miRNA-mediated loss of m⁶A increases nascent translation in glioblastoma

Abstract

Within the glioblastoma cellular niche, glioma stem cells (GSCs) can give rise to differentiated glioma cells (DGCs) and, when necessary, DGCs can reciprocally give rise to GSCs to maintain the cellular equilibrium necessary for optimal tumor growth. Here, using ribosome profiling, transcriptome and m6A RNA sequencing, we show that GSCs from patients with different subtypes of glioblastoma share a set of transcripts, which exhibit a pattern of m6A loss and increased protein translation during differentiation. The target sequences of a group of miRNAs overlap the canonical RRACH m6A motifs of these transcripts, many of which confer a survival advantage in glioblastoma. Ectopic expression of the RRACH-binding miR-145 induces loss of m6A, formation of FTO/AGO1/ILF3/miR-145 complexes on a clinically relevant tumor suppressor gene (CLIP3) and significant increase in its nascent translation. Inhibition of miR-145 maintains RRACH m6A levels of CLIP3 and inhibits its nascent translation. This study highlights a critical role of miRNAs in assembling complexes for m6A demethylation and induction of protein translation during GSC state transition.Author SummaryCellular plasticity and epigenetic adaptation of human glioblastoma stem cells to the tumor microenvironment is a hallmark of this devastating disease. With our present work, we discover the relationship between miRNAs and the RNA methylation machinery in human glioblastoma and show how miRNA-induced loss of m6A results in increase in protein translation of clinically important transcripts during glioblastoma stem cell differentiation. Leveraging the dynamic functions of these miRNAs can be important in the design of optimal therapeutics targeted at cancer cell plasticity.

Chi3l1 is a modulator of glioma stem cell states and a therapeutic vulnerability for glioblastoma

“…S4B and C). To determine the in vivo efficacy of anti-Chi3l1 antibody as localized treatment for glioblastoma, we generated orthotopic xenograft glioblastoma in immunocompromised mice using patient derived GSCs as shown before (16,17). 28 days following the stereotactic implantation of GSCs, mice were implanted with an intracranial catheter connected to an osmotic pump (Alzet) for continuous infusion of anti-Chi3l1 antibody.…”

“…GSCs from patients with IDH wild type primary glioblastoma have been characterized by RNA-seq and shown to recapitulate the patient's tumor in orthotopic xenografts (16,17). GSC1 and GSC2 both exhibit chromosome 10 deletion and amplification of chromosome 7.…”