Fig S1. SF3B1 mutant CLL samples had pervasive changes in 3’ splice site.
Fig S2. Omics analyses identify widespread post-transcriptional upregulation of splicing factors in CLL.
Fig S3. Abundance of spliceosome complexes and RNA-binding proteins are associated with clinical outcomes in CLL.
Fig S4. METTL3 is consistently upregulated along with differential m6A modification on transcripts of RNA splicing process in CLL.
Fig S5. KO or pharmacological inhibition of METTL3 impacts cell growth.
Fig S6. KO or pharmacological inhibition of METTL3 impacts apoptosis, cell cycle, and splicing factor abundance.
Fig S7. Splicing factors are either direct or indirect targets of METTL3.
Fig S8. Validation of association between m6A and splicing factor abundance using dCasRx-METTL3.
ARTICLE ABSTRACT
RNA splicing dysregulation underlies the onset and progression of cancers. In chronic lymphocytic leukemia (CLL), spliceosome mutations leading to aberrant splicing occur in ∼20% of patients. However, the mechanism for splicing defects in spliceosome-unmutated CLL cases remains elusive. Through an integrative transcriptomic and proteomic analysis, we discover that proteins involved in RNA splicing are posttranscriptionally upregulated in CLL cells, resulting in splicing dysregulation. The abundance of splicing complexes is an independent risk factor for poor prognosis. Moreover, increased splicing factor expression is highly correlated with the abundance of METTL3, an RNA methyltransferase that deposits N6-methyladenosine (m6A) on mRNA. METTL3 is essential for cell growth in vitro and in vivo and controls splicing factor protein expression in a methyltransferase-dependent manner through m6A modification-mediated ribosome recycling and decoding. Our results uncover METTL3-mediated m6A modification as a novel regulatory axis in driving splicing dysregulation and contributing to aggressive CLL.
METTL3 controls widespread splicing factor abundance via translational control of m6A-modified mRNA, contributes to RNA splicing dysregulation and disease progression in CLL, and serves as a potential therapeutic target in aggressive CLL.See related commentary by Janin and Esteller, p. 176.This article is highlighted in the In This Issue feature, p. 171
