Abstract 25: Multimodal single-cell analysis of lifileucel tumor-infiltrating lymphocyte (TIL) product identifies additional high-resolution potential features

Abstract

Abstract Introduction: Autologous TIL cell therapies such as lifileucel have demonstrated durable responses in patients (pts) with various solid tumors including melanoma and lung cancer. The TIL drug product (DP) phenotype was previously assessed and extensively characterized based on the bulk population. The current research further characterizes the TIL DP at a single-cell level using high-dimension multimodal sequencing and explores features that have a potential to inform future development of TIL therapies. Methods: Manufactured lifileucel TIL DP from 20 pts (best overall response [BOR]: 6 complete response [CR], 4 partial response, 5 stable disease, 5 progressive disease [PD]) from the registrational melanoma C144-1 trial were analyzed using single-cell RNA and T-cell receptor (TCR) sequencing, resulting in 153K single-cell transcriptomes. To aid with cell-type annotation, 130 surface proteins on TIL DP samples from a subset of 4 pts (BOR: 2 CR, 2 PD) were detected via Cellular Indexing of Transcriptomes and Epitopes by sequencing. Multimodal weighted nearest-neighbor analysis combined with manual cluster annotation (via known marker genes and proteins), cell-type-specific gene signatures, and automated annotation were used to develop a single-cell TIL (scTIL) reference map, resulting in high-resolution subsets of cells. TCR clonotypes from lifileucel TIL DP were compared to those from respective pretreatment tumors previously identified by bulk TCR sequencing. Results: Mapping of the full dataset to the novel scTIL reference revealed a CD8+ TIL-dominant composition of responder TIL DP. TIL from pts with BOR PD exhibited reduced CD8+ effector memory (Tem)-like and resident memory (Trm)-like T cells. Differential expression analysis showed that responder CD8+ TIL had increased expression of TCR signaling genes while responder CD4+ TIL exhibited gene expression consistent with a more cytotoxic-like phenotype. Relative to responders, CD8+ TIL of pts with BOR PD had lower expression of the CD39−CD69− (stem-like) gene signature and higher expression of the CD39+CD69+ (terminal differentiation) gene signature. Pseudotime trajectory analysis found that both CD8+ and CD4+ TIL of pts with BOR PD were more terminally differentiated. Single-cell TCR sequencing revealed that CD8+ T-cell clusters had greater clonal overlap than CD4+ T-cell clusters. Expanded clonotypes in pretreatment tumor tissues were more prevalent in TIL TCR repertoires of responders and were more likely to be expressed by CD8+ (specifically CD8+ Tem- and Trm-like TIL) than CD4+ T cells. Conclusions: Collectively, these results shed additional light on the cellular and molecular characteristics of ex vivo expanded lifileucel TIL DP and signal additional features with a potential to guide future TIL product development. Citation Format: Joe Dean, Joe Yglesias, Hequn Yin, Rongsu Qi. Multimodal single-cell analysis of lifileucel tumor-infiltrating lymphocyte (TIL) product identifies additional high-resolution potential features [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 25.