Autologous hematopoietic stem cell transplantation (HSCT) is commonly employed for hematologic and non-hematologic malignancies. In clinical trials, HSCT has been evaluated for severe autoimmunity as a method to "reset" the immune system and produce a new, non-autoimmune repertoire. While the feasibility of eliminating the vast majority of mature T cells is well established, accurate and quantitative determination of the relationship of regenerated T cells to the baseline repertoire has been difficult to assess. Here, in a phase II study of HSCT for poor-prognosis multiple sclerosis, we used high-throughput deep TCRβ chain sequencing to assess millions of individual TCRs per patient sample. We found that HSCT has distinctive effects on CD4 + and CD8 + T cell repertoires. In CD4 + T cells, dominant TCR clones present before treatment were undetectable following reconstitution, and patients largely developed a new repertoire. In contrast, dominant CD8 + clones were not effectively removed, and the reconstituted CD8 + T cell repertoire was created by clonal expansion of cells present before treatment. Importantly, patients who failed to respond to treatment had less diversity in their T cell repertoire early during the reconstitution process. These results demonstrate that TCR characterization during immunomodulatory treatment is both feasible and informative, and may enable monitoring of pathogenic or protective T cell clones following HSCT and cellular therapies.
IntroductionWhen employed for immunomodulation, the goal of autologous hematopoietic stem cell transplantation (HSCT) is to create a non-autoreactive immune compartment by altering the immune repertoire and/or function of autoreactive cells (1-3). Using T cell receptor excision circle analysis in HSCT-treated MS patients, we showed previously that even in adults, thymic output contributed to the post-treatment TCR repertoire (2, 4) and that this, plus expansion of residual cells not eliminated during conditioning, regenerated the T cell compartment (5).However, the clonal specificities of a regenerated repertoire following high-dose immunosuppressive therapy (HDIT) and autologous HSCT have not been well explored, as previous studies used CDR3 spectratyping for TCR clonal analysis, which made it impractical to sequence more than several dozen TCRs. Only a single patient receiving HSCT for autoimmune disease (ankylosing spondylitis) has had a fuller analysis of their TCR repertoire reported (6). Here, as part of a new phase II trial for poor-prognosis MS (see Methods), we have taken advantage of high-throughput deep TCRβ chain sequencing (7) to directly assess millions of TCRs per individual before and at two time points after autologous HSCT in a cohort of 24 patients.