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BackgroundCellular immunotherapies using autologous tumor-infiltrating lymphocytes (TIL) can induce durable regression of epithelial cancers in selected patients with treatment-refractory metastatic disease. As the genetic engineering of T cells with tumor-reactive T-cell receptors (TCRs) comes to the forefront of clinical investigation, the rapid, scalable, and cost-effective detection of patient-specific neoantigen-reactive TIL remains a top priority.MethodsWe analyzed the single-cell transcriptomic states of 31 neoantigen-specific T-cell clonotypes to identify cell surface dysfunction markers that best identified the metastatic transcriptional states enriched with antitumor TIL. We developed an efficient method to capture neoantigen-reactive TCRs directly from resected human tumors based on cell surface co-expression of CD39, programmed cell death protein-1, and TIGIT dysfunction markers (CD8+ TILTP).ResultsTILTP TCR isolation achieved a high degree of correlation with single-cell transcriptomic signatures that identify neoantigen-reactive TCRs, making it a cost-effective strategy using widely available resources. Reconstruction of additional TILTP TCRs from tumors identified known and novel antitumor TCRs, showing that at least 39.5% of TILTP TCRs are neoantigen-reactive or tumor-reactive. Despite their substantial enrichment for neoantigen-reactive TCR clonotypes, clonal dynamics of 24 unique antitumor TILTP clonotypes from four patients indicated that most in vitro expanded TILTP populations failed to demonstrate neoantigen reactivity, either by loss of neoantigen-reactive clones during TIL expansion, or through functional impairment during cognate neoantigen recognition.ConclusionsWhile direct usage of in vitro-expanded CD8+ TILTP as a source for cellular therapy might be precluded by profound TIL dysfunction, isolating TILTP represents a streamlined effective approach to rapidly identify neoantigen-reactive TCRs to design engineered cellular immunotherapies against cancer.

BackgroundAdoptive transfer of T-cell receptor-engineered T cells (TCR-T cells) has shown promising efficacy in solid tumor treatment, but achieving clinical benefit typically requires infusion of tens of billions of cells. The commonly used rapid expansion protocol (REP), based on the CD3-agonistic OKT3 antibody and irradiated allogeneic feeder cells, exponentially expands tumor-infiltrating lymphocytes (TILs). However, the effect of REP on TCR-T cell frequency and phenotype remains unclear. This study aimed to evaluate the impact of REP on TCR-T cells and to assess the potential of a neoantigen-specific stimulation platform, NeoExpand, as a strategy to selectively expand TCR-T cells with favorable phenotypes.MethodsWe compared the effects of REP and NeoExpand on the frequency, yield, and phenotype of TCR-T cells engineered against shared neoantigens. Various autologous antigen-presenting cell (APC) types, including dendritic cells and bulk peripheral blood mononuclear cells (PBMCs), were tested as stimulators in NeoExpand. Additionally, we combined NeoExpand with CD3 activation, with or without allogeneic feeders, to improve scalability. The role of exogenous interleukin (IL)-21 in shaping TCR-T cell phenotypes was also investigated.ResultsREP impaired the frequency and phenotype of TCR-T cells, particularly CD4+ and CD8+ subsets matched to their engineered TCRs. In contrast, NeoExpand selectively increased TCR-T cell frequency and improved their phenotypes but did not consistently achieve higher total yields compared with REP. Among the tested autologous APCs, PBMCs effectively supported selective expansion. Further optimization using PBMCs as APCs revealed that combining NeoExpand with CD3 activation enabled exponential expansion without compromising selectivity. Inclusion of IL-21 during NeoExpand promoted a naïve/stem-like phenotype in CD8+ TCR-T cells, with minimal effect on CD4+ TCR-T cells.ConclusionsThese findings demonstrate that NeoExpand enables selective expansion of TCR-T cells while preserving favorable phenotypes and scalability. The approach supports further clinical evaluation of NeoExpand as a strategy to generate high-quality TCR-T cell products for adoptive cell therapy.

BackgroundThe use of tumor-infiltrating T lymphocytes (TIL) that recognize cancer neoantigens has led to lasting remissions in metastatic melanoma and certain cases of metastatic epithelial cancer. For the treatment of the latter, selecting cells for therapy typically involves laborious screening of TIL for recognition of autologous tumor-specific mutations, detected through next-generation sequencing of freshly resected metastatic tumors. Our study explored the feasibility of using archived formalin-fixed, paraffin-embedded (FFPE) primary tumor samples for cancer neoantigen discovery, to potentially expedite this process and reduce the need for resections normally required for tumor sequencing.MethodWhole-exome sequencing was conducted on matched primary and metastatic colorectal cancer samples from 22 patients. The distribution of metastatic tumor mutations that were confirmed as neoantigens through cognate TIL screening was evaluated in the corresponding primary tumors. Mutations unique to primary tumors were screened for recognition by metastasis-derived TIL and circulating T lymphocytes.ResultsWe found that 25 (65.8%) of the 38 validated neoantigens identified in metastatic tumors from 18 patients with colorectal cancer were also present in matched primary tumor samples. This included all 12 neoantigens encoded by putative cancer driver genes, which are generally regarded as superior targets for adoptive cell therapy. The detection rate for other neoantigens, representing mutations without an established role in cancer biology, was 50% (13/26). Gene products encoding neoantigens detected in the primary tumors were not more likely to be clonal or broadly distributed among the analyzed metastatic lesions compared with those undetected in the primary tumors. Additionally, we found that mutations detected only in primary tumor samples did not elicit recognition by metastatic tumor-derived TIL but could elicit specific recognition by the autologous circulating memory T cells.ConclusionsOur findings indicate that primary FFPE tumor-derived screening libraries could be used to discover most neoantigens present in metastatic tumors requiring treatment. Furthermore, this approach can reveal additional neoantigens not present in resected metastatic tumors, prompting further research to understand their clinical relevance as potential therapeutic targets.