Characteristics of Post-Infusion Chimeric Antigen Receptor (CAR) T Cells and Endogenous T Cells Associated with Early and Long-Term Response in Lisocabtagene Maraleucel (liso-cel)-Treated Relapsed or Refractory (R/R) Large B-Cell Lymphoma (LBCL)
Authors: Thorpe Jerill , Jiang Yue , Rytlewski Julie A , Kostic Ana , Kim Yeonhee , Peiser Leanne 
Published: November 2021

Abstract
Background: Liso-cel is an autologous, CD19-directed, defined composition, 4-1BB CAR T cell product administered at equal target doses of CD8 + and CD4 + CAR + T cells. In the pivotal TRANSCEND NHL 001 study (NCT02631044) in patients (pts) with R/R LBCL after ≥ 2 prior lines of therapy, liso-cel demonstrated significant clinical activity with an objective response rate of 73%, complete response (CR) rate of 53%, and median duration of response (DOR) not reached at 12 months' median DOR follow-up, and a low incidence of severe cytokine release syndrome (2%) and neurological events (10%; Abramson et al. Lancet 2020;396:839-852). While CAR T cells have shown remarkable efficacy in treating LBCL, with a well-understood mechanism of direct CAR T cell tumor killing, the contribution of the endogenous immune system in this response is currently unclear. Previously, histologic and gene expression analysis of pre- and posttreatment tumor biopsies from pts who received liso-cel in TRANSCEND NHL 001 showed a relationship between tumor-infiltrating CAR-negative (endogenous) T cells and early and durable response [Reiss et al. Blood 2019;134(suppl 1):202].
Here we examine, by gene expression and flow cytometry, post-infusion characteristics of liso-cel and peripheral endogenous T cells in pts from TRANSCEND NHL 001 with early (CR at 1 or 3 months) and long-term (CR at 9 or 12 months) response versus pts with progressive disease (PD) before or at the same time points.
Methods: CAR and endogenous T cells were assayed using a novel cell-sorting and low-input RNA-seq method. CAR and endogenous T cells were isolated from peripheral blood mononuclear cell samples from 39 pts at time to maximum concentration of liso-cel (T max; Day 8-22), 1 month, and 2 months after liso-cel infusion. In addition, samples from 44 pts were assayed only at T max by RNA-seq. A subset of these samples was assessed by flow cytometry for expression of the T cell differentiation markers CD4, CD8, CD45RA, CCR7, CD27, and CD28.
All RNA-seq analyses were performed in R version 4.0.2. Differential expression analysis was performed with the DESeq2 package with gene set enrichment analysis using clusterProfiler and GSVA packages with gene sets obtained from MSigDB. Comparisons of 2 groups were made with a Wilcoxon rank sum test. Association with the time-to-event outcome of progression-free survival (PFS) was assessed using Cox proportional hazards model or log rank test.
Results: Characteristics consistent with less differentiated CAR T cells and endogenous T cells were significantly associated with early and long-term response. Elevated CAR T cell expression of CD27 at T max was associated with CR at 1 month and longer PFS. Expression of CCR7 by CAR T cells at 1 and 2 months was associated with CR at 9 months. Additionally, at T max, gene sets associated with T cell effector differentiation and metabolism were enriched in CAR T cells from pts with early relapse (pts with CR vs PD at 3 months).
In endogenous T cells, elevated expression of CCR7 and CD28 at T max was associated with early response (CR at 1 and 3 months). Additionally, expression of CCR7 and CD28 in T cells isolated at 1 and 2 months was associated with long-term response (CR at 9 and 12 months). Furthermore, expression of the immune checkpoint receptor LAG3 by endogenous T cells was associated with PD from month 3 to month 12.
Conclusions: In summary, the data from our study show the relationship between CAR T cell differentiation status and achieving response over time, and provide new evidence for the involvement of endogenous T cells in the therapeutic efficacy of CAR T cell therapy.

Disclosures
Thorpe: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company. Jiang: Bristol Myers Squibb: Ended employment in the past 24 months. Rytlewski: Adaptive Biotechnologies: Current equity holder in publicly-traded company, Divested equity in a private or publicly-traded company in the past 24 months; Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company, Patents & Royalties. Kostic: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company. Kim: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company. Peiser: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company.