Rewiring the transcriptome: diagnostic and therapeutic implications of alternative splicing in solid cancers

Alternative splicing (AS) is a fundamental mechanism of pre-mRNA processing that allows one gene to create numerous transcript and protein isoforms, thereby substantially increasing the diversity of the human proteome. AS occurs co-transcriptionally (when the nascent pre-mRNA is still being generated from chromatin) or post-transcriptionally after the release of the transcript, and both modalities contribute to the control of isoform expression in a tissue- and context-dependent manner. Under normal physiological conditions, AS is tightly regulated in a tissue- and context-dependent manner. However, in malignancies, this regulatory precision is often lost, leading to extensive splicing aberrations that promote oncogenic transformation, tumor progression, and resistance to therapy. Solid tumors, in particular, exhibit a high frequency of aberrant splicing events, which frequently give rise to oncogenic isoforms or the suppression of tumor-inhibitory variants. These disruptions contribute to key cancer hallmarks such as uncontrolled proliferation, resistance to apoptosis, neoangiogenesis, and epithelial-mesenchymal transition (EMT). Recent findings underscore the clinical relevance of splicing-derived molecular signatures. Distinct splicing profiles have been correlated with diagnostic, prognostic, and predictive outcomes in multiple solid tumors-including breast, prostate, lung, colorectal, and central nervous system malignancies. Notably, tumor-specific alternative splice variants often generate unique exon-exon junctions (neojunctions) that encode immunogenic peptides, representing a promising class of neoantigens for immunotherapy. These neoantigens are fueling the development of personalized treatment modalities such as splicing-directed vaccines and T cell-based therapies. The advent of advanced technologies-including long-read sequencing, single-cell transcriptomics, and proteogenomics-has enabled high-resolution mapping of cancer-specific splice variants and enhanced our understanding of their functional relevance. Therapeutic strategies targeting aberrant splicing are also advancing, with splice-switching oligonucleotides, small-molecule modulators, and CRISPR-based RNA-editing platforms emerging as innovative approaches. Despite these advances, challenges such as splicing heterogeneity, off-target effects, and incomplete protein-level validation continue to hinder clinical translation. This review offers an integrated overview of the molecular drivers and clinical implications of alternative splicing in cancer. It emphasizes the potential of AS-based diagnostics and therapeutics within precision oncology and highlights the importance of multi-omic integration and clinical validation to fully harness the therapeutic opportunities of splicing dysregulation.