Characterization of Allogeneic T Cells Expressing Inducible Caspase-9 Following Adoptive Transfer in Children Receiving an HLA-Haploidentical Hematopoietic Stem Cell Transplant for the Treatment of Myeloid Malignancies

Background: Adoptive transfer of allogeneic donor T cells can be an effective treatment for hematological malignancies through recognition of leukemia-associated antigens (LAAs) on tumor cells or through alloreactivity. However, alloreactive T cells can also cause graft-versus-host disease (GvHD) limiting their use as an immunotherapy. To leverage the anti-tumor effects of allogeneic polyclonal T cells while minimizing GvHD, we have genetically modified donor T cells with the inducible caspase-9 (iC9) safety switch, which induces apoptosis following exposure to the small molecule ligand rimiducid. Here we show that iC9-modified allogeneic T cells (BPX-501) persist, expand and contain functional LAA-specific T cells in children receiving an alpha/beta TCR and CD19-depleted HLA-haploidentical hematopoietic stem cell transplant (haplo-HSCT) for the treatment of myeloid malignancies.

Methods: Pre-infusion products (BPX-501: donor T cells modified with the bicistronic retroviral vector encoding iC9 and truncated CD19 (ΔCD19)) and patient peripheral blood mononuclear cells (PBMCs) were analyzed from twelve patients (AML (10), MDS (1), JMML (1)) receiving BPX-501 (1x10⁶ cells/kg) following an alpha/beta T cell and CD19 B cell-depleted haplo-HSCT (BP-004U: NCT03301168). Engraftment and persistence were measured by coexpression of CD3 and CD19 by flow-cytometry. Endogenous and gene-modified T cells were also phenotyped for CD4:CD8 ratios, memory cell composition (T_N, T_CM, T_EM, T_EMRA; CD45RA and CD62L) and T cell receptor Vβ diversity. BPX-501 products and post-treatment samples were characterized for LAA-specific T cells using IFN-γ ELISpot against peptide pools (15 aa overlapping by 5 aa) derived from WT1, PRAME, MAGE (A1, C1, C3), NE and PR3, with and without exposure to 10 nM rimiducid to determine the anti-leukemic contribution of BPX-501.

Results: BPX-501 was infused at a median time of 22.5 days after HSCT (range 12-34, one patient was infused at day 89 and one patient was infused at day 147). BPX-501 cells (CD3⁺CD19⁺) were detectable in the peripheral blood at 1-2 weeks after infusion in all 12 patients, reaching a peak expansion frequency of a median of 24% ± 17% of total CD3⁺ T cells, and an absolute cell number of 66.9 ± 112 cells/µl at 2 months post-infusion and could be detected for up to 24 months. BPX-501 T cells showed a CD8-skewed phenotype whereas endogenous T cells exhibited a more balanced CD4:CD8 ratio. BPX-501 were predominantly CD45RA^-CD62L⁺ and CD45RA^-CD62L^- central and effector memory T cells, respectively. In BPX-501 products, we detected LAA-specific T cells by ELISpot using overlapping peptide pools to WT1, PRAME, MAGE, NE and PR3, and in peripheral blood samples obtained 2 to 5 months post-T cell infusion. Importantly, LAA-reactivity was greatly diminished with exposure to iC9-activating rimiducid. Further, we measured the TCR Vβ usage and observed highly-skewed TCR repertoire in BPX-501 T cells compared to endogenous T cells in 6 months after HSCT indicating selection and expansion of TCR clones. Three patients engrafted BPX-501 were treated with rimiducid to control GvHD resulting in a rapid decrease (62% ± 12%) of CD3⁺CD19⁺ T cells in the peripheral blood. In patients treated with rimiducid, CD3⁺CD19⁺ T cells recover without further instances of GvHD suggestive of in vivo depletion of alloreactive T cell clones using iC9.

Summary: Allogeneic T cells engineered with the iC9 safety switch engraft, expand and demonstrate long-term persistence following adoptive transfer into patients receiving a haplo-HSCT. LAA-specific T cells and alloreactive T cells within the BPX-501 product are detectable in the peripheral blood following infusion and likely contribute to elimination of myeloid malignancies.