Single Nucleus RNA-Sequencing Reveals Overall Conservation of Hypothalamic Cell Identities but Differential Expression of Specific Genes in the Magel2 Null Mouse Model of Prader-Willi Syndrome

Abstract

Abstract Prader-Willi syndrome (PWS) is a genetic disorder affecting 1 in 10,000 to 30,000 live births. Diagnostic features of PWS including insatiable appetite and obesity are well-defined and many are associated with disruption of hypothalamic function. PWS is caused by sporadic or inherited loss of expression from the paternal allele of one or more maternally imprinted/silenced genes located in chromosomal region 15q11-q13 that encompasses five protein coding genes Mkrn3, Magel2, Necdin and Snurf-Snprn and a family of snoRNAs. Seminal studies have indicated that isolated Magel2 gene silencing plays a pivotal role in the development of many, but not all, clinical features of PWS. Magel2 is highly expressed in the hypothalamus and loss of function studies revealed substantial cellular and molecular changes in hypothalamic neurons located in the suprachiasmatic, paraventricular, supraoptic and arcuate nuclei and the lateral hypothalamus. In addition to neuronal alterations, loss of MAGEL2 increases the density and activation of microglia in adult hypothalamus. In the current study, we characterized global changes in hypothalamic gene expression and searched for novel cell populations associated with loss of Magel2 expression using single nucleus RNA sequencing. Single cell nuclei were isolated in two technical replicates per group from hypothalami of adult male and female Magel2-null (C57BL/6-Magel2tm1Stw/J) and wild type sibling mice for the 10X genomics scRNA-seq pipeline. A total of 63,470 cells divided approximately equally by sex and Magel2 genotype were analyzed. Unsupervised cell clustering identified 19 distinct clusters in males (10 neuronal and 9 non-neuronal) and 21 clusters in females (11 neuronal and 10 non-neuronal) based on their transcriptional profiles of signature genes. The percentages of total cells and the transcriptional profiles of each defined cluster from all four combinations of genotype and sex were nearly identical, indicating that loss-of-function of Magel2 does not alter overall cell cluster identities in the hypothalamus. However, a quantitative analysis of gene expression profiles from all individual clusters demonstrated upregulation of a set of genes including Fkbp5, Zbtb16, Htra1, 2900097C17Rik and 1700030F04Rik predominantly in oligodendrocytes and astrocytes in both sexes of Magel2 null mice. In contrast, the majority of down-regulated genes were found in neuronal cell clusters in both sexes of Magel2 null mice. Our current study is the first to characterize cellular and genetic changes in the whole hypothalamus due to the lack of MAGEL2. The data provide a valuable resource for elucidating the regulatory mechanisms of MAGEL2 for the pathogenesis of PWS and shed light on the discovery of new candidate targets for the potential treatment of PWS. This study is supported by the Foundation for Prader-Willi Research and NIH grant R01DK068400.