Single-cell, whole-embryo phenotyping of mammalian developmental disorders

Huang, Xingfan; Henck, Jana; Qiu, Chengxiang; Sreenivasan, Varun K. A.; Balachandran, Saranya; Amarie, Oana V.; de Angelis, Martin Hrabě; Behncke, Rose Yinghan; Chan, Wing-Lee; Despang, Alexandra; Dickel, Diane E.; Duran, Madeleine; Feuchtinger, Annette; Fuchs, Helmut; Gailus-Durner, Valerie; Haag, Natja; Hägerling, Rene; Hansmeier, Nils; Hennig, Friederike; Marshall, Cooper; Rajderkar, Sudha; Ringel, Alessa; Robson, Michael; Saunders, Lauren M.; da Silva-Buttkus, Patricia; Spielmann, Nadine; Srivatsan, Sanjay R.; Ulferts, Sascha; Wittler, Lars; Zhu, Yiwen; Kalscheuer, Vera M.; Ibrahim, Daniel M.; Kurth, Ingo; Kornak, Uwe; Visel, Axel; Pennacchio, Len A.; Beier, David R.; Trapnell, Cole; Cao, Junyue; Shendure, Jay; Spielmann, Malte

doi:10.1038/s41586-023-06548-w

Title: Single-cell, whole-embryo phenotyping of mammalian developmental disorders

Journal Article · 14 November 2023 · Nature (London)

DOI: https://doi.org/10.1038/s41586-023-06548-w · OSTI ID:2349056

Huang, Xingfan ^[1]; Henck, Jana ^[2];

^[1];

^[3]; Balachandran, Saranya ^[3];

^[4];

^[5];

^[6]; Chan, Wing-Lee ^[6]; Despang, Alexandra ^[7];

^[8];

^[1]; Feuchtinger, Annette ^[4];

^[4];

^[4]; Haag, Natja ^[9]; Hägerling, Rene ^[10];

^[10]; Hennig, Friederike ^[11]; Marshall, Cooper ^[1] more »

Univ. of Washington, Seattle, WA (United States)
Univ. of Lübeck (Germany); Kiel Univ., Lübeck (Germany); Max Planck Inst. for Molecular Genetics, Berlin (Germany)
Univ. of Lübeck (Germany); Kiel Univ., Lübeck (Germany)
German Research Center for Environmental Health (GmbH), Neuherberg (Germany)
German Research Center for Environmental Health (GmbH), Neuherberg (Germany); Technische Univ. München, Freising (Germany); German Center for Diabetes Research (DZD), Neuherberg (Germany)
Inst. of Medical Genetics and Human Genetics of the Charité, Berlin (Germany); Universitätsmedizin Berlin, (BCRT) (Germany)
Max Planck Inst. for Molecular Genetics, Berlin (Germany); Universitätsmedizin Berlin, (BCRT) (Germany)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
RWTH Aachen Univ. (Germany)
Max Planck Inst. for Molecular Genetics, Berlin (Germany); Inst. of Medical Genetics and Human Genetics of the Charité, Berlin (Germany); Universitätsmedizin Berlin, (BCRT) (Germany)
Max Planck Inst. for Molecular Genetics, Berlin (Germany)
Max Planck Inst. for Molecular Genetics, Berlin (Germany); Inst. of Medical Genetics and Human Genetics of the Charité, Berlin (Germany)
German Center for Diabetes Research (DZD), Neuherberg (Germany)
Univ. Medical Center Göttingen (Germany)
Univ. of Washington, Seattle, WA (United States); Seattle Children’s Research Inst., WA (United States)
Univ. of Washington, Seattle, WA (United States); Allen Discovery Center for Cell Lineage Tracing, Seattle, WA (United States)
Rockefeller Univ., New York, NY (United States)
Univ. of Washington, Seattle, WA (United States); Allen Discovery Center for Cell Lineage Tracing, Seattle, WA (United States); Howard Hughes Medical Inst., Seattle, WA (United States)
Univ. of Lübeck (Germany); Kiel Univ., Lübeck (Germany); Max Planck Inst. for