m6A Demethylase ALKBH5 Maintains Tumorigenicity of Glioblastoma Stem-like Cells by Sustaining FOXM1 Expression and Cell Proliferation Program

Abstract

The dynamic and reversible N⁶-methyladenosine (m⁶A) RNA modification installed and erased by N⁶-methyltransferases and demethylases regulates gene expression and cell fate. We show that the m⁶A demethylase ALKBH5 is highly expressed in glioblastoma stem-like cells (GSCs). Silencing ALKBH5 suppresses the proliferation of patient-derived GSCs. Integrated transcriptome and m⁶A-seq analyses revealed altered expression of certain ALKBH5 target genes, including the transcription factor FOXM1. ALKBH5 demethylates FOXM1 nascent transcripts, leading to enhanced FOXM1 expression. Furthermore, a long non-coding RNA antisense to FOXM1 (FOXM1-AS) promotes the interaction of ALKBH5 with FOXM1 nascent transcripts. Depleting ALKBH5 and FOXM1-AS disrupted GSC tumorigenesis through the FOXM1 axis. Our work uncovers a critical function for ALKBH5 and provides insight into critical roles of m⁶A methylation in glioblastoma.

Keywords: ALKBH5; FOXM1; glioblastoma; m(6)A modification.

Figure 1. ALKBH5 is Required for GSC Self-Renewal and Predicts Poor Survival of GBM Patients

(A) Correlation between ALKBH5 mRNA expression and survival of GBM patients in the TCGA data set. Overall patient survival in groups of high, intermediate, and low expression was analyzed by Kaplan-Meier survival curve. The median overall survival duration of patients with high ALKBH5 expression (9.9 months) versus with low ALKBH5 expression (16.6 months) was compared by log-rank test (p=0.037). (B) Western blotting of ALKBH5 in NHAs, glioma cells, and GSCs. Actin served as a loading control. (C) Correlation between ALKBH5 and SOX2 protein expression in GBM specimens. Tumor sections from 15 GBM specimens were immunofluorescence (IF)-stained with anti-ALKBH5 and anti-SOX2 antibodies. Left, representative images are shown. Right, in 5 random selected microscope fields of each tumor, the percentage of ALKBH5 positive cells among SOX2 positive versus SOX2 negative cells was compared by t-test. Lines show mean and SD. (D) The Pearson correlation between ALKBH5 and SOX2 mRNA expression (RNAseq V2 RSEM [log2]) in the TCGA GBM data set. (E) ALKBH5 mRNA expression in GSCs and paired matching tumors by RNA-seq analysis. (F) In vitro limiting dilution assays plating decreasing number of GSCs with or without ALKBH5 knockdown calculated with extreme limiting dilution assay analysis (top left), representative images of tumorspheres in dose of 100 cells/well were shown in top right panel. Scale bar, 20 μm. Stem cell frequencies from GSCs with or without ALKBH5 knockdown were estimated as the ratio 1/x with the upper and lower 95% confidence intervals, where 1 = stem cell and x = all cells (bottom). See also Figure S1 and Table S1

Figure 2. Inhibition of ALKBH5 Impairs GSC Proliferation and Tumorigenecity

(A) Proliferation of GSCs with or without ALKBH5 knockdown as determined by cell counting. n=3. ^*p<0.05, ^**p<0.01, ^***p<0.001. (B) Proliferation of GSCs with or without ALKBH5 knockdown as assessed by BrdU (5-bromo-2′-deoxyuridine) incorporation for 3 hr. Scale bar, 20 μm. (C) Random selected microscope fields of (B) were quantified for BrdU-positive GSCs. n=5. (D) Survival analysis of mice intracranially implanted with GSCs with or without ALKBH5 knockdown. GSCs were implanted intracranially into nude mice, and tumor formation was determined by histology. (E) Top, histograms show tumor volumes formed by indicated GSC17 cells in mouse brains. Bottom, representative images of H&E staining for tumor formation. n=8. All bar plot data are the means ± SEMs. See also Figure S2

Figure 3. Characterization of m⁶A Modification and Gene Expression Changes in the ALKBH5-Deficient Cells

