Adoptive T cell therapy with pathogen specific T cells for the treatment of immune deficiency following allogeneic haemopoietic stem cell transplant (HSCT) has shown clinical efficacy with little toxicity. Graft manipulation strategies and adoptive cell transfer after HSCT are ever more complex but the biological effects are not well understood. Small patient numbers and complex clinical features pose significant challenges.
We have employed high dimensional mass cytometry and a bioinformatics pipeline to study immune reconstitution in recipients of allogeneic HSCT with and without adoptive T cell therapy using a 37 marker panel producing 75 gated canonical cell subsets per patient sample. We have used bioinformatics tools including t-stochastic neighbour embedding (t-SNE), principle component analysis (PCA) and unsupervised consensus clustering algorithm SC3 to analyse this large dataset. Immunological profiles have been identified that are influenced by clinical parameters such as transplant conditioning, donor source, T cell depletion and post-transplant events, in particular, CMV reactivation, adoptive T cell transfer of pathogen specific T cells and time post-transplant. Immune recovery within each individual can be visualised in detail using spanning-tree progressive algorithm of density normalised events (SPADE) or visualisation of t-SNE (ViSNE).
The system level immunological changes form cell therapy interventions can be understood using mass cytometry immune profiling. This technology has numerous potential applications in cancer immunotherapy.