The Role of KDM2A and H3K36me2 Demethylation in Modulating MAPK Signaling during Neurodevelopment [RNA-seq]

To explore how KDM2A regulates downstream genes and impacts NPC function, we generated KDM2A knockdown H9 ESC lines using shRNA lentivirus. We designed five siRNAs and selected the two most effective ones for shRNA creation, which were then packaged into shRNA lentivirus (sh1, sh4). Subsequently, we induced these cells into NPCs and cerebral organoids. Through RNA-seq and DEG analysis, we observed that DEGs in NPCs were associated with the MAPK signaling pathway, a finding also present in cerebral organoids. We conducted a disease enrichment analysis on the obtained gene lists, revealing enrichment in neurodevelopmental disorders such as intellectual disability (ID) and autism spectrum disorder (ASD). This finding indirectly suggests that KDM2A plays a role in early neurodevelopmental processes. Overall design: We generated KDM2A knockdown H9 ESC lines using shRNA lentivirus. We designed five siRNAs and selected the two most effective ones to create shRNA, which were then packaged into shRNA lentivirus (sh1, sh4). Next, we induced these cells into NPCs and cerebral organoids. NPCs and Day 30 cerebral organoids underwent RNA-seq (150 bp, paired-end) on the Illumina NovaSeq 6000 system. DESeq2 identified DEGs(FDR< 0.05, |log2FC| >=1) between KDM2A knockdown and control samples. DEGs were utilized for Gene Ontology, KEGG pathway analysis and PPI.