Identification of HLA class II-restricted T cell receptors against shared PIK3CA mutations in patients with epithelial cancers

PIK3CA is the third most common mutated gene in epithelial cancers, behind only TP53 and KRAS. Somatic PIK3CA mutations occur predominantly in the protein's hotspot locations H1047, E545, E542 and N345, and evidence of those alterations eliciting immune responses has been limited. HLA class I-restricted TCRs against E545K and H1047L have, only recently, been identified following in vitro sensitization (IVS) with peripheral blood lymphocytes (PBL) from normal donors. In this study, we examined the immunogenicity of PIK3CA in patients with epithelial cancers of diverse histology, by testing TIL and antigen-experienced PBL against autologous hotspot PIK3CA mutations. Two distinct TCRs specific to PIK3CA^N345K, restricted by HLA-class II pair DPB1*04:01/DPA1*01:03, were identified in a patient with colon cancer, following independently a TIL screen and an IVS of memory CD4 + T cells from the peripheral blood. Patient PBL engineered to express each TCR suppressed the in vitro growth of two cell lines modified to express the DPB1*04:01/DPA1*01:03 pair and full length PIK3CA^N345K protein. A TCR specific to the PIK3CA^E545K, restricted by HLA-DRB1*04:01, was also identified following IVS of memory CD4 + PBL from another patient, with rectal cancer. Autologous PBL, gene engineered to express the PIK3CA^E545K-specific TCR, suppressed the in vitro growth of two cancer cell lines, which endogenously expressed the PIK3CA^E545K neoantigen. This study identified three PIK3CA-specific TCRs against two shared mutations, restricted by common HLA-class II molecules, using antigen-experienced TIL and memory PBL from patients with epithelial cancers and may further allow the development of off-the-shelf T cell immunotherapy strategies targeting PIK3CA.