This review integrates the molecular logic of splice-site selection with the cancer-specific mechanisms that perturb it, summarizes representative isoform switches across the hallmarks of cancer, evaluates emerging technologies and clinical biomarkers, and discusses the opportunities and constraints of translating splicing biology into precision oncology.
Abstract
Alternative pre-mRNA splicing is a central layer of gene regulation that enables a limited number of genes to generate a far larger and more context-dependent transcriptome and proteome. In cancer, splicing is disrupted by mutations in cis-regulatory sequences, recurrent lesions in spliceosome components, altered abundance or activity of RNA-binding proteins, and changes in transcription, chromatin, RNA modification, metabolism and stress signalling. These alterations are not merely by-products of malignant transformation. They can create oncogenic protein isoforms, eliminate tumour-suppressive products, remodel cellular identity, promote metastasis and drug resistance, and generate tumour-restricted peptides that are visible to the immune system. Large pan-cancer datasets, long-read sequencing, single-cell isoform profiling, proteogenomics and functional perturbation screens are now resolving this complexity at unprecedented scale. In parallel, multiple therapeutic strategies are advancing, including modulators of the SF3B complex, molecular glues that degrade RBM39, inhibitors of protein arginine methyltransferases and splicing kinases, splice-switching oligonucleotides, programmable RNA-targeting systems, and vaccines or T-cell receptors directed against splicing-derived neoantigens. This review integrates the molecular logic of splice-site selection with the cancer-specific mechanisms that perturb it, summarizes representative isoform switches across the hallmarks of cancer, evaluates emerging technologies and clinical biomarkers, and discusses the opportunities and constraints of translating splicing biology into precision oncology. Particular emphasis is placed on tumour specificity, intratumoural heterogeneity, proteomic validation, therapeutic windows and rational combination strategies.
RNA splicing expands the functional output of eukaryotic genomes by enabling individual precursor messenger RNA (pre-mRNA) to generate multiple mature transcripts with protein‑coding and regulatory properties. Its fidelity and plasticity depend on coordinated interactions among the spliceosome, trans-acting splicing factors, cis-regulatory elements, and chromatin- and RNA-associated regulatory mechanisms. However, how these components collectively generate cell- and tissue-specific splicing programs, and how their disruption drives disease, remain incompletely understood. In this review, we integrate the molecular regulation of RNA splicing with its physiological, pathological and therapeutic consequences. We describe how spliceosome assembly, splicing regulatory elements, splicing factors, epigenetic modifications, and post-transcriptional processes determine splice-site selection. We then examine how regulated isoform programs support development, tissue specialization, homeostasis, circadian timing, and stress adaptation, and how their failure contributes to cancer and diverse non-neoplastic diseases. In cancer, we highlight the bidirectional interplay between splicing dysregulation and the tumor microenvironment, through which metabolic reprogramming and immune suppression reinforce aberrant splicing. Finally, we assess strategies that modulate the spliceosome, splicing-factor activity, or disease-associated transcripts, and present a perspective on how multi-omics, artificial intelligence, targeted delivery, and combination with immunotherapy could collectively advance the discovery and precision of splicing-directed therapies. We suggest that safe clinical translation will require greater selectivity, reduced off-target toxicity, and preservation of essential physiological splicing.
Huining Huang, Yao Yu, Qian Zhou et al.· Molecular Biomedicine· 0 citations
This review examines how different types of ncRNAs contribute to cancer initiation, progression, and treatment resistance, and assesses their potential as diagnostic markers, prognostic factors, and therapeutic targets.
Akanksha Samuel, G. Calin· Carcinogenesis· 0 citations
This study instigated a gene-specific targeted strategy by unlocking the regulatory network, and designed antisense oligonucleotides (ASOs) targeting important regulatory sites, demonstrating that ASO pharmacology is an actionable strategy for clinical development, challenging the existing paradigms in SF-mutated cancers.
Alternative splicing is a pervasive mechanism that expands the coding potential and functional complexity of the human genome. Dysregulated isoform usage alters gene functions and contributes broadly to human disease across developmental, neurodegenerative, and cancer settings. Technologies for characterizing splicing and isoforms have advanced rapidly, evolving from Sanger sequencing of individual cDNA clones to high-throughput next-generation sequencing of splice junctions, and more recently to long-read sequencing that resolves full-length transcripts at bulk, single-cell, and spatial resolutions. With the growing recognition of their critical roles in human disease, multiple therapeutic modalities have been developed to precisely target splicing and isoform regulation at the DNA, RNA, and protein levels. Clinical-grade small molecules and antisense oligonucleotides that modulate aberrant RNA splicing and isoform switching have become available, offering new hope for previously incurable diseases. Here, we review this crucial yet underexplored layer of transcriptomic regulation in human disease, encompassing regulatory mechanisms, technological advances, therapeutic strategies, and future directions.
Hepatocellular carcinoma (HCC) is a malignant neoplasm characterized by high incidence and mortality rates globally. Its pathogenesis and progression are intricate and multifaceted, necessitating comprehensive analysis and elucidation. Recent studies have demonstrated that non-coding RNAs (such as long non-coding RNAs, circular RNAs, and microRNAs) and alternative splicing, which are central to post-transcriptional regulation, engage in extensive regulatory interactions. These interactions form a complex regulatory network that significantly influences the malignant properties such as stemness, proliferation, invasion, metastasis, metabolic reprogramming, tumor microenvironment, and drug sensitivity in liver cancer cells. This review systematically explores the molecular mechanisms underlying the interactions between non-coding RNAs and alternative splicing events, highlighting the role of this regulatory network in modulating the expression of oncogenes and tumor suppressor genes in HCC. Additionally, this review investigates the prospective application of pivotal molecules within this regulatory network as novel diagnostic biomarkers and therapeutic targets. It also analyzes the challenges and obstacles encountered in the clinical translation process, thereby providing new insights for research on the precision diagnosis and treatment of HCC.
ABSTRACT RNA‐binding proteins (RBPs) are central regulators of post‑transcriptional gene expression, controlling RNA stability, localization, translation, and alternative splicing. Their functions arise not only from intrinsic RNA‐binding domains but also from dynamic interactions with noncoding RNAs, metabolites, cofactors, and other RBPs. Here, we summarize the structural diversity and core biological activities of canonical and noncanonical RBPs, and delineate how competitive and cooperative regulatory networks dictate RBP function in disease, with an emphasis on cancer. Competitive mechanisms, including lncRNA‐mediated sequestration, antagonistic crosstalk between miRNAs and RBPs, and competition among RBPs for shared substrates, can redirect RNA fate. In contrast, cooperative mechanisms assemble multimolecular ribonucleoprotein complexes that reinforce oncogenic or tumor‐suppressive programs. Dysregulation of these networks promotes proliferation, metastasis, immune evasion, and therapy resistance. We also review emerging therapeutic strategies that target RBP‐centered regulatory circuits, including antisense oligonucleotides, small molecules, protein degraders, and natural products, and we evaluate representative preclinical studies and clinical trials. By integrating mechanistic principles with translational evidence, this review provides a network‐based framework for exploiting RBPs as therapeutic vulnerabilities and for advancing next‐generation precision oncology.
Ling Li, Xiu-Li Yan, Qing Ji et al.· MedComm· 0 citations