Characterization of CMV induced alpha/beta and gamma/delta T cells after allogeneic stem-cell
transplantation utilizing single cell RNA seq
Allogeneic stem cell transplantation (allo-SCT) remains the only curative option for
various high risk hematological malignancies. To reduce the risk of graft versus host disease, we
perform ex vivo αβT cell depletion before infusion, which is expected to result in an increased risk of
viral reactivations such as cytomegalovirus (CMV). We and others have previously shown that after
αβT cell depleted allo-SCT, early immune reconstitution and viral immunity relies predominantly on
γδT and NK cells. Here we study how CMV contributes to the development of the innate and adaptive
immune repertoires after T cell deplete and T cell replete allo-SCT.
Numerical reconstitution of αβT and γδT cells was analyzed in a retrospective cohort of
patients who had received an αβT cell depleted allo-SCT (n=146) or T cell replete allo-SCT (n=67).
For 30 αβT cell depleted allo-SCT patients, detailed flow cytometric analyses and next generation
sequencing of the δ and β chain were performed. Furthermore, we performed 5’ single cell RNA
sequencing (scRNAseq) on patient samples ~1 year after SCT. We included patients that had
undergone an αβT cell depleted allo-SCT (n=3) or T cell replete allo-SCT (n=3) and experienced a
CMV reactivation after allo-SCT.
In αβT cell depleted allo-SCT recipients both Vδ2- and Vδ2+ γδT cells reconstituted early,
reaching reference values within the first 100 days. CMV reactivation enhanced recovery of Vδ2- T
cells and CD8+ αβT cells. CD8+ αβT cell and Vδ1+ γδT cell expansion after CMV reactivation was
driven by CD27low Teffector cells. Interestingly, we observed that the dominance of Vδ2- γδT cells within
the γδT cell repertoire lasted up to 3 years after allo-SCT, resulting in an inversed ratio of Vδ2+/Vδ2-
γδT cells and associated with slow CD4+ αβT cell reconstitution. This was confirmed by 5’ scRNAseq
analyses 1 year post allo-SCT, where the major γδT cell population was Vδ2- and CD4+ αβT cells
were scarce.
Early immune reconstitution after αβ T cell depleted allo-SCT results in a marked
expansion of Vδ2- γδT cells and CD8+ αβT cells, which is further increased by CMV reactivation.
Moreover, the inversed ratio of Vδ2+/Vδ2- γδT cells in our cohort suggests Vδ2- γδT cells might
contribute as regulators to balance the immune system during the absence of CD4+ αβT cells.