Sensitive identification of neoantigens and cognate TCRs in human solid tumors

Marion Arnaud,Brian J Stevenson,Marta A S Perez,Petra Baumgaertner,Blanca Navarro Rodrigo,Daniel E Speiser,Philippe Guillaume,Lana E Kandalaft,Sara Bobisse,Florian Huber,Julien Schmidt,Vincent Zoete,Raphaël Genolet ,Melita Irving,Johanna Chiffelle,George Coukos,David Gfeller,Michal Bassani-Sternberg,Tu Nguyen-Ngoc,Morgane Magnin,Chloé Chong ,Alexandre Harari

doi:10.1038/s41587-021-01072-6

Abstract

The identification of patient-specific tumor antigens is complicated by the low frequency of T cells specific for each tumor antigen. Here we describe NeoScreen, a method that enables the sensitive identification of rare tumor (neo)antigens and of cognate T cell receptors (TCRs) expressed by tumor-infiltrating lymphocytes. T cells transduced with tumor antigen-specific TCRs identified by NeoScreen mediate regression of established tumors in patient-derived xenograft mice.

Highlights

As proof of principle, we first validated the contribution of the Neoscreen approach by interrogating TILs from two tumor specimens where we could readily identify four neoepitope reactivities among TILs expanded with IL-2
The location of CDR3α and CDR3β loops is shown by arrows. d, Violin plots display frequencies of TCRβ-A, TCRβ-B and TCRβ-C in bulk T cell receptors (TCRs) repertoires of the different TIL cultures and of the original tumor. e, Heat maps depict the frequencies of tumor antigen-specific TCRβ clonotypes (n = 50) within the different bulk TIL populations
P value was determined with a one-tailed paired t-test. g, Proportions of neoepitope- versus tumor-associated antigen (TAA)-specific TCRβ among enriched versus newly detected clonotypes. h, ACT of TCR-transduced T cells in autologous patient-derived xenograft tumor model. i, In vivo efficacy of adoptively transferred tyrosinase[508–514] TCR-transduced

Summary

Introduction

We first validated the contribution of the Neoscreen approach by interrogating TILs from two tumor specimens (patients 6 and 7; Supplementary Tables 1 and 4) where we could readily identify four neoepitope reactivities among (conventional) TILs expanded with IL-2. We purified tumor antigen-specific NeoScreen TILs using pMHC-multimers or 4-1BB upregulation and performed bulk TCRα and TCRβ sequencing of isolated T cells (Fig. 2a, Extended Data Fig. 6 and Supplementary Table 5).

Results

Conclusion