| Down syndrome (DS; trisomy21) is characterized by a complete, or occasionally partial, triplication of chromosome21(Hsa21). With an incidence of about one in650～1000births, DS is the most common autosomal abnormality affecting live-born infants. More than80clinical features, with variation in number and in severity, are reported in DS. Mental retardation and congenital heart defects are typically clinical traits in DS individuals and widely studied.In studies of DS, researchers reported that the symptomatic onset of some neurological complications in DS individuals is age-specific, because certain complications will arise in childhood and other complications will arise in adulthood. For instance, after the first fourth decade of life, DS individuals start to display many of the same neuropathological features as individuals with Alzheimer’s disease. These findings suggest that temporal regulation of trisomic genes and its downstream effects (either directly or indirectly) on the expression of non-Hsa21genes in DS could occur, and consequently impact on DS phenotypes at different developmental stages. Therefore, investigating the expression profile in a temporal manner may provide a more comprehensive picture of DS phenotypes, leading to a better understanding of this syndrome. Nevertheless, due to the difficulty in accessing sufficient amounts of the desired tissues from DS individuals, the knowledge of transcriptome variation in a temporal dimension is quite sparse. Peripheral blood is one of the most readily available tissue sources for gene-expression studies. And there are multiple blood cell-related phenotypes, including increased risk to develop leukemia, decreased lymphocyte peripheral counts, as well as vulnerability to recurrent bacterial and viral infections. Therefore, in this study, peripheral blood samples from DS children and neonates and age-matched control were collected. Using exon array, we measured gene-expression profiles in peripheral blood cells from DS and age-matched control samples at the two developmental stages and performed functional analysis. A total of174transcript clusters (gene-level) with eight located on Hsa21in neonate (N) group and383transcript clusters including57on Hsa21in childhood (C) group were significantly dysregulated in DS individuals.Only22dysregulated genes were shared at both of the two stages, reflecting temporally dynamic variation in gene expression in DS. Further functional analysis revealed that the dysregulated genes in DS were significantly enriched in two KEGG pathways in N group and six pathways in C group. These pathways included leukocyte trans-endothelial migration, B cell receptor signaling pathway and primary immunodeficiency, etc., which causally implicated dysfunctional immunity in DS. Our results provided a comprehensive picture of expression patterns of DS at the two developmental stages and point towards candidate genes and molecular pathways potentially associated with the immune defects in DS.Furthermore, using the exon array, we firstly explored splicing variation of mRNA between DS peripheral blood cells and age-matched control at the two stages. Our result showed that104candidate genes including4Hsa21genes and299including13Hsa21genes were differentially spliced between DS and control individuals. No identical splicing event in these splice variants were observed between DS children and neonates. Overwhelming majority (>90%) of candidate splice variants occurred within coding regions of the genes, most (>60%) of the transcript isoforms in DS were removal of the exons, suggesting that protein sequence variation, even functional defects in DS, and therefore contribute to DS phenotypes.Genome-wide expression analysis in DS PBCs revealed that only a part of Hsa21genes in DS were dysregulated, with many trisomic genes displaying normal expression, which were widely observed in other’s reports. Some researchers attributed it to gene dosage compensation effects. One hypothesis suggests that the trisomic genes with normal expression in DS might be epigenetically regulated by altered methylation pattern of these genes. However, a comprehensive analysis of DNA methylation profile of Hsa21in DS is undefined. Here, a high-content chromosome21tilling array wasspecifically designed to explore DNA methylatioin pattern and evaluate the hypothesis. We used immunoprecipitation (IP) approach followed by tilling array analysis to generate methylation pattern of Hsa21in DS PBLs. Our results revealed that DNA methylation of Hsa21in DS PBL was not varied in comparison with controls, and most of promoter CpG island on Hsa21wereunmethylated. Therefore, we concluded that DNA methylation is not a general dosage compensation mechanism underlying widely normally expressed trisomic chromosome21in DS... |
PDF Full Text Request