The contribution of X-chromosome-linked genes to cellular phenotypes and AD-related pathology in Down Syndrome

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Abstract Down Syndrome (DS) is caused by triplication of human chromosome 21 (HSA21), resulting in intellectual disability, motor dysfunction, and early onset Alzheimer’s Disease (AD). The mechanistic connection between triplicated genes in DS and the all-encompassing imbalance in gene expression underlying the abnormalities seen in DS brain cells has not been established. It is also unknown how this global transcriptomic disbalance leads to intellectual disability and early development of AD-related pathology in DS, nor what genes play a key role in these processes. In our preliminary studies, we generated oligocortical spheroids (OLS) derived from DS isogenic induced pluripotent stem cell (iPSCs) lines. Trisomic OLS recapitulate DS and AD- related cellular phenotypes, including reduced cortical volume, aberrant myelination and pathological depositions of amyloid beta and hyper-phosphorylated tau. Through our single-cell RNA sequencing (scRNA-seq) analysis of euploid and trisomic OLS, we identified a cluster of X- linked genes containing brain expressed X-linked/transcription elongation factor A (SII) (BEX/TCEAL) family members, that is downregulated in trisomy. At the same time, trisomic cells showed a significantly increased expression of non-coding X-inactive specific transcript (XIST), responsible for the X-chromosome inactivation. Importantly, the dysregulation of BEX/TCEAL is linked to psychiatric disorders, intellectual deficits, neurodegeneration, and AD. Noticeably, other recent studies, including those performed in DS cell lines and human postmortem brains, showed downregulated expression of different genes in this cluster accompanied by enhanced XIST levels. However, the aberrant expression of these transcription factors and their potential connection to brain pathology in trisomy has been neglected. Herein, we hypothesize that downregulation of BEX/TCEAL is causatively related to abnormal brain development and AD pathology in DS. In our studies, we will determine the contribution of X-chromosome-linked genes’ repression to DS-related pathology by assessing whether reducing XIST or restoring BEX/TCEAL gene expression can mitigate DS-associated cellular phenotypes. We will specifically focus on the effect of BEX2 and TCEAL7 downregulation in DS since their expression was most consistently downregulated across multiple developmental periods in DS human transcriptomic study, further supporting our preliminary data. We will also define the genome-wide downstream targets of BEX2 and TCEAL7 and their significance in trisomy. Our translational, human-directed study will ultimately test the causative link between the dysregulation of X- chromosome-linked genes’, and transcriptional and phenotypical alterations in trisomy.