Achieving a better understanding of the pathogenesis of Down syndrome (DS; trisomy 21) is important for improving the quality of life of people with DS and for understanding major phenotypes, including intellectual disability, autoimmunity, cardiac defects, Alzheimer?s disease, and cancer susceptibility and resistance, which are prominent in DS and are also highly relevant to the general population. Recently we carried out epigenetic profiling, focusing on DNA methylation, in grey matter and purified neurons and glial cells from autopsy brains, as well as T-lymphocytes, from individuals with DS vs. matched normal controls. We found highly recurrent DS-specific differences in methylation patterns (DS-DM), and observed tissue-specificity of the DS-DM, onset of the altered methylation patterns at the fetal stage, and altered mRNA expression (DS-DE) of only a subset of the affected genes. We found that CpGs in specific classes of transcription factor binding sites (TFBS) were preferentially affected, implicating altered TFBS occupancy as a mechanism in shaping the patterns of DS-DM. Additionally, we carried out whole genome bisulfite sequencing (WGBS) on brains from mouse models of DS, compared to wild-type littermates, and found alterations in methylation patterns that significantly paralleled those in the human brains. Motivated by these findings, we now seek to answer three questions ? all using well-controlled mouse models of DS carrying chromosomal triplications. First, to understand the molecular consequences of DS-DM we will identify DM genes in the mouse models and determine which of them have differential mRNA expression. We will address this question in purified cell types: T cells and GABAergic neurons. Second, we will test two hypotheses for the trans-acting mechanisms of DS-DM: (i) the abnormal methylation is due to over-expression of methylation pathway genes, including Dnmt3l and others, in the triplicated chromosome regions, and/or (ii) the abnormal patterns of methylation are shaped by overexpression of specific TF genes in the triplicated regions, leading to altered TFBS occupancy followed by altered CpG methylation in and around these sites. We will transfer segmental deletions and/or knockout alleles of individual genes into the DS mouse models to normalize gene dosage, and use WGBS and phenotyping to ask whether specific components of the DM and specific phenotypes are affected, respectively, in the offspring carrying the compound mutations. Third, we will apply state-of-the-art genomic assays to ask whether chromatin architecture within the cell nucleus is altered by the presence of the extra genetic material, and whether this alteration in turn affects DNA methylation, gene expression and phenotypes. Success of our project will identify effector and target genes for DS-DM and unravel the mechanisms underlying DS-DM. We expect that these data will significantly improve our understanding of DS pathogenesis and have broad implications for trans-acting genetic epigenetic interactions in other human developmental and neoplastic disorders that are associated with chromosomal aneuploidies.
Recently we demonstrated recurrent abnormalities in DNA methylation patterns (DS-DM) in multiple tissues from human Down syndrome (DS), and we showed that this epigenetic response to the trisomic chromosome is partly recapitulated in mouse models of DS. Here we will generate and analyze specifically designed mouse models of DS using various strategies, including Nextgen methylation sequencing and phenotypic characterization, to investigate the molecular mechanisms and biological consequences of DS-DM. Successful outcomes of this project will reveal how the extra chromosomal material (trisomy 21) affects DS phenotypes through epigenetic mechanisms, and will also have broader implications regarding the mechanisms by which chromosomal or sub-chromosomal aneuploidies produce altered epigenetic patterning in other human developmental syndromes, and in neuropsychiatric diseases and cancers.