Neoantigen-specific CD4+ tumor-infiltrating lymphocytes are potent effectors identified within adoptive cell therapy products for metastatic melanoma patients

BACKGROUND

Adoptive cell therapy (ACT) with tumor-infiltrating lymphocytes (TILs) is a promising immunotherapeutic approach for patients with advanced solid tumors. While numerous advances have been made, the contribution of neoantigen-specific CD4+T cells within TIL infusion products remains underexplored and therefore offers a significant opportunity for progress.

METHODS

We analyzed infused TIL products from metastatic melanoma patients previously treated with ACT for the presence of neoantigen-specific T cells. TILs were enriched on reactivity to neoantigen peptides derived and prioritized from patient sample-directed mutanome analysis. Enriched TILs were further investigated to establish the clonal neoantigen response with respect to function, transcriptomics, and persistence following ACT.

RESULTS

We discovered that neoantigen-specific TIL clones were predominantly CD4+ T cells and were present in both therapeutic responders and non-responders. CD4+ TIL demonstrated an effector T cell response with cytotoxicity toward autologous tumor in a major histocompatibility complex class II-dependent manner. These results were validated by paired TCR and single cell RNA sequencing, which elucidated transcriptomic profiles distinct to neoantigen-specific CD4+ TIL.

CONCLUSIONS

Despite methods which often focus on CD8+T cells, our study supports the importance of prospective identification of neoantigen-specific CD4+ T cells within TIL products as they are a potent source of tumor-specific effectors. We further advocate for the inclusion of neoantigen-specific CD4+ TIL in future ACT protocols as a strategy to improve antitumor immunity.

Abstract 4049: TIDAL-01: A selected TIL process that enriches for neoantigen reactive TIL in solid tumors

Background: Tumor infiltrating lymphocyte (TIL) therapy is capable of mediating durable complete responses in melanoma. While solid tumors such as colorectal cancer (CRC), non-small cell lung cancer (NSCLC), ovarian and breast have been shown to contain neoantigen reactive TIL, the success of bulk TIL therapy in these tumors has been limited. Enhancing tumor reactivity through the selective expansion of neoantigen-reactive subpopulations, has demonstrated success in cancers outside of melanoma underscoring the potential of a neoantigen selected TIL approach in indications with lower tumor mutational burdens. Here we demonstrate that the TIDAL-01 process, which utilizes tumor-specific mutation containing peptides to select neoantigen reactive TIL produces TIL products significantly enriched in neoantigen reactivity.

Methods: Fresh tumors were cut into fragments or dissociated and cultured in a primary expansion (preREP). Antigen presenting cells (APCs) were isolated and expanded from patient matched blood. Whole exome and RNA sequencing was performed on tumor tissue and autologous PBMCs and used to predict and prioritize neoantigen mutations. Peptides encoding the mutations were synthesized, loaded onto APCs and co-cultured with autologous TIL. Neoantigen reactive TIL were selected by fluorescence activated cell sorting (FACS), based on the upregulation of the activation markers CD134 and CD137 and expanded with a rapid expansion protocol (REP). Bulk and unselected TIL were expanded alongside for comparison. Neoantigen reactivity was quantified and deconvoluted by cytokine secretion, degranulation, upregulation of CD134/CD137 by flow and when practical, killing of autologous tumor cell lines or organoids.

Results: Successful TIL expansion was achieved in 31/34 (91%) tumors (14/17 CRC, 10/10 NSCLC, 3/3 ovarian and 3/3 melanoma) using both tumor fragments and dissociated tumors. CRC tumors accounted for half of the samples (17/34), and the tumor mutational burden within these samples varied substantially, ranging from 229 to 5436 mutations. Upregulation of CD134 and CD137 and increased IFN-γ production was observed in all samples upon co-culture with peptide loaded APCs. Peptide restimulation and deconvolution revealed that the TIDAL-01 process is capable of enriching for both CD4 and CD8 reactivities. Selected TIL products produced up to 50x more IFN-γ, TNF-α and Granzyme B than bulk TIL and at least 2x higher levels of degranulation, indicative of greater killing potential.

Conclusions: TIL from metastatic CRC, melanoma, NSCLC and ovarian tumors were successfully expanded from the majority of patients. Co-culture of TIL and peptide loaded APCs followed by FACS significantly enriched for neoantigen reactivity compared to bulk TIL, demonstrating the potential of the TIDAL-01 process to produce selected TIL products for the treatment of non-melanoma tumors.

Citation Format: Larissa A. Pikor, Antoine Bernard, Nathalie Brassard, Anna Fritzsche, Anna Kluew, Zachary K. Jilesen, Jake Nikota, Rohan Bareja, Christian Laing, David F. Stojdl, TJ Langer, Stewart Abbot, Barbara Sennino, Simon Turcotte. TIDAL-01: A selected TIL process that enriches for neoantigen reactive TIL in solid tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4049.

385 Identification and enrichment of neoantigen-reactive T cells to optimize adoptive cell transfer with tumor-infiltrating lymphocytes (TIL)

Background

Adoptive cell transfer (ACT) using tumor-infiltrating lymphocytes (TIL) has achieved an overall response rate of 39% in metastatic melanoma patients at Moffitt Cancer Center. In these trials, a substantial fraction of patients were non-responders by RECIST, but demonstrated a mixed response to therapy. These results suggest that the infused TIL product contained tumor-reactive T cells with therapeutic potential, which could be further optimized to improve ACT with TIL. We hypothesized that outcomes might be improved by identifying and enriching neoantigen-reactive TIL within bulk products. The purpose of this study is to define approaches to optimize ACT with TIL, by identifying, enriching, and analyzing neoantigen reactive TIL from the ACT infusion product of previously treated metastatic melanoma patients.

