Treatment-Free Intervals during CD19xCD3 BiTE ® Construct-Mediated T-Cell Stimulation Induce Functional Reinvigoration and Transcriptional Reprogramming of Exhausted T Cells
Authors: Zieger Nora , Kazerani Pasikhani Maryam , Straub Tobias , Nicholls Alyssa , Hänel Gerulf , Wulf Jan , Scheurer Michaela , Nixdorf Daniel , Sponheimer Monika , Lacher Sonja M , Brauchle Bettina , Marcinek Anetta , Rohrbacher Lisa , Leutbecher Alexandra , von Bergwelt Michael , Spiekermann Karsten , Weigert Oliver , Theurich Sebastian , Buecklein Veit L , Kischel Roman , Subklewe Marion 
Published: November 2021

Abstract
Blinatumomab is a bispecific T-cell engager (BiTE ®) construct approved for treatment of relapsed/refractory (r/r) B-cell precursor acute lymphoblastic leukemia (BCP-ALL). It is applied as continuous infusion over 28 days and induces remissions in 43 % of r/r patients. Responses correlated to T-cell expansion (Topp et al. 2011, Zugmaier et al. 2015). Mimicking the clinical application in an in vitro model system, we showed previously that continuous stimulation (CONT) with AMG 562, a half-life extended CD19xCD3 BiTE ® construct, induces T-cell exhaustion, as seen in chronic infections. Also, we could enhance T-cell function in vitro by treatment-free intervals (TFI) (Zieger et al. ASH 2020). To identify genetic drivers of enhanced T-cell function that could provide anti-exhaustion targets for clinical use, we aimed to characterize the transcriptome of exhausted vs rested T cells by bulk RNA sequencing of CONT and TFI T cells.

To simulate CONT vs TFI AMG 562 stimulation, cocultures of healthy donor T cells and CD19 + OCI-Ly1 cells were set up for 28 days under CONT or TFI (7 days on/7 days off) AMG 562 exposure. On day 0, 7, 14 and 21, we sorted 5x10 5 CD3 + T cells for transcriptome assessment (n=3). In parallel, function of TFI vs CONT T cells was analyzed in vitro: (1) AMG 562-mediated killing was evaluated as specific lysis of CD19 + Ba/F3 cells after 72h, (2) T-cell expansion during the killing assay was calculated as fold change (FC) of CD2 + counts, (3) AMG 562-mediated cytokine secretion was evaluated via intracellular staining.

