Genomic, transcriptomic and metabolomic analysis of trisomy 21

Down syndrome (DS) is caused by three copies of chromosome 21 (Hsa21). The pathogenetic mechanism underlying cognitive delay in individuals with DS is unclear, and there is no therapeutic strategy to improve this condition. In this work, the genotype-phenotype correlation was investigated in trisomy (T21) at the genomic, transcriptomic, and metabolomic levels to expand knowledge about the molecular mechanisms underlying the pathogenesis of DS. Two different research strategies were followed to approach this complex purpose. The first research strategy was to start from the sequence of Hsa21. The highly restricted-DS critical region (HR-DSCR) is the “minimal” region always associated with a diagnosis of DS in partial T21 cases and likely associated with DS “core” features, particularly intellectual disability (ID). We re-confirmed the HR-DSCR genomic limits, and we characterized the locus through in-silico and in-vitro gene expression analyses. We developed a new T21 cell model having a deletion of the HR-DSCR to re-establish the normal copy number of this region and study the phenotypic changes that this deletion resulted in. The second research strategy was to start from the metabolism, searching for alterations that could cause ID in DS. We focused on one-carbon metabolism, dosing central metabolite levels in the plasma and urine samples of DS and control groups, finding some dysregulated metabolic intermediates. The expression of genes involved in the one-carbon pathway was studied in silico using our previously published blood transcriptome map (DS vs control) and in vitro on a broader number of samples. Several differential expressed genes and statistically significant correlations emerged, confirming the complexity and the dysregulation of this pathway. Moreover, the quality of microarray-derived expression data was improved. These results could strengthen our clinical trial proposal that rebalancing the one-carbon pathway through administering a metabolic intermediate to children with DS could improve their cognitive status.