Targeting cancer: tumor-specific splicing events give rise to immunogenic, tumor-wide neoantigens

In a recent study published in Nature, 1 Kwok et al. identified tumor-wide antigens that derived from tumor-specific splicing events, known as neojunctions (NJs) (Fig. 1a).The study identified two distinct neopeptide-encoding NJs (NEJs) that were spatially and temporally conserved in glioblastoma (GBM) patients and induced an HLA-dependent T cell response.The discovery of these NEJs, as well as the pipeline used for their identification, harbors significant potential for the development of tumor vaccines and adoptive cell therapies that might be effective across various cancer entities.Immunotherapies have transformed the landscape of cancer therapy.However, treatment efficacy is often limited by the scarcity of tumor-wide and tumor-specific antigens. 2While certain cancers, such as B cell lymphoma, possess well-defined, targetable antigens (e.g., CD19), many other cancers either lack tumorspecific antigens due to low mutational burden (e.g.acute myeloid leukemia) 3 or exhibit high intratumoral heterogeneity (ITH) (e.g.GBM), 4 meaning that neoantigens are expressed only in a subset of tumor cells.In such cases, targeted vaccines or adoptive cell therapies are often rendered ineffective.Previous studies have successfully explored the use of NJs for the identification of tumor-specific neoantigens. 5However, a comprehensive analysis of the spatial distribution and temporal consistency of NJ-derived neoantigens is still lacking.Kwok et al. addressed this gap by identifying NEJs that are spatially conserved and expressed across multiple patients and tumor types.Initially, the authors analyzed publicly available datasets from The Cancer Genome Atlas (TCGA) (Fig. 1b).They demonstrated that NJs are present in 12 different tumor types and that some NJs are public, meaning that they are present across multiple tumor entities.To further investigate ITH in the context of NJs, the authors examined multi-site intratumoral sampling data from four tumor types and additionally analyzed spatial NJ distribution in 51 glioma patients by obtaining 10 spatially separated intratumoral biopsies per patient (Fig. 1c).Their analysis revealed tumor-wide NJs in all tested tumors.Additionally, also temporally conserved NJs were detected, as evidenced by their presence in the original as well as metastatic and recurrent post-treatment cancers (Fig. 1d).Next, the authors sought to determine whether tumor-wide NJs could be detected on mRNA and protein level (Fig. 1e).Given the high ITH and poor immunotherapy outcomes in glioma patients, they focused their analysis on this tumor type.By analyzing publicly available RNA sequencing and mass spectrometry (MS) data sets, they were able to map neopeptides to 302 distinct