Codon Optimization of the Human Papillomavirus E7 Oncogene Induces a CD8+ T Cell Response to a Cryptic Epitope Not Harbored by Wild-Type E7

Abstract

Codon optimization of nucleotide sequences is a widely used method to achieve high levels of transgene expression for basic and clinical research. Until now, immunological side effects have not been described. To trigger T cell responses against human papillomavirus, we incubated T cells with dendritic cells that were pulsed with RNA encoding the codon-optimized E7 oncogene. All T cell receptors isolated from responding T cell clones recognized target cells expressing the codon-optimized E7 gene but not the wild type E7 sequence. Epitope mapping revealed recognition of a cryptic epitope from the +3 alternative reading frame of codon-optimized E7, which is not encoded by the wild type E7 sequence. The introduction of a stop codon into the +3 alternative reading frame protected the transgene product from recognition by T cell receptor gene-modified T cells. This is the first experimental study demonstrating that codon optimization can render a transgene artificially immunogenic through generation of a dominant cryptic epitope. This finding may be of great importance for the clinical field of gene therapy to avoid rejection of gene-corrected cells and for the design of DNA- and RNA-based vaccines, where codon optimization may artificially add a strong immunogenic component to the vaccine.

Identification of novel HLA-A*11:01-restricted HPV16 E6/E7 epitopes and T-cell receptors for HPV-related cancer immunotherapy

“…Different HPV epitopes have been targeted with TCR gene-engineered T cells. [16][17][18] It was reported that the TCR gene engineered T cells that recognized human leukocyte antigen (HLA)-A*02:01-restricted epitopes of HPV16 E6 (E6 29-38 ) 19 or E7 (E7 11-19 ) 20 can successfully target HPV + tumor cells. Furthermore, both TCRs are currently under investigation in clinical trials.…”

Unbiased Identification of T-Cell Receptors Targeting Immunodominant Peptide–MHC Complexes for T-Cell Receptor Immunotherapy

“…4A ). 39 T cells transduced with the optimized E5 TCR recognized target cells carrying the 189 nt short minigene of E5, but did not recognize target cells expressing minigenes shorter than 126 nt ( Fig. 4A ).…”

Strategies to Genetically Modulate Dendritic Cells to Potentiate Anti-Tumor Responses in Hematologic Malignancies

“…For the delivery of mRNA, transcription can be excluded as a relevant parameter for improvement, but all others may be useful. It was reported that codon-optimization of the human papillomavirus (HPV) E7 oncoprotein sequence resulted in much higher protein translation and induced CD8+ T cell responses to cryptic epitopes not harbored by wildtype E7 ( 40 ). Codon-optimization could, therefore, confer additional advantages then using native mRNA sequences.…”