Figure 3.

Combinatory analyses of MeRIP-seq, RNA-seq, CLIP-seq, and patients' survival data identified CDC5L mRNA as a potential target of IGF2BP1 in MM. (A) The numbers of predicted m⁶A site classification based on reliability in NCI-H929 cells were predicted by the SRAMP tool. (B) The top 30 significant enriched KEGG pathways for the 2608 peak-related genes in MeRIP-seq were plotted according to enrichment score and pathways. The P-value and number of genes are denoted by color darkness and size of cycle, respectively. (C, D) The top 20 obviously enriched KEGG pathways of down-regulated differentially expressed gene (DEGs) (n = 230; C) and up-regulated DEGs (n = 504; C) in the IGF2BP1-KD RNA-seq data were plotted according to enrichment scores and pathways (D). (E) The top 10 significant enriched KEGG pathways of the target genes of IGF2BP1 from Clip-seq data analysis were plotted. (F) The overlapping of differentially expressed mRNAs for m⁶A-seq, IGF2BP1-KD RNA-seq, and IGF2BP1 CLIP-seq versus control are shown in the Venn diagram. (G) The relationship between CDC5L expression levels and six classical CAs of MM patients in the MMRF dataset. (H) In MM patients with 1q+, patients with a higher CDC5L mRNA expression level exhibited worse prognosis in terms of progression-free survival (PFS) and overall survival (OS) as compared with the patients with a lower CDC5L mRNA level. IGF2BP1, insulin-like growth factor 2 mRNA binding protein 1; MM, multiple myeloma; CAs, cytogenetic abnormalities; CDC5L, cell division cycle 5-like; MeRIP-seq, methylated RNA immunoprecipitation sequencing; CLIP-seq, crosslinking immunoprecipitation sequencing; RNA-seq, RNA sequencing.