Clinical Response after Allogeneic CAR T Cell Therapy Is Linked to Expansion of Identical CD8+ Effector-like T Cell Clones

Efficacy of chimeric antigen receptor (CAR) T cell therapies relies on their ability to expand within the recipient. A detailed understanding of the mechanisms driving this process is difficult to obtain in the autologous setting due to the single-use, patient-derived nature of each infusion product (IP). Nevertheless, several studies have suggested that T cell phenotype in the IP plays a key role. Allogeneic products provide a unique opportunity to distinguish cell-intrinsic from cell-extrinsic mechanisms of CAR T cell expansion as a single lot may be administered to multiple recipients. We hypothesized that the cell-intrinsic molecular characteristics of individual T cell clones in the IP would lead to preferential expansion of some of these clones after infusion.

We identified patients with relapsed/refractory large B-cell lymphoma treated on the ALPHA-2 phase 1 trial (NCT04416984) with a single lot of ALLO-501A, a healthy donor-derived CD19 CAR T with T cell receptor (TCR) and CD52 knockout using Cellectis technologies. Among six patients showing robust expansion (median maximum CAR vector copy number 21,571; range 10,296-104,784), peak expansion occurred at day 14 and a high frequency (5/6 = 83%) of clinical responses was observed.

To understand the nature of the allogeneic CAR T cells expanding in these patients, we performed single-cell (sc) T-cell receptor (TCR)/RNA/surface protein (CITE)-seq on the IP and bulk TCRseq on post-treatment peripheral blood mononuclear cell (PBMC) samples. We identified preferentially expanding T cell clones by comparing the observed post-treatment frequencies and AUCs of each clone with expected values based on their IP frequencies in a first-order kinetic model. Interestingly, identical clones (93.8% CD8+) were observed to preferentially expand and contract in four expanders displaying oligoclonal expansion patterns. Overall, of the top 2000 IP clones, 81 expanding (in at least 3 out of 4 patients) and 27 contracting (in at least 2 out of 4 patients) clones were identified at the p < 0.05 level.

Of 10 transcriptional states (clusters) identified in the IP CD8+ T-cell scRNA-seq data, we identified one significantly enriched in expanding clones (odds ratio (OR) 5.66; p<1e-15) and three enriched in contracting clones (OR range 2.41-25.71; p<1e-15). Neither the proportion of CAR+ cells (p = 0.52) nor the level of CAR expression (p = 0.48) differed among these states, suggesting that distinct cell-intrinsic transcriptional programs may influence cell fate.

To elucidate these pathways, we compared the transcriptional profiles of expanding versus contracting clones. We observed that expanding clones exhibited higher expression of effector and differentiation markers including GZMK, GZMH, NKG7, and KLRG1; higher scores for “CD8+ cytotoxicity” (NES = 1.96, FDR = 0.0052), “NK-like activation” (NES = 1.77, FDR = 0.0053), and “effector memory” (Wilcoxon p = 7.35E-5); and lower “central memory” scores (Wilcoxon p < 2.2E-16) than contracting clones. Interestingly, analysis of the donor PBMCs used to generate the IP showed a similar phenotype among these clones, suggesting that this phenotype exists prior to manufacturing and is maintained throughout the manufacturing process.

In conclusion, we found that identical CD8⁺ clones exhibiting an effector-like phenotype preferentially expanded in multiple recipients after allogeneic CD19 CAR T cell treatment. To our knowledge, this is the first study to compare clonal expansion patterns among recipients of a single lot of allogeneic CAR T cells. The striking similarity of expansion patterns across recipients demonstrates the importance of cell-intrinsic transcriptional programs in driving cell expansion after CAR T cell infusion. Moreover, our data highlight clones with effector-like molecular states as a key subset which could mediate antitumor responses to allogeneic CAR T cell products. These findings, as well as the presence of this phenotype in donor PBMCs prior to manufacturing, carry important implications for future development of these therapies.