A mosaic Down syndrome model system comparing isogenic trisomic/disomic cells to unmask trisomy-21 related genomic, epigenomic, and senescence changes acquired across the lifespan

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PROJECT SUMMARY Down syndrome (Ds) has been associated with multiple, co-occurring health and behavioral conditions, as well as precocious (or accelerated) aging. The results of recent clinical studies are providing a clearer picture of health outcomes in childhood, adolescence, and early adulthood in people with Ds; yet very little is known about the cascade of trisomy 21-related biological changes that arise to culminate in the development of co-occurring conditions. The recent discovery of cytosolic DNA as an “integrator” of changes acquired in somatic cells provides a new research direction for identifying age- and trisomy 21-related biological alterations. Cells can acquire cytosolic DNA via micronuclei (MN) formation and extrachromosomal telomere circles (t-circles). A subset of this cytoplasmic self-DNA is recognized by innate immune surveillance pathways, which, in turn, lead to increased levels of senescence. We hypothesize that trisomy 21 increases MN levels and telomere attrition, leading to a perpetuating cycle of senescence and methylation alterations that accumulate/increase in frequency with age. One powerful approach for discovering trisomy 21-specific alterations is to evaluate biological attributes in cells from people with mosaicism for trisomy 21 (mDs). One can unmask and quantify trisomy 21-induced changes by “subtracting” values observed in isogenic disomic cells from those present in trisomic cells (thereby removing the confounding effects due to total background genetic make-up, as well as environmental influences). Thus, to identify the impact of a trisomy 21 imbalance on cytosolic DNA pathways, we will longitudinally compare biological measures in isogenic trisomic versus disomic cells from 65 people with mDs over 3 time points, (including baseline data, and spanning as much as 30 years of follow-up). To test our study hypothesis, we will quantify: (1) cytosolic self-DNA via a MN assay; (2) subtelomere/telomere alterations or dysfunction; (3) senescence patterns and cytokine levels; and (4) DNA methylation patterns. Each of these biological factors will be analyzed with “state of the art” tools we developed/optimized, which include: chromosome-specific assays for MN [SKY/FISH MN assay]); novel telomere/subtelomere length assays [Q-FISH & nanomapping]; telomere dysfunction assays; senescence, transcriptome, and cytokine marker assays; genome-wide studies for DNA methylation; and bioinformatic modeling. We will also collect/evaluate deep phenotype data. By interrogating relationships among and between biological measures with phenotypic traits, we will discover their role in mediating health outcomes. In summary, this longitudinal study of isogenic trisomic/disomic cells will enable us to “unmask” trisomy 21-associated changes in biological cascades and will provide the first assessment of the role of cytosolic DNA in health conditions associated with Ds/mDs. By identifying driver/mediator relationships between biomarkers, we will create new algorithms that will help physicians recognize health conditions at an earlier age in people with Ds/mDs. Importantly, we will identify new therapeutic targets that could transform our approach for developing treatments to alleviate symptoms of health conditions acquired by people with mDs/Ds.