T cell therapy for COVID-19 with single cell immune sequencing

The coronavirus disease has plagued the world for months, with over 100 million confirmed cases worldwide and a growing death toll. Researchers all over the world have been seeking alternate solutions to combat the virus and quell the disease – one novel solution is T cell therapy. Using a single-cell immune sequencing technique, a group of researchers at the Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and University Hospital Erlangen in Germany made headway with their discovery of T cells with protective response to the virus.  

Given the prevalence of the coronavirus disease, treatments and vaccines have been rapidly mass-produced for the public. Available vaccines, while helpful for some, cannot protect everyone. Cancer patients who have undergone hematopoietic stem cell transplant are quite vulnerable to side effects and complications of infections. The long-term effects of the virus infiltrating organ systems such as the brain or pancreas are also a source of concern.^1,2 These highlight the relevance for new treatments that would boost the immune response to SARS-CoV-2 in infected, immunocompromised individuals. 

During the Spanish Flu outbreak in 1918, convalescent plasma was prominently used to confer adaptive immunity to the virus via the transfer of neutralizing antibodies. Transferring convalescent plasma in the case of COVID-19 has proved successful in mild to moderate cases.^3,4 In severe cases where patients need mechanical ventilation, it has been less successful. Also, recent reports have warned that this method may promote the evolution of the virus – which would then be problematic for vaccine efficacy.  

Neutralizing antibodies are not the only immunological protection against COVID-19, the long-lasting T cells also mediate immune protection. On this basis, T cell immunity against several SARS-CoV-2 proteins not only represents a major component of the healthy immune response^5,6 but also presents a new avenue for immunotherapy. T cell therapy is a type of immunotherapy that uses immune T cells to fight specific foreign or invading cells. To this end, Verhagen et al. set out to characterize T cells from COVID-19 patients with potentially protective response to SARS-CoV-2. They recently described their findings in an article in Clinical and Experimental Immunology.⁷ 

With participants’ consent, peripheral blood mononuclear cells (PBMCs) were obtained from healthy and SARS-CoV-2 infected donors. On assessment, the Verhagen group found that COVID-19 patients had higher HLA-DR and CD38 expression of both CD4⁺ and CD8⁺ T cells – suggesting an ongoing antiviral response. They examined both groups for responses to Spike and Nucleocapsid proteins, two major antigens of the SARS-CoV-2 virus, and found only three of the COVID-19 patients responded strongly to both antigens.  

To study the antigen-specific T cell response from the three highly reactive patients, they generated clones of virus-reactive CD4⁺ T cells, confirmed a set of nine immunodominant epitopes, and characterized T cell responses against these. Subsequently, they examined the response of each T cell clone to its target epitope, providing a collection of T cells with outstanding characteristics that could potentially target multiple epitopes.  

Finally, the group used the iRepertoire iPair single cell immune sequencing service to investigate the TCR repertoire of T cell clones. Using a single cell workflow, they sequenced small clonal populations and acquired paired chain sequences for all samples, with sufficient data to identify the exact TCR. This “mini-bulk” approach enabled them to characterize paired chains of individual T cell clones.   

Using this approach, sequences can be selected from the T cell clones with the most advantageous qualities to generate SARS-CoV-2 antigen-specific TCR-transgenic T cells using endogenous T cells from patients or from HLA-matched donors. An encouraging similarity in TCR sequences was also observed across HLA backgrounds, suggesting transgenic virus-reactive T cells may be broadly transferable. It should be noted that the donors in this study, came from a limited, German population. A global approach would still need to investigate antigen-specific responses in donors from a much more diverse background; however, this work constitutes a significant first step toward TCR-transgenic CD4+ T cell therapy of COVID-19. 

References

1. Meinhardt, Jenny, et al. “Olfactory Transmucosal SARS-CoV-2 Invasion as a Port of Central Nervous System Entry in Individuals with COVID-19.” Nature Neuroscience, vol. 24, no. 2, 2020, pp. 168–175., doi:10.1038/s41593-020-00758-5. 
2. Müller, Janis A., et al. “SARS-CoV-2 Infects and Replicates in Cells of the Human Endocrine and Exocrine Pancreas.” Nature Metabolism, vol. 3, no. 2, 2021, pp. 149–165., doi:10.1038/s42255-021-00347-1.
3. Libster, Romina, et al. “Early High-Titer Plasma Therapy to Prevent Severe Covid-19 in Older Adults.” New England Journal of Medicine, vol. 384, no. 7, 2021, pp. 610–618., doi:10.1056/nejmoa2033700.
4. Joyner, Michael J., et al. “Convalescent Plasma Antibody Levels and the Risk of Death from Covid-19.” New England Journal of Medicine, vol. 384, no. 11, 2021, pp. 1015–1027., doi:10.1056/nejmoa2031893. 
5. Grifoni, Alba, et al. “Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals.” Cell, vol. 181, no. 7, 2020, doi:10.1016/j.cell.2020.05.015.
6. Tarke, Alison, et al. “Comprehensive Analysis of T Cell Immunodominance and Immunoprevalence of SARS-CoV-2 Epitopes in COVID-19 Cases.” Cell Reports Medicine, vol. 2, no. 2, 2021, p. 100204., doi:10.1016/j.xcrm.2021.100204.
7. Verhagen, Johan, et al. “Human CD4 + T Cells Specific for Dominant Epitopes of SARS‐CoV‐2 Spike and Nucleocapsid Proteins with Therapeutic Potential.” Clinical & Experimental Immunology, 2021, doi:10.1111/cei.13627.