Members of the research team including Dr Aya El Helali (front row, right), Dr Brian Hon-Yin Chung (front row, left) and Prof Gilberto Ka-Kit Leung (back row, left).Researchers from the Clinical Neuroscience Consortium (CNC), a collaborative platform jointly established by the University of Hong Kong (HKU) and Queen Mary Hospital in collaboration with the Hong Kong Genome Institute (HKGI), have achieved a major breakthrough in brain cancer research, uncovering thousands of previously unannotated isoforms and identifying potential targets for both precision therapeutics and personalized cancer vaccines.
“Using single-cell long-read sequencing [scLR-seq] and data from >210,000 individual cells from 27 patients with glioblastoma multiforme [GBM], the research team built the most comprehensive map of isoform diversity to date, encompassing both tumour cells and the surrounding immune and stromal cells that make up the tumour microenvironment,” reported Dr Aya El Helali of the Department of Clinical Oncology, HKU, who is also CNC Chapter Lead (Brain Tumour). “The study identified 6,524 previously unannotated isoforms, including 179 that are tumour-specific.” [Nat Commun 2026;17:5640]
While single-cell RNA sequencing has revealed diverse cellular states within GBM, conventional short-read approaches cannot resolve full-length isoforms, limiting insights into the functional consequences of splicing. This new study addressed this gap by directly applying scLR-seq to construct an isoform-level atlas of GBM. By capturing full-length transcripts at single-cell resolution, hundreds of isoforms with differential transcript usage across distinct tumour cell populations were identified.
The team also developed a framework to prioritize tumour-restricted isoforms and identify surface-intracellular target pairs. Utilizing the differentially expressed annotated isoforms in GBM, they elucidated a methodology to pinpoint 40 patient-specific target pairs for tailored targeted therapeutics for seven GBM patients.
GBM remains the most aggressive and lethal primary brain tumour in adults. In Hong Kong, the median overall survival of GBM patients is approximately 10 months despite standard-of-care surgery, radiotherapy and temozolomide chemotherapy. A major contributor to this poor clinical outcome is the profound intratumoral heterogeneity, and widespread dysregulation of RNA splicing, which drives treatment resistance (eg, poor response to immune checkpoint inhibitors), recurrence and immune evasion. [Neuro Oncol 2022;10:5061; Nat Rev Cancer 2023;23:135-155]
However, antigen-specific immunotherapies, including CAR-T cell therapies and neoantigen-based vaccines, have shown greater promise. Early-phase clinical trials of multi-peptide vaccines have demonstrated favourable safety profiles and immunogenicity in GBM patients. [N Engl J Med 2024;390:1290-1298; Nat Commun 2024;15:6870; Clin Cancer Res 2022;28: 5368-5382]
“Our discovery of tumour-specific isoforms reveals a new class of potential neoantigens and suggests that many promising therapeutic targets may have remained entirely invisible to existing approaches,” said Dr Brian Hon-Yin Chung of the Department of Paediatrics & Adolescent Medicine, HKU, who is also Interim CEO of the HKGI. “By expanding the pool of candidate neoantigens available for personalized cancer vaccines and immunotherapies, our research findings represent an important step towards next-generation immunotherapies for brain cancer, opening the door to more precise and individualized treatment strategies for patients with GBM.”