Methods

Patient-derived cryopreserved tumor tissue, PBMC, and TIL from completed metastatic melanoma TIL trials were used for this study. Whole exome and RNA sequencing were performed on DNA and RNA extracted from tumor tissue and compared to DNA from autologous PBMC. Genetic sequencing and gene expression data were utilized to determine protein-modifying somatic mutations. Peptides were then predicted for their ability to be presented on MHC molecules, prioritized, and up to 192 custom 25-mers were synthesized per patient sample. Neoantigen peptides were loaded onto patient-derived dendritic cells (DC) and co-cultured with autologous TIL. These TIL were then sorted by FACS on their ability to upregulate 41BB and OX40 and expanded through the rapid expansion protocol (REP). Enriched TIL were subsequently screened for neoantigen reactivity by 41BB/OX40 upregulation, cytokine release, and degranulation.

Results

Protein-altering somatic mutations from metastatic melanoma tissues ranged from 49 to 1631 mutations (median = 389). On average, 16.2% of TIL were sorted for upregulation of 41BB/OX40 upon co-culture with DC pulsed with the neoantigen peptide pool (range: 2.7–31.1%). CD4+ TIL displayed a 3.75-fold upregulation of 41BB/OX40, while CD8+ TIL saw a 1.88-fold increase (n=6). This coincided with substantial production of IFNγ, TNFα, and granzyme B (n=6). Neoantigen-reactive (41BB+/OX40+) and non-reactive (41BB-/OX40-) TIL expanded to similar degrees in REP (average of 639-fold vs. 611-fold; n=6). Restimulation of enriched neoantigen-specific TIL resulted in superior pro-inflammatory functionality (granzyme B, IFNγ, and TNFα) when compared to non-reactive TIL.

Conclusions

TIL from metastatic melanoma patient samples were successfully enriched for neoantigen-reactive TIL, which maintained increased reactivity against these predicted peptides upon restimulation when compared non-reactive TIL. These data support further investigation into the use of neoantigen-enriched TIL products to enhance efficacy of ACT.

Trial Registration

NCT01005745, NCT01659151, NCT01701674

Ethics Approval

NCT01005745 was approved by USF IRB approval number Ame5_107905.NCT01659151 was approved by Advarra IRB approval number 14.03.0083.NCT01701674 was approved by USF IRB approval number Ame13_Pro00009061.All participants gave informed consent before taking part.

384 An investigation into the role of CD4+ tumor-infiltrating lymphocytes (TIL) in metastatic melanoma patients with a complete response to adoptive cell therapy

Background

Immunotherapy for cancer has long been focused on the generation of CD8+ cytotoxic T lymphocyte responses, independent of their dynamic CD4+ T cell counterpart. One promising approach, adoptive cell transfer (ACT) of tumor-infiltrating lymphocytes (TIL), has yielded response rates ranging from 28–55%.1–2 Investigation into the role of CD4+ TIL in this setting remains critically underexplored as an opportunity to improve upon these successes.

Methods

Two metastatic melanoma patients (PT1 and PT2) were treated with TIL on a completed clinical trial at Moffitt Cancer Center (NCT01005745). Tumor recognition by TIL was assessed via co-culture with tumor. Whole exome (WES) and RNA Sequencing were performed on cryopreserved tumor sections and mutant peptide-MHC binding was predicted. TIL were stimulated with antigen presenting cells (APCs) loaded with neoantigen-derived 25mer peptides and sorted based on 41BB/OX40 upregulation, followed by functional immunologic assays. TCR sequencing was conducted on patient peripheral blood as well as isolated neoantigen-specific TIL clones to determine persistence in vivo and cognate peptide-MHC targets were determined empirically.

Results

PT1, infused with predominantly CD4+ TIL (88%), achieved a complete response (CR) despite lack of IFNγ detection with conventional in vitro tumor co-culture methods. Infusion product TIL were sorted by upregulation of OX40 and 41BB upon stimulation with APCs loaded with the mutant peptide pool. Neoantigen reactivity arose from a single peptide sequence, which conferred recognition by a CD4+ TIL clone, which comprised 17% of the infusion product and enriched to greater than 80% after sorting via FACS. These CD4+ TIL produced IFNγ, TNFα, and granzyme B in response to peptide-loaded APCs in an HLA-DR dependent manner. TCRβ overlap revealed this CD4+ clone peaked at two weeks post-infusion (40%) and persisted after infusion for at least six weeks. PT2 was infused with highly reactive, primarily CD8+ (88%) TIL and also achieved a CR. Isolated CD4+ TIL were also responsive to tumor antigens in the context of MHC Class II in vitro. Tumor-reactive CD4+ TIL were enriched by IFNγ capture and delayed xenograft growth in vivo (p<0.01). Neoantigen peptides stimulated predominantly CD4+ TIL to upregulate OX40/41BB and produce IFNγ, TNFα, and granzyme B.

Conclusions

Investigation of these case studies demonstrated evidence of CD4+ TIL involvement in complete clinical responses after ACT. Ongoing studies will define the precise role of tumor-reactive CD4+ T cells in the anti-tumor immune response and provide the framework for future investigation into their function and therapeutic efficacy.

Trial Registration

NCT01005745

References

Bailey SR, et al. Human CD26high T cells elicit tumor immunity against multiple malignancies via enhanced migration and persistence. Nat Commun 2017;8(1):1961.

Tran E, et al. Cancer immunotherapy based on mutation-specific CD4+ T cells in a patient with epithelial cancer. Science 2014;344(6184):641–5.

Ethics Approval

Approved by USF IRB approval number Ame5_107905. All participants gave informed consent before taking part.