RNA splicing analysis deciphers developmental hierarchies and reveals therapeutic targets in adult glioma

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Abstract
Widespread alterations in RNA alternative splicing (AS) have been identified in adult gliomas. However, their regulatory mechanism, biological significance, and therapeutic potential remain largely elusive. Here, using a computational approach with both bulk and single-cell RNA-Seq, we uncover a prognostic AS signature linked with neural developmental hierarchies. Using advanced iPSC glioma models driven by glioma driver mutations, we show that this AS signature could be enhanced by EGFRvIII and inhibited by in situ IDH1 mutation. Functional validations of 2 isoform switching events in CERS5 and MPZL1 show regulations of sphingolipid metabolism and SHP2 signaling, respectively. Analysis of upstream RNA binding proteins reveals PTBP1 as a key regulator of the AS signature where targeting of PTBP1 suppresses tumor growth and promotes the expression of a neuron marker TUJ1 in glioma stem-like cells. Overall, our data highlights the role of AS in affecting glioma malignancy and heterogeneity and its potential as a therapeutic vulnerability for treating adult gliomas.
Funding Information
  • U.S. Army Medical Research Acquisition Activity (W81XWH-22-10373,W81XWH-22-1-0374)
  • United States National Institutes of Health (NS115403,NS122375,NS126810,NS125318,CA234799,CA279896,NS117104,NS119039,CA209345,NS080939,NS116802,CA258248)
  • Fundação de Amparo à Pesquisa do Estado de São Paulo, Brazil (2020/03714-8)

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