Cancer immunotherapy has achieved remarkable success; however, the identification of targetable tumor antigens (TAs) remains a significant challenge for T cell receptor (TCR) and chimeric antigen receptor T cell (CAR-T) therapies. Besides genomic mutations, an alternative underexplored source of immunotherapy targets may be derived from dysregulation of RNA processing. Aberrant RNA processing is widespread in cancer and can generate aberrant proteins and immunogenic peptides in cancer cells. Long-read RNA-sequencing (RNA-seq), as opposed to the widely-used short-read RNA-seq, offers advantages in resolving full-length transcript isoforms and complex RNA processing events. This advancement enables the profiling of complete transcripts, facilitating antigen discovery through the inference of topology and structure for corresponding translated proteins.In the first part of the dissertation, we present TEQUILA-seq, a versatile, cost-effective method for targeted long-read RNA-seq. Even though long-read RNA-seq is a powerful technology for transcriptome analysis, the relatively low throughput of current long-read sequencing platforms limits transcript coverage. One strategy for overcoming this bottleneck is targeted long-read RNA-seq for preselected gene panels. Utilizing isothermally linear-amplified capture probes, TEQUILA-seq enriches transcript coverage while preserving quantification. Profiling full-length transcript isoforms of 468 cancer-related genes across 40 breast cancer cell lines, we reveal a common RNA-associated mechanism for tumor suppressor gene inactivation. TEQUILA-seq reduces the per-reaction cost of targeted capture by 2-3 orders of magnitude, as compared to a standard commercial solution. We believe that TEQUILA-seq can be broadly used for targeted sequencing of full-length transcripts in diverse biomedical research settings. In the second part of dissertation, we introduce IRIS-long, an in silico platform harnessing long-read RNA-seq data from tumor and normal transcriptomes to discover and prioritize RNA dysregulation-derived immunotherapy targets. Applying IRIS-long to analyze long-read RNA-Seq data from 49 melanoma cell lines, we identified candidate CAR-T targets and validated their protein localization by confocal microscopy imaging. This work provides insights into the contribution of RNA dysregulation to the repertoire of TAs in cancer cells, and demonstrate the utility of IRIS-long in discovering RNA dysregulation-derived targets, thereby expanding the scope of cancer immunotherapies.