Gastrulation-stage gene expression in Nipbl+/- mouse embryos foreshadows the development of syndromic birth defects

In animal models, Nipbl-deficiency phenocopies gene expression changes and birth defects seen in Cornelia de Lange Syndrome (CdLS), the most common cause of which is Nipbl-haploinsufficiency. Previous studies in Nipbl+/- mice identified aberrant gene expression and heart defects as early as cardiac crescent (CC) stage. Here, we performed single-cell RNA-sequencing on wildtype (WT) and Nipbl+/- mouse embryos at CC- and earlier (gastrulation) stages. Nipbl+/- embryos had fewer mesoderm cells than WT and altered proportions of mesodermal cell subpopulations. These findings were associated with an underexpression of genes implicated in driving specific mesodermal lineages. Nipbl+/- embryos also misexpressed developmentally-critical genes, including the transcription factor, Nanog, and genes governing left-right and anterior-posterior patterning. These events of cell misallocation and transcriptional dysregulation foreshadowed defects in tissue composition and patterning that arise later in Nipbl+/- mice, offering insights into early developmental contributions to birth defects in CdLS. We performed single cell RNA sequencing (10X Genomics Chromium) on 2 pairs of E7.4 early bud wildtype mouse embryos, 5 pairs of E7.5 late bud Nipbl Flox/+ (which express Nipbl at wildtype levels) embryos, 6 pairs of E7.5 late bud Nipbl FIN/+ (which express Nipbl at Nipbl +/- levels) embryos, 2 pairs of E7.6 early head fold wild type embryos, 8 E7.75 cardiac crescent Nipbl Flox/+ embryos, and 8 E7.75 cardiac crescent Nipbl FIN/+ embryos. Update: [09-22-2023] GSM4586367 (LB_FLOX_2) was removed because the sample contained cells of mixed genotype. Update: [10-17-2023] Additional samples, and processed data generated from multiple/merged samples (as detailed in the readme.txt) have been included.