To characterize activation gene signatures and T-Cell Receptor (TCR) repertoire of ATA188 allogeneic EBV-specific T cells.

Accumulating evidence indicates that Epstein-Barr virus (EBV) is implicated in the development of MS. We have developed a novel allogeneic T-cell therapy targeting EBV-encoded antigens, ATA188, that has shown safety and initial efficacy in Progressive MS patients (NCT03283826). Transcriptional and TCR-repertoire profiling of ATA188 T cells was employed to delineate activated gene sets, molecular signatures and underlying functional pathways associated with effector cell function and therapeutic potential.

ATA188 T cells were profiled with a curated 326-gene panel using the NanoString nCounter® platform. Total RNA from control and antigen-activated EBV-specific CD8+ T cells were sorted following EBV stimulation, sequenced, and analyzed. Individual genes differentially expressed were identified and further subjected to enrichment analyses. Additionally, deep TCRβ chain sequencing (TCR-seq) was conducted to define TCR clonal diversity and identity in ATA188 cells.

Despite being derived from unrelated healthy donors, the ATA188 T cells showed considerable concordance in expression profiles (Spearman>0.80; p<E-10) within the resting and activated states. In total, significantly differentially expressed genes (fold change>1.5, p<0.01) were identified, representing a distinct activation signature for ATA188 cells. The activated states in-part identified upregulation of IL-2, IFNG, XCL1, CCL4, CSF2, TNFRSF9, and downregulation of KLF2. These were consistent with activation (p<E-05) of cytokine-receptor, JAK-STAT, T-cell receptor, and chemokine signaling pathways. Finally, TCR-seq analysis showed that ATA188 cells contain varying EBV-specific TCR clonotypes associated with specific restriction through one or more HLA alleles.

Transcriptional and TCR repertoire profiling of ATA188 revealed T-cell-intrinsic signatures and clonotypes associated with defined EBV-specific TCR repertoire, EBV-specific T-cell activation, and functional signaling pathways. These combined analyses of T cells comprising ATA188 are consistent with its proposed mechanism of targeting EBV infected B cells by recognizing MS-relevant EBV antigens on these cells via defined TCRs.