(A) Venn diagrams show 206 genes with over 2-fold expression change in shALKBH5 compared with shCtrl in both GSC11 and GSC17 (top). IPA identified the enriched gene ontology processes of the 206 genes (bottom). (B) Top consensus motif identified by HOMER with m⁶A-seq peaks in GSC11 cells with or without ALKBH5 knockdown. (C) Number of m⁶A peaks identified in m⁶A-seq in shCtrl and shALKBH5 GSC11 cells. (D) Number of m⁶A-modified genes identified in m⁶A-seq. Common m⁶A genes contain at least 1 common m⁶A peak, while unique m⁶A genes contain no common m⁶A peaks. (E) Graphs of m⁶A peak distribution showing the proportion of total m⁶A peaks in the indicated regions in control and ALKBH5-deficient cells (top) and the appearance of new m⁶A peaks (unique peaks in shALKBH5) or loss of existing m⁶A peaks (unique peaks in shCtrl) after ALKBH5 knockdown (bottom). (F) Schematic of ALKBH5 downstream analysis. (G) Relative mRNA levels of FOXM1 downstream targets from microarray analysis. Data are the means ± SEMs for GSC11 and GSC17 cells. Combined analysis of 2 independent biological replicates in (B–E). See also Figure S3 and Table S2–S5

Figure 4. ALKBH5 Maintains FOXM1 Expression by Demethylating FOXM1 Nascent Transcripts

(A) qPCR analysis of FOXM1 mRNA expression in GSC11 with or without ALKBH5 knockdown. Samples were normalized to GAPDH mRNA. (B) Western blotting of FOXM1 in GSCs with or without ALKBH5 knockdown. (C) Western blotting of FOXM1 and SOX2 in GSC17 cells treated with control or ALKBH5 siRNAs. (D) Correlation between FOXM1 and ALKBH5 mRNA expression (RNAseq V2 RSEM [log2]) in the TCGA GBM data set. (E) Correlation between ALKBH5 and FOXM1 protein expression in GBM specimens. Left, representative IF images of 15 GBM specimens. Scale bar, 20 μm. Right, in 5 random selected microscope fields of each tumor, the percentage of FOXM1 positive cells among ALKBH5 positive versus ALKBH5 negative cells was compared by t-test. Lines show mean and SD. (F) qPCR analysis of FOXM1 pre-mRNA in GSCs with or without ALKBH5 knockdown. (G) Cytoplasmic (C), nucleoplasmic (N), and insoluble (I) fractions of GSC11 cells treated with or without 5 μg/ml ActD (actinomycin D) for 2 hr were subjected to Western blotting for indicated proteins. (H) Distribution of FOXM1 transcripts in subcellular fractions assessed by qPCR. (I) RIP (RNA immunoprecipitation) analysis of transcripts from the nuclear extracts of GSC17 cells expressing exogenous ALKBH5 with or without FLAG tag. Enrichment of FOXM1 mature and pre-mRNA with FLAG was measured by qPCR and normalized to input. Western blotting of ALKBH5 showing equal expression of tagged or untagged proteins. (J) MeRIP-qPCR analysis of m⁶A levels of FOXM1 pre-mRNA in GSC17 cells with or without ALKBH5 knockdown. (K) Western blotting of FOXM1 in GSC17 with or without ALKBH5 knockdown and transfected with control, wild-type or mutant ALKBH5 plasmid. All bar plot data are the means ± SEMs of 3 independent biological replicates. ^*p<0.05, ^**p<0.01, ^***p<0.001. See also Figure S4

Figure 5. The FOXM1 3′UTR Mediates ALKBH5 Regulation

(A) Left, peaks show the relative abundance of m⁶A sites along FOXM1 mRNA in GSC11-shALKBH5 cells. The blue and red reads are from the non-IP control input and MeRIP of GSC11-shALKBH5, respectively. Right, identification of a unique peak at 3′UTR. (B) MeRIP-qPCR analysis of fragmented or intact FOXM1 RNA from GSC11 with or without ALKBH5 knockdown. Left: peak region enrichment in fragmented RNA. Right: enrichment of m⁶A-marked FOXM1 mature and pre-mRNA in intact RNA. Up: half samples were fragmented. (C) MeRIP-qPCR analysis of fragmented FOXM1 RNA in GSC17 with or without ALKBH5 knockdown. (D) Western blotting of FLAG-FOXM1 in GSCs seeded in 12-well plates and transfected with 50 ng FOXM1 CDS-3′UTR or FOXM1 CDS plasmid and treated with control or ALKBH5 siRNAs. (E) Relative activity of the wild-type or mutant FOXM1 3′UTR firefly luciferase reporter in GSC17 cells treated with control or ALKBH5 siRNAs. (F) RIP analysis of the interaction of FLAG with FOXM1 pre-mRNA using total cell lysates of GSC17 cells expressing exogenous HuR with or without FLAG tag and treated with control or ALKBH5 siRNAs. Enrichment of FOXM1 pre-mRNA with FLAG was measured by qPCR and normalized to input. Western blotting of HuR showing equal expression of tagged or untagged proteins. (G) qPCR analysis of FOXM1 in GSCs treated with control or HuR siRNAs. (H) Western blotting of FOXM1 RNA expression in GSCs treated with control or HuR siRNAs. All bar plot data are the means ± SEMs of 3 independent experiments except (B) and (C) where error bars denote SD of technical triplicates. ^*p<0.05, ^**p<0.01, ^***p<0.001. See also Figure S5

