Tumor Microenvironment Cellular Crosstalk Predicts Response to Adoptive TIL Therapy in Melanoma

Abstract

Adoptive cell therapy (ACT) using ex vivo expanded tumor-infiltrating T lymphocytes (TILs) can mediate responses in metastatic melanoma, but long-term efficacy remains limited to a fraction of patients. Here we interrogated tumor-microenvironment (TME) cellular states and interactions of longitudinal samples from 13 metastatic melanoma patients treated with TIL-ACT in our clinical study (NCT03475134). We performed single-cell RNA-seq and spatial proteomic analyses in pre- and post-ACT tumor tissues and showed that responders exhibited higher tumor cell-intrinsic immunogenicity. Also, endogenous CD8+ TILs and myeloid cells of responders were characterized by increased cytotoxicity, exhaustion and costimulation and type-I IFN signaling, respectively. Cell-cell interaction prediction analyses corroborated by spatial neighborhood analyses revealed that responders have rich baseline intratumoral and stromal tumor-reactive T-cell networks with activated myeloid populations. Successful TIL-ACT therapy further reprogrammed the myeloid compartment and increased TIL-myeloid networks. Our systematic target discovery study reveals CD8+ T-cell network-based biomarkers that could improve patient selection and guide the design of ACT clinical trials.

Tumor-reactive clonotype dynamics underlying clinical response to TIL therapy in melanoma

“…To gain insights into T-cell dynamics and the in vitro and in vivo fates of cells in the context of TIL-ACT, we interrogated deeply and longitudinally T cells in 13 metastatic melanoma patients who received TIL-ACT in a phase-I clinical trial (NCT03475134). The objective response rate (ORR) in this study was 46.2% (n=6/13) 25 . We examined, by integrated single-cell analyses, the profile of 122'000 T cells, and using bulk TCR-seq we tracked the dynamics of over 2.8x10 6 clonotypes.…”

“…The number of adoptively-transferred tumor-specific T cells predicts efficacy in preclinical models and clinical ACT studies [26][27][28] . For translational purposes, we classified patients as responders (Rs) when they had a complete or partial response (by RECIST criteria v1.1, n=6) vs. non-responders (NRs) when they experienced stable or progressive disease (n=7) 25 . We found that responding patients received more total T cells (Fig.…”

“…Taking advantage of the collection of scRNA/scTCR-seq data from the above validated tumor-reactive CD8 + clonotypes, we built a bestowed signature of tumor reactivity for TILs from our melanoma patients progressing after anti-PD1 or anti-PD1/CTLA-4 therapy 25 (Supplementary Table 3). This was concordant with reported signatures of tumor-specific 21 or neoantigen-specific cells [16][17][18] in melanoma or epithelial cancers (Extended Data Fig.…”

“…Among the 249 CD8 + TIL clonotypes characterized, 123 were proven tumor-specific, and these were indeed distributed across canonical exhausted (Tex), precursor-exhausted (Pex) and interferon-stimulated gene (ISG) states, although a large fraction of them were also effector- 25 (Fig. 4A).…”

Tertiary lymphoid structure-related immune infiltrates in NSCLC tumor lesions correlate with low tumor-reactivity of TIL products

“…Also for TIL therapy, first indications of the influence of the TME composition in generating TIL products have been collected. In melanoma patients, the T cell differentiation status was proposed to correlate with the efficacy of the TIL product 5,26 , and in a small cohort, a correlation with the activation status of macrophages and dendritic cells was observed 27 . For NSCLC-derived TIL products, such correlations with the immune cell infiltrates in tumor lesions have, to our knowledge, not yet been reported.…”