We could confirm that function of Day 14 TFI vs CONT T cells was significantly enhanced (% specific lysis: TFI=99±2.2, CONT=34±4.2, p&lt;0.0001; T-cell expansion as FC: TFI=4±0.8, CONT=1±0.6, p&lt;0.01; Granzyme B MFI ratio of CD8 +: TFI=451±168, CONT=144±33, p&lt;0.0001). RNA sequencing and differentially expressed gene (DEG) analysis of Day 14 TFI vs CONT T cells identified 1902 significantly up- and 2603 downregulated genes (p adj&lt;0.05). Unsupervised clustering of the top 100 DEG showed striking similarity in gene expression patterns in unstimulated (Day 0) and Day 14 TFI vs CONT T cells. Intriguingly, genes related to memory and stemness were highly enriched on Day 0 and Day 14 TFI (TCF7, IL7R, SELL). Among the top downregulated genes in Day 14 TFI vs CONT T cells, we identified genes related to cell cycle (CCNB1, CDK1) and activation (IL2RA). Exhaustion-associated genes were significantly downregulated in Day 14 TFI vs CONT T cells (LAG-3, PDCD1, NR4A3, IRF4). Pathway analysis of Day 14 TFI vs CONT T cells confirmed downregulation of cell cycle (G2M checkpoint, normalized enrichment score (NES)=-2.47, E2F Targets, NES=-2.64; p adj=6.3E -10) and metabolism (MTORC1 signaling, NES=-2.27, OXPHOS, NES=-2.03; p adj=6.3E -10). Gene set enrichment analysis (GSEA) also showed reduction of effector compared to memory-related genes in Day 14 TFI vs CONT (GSE9650, NES=-1.95, FDR q=0.0).
After restimulation of TFI T cells with AMG 562 (Day 21 TFI) we observed higher effector function in TFI vs CONT T cells (% specific lysis, TFI=51±8, CONT=23±7, p&lt;0.0001). DEG analysis of Day 21 TFI vs CONT identified 1417 significantly up- and 1821 downregulated genes (p adj&lt;0.05). Unsupervised clustering of the top 100 DEG revealed a unique gene set in Day 21 CONT T cells enriched in apoptosis-related genes (TRAF1, ELAPOR1, BMF). Among the top upregulated genes in Day 21 TFI T cells were genes involved in activation and growth (DPP4, SLC3A2) and cell cycle (CDK1, PLK1), induced by AMG 562 restimulation after TFI. Exhaustion-related genes were downregulated in Day 21 TFI vs CONT T cells (LAG-3, BTLA, NFATC1). Remarkably, identical pathways downregulated on Day 14 TFI were enriched in Day 21 TFI T cells (G2M checkpoint, NES=2.63, MTORC1 signaling, NES=2.36, OXPHOS, NES=2.42; p adj=7.1E -10). Accordingly, GSEA showed enrichment of effector- rather than memory-related genes on Day 21 TFI vs CONT (GSE9650, NES=1.75, FDR q=0.0).
Together, our data suggest that TFI functionally and transcriptionally rejuvenates T cells. Upon restimulation (Day 21 TFI), T cells reengage an effector program and are less exhausted compared to CONT T cells. In future analyses we will correlate RNA expression levels to functional traits using whole genome co-expression network analysis (WGCNA). Thereby we aim to identify gene clusters critical for persistent T-cell function that might serve as targets to improve efficacy of T-cell based immunotherapies.
Figure 1 Figure 1.

Disclosures
Lacher: Roche: Research Funding. Brauchle: Adivo: Current Employment. von Bergwelt: Kite/Gilead: Honoraria, Research Funding, Speakers Bureau; Miltenyi: Honoraria, Research Funding, Speakers Bureau; MSD Sharpe & Dohme: Honoraria, Research Funding, Speakers Bureau; Roche: Honoraria, Research Funding, Speakers Bureau; Mologen: Honoraria, Research Funding, Speakers Bureau; Novartis: Honoraria, Research Funding, Speakers Bureau; Astellas: Honoraria, Research Funding, Speakers Bureau; BMS: Honoraria, Research Funding, Speakers Bureau. Weigert: Janssen: Speakers Bureau; Epizyme: Membership on an entity's Board of Directors or advisory committees; Roche: Research Funding. Theurich: Amgen: Consultancy, Honoraria; BMS/Celgene: Consultancy, Honoraria; GSK: Consultancy, Honoraria; Janssen: Consultancy, Honoraria; Pfizer: Consultancy, Honoraria; Sanofi: Consultancy, Honoraria; Takeda: Consultancy, Honoraria. Buecklein: Miltenyi: Research Funding; Novartis: Consultancy, Other: congress and travel support, Research Funding, Speakers Bureau; BMS/Celgene: Consultancy, Research Funding; Pfizer: Consultancy, Honoraria, Speakers Bureau; Amgen: Consultancy, Honoraria; Kite/Gilead: Consultancy, Honoraria, Other: Congress and travel support, Research Funding. Kischel: Amgen GmbH Munich: Current Employment. Subklewe: Klinikum der Universität München: Current Employment; Takeda: Speakers Bureau; Pfizer: Consultancy, Speakers Bureau; Janssen: Consultancy; Seattle Genetics: Consultancy, Research Funding; Roche: Research Funding; Novartis: Consultancy, Research Funding, Speakers Bureau; MorphoSys: Research Funding; Miltenyi: Research Funding; Gilead: Consultancy, Research Funding, Speakers Bureau; Amgen: Consultancy, Research Funding, Speakers Bureau; BMS/Celgene: Consultancy, Research Funding, Speakers Bureau.