Transcriptome and Proteome Profiling of Neural Induced Pluripotent Stem Cells from Individuals with Down Syndrome Disclose Dynamic Dysregulations of Key Pathways and Cellular Functions

Abstract

Down syndrome (DS) or trisomy 21 (T21) is a leading genetic cause of intellectual disability. To gain insights into dynamics of molecular perturbations during neurogenesis in DS, we established a model using induced pluripotent stem cells (iPSC) with transcriptome profiles comparable to that of normal fetal brain development. When applied on iPSCs with T21, transcriptome and proteome signatures at two stages of differentiation revealed strong temporal dynamics of dysregulated genes, proteins and pathways belonging to 11 major functional clusters. DNA replication, synaptic maturation and neuroactive clusters were disturbed at the early differentiation time point accompanied by a skewed transition from the neural progenitor cell stage and reduced cellular growth. With differentiation, growth factor and extracellular matrix, oxidative phosphorylation and glycolysis emerged as major perturbed clusters. Furthermore, we identified a marked dysregulation of a set of genes encoded by chromosome 21 including an early upregulation of the hub gene APP , supporting its role for disturbed neurogenesis, and the transcription factors OLIG1 , OLIG2 and RUNX1 , consistent with deficient myelination and neuronal differentiation. Taken together, our findings highlight novel sequential and differentiation-dependent dynamics of disturbed functions, pathways and elements in T21 neurogenesis, providing further insights into developmental abnormalities of the DS brain. Electronic supplementary material The online version of this article (10.1007/s12035-019-1585-3) contains supplementary material, which is available to authorized users.

DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors

“…Herein, we set out to analyze the methylation pattern of all known CpG regions and promoters in trisomic and matched euploid iPSCs differentiated into the neural lineage. The iPSCderived neural model used in this study has shown a transcriptional profile comparable to that of fetal brains at the early and mid-gestational stages, respectively [10]. We present herein the identification of CpGs regions and promoters across the genome with a consistent pattern of differential methylation pattern in T21 neural cells at two distinct stages of differentiation when compared to euploid cells.…”

“…Staining and RNA sequence analysis of neural markers confirmed that the composition of major neural cell types was comparable in trisomic and euploid cultures, and at both differentiation stages (Additional file 1a, b). The transcriptional profiles at the NPC and DiffNPC stages correspond to that of different brain regions, including the hind-and midbrain, at early-and mid-gestation, respectively [10].…”

“…Genomic DNA for methylation analysis of known CpG regions and promoters across the genome was isolated from previously established neural iPSC cultures derived from one male and one female (DS1 and DS2) with characteristic DS features and a full T21, as well as from two age and gender-matched euploid donors (Ctrl1 and Ctrl2) [10]. The DNA was obtained from iPSC derived neural progenitor cells (NPCs) [24], and further differentiated for 30 days (DiffNPC) using an undirected protocol ( [10]; Fig. 1).…”

“…As methylation of CGIs and flanking regions are likely to cause transcriptional repression of a nearby gene, we asked if the altered methylation pattern of CGI+ of the 37 enriched genes correlated with differential expression. To this end, we revisited our gene expression data from T21 and euploid lines obtained from the DiffNPC differentiation stage [10]. The analysis revealed that 12 out of the 37 genes (32%) were differentially expressed (p < 0.05) in T21 DiffNPCs (Table 1).…”

“…The supernumerary chromosome 21 causes major regional brain abnormalities and a broad range of distinct clinical features [2][3][4]. We and others have previously shown global gene expression changes in neural cells and brain specimens with T21 [5][6][7][8][9][10] and it is now generally accepted that DS is the result of complex transcriptomic changes induced by a genomic imbalance of human chromosome 21 (HSA21) [5][6][7][8][9][10]. While these earlier reports have shown several dysregulated genes in neural cells and brain tissues with T21, the precise mechanisms mediating the genome-wide transcriptomic alterations are still largely unknown.…”