Our work uses cellular and molecular technologies to analyze the complex heterogeneity of T cell responses at the level of single cells. Despite organized in cell populations and performing similar functions, every cell in the immune system is different. Therefore single cell analysis is a very powerful tool to identify rare functions that otherwise would be missed by bulk analysis (i.e. of the average population). In this regard, we recently optimized a unique technology, 28-color, 30-parameter flow cytometry and used it to study antigen-specific T cells in the context of haploidentical stem cell transplantation with post-transplant cyclophosphamide (HSCT with pt-cy).
We defined the phenotype, functionality and T cell receptor diversity of T cells that are adoptively transferred with the graft. We used cytomegalovirus (CMV)-specific T cells as a model, as we have demonstrated in the past that CMV-specific T cells infused with the graft are capable to persist in the patient and clonally expand following viral reactivation. We developed 30-parameter flow cytometry panels to investigate multiple features of T cells and found that CMV-specific T cells are primed early post HSCT, initially display a proliferating/activated phenotype, that is replaced by a terminal effector phenotype. One year after transplant, CMV-specific T-cell profiles were similar to those of the CMV-seropositive donor, suggesting reestablishment of physiological homeostasis. Uncontrolled viral replication associated with lower abundance of distinct CMV-specific CD4+ T-cell immunophenotypes, hinting at a possible role of these cells in CMV control following haplo-HSCT with pt-cy. Analysis of the blood of patients receiving infusions of immune cells from the donor revealed that CMV-specific T cells are capable to persist, thereby indicating they can provide anti-viral immunity in the long term.
We combined single cell technologies, such as sequencing and 30-parameter flow cytometry, to study the complexity of memory T cells in humans. We recently developed new pipelines of computational analysis to dissect the complexity of single cell data, and were able to identify previously unrecognized populations of cells that have long-lived characteristics but at the same time share features with those dysfunctional cells found in solid tumors. Intriguingly, these cells are the preferential targets of immunotherapy approaches directed to reinvigorate the function of the immune system in solid tumors (i.e. those with checkpoint blockade). We have elucidated the molecular characteristics of these dysfunctional cells, and are currently exploiting this information to improve the function of T cells in response to checkpoint blockade immunotherapy or in response to an additional immunotherapeutic approach that is very effective for the treatment of hematological malignancies, i.e. infusion of anti-tumor T cells generated in the lab. In particular, we have shown that growing T cells in the lab in the presence of inexpensive antioxidants improves the anti-tumor immune response considerably at the preclinical level. We have also identified novel transcription factors (molecules capable to regulate the expression of hundreds of genes) that block the function of these potent T cells. We anticipate the genetic engineering of T cells aiming to disrupt these inhibitory networks will improve the anti-tumor immune response in the long term.
