this report, we demonstrate that SARS-CoV-2-specific T-cells can be expanded from convalescent donors, and recognize immunodominant viral epitopes in conserved regions of membrane, spike, and nucleocapsid. Following in vitro expansion using a GMP-compliant methodology (designed to allow the rapid translation of this novel SARS-CoV-2 T-cell therapy to the clinic), membrane, spike, and nucleocapsid peptides elicited IFN-γ production, in 27 (59%), 12 (26%), and 10 (22%) convalescent donors (respectively), as well as in 2 of 15 unexposed controls. We identified multiple polyfunctional CD4-restricted T-cell epitopes within a highly conserved region of membrane protein, which induced polyfunctional T cell responses, which may be critical for the development of effective vaccine and T cell therapies. Hence, our study shows that SARS-CoV-2 directed T-cell immunotherapy targeting structural proteins, most importantly membrane protein, should be feasible for the prevention or early treatment of SARS-CoV-2 infection in immunocompromised patients with blood disorders or after bone marrow transplantation to achieve anti-viral control while mitigating uncontrolled inflammation.

Rapid GMP-Compliant Expansion of SARS-CoV-2–Specific T Cells From Convalescent Donors for Use as an Allogeneic Cell Therapy for COVID-19

“…Various manufacturing methods have been developed, but cytokine capture has proved effective for isolation of T cells for clinical therapy (17)(18)(19). Other methods for isolation and/ or expansion of antigen-specific T cells have been developed, including isolation of tetramer-binding T cells (40), selection of activated T cells post antigen-exposure using CD137 selection (41), and expansion of virus-specific T cells through optimized in vitro stimulation with peptides and cytokines (36).…”

“…We are concentrating on manufacturing an HLA-typed bank of donated cells, as even a modest manufacturing process would yield 100 to 200 doses at a target dose of 10 7 cells per treatment. This approach could also be achieved using the recently published methods (also based on previous work with other virus infections such as CMV/ADV) by Keller et al in October 2020 (36).…”

Influence of HLA class II polymorphism on predicted cellular immunity against SARS-CoV-2 at the population and individual level

“…We focused on the two largest datasets recently described by Snyder et al 22, 23 (336 HLA class II peptides) and by Mateus et al 24 (135 HLA class II peptides) that contain peptides from the entire SARS-CoV-2 proteome. We also examined two relatively small datasets encompassing 9 nucleocapsid and 25 structural protein-derived (Spike, nucleocapsid or membrane) peptides 25, 26 . In the aforementioned datasets, the HLA restriction was not known and validation focused on positive identification of experimental peptides by the computational models (supplementary information).…”

Expanding the toolbox to combat a pandemic

“…Understanding immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for optimizing treatment of COVID-19. In this issue of Blood , Keller and colleagues 1 generated SARS-CoV-2–specific cytotoxic T lymphocytes (CTLs) from the blood of individuals recovered from infection. The rapid application of this good manufacturing practice (GMP)-compliant system raises the possibility that banked third-party SARS-CoV-2 CTLs could be used for treatment.…”

“…Recent efforts have seen progress in increasing the number of viruses targeted and improving accessibility to these therapies by more rapid production methods and/or the use of banks of “off-the-shelf” third-party products. 1 , 5 Progress in tracking the in vivo expansion and durability of the transferred T cells has not kept pace with the clinical expansion of these therapies, but novel approaches to immune monitoring and the potential for deep sequencing of infused populations are changing that. Meanwhile, commercialization of banked viral-specific T-cell therapies is on the horizon.…”