Project Summary/Abstract The presence of an extra chromosome (trisomy or marker chromosome) is a common cause of congenital anomalies and developmental disabilities. Approximately 1% of chromosomal abnormalities are mosaic, and these patients have two cellular populations with and without chromosomal abnormalities. Pallister-Killian syndrome (PKS) is a common mosaic chromosomal disorder, and this syndrome is caused by the presence of an extra supernumerary marker chromosome, isochromosome 12p (i(12p), composed of two 12p arms that are mirror-images). We previously demonstrated that the i(12p) in PKS is formed during meiosis. All PKS zygotes contain i(12p), but during mitosis, some cells lose the i(12p) through a process known as aneuploid rescue. Consequently, all patients with PKS demonstrate mosaicism. In mosaic chromosomal disorders, altered gene dosage is believed to be the primary driver of the clinical phenotype, and the rescued cells without the chromosome abnormality are thought to be “normal.” Based on this premise, it has been proposed that there exists a correlation between the mosaic ratio (proportion of the cells possessing chromosomal abnormality in any given tissue) and the severity of patient’s clinical symptoms, but we previously demonstrated the lack of such a correlation in PKS. One possible explanation for the lack of correlation is that cells that have lost the extra chromosome continue to demonstrate functional alterations. By taking advantage of the mosaic nature of chromosomal abnormality seen in PKS, we assessed if aneuploid-rescued PKS cells retain gene expression and epigenetic abnormalities without i(12p), and we discovered similar transcriptome and histone modification profiles between PKS cells with and without the extra 12p. Hence, our data points to an ongoing “memory” effect of the i(12p) on both the transcriptome and epigenome that are not restored after the elimination of i(12p) by aneuploid rescue. The long-term goal of this project is to identify treatments to improve the clinical features associated with PKS and other numerical chromosomal disorders in children. Our preliminary data suggest that, for the full restoration of cellular functions in PKS, not only elimination of the extra chromosome but also epigenetic resetting is needed. The overall objective of this study is to investigate the role of i(12p) in the transcriptional and epigenetic alterations observed in PKS. To achieve our overall objective, we will perform further genomic analyses through two Specific Aims. In Aim 1, we will investigate gene expression alterations at the single-cell level using single-cell RNA-sequencing and mosaic PKS skin fibroblast cell lines. In Aim 2, we will investigate whether induced pluripotent stem cell reprogramming can alleviate transcriptome and epigenome alterations seen in PKS cells without i(12p). This project has a potential to drive a paradigm shift in our understanding of the basic pathobiology of mosaic chro...