Description

Identification and evaluation of immune recognition towards mutation derived epitopes in non‑small cell lung cancer for cancer immunotherapy

Sunil Kumar Saini¹, Sofie Ramskov¹,Amalie Kai Bentzen¹, Rikke Lyngaa¹, James Reading², Andrew J.S. Furness^2,3, Charles A.Swanton⁴, Sergio A. Quezada^2,3, Sine Reker Hadrup¹

¹Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870 Frederiksberg C

²CRUK Lung Cancer Center of Excellence, UCL Cancer Institute, London, UK.

³Cancer Immunology Unit, University College London Cancer Institute, University College London, UK.

⁴The Francis Crick Institute, London, UK

Increasing evidence point to important role of mutation-derived antigens in immune recognition of cancer and their potential use in therapeutic approach towards cancer immunotherapy. For non-small cell lung cancer (NSCLC), we are focused on assessing immunoreactivity towards mutation derived antigens (neoantiges) from individual mutational landscape. We identified CD8 T-cells reactive to these neoantigens and suggested their correlation with genetic heterogeneity (McGranahan et al., Science 2016). Expanding on this, we are now analyzing neaontigen specific immunoreactivity with a larger patient cohort covering several different HLA types to understand and utilize neoantigens specific immune response for cancer immunotherapy. For this analysis, we employed a newly developed technology by our group that uses DNA-barcode labeled MHC multimers to detect multiple, potentially >1000 different neoepitope specific T-cell populations in a single sample (Bentzen et al., Nature Biotechnology, 2016).

We generated personalized neo-epitope libraries (varying from 150 to 500 epitopes per patient) based on tumor specific mutations, and used the multiplex technology to discover the T‑cell recognition of neoantigens. For a comparative analysis we used unexpanded tumor infiltrating lymphocytes (TILs), expanded TILs from NSCLC tumors, and peripheral blood mononuclear cells (PBMCs). We identified several CD8⁺ T‑cell responses toward neoantigens; interestingly primarily recognizing clonally expressed neoantigens. Furthermore, we found higher number of CD8⁺ T‑cell responses in unexpanded TILs as compared to expanded TILs, suggesting loss of potential antigenic response during the in-vitro expansion of TILs. In conclusion, we demonstrate here the use of new multiplex technology to screen large neoepitope libraries by successfully identifying neoepitope specific T‑cells. Our results demonstrate that looking into personalized neoepitope libraries could lead to identification of tumor specific antigenic response that could be utilized in immunotherapy approaches such as in combination with checkpoint inhibitors.