An Efficient Single-Cell RNA-Seq Approach to Identify Neoantigen-Specific T Cell Receptors

Yong Chen Lu, Zhili Zheng, Paul F. Robbins, Eric Tran, Todd D. Prickett, Jared J. Gartner, Yong F. Li, Satyajit Ray, Zulmarie Franco, Valery Bliskovsky, Peter C. Fitzgerald, Steven A. Rosenberg

Research output: Contribution to journalArticlepeer-review

32 Scopus citations


The adoptive transfer of neoantigen-reactive tumor-infiltrating lymphocytes (TILs) can result in tumor regression in patients with metastatic cancer. To improve the efficacy of adoptive T cell therapy targeting these tumor-specific mutations, we have proposed a new therapeutic strategy, which involves the genetic modification of autologous T cells with neoantigen-specific T cell receptors (TCRs) and the transfer of these modified 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)-transfected or peptide-pulsed autologous antigen-presenting cells (APCs) and the single-cell RNA sequencing (RNA-seq) analysis of T cells to identify paired TCR sequences associated with cells expressing high levels of interferon-γ (IFN-γ) and interleukin-2 (IL-2). Following this new approach, multiple TCRs were identified, synthesized, cloned into a retroviral vector, and then transduced into donor T cells. These transduced T cells were shown to specifically recognize the neoantigens presented by autologous APCs. In conclusion, this approach provides an efficient procedure to isolate neoantigen-specific TCRs for clinical applications, as well as for basic and translational research. The identification of antigen-specific T cell receptors (TCRs) is a complicated process, which is technically challenging and not suitable for clinical applications. To simplify this process, Lu and colleagues developed an efficient single-cell approach, which can significantly reduce the labor and time for the TCR isolation.

Original languageEnglish (US)
Pages (from-to)379-389
Number of pages11
JournalMolecular Therapy
Issue number2
StatePublished - Feb 7 2018
Externally publishedYes


  • cancer immunotherapy
  • gene therapy
  • single cell

ASJC Scopus subject areas

  • Molecular Medicine
  • Molecular Biology
  • Genetics
  • Pharmacology
  • Drug Discovery


Dive into the research topics of 'An Efficient Single-Cell RNA-Seq Approach to Identify Neoantigen-Specific T Cell Receptors'. Together they form a unique fingerprint.

Cite this