Investigating epigenetic mechanisms in Down syndrome using human cellular models

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SUMMARY Down syndrome (DS), driven by an extra copy of chromosome 21 (HSA21), is associated with a broad spectrum of neurological and non-neurological phenotypes, profound interindividual variation and significant changes in genome-wide gene expression and DNA methylation patterns, although underlying mechanisms remain incompletely resolved. Epigenetic re-wiring is a promising candidate for achieving the types of genome- wide changes that are observed in DS as well as contributing to interindividual variation in disease phenotypes. However, this area of investigation, particularly at the level of chromatin states, remains almost entirely unexplored in DS. Leveraging human induced pluripotent stem cell (iPSC) models, we recently conducted a novel, unbiased, and comprehensive survey of the relative abundance of over 80 different histone post- translational modifications (PTMs) in DS versus euploid controls using histone mass spectrometry. These results, coupled with additional validation experiments, revealed a set of novel disruptions to H3K36me2, H3K4me1 and H3K23ac abundance which we predict contribute to DS disease biology. In this proposal, we aim to expand our analyses to obtain, for the first time, a comprehensive view of how trisomy 21 disrupts histone PTMs and the downstream impacts on molecular and cellular function. Importantly, this proposal moves away from a HSA21/gene-centric view of DS, traditionally studied using murine models, to explore how epigenetic re-wiring may intersect with a set of key unanswered questions in the field using physiologically relevant human cellular models. Conceptually, our experiments are designed to explore questions around the significant changes in dosage of genes encoded on euploid chromosomes, the profound interindividual variation in DS, how different cell types may be impacted by trisomy 21 in divergent or convergent ways, and how DS mechanisms may overlap with other diseases. Specifically, in Aim I, we will systematically define the scope of histone PTM abundance phenotypes in DS using a cohort of different donor individuals and cell types to analyze interindividual and cell-type variation, and then connect these changes to chromatin binding and transcriptional output for select modifications to elucidate fundamental mechanisms. In Aim II, we will test the molecular reversibility of histone phenotypes in DS using pharmacological and CRISPRa approaches to identify potential clinically relevant targets in DS. In Aim III, we will test the hypothesis that dysregulation of histone PTMs drives core neurobiological phenotypes in DS to further understand their functional relevance and potentially map known cellular phenotypes to novel molecular mechanisms. Collectively, the rigorous and innovative analyses in this Transformative Research Award application will illuminate new mechanisms of epigenetic dysregulation in DS, explore a set of key unanswered questions in the field and may ultimately inform on therapeutic strategies for DS patients.