PROJECT SUMMARY. Down syndrome (DS), the genetic condition caused by trisomy 21 (T21), is the most prevalent chromosomal abnormality and a leading cause of intellectual and developmental disability. T21 affects the development and/or function of nearly every organ system, predisposing individuals with DS to many co-occurring conditions such as Alzheimer’s disease, congenital heart defects, and autoimmune disorders, among others. Although it is accepted that T21 causes genome-wide dysregulation of gene expression programs, little is known about how T21 affects gene expression across different tissues and organs, and how these effects contribute to the etiology of the co-occurring conditions of DS. Therefore, there is a clear need to understand the complex cause-effect relationships between T21, altered gene expression, and organ development and pathophysiology. Several mouse models of DS recapitulate key phenotypes of DS and have been used to study gene expression dysregulation in DS. Additionally, induced pluripotent stem cell (iPSC) systems have been employed to study the effects of T21 in human cell types. Therefore, in clear response to the Funding Opportunity Announcement PAR- 22-247, we propose here to generate a Trisomy 21 Model Atlas of tissue-specific murine and human transcriptomes, matched to detailed metrics of organ development and architecture. The use of mouse models will provide insights into tissue- and developmental stage-specific transcriptome changes and pathophysiology, while human cell types differentiated from iPSCs will dissect cell-intrinsic features of T21 and validate findings from the mouse models. Our Specific Aims are: 1. Generate an atlas of gene expression programs affected by trisomy 21 across model systems. Supported by strong preliminary data, we propose here to complete an atlas of transcriptome changes in ten organs across three developmental stages in mice and matched data from human cell types derived from iPSCs. 2. Define the impact of trisomy 21 on organ development and pathophysiology at the cellular level. To investigate the link between dysregulated gene expression and tissue dysfunction, we will assess organ development and pathophysiology through histopathological profiling, multiplexed immunofluorescence imaging, single-cell RNA-sequencing, and characterization of human organoids derived from iPSCs. 3. Curate, organize, and share all data for open access through the INCLUDE Data Hub. We will ensure that all data is made publicly available in the INCLUDE Data Hub by completing careful file curation and organization, developing a metadata schema, and creating a code repository. This will ensure that the atlas becomes a lasting resource that can be used beyond the scope of this grant. Altogether, this resource will advance our understanding of the effects of T21 on organ development and pathology, while enabling findings cross-validated in mouse models and human cell types.

PROJECT NARRATIVE. Down syndrome (DS), the genetic condition caused by triplication of chromosome 21 (T21), is the most common chromosomal abnormality and a leading cause of intellectual and developmental disability. Although it is accepted that T21 causes genome-wide dysregulation of gene expression programs, little is known about how T21 affects gene expression across different tissues and organs, and how these effects contribute to the developmental and clinical hallmarks of DS. To address this knowledge gap, this proposal aims to generate a comprehensive atlas of tissue-specific gene expression changes caused by T21, matched to detailed metrics of organ development and architecture.