Figure 6. FOXM1-AS Is a Nuclear lncRNA That Facilitates the Interaction between ALKBH5 and FOXM1 Nascent Transcripts

(A) Physical map of FOXM1 and FOXM1-AS (F-AS) transcription units. Arrows indicate the direction of transcription. Vertical bars indicate exons. (B) qPCR analysis of indicated RNA expression in glioma cells and GSCs. (C) Top, RNA distribution in subcellular fractions assessed by qPCR. Bottom, Western blotting of indicated proteins in 2 independent experiments. (D and E) Analysis of the interaction between F-AS and ALKBH5 by an RIP assay using anti-FLAG antibodies in the nuclear extracts of GSC17 cells expressing exogenous ALKBH5 with or without FLAG tag (D) and an RNA pull-down assay using biotinylated probes to capture F-AS in the nuclear extracts of GSC17 cells (E). The RNA and protein in the RNA-protein complex were then detected by qPCR and Western blotting, respectively. HuR and antisense probes consisted of complementary sequence to F-AS probes served as negative controls. (F) RNA pull-down assay of F-AS–associated RNA from GSC17 cells. Biotinylated F-AS probes or antisense probes were incubated with AMT-crosslinked or untreated RNA and collected with streptavidin beads. Interaction with F-AS was quantified by qPCR. (G) RIP analysis of the interaction of FOXM1 pre-mRNA with FLAG in the nuclear extracts of GSC17 cells expressing exogenous ALKBH5 with or without FLAG tag and treated with control or F-AS siRNAs. Enrichment of FOXM1 pre-mRNA with FLAG was measured by qPCR and normalized to input. (H) MeRIP-qPCR analysis of m⁶A levels of FOXM1 pre-mRNA in GSC17 cells with or without F-AS knockdown. (I) Western blotting of FOXM1 and ALKBH5 in GSC17 cells and transfected with FOXM1 CDS-3′UTR or FOXM1 CDS plasmid before treatment with indicated siRNAs. (J) Relative activity of the FOXM1 3′UTR firefly luciferase reporter in GSC17 cells treated with control or F-AS siRNAs. (K) RIP analysis of the interaction of FOXM1 pre-mRNA with HuR in GSC17 cells with or without F-AS knockdown. Enrichment of FOXM1 pre-mRNA with HuR was measured by qPCR. All bar plot data are the means ± SEMs of 3 independent experiments. ^*p<0.05, ^**p<0.01, ^***p<0.001. N.S., no significance. See also Figure S6

Figure 7. Knocking Down FOXM1-AS Impairs FOXM1 Expression and Self-renewal in GSCs

(A) qPCR analysis of indicated RNA in GSC17 cells with or without F-AS knockdown. (B) Western blotting of FOXM1 in GSCs with or without F-AS knockdown. (C) The Pearson correlation between F-AS and FOXM1 RNA expression in 45 tumor regions by laser-capture microdissection from 15 GBM specimens. 3 different tumor regions from the same tumor were represented in one color. (D) Proliferation of GSCs with or without F-AS knockdown, as determined by cell counting. (E) Representative IF images of GSCs incorporated with BrdU overnight. (F) Tumorsphere formation efficiency of GSC11 cells with or without F-AS knockdown after 7 days of incubation in a 96-well plate, as calculated by the number of spheres per 100 single cells. (G) Fluorescence and bright-field micrographs of GSCs with or without F-AS knockdown. All bar plot data are the means ± SEMs of 3 independent experiments, except those in (F), where n=5. ^*p<0.05, ^**p<0.01, ^***p<0.001. Scale bar, 20 μm. See also Figure S7

Figure 8. FOXM1 Reinstates the Tumor Growth of GSCs with Depleted ALKBH5 or FOXM1-AS

(A) qPCR analysis of the indicated mRNAs in GSC11 cells with or without ALKBH5 knockdown and in GSC11 cells with ALKBH5 knockdown rescued by exogenous FOXM1. Error bars: ± SEM of 3 independent experiments. ^*p<0.05, ^**p<0.01 (shALKBH5 + FOXM1 versus + Vector) (B) Top, representative images of H&E staining for tumor formation. Bottom, histograms show tumor volumes. Error bars: ± SEM. n=8. (C) Representative IF images of the indicated proteins in GSC17 xenografts. Scale bar, 50 μm. See also Figure S8