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A rapid single-cell RNA-seq approach to identify neoantigen-specific T-cell receptors targeting tumor-specific mutations for use in gene-engineered T-cell immunotherapy

Accumulated evidence suggested that effective cancer immunotherapies were associated with neoantigen-reactive T cells, and adoptive transfer of neoantigen-reactive tumor infiltrating lymphocytes (TILs) could result in tumor regressions. To improve the efficacy of adoptive T-cell therapy targeting tu...

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Bibliographic Details
Published in:The Journal of immunology (1950) 2017-05, Vol.198 (1_Supplement), p.126-126.14
Main Authors: Lu, Yong-Chen William, Zheng, Zhili, Robbins, Paul F, Tran, Eric, Prickett, Todd D, Gartner, Jared J, Li, Yong F, Ray, Satyajit, Bliskovsky, Valery, Fitzgerald, Peter C, Rosenberg, Steven A
Format: Article
Language:English
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Summary:Accumulated evidence suggested that effective cancer immunotherapies were associated with neoantigen-reactive T cells, and adoptive transfer of neoantigen-reactive tumor infiltrating lymphocytes (TILs) could result in tumor regressions. To improve the efficacy of adoptive T-cell therapy targeting tumor-specific mutations, we have proposed a new therapeutic approach, which involves the genetic modification of autologous T cells with neoantigen-specific TCRs and the transfer of these T cells back to cancer patients. However, the current techniques to isolate neoantigen-specific TCRs are labor-intensive, time-consuming and technically challenging, not suitable for clinical applications. To facilitate this process, a new approach was developed, which included the co-culture of TILs with tandem minigene (TMG)-pulsed antigen-presenting cells, single-cell RNA-seq analysis of T cells and the identification of paired TCR sequences associated with cells expressing high levels of IFN-γ and IL-2 mRNA. In this study, TIL fragment cultures were grown from tumors resected from three patients with metastatic gastrointestinal cancers, and then were screened against TMG libraries encoding tumor-specific mutations identified by whole-exome sequencing. Following this new approach, three TCRs were identified, synthesized and cloned into a retroviral vector. These TCRs were then transduced into donor T cells, and these transduced T cells were shown to specifically recognize the following neoantigens encoded by the TMGs: USP8 (R667H), KRAS (G12D) and NBAS (C144S). In conclusion, this approach provides a rapid procedure to isolate neoantigen-specific TCRs for basic and translational research, as well as clinical applications.
ISSN:0022-1767
1550-6606
DOI:10.4049/jimmunol.198.Supp.126.14