Quantification of gene expression patterns to reveal the origins of abnormal morphogenesis

Abstract

16The earliest developmental origins of dysmorphologies are poorly understood in many congenital 17 diseases. They often remain elusive because the first signs of genetic misregulation may initiate as 18 subtle changes in gene expression, which can be obscured later in development due to secondary 19 phenotypic effects. We here develop a method to trace back the origins of phenotypic abnormalities by 20 accurately quantifying the 3D spatial distribution of gene expression domains in developing organs. By 21 applying geometric morphometrics to 3D gene expression data obtained by Optical Projection 22 Tomography, our approach is sensitive enough to find regulatory abnormalities never previously 23 detected. We identified subtle but significant differences in gene expression of a downstream target of 24 the Fgfr2 mutation associated with Apert syndrome. Challenging previous reports, we demonstrate that 25Apert syndrome mouse models can further our understanding of limb defects in the human condition. 26Our method can be applied to other organ systems and models to investigate the etiology of 27 malformations. 28

Combined method of whole mount and block‐face imaging: Acquisition of 3D data of gene expression pattern from conventional in situ hybridization

“…However, since μCT measures X-ray transmissivity and cannot distinguish colors, it can provide fine structural data, but not suitable gene expression pattern data. Opticalbased 3D imaging systems, such as light sheet fluorescence microscopy (LSFM) and optical projection tomography (OPT), enable the creation of 3D reconstructed images of specific gene expression patterns and 2D optical cutting planar images (Keller, 2013;Martínez-Abadías et al, 2018). Both LSFM and OPT are useful for obtaining 3D gene expression data; however, 2D planar images from these methods are virtual sections and cannot be re-used for various labeling methods, as can be done using the CoMBI method.…”

Quantifying the relationship between cell proliferation and morphology during development of the face

“…Connecting these mechanisms to 3D change in organismal form requires quantification of cellular processes in whole embryonic structures over developmental time. While three dimensional morphology can be quantified from microCT and optical projection tomography images (Parsons et al, 2008;Boughner et al, 2008;Xu et al, 2015;Martínez-Abadías et al, 2018), cellular dynamics are much less accessible in three dimensions. This is because the vast majority of quantification of cellular dynamics is based on analysis of serial histological sections, with localized sampling rather than whole embryonic structures (Ramaesh and Bard, 2003;Miklius and Hilgenfeldt, 2011;Russ and Dehoff, 2012).…”