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

View ORCID ProfileNeus Martinez-Abadias, View ORCID ProfileRoger Mateu Estivill, View ORCID ProfileJaume Sastre Tomas, Susan Motch Perrine, Melissa Yoon, View ORCID ProfileAlex Robert-Moreno, View ORCID ProfileJim Swoger, Lucia Russo, Kazuhiko Kawasaki, Joan Richtsmeier, View ORCID ProfileJames Sharpe
doi: https://doi.org/10.1101/246256
Neus Martinez-Abadias
European Molecular Biology Lab (EMBL);
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  • For correspondence: nieves.martinez@embl.es
Roger Mateu Estivill
Universitat de Barcelona (UB);
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Jaume Sastre Tomas
Universitat de les Illes Balears (UIB);
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Susan Motch Perrine
Pennsylvania State University;
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Melissa Yoon
Pennsylvania State University;
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Alex Robert-Moreno
European Molecular Biology Lab (EMBL);
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Jim Swoger
European Molecular Biology Lab (EMBL);
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Lucia Russo
Center for Genomic Regulation (CRG)
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Kazuhiko Kawasaki
Pennsylvania State University;
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Joan Richtsmeier
Pennsylvania State University;
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James Sharpe
European Molecular Biology Lab (EMBL);
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Abstract

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

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The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
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  • Posted January 11, 2018.

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Quantification of gene expression patterns to reveal the origins of abnormal morphogenesis
Neus Martinez-Abadias, Roger Mateu Estivill, Jaume Sastre Tomas, Susan Motch Perrine, Melissa Yoon, Alex Robert-Moreno, Jim Swoger, Lucia Russo, Kazuhiko Kawasaki, Joan Richtsmeier, James Sharpe
bioRxiv 246256; doi: https://doi.org/10.1101/246256
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Quantification of gene expression patterns to reveal the origins of abnormal morphogenesis
Neus Martinez-Abadias, Roger Mateu Estivill, Jaume Sastre Tomas, Susan Motch Perrine, Melissa Yoon, Alex Robert-Moreno, Jim Swoger, Lucia Russo, Kazuhiko Kawasaki, Joan Richtsmeier, James Sharpe
bioRxiv 246256; doi: https://doi.org/10.1101/246256

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