Long‐Read Pan‐Cancer Transcriptomics Unravel Distinct Alteration Trends Between Gene and Isoform Expression in Tumorigenesis

ABSTRACT Tumorigenesis involves transcriptomic alterations at both gene and isoform levels. While short‐read RNA‐seq can't fully resolve isoform‐level changes, long‐read RNA sequencing (lrRNA‐seq) overcomes this limitation. In this study, we analyzed 144 paired tumor‐normal transcriptomes across 10 organs using lrRNA‐seq. Our pan‐cancer analysis revealed convergent gene expression associated with oncogenic dedifferentiation, contrasting with variable, organ‐specific isoform‐level alterations. Isoform‐level changes, including aberrant fusion transcripts and disrupted isoform composition, were widespread and partially linked to altered splicing factor expression. Notably, many genes showed significant isoform alterations without corresponding gene expression differences. Integrating gene and isoform‐level data, we developed a pan‐cancer scoring framework to identify candidate prognostic correlates and potential therapeutic targets for further validation. This framework uncovered multiple underappreciated pan‐cancer susceptibility genes, such as IBSP and FANCL , whose dysregulation occurs predominantly at the isoform level. Our findings advance understanding of tumor transcriptomics and provide a resource for future biomarker and therapeutic development.