Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells

Abstract

Significant tumor regressions have been observed in up to 70% of patients receiving adoptively transferred autologous melanoma-reactive tumor infiltrating lymphocytes (TIL) 1,2, and in pilot trials, 40% of treated patients experienced complete regressions of all measurable lesions for at least five years following treatment 3. To evaluate the potential association between the ability of TIL to mediate durable regressions and their ability to recognize potent antigens that presumably include mutated gene products, a novel screening approach was developed that involved mining whole exome sequence data to identify the mutated proteins that were expressed in patient tumors. Candidate mutated T cell epitopes that were identified using an MHC binding algorithm 4 were then synthesized and evaluated for recognition by TIL. Using this approach, mutated antigens expressed on autologous tumor cells were identified as targets of three TIL that were associated with objective tumor regressions following adoptive transfer. This simplified approach, which avoids the need to generate and laboriously screen cDNA libraries from tumors, may represent a generally applicable method for identifying mutated T cell antigens expressed in melanoma as well as other tumor types.

Predicting T cell recognition of MHC class I restricted neoepitopes

“…most are not immunogenic. 24,28,46 Especially in patients with high mutational load, hundreds or even thousands of mutated peptides are commonly found based on sequencing approaches, highlighting the need to further narrow down this candidate list and increase the specificity in detecting immunogenic neoepitopes.…”

“…Several of the peptides from the NCI dataset were also published, 46,61–63 which resulted in an overlap with the curated literature dataset. To keep the datasets distinct from each other, we filtered the literature dataset and removed all peptides included in the NCI dataset for all bioinformatics and statistical analyses.…”

Immune targets and neoantigens for cancer immunotherapy and precision medicine

“…These studies demonstrate that neoantigens can be rapidly identified within a few weeks and can serve as tumor-specific targets for T cell-mediated recognition and destruction of tumor cells. Similarly, several neoantigens have been identified from human cancer recognized by CD8 + and CD4 + T cells through exome sequencing and screening for T cell responses [221][222][223]. More recently, it has been further demonstrated that neoantigen-specific T cells can be isolated from patient PBMCs using FACS analysis and purification, although their frequencies are much lower than neoantigen-specific T cells in the corresponding TIL populations [45,224].…”

“…In subsequent validation steps, tumor-reactive T cells are the key to screening and identification of T cell-recognized neoantigens (Table 3). TILs can be isolated from freshly obtained tumor tissues and used for screening candidate neoantigens [221]. Alternatively, neoantigen-specific T cells may be isolated from the patient's PBMCs based on upregulation of activation markers such as 4-1BB, OX-40 and PD-1 on T cells [224,235].…”

Cancer immunotherapy: exploiting neoepitopes

“…First, in-depth evaluation of the T-cell response in melanoma patients who responded to TIL-therapy, and infusion of ex vivo expanded tumor-infiltrating T cells, revealed that the T-cell clones driving therapeutic efficacy were not directed against lineage-specific and cancer testis antigens, but instead against neo-epitopes encoded by the tumor mutanome [3]. Essentially the same observation was subsequently made in patients responding to so-called checkpoint inhibitors, antibodies against cytotoxic T-lymphocyte-associated Protein 4 (CTLA-4) or the programmed cell death (PD)-1/PD-L1 axis, that can activate T cells by neutralizing inhibitory pathways in T cells [4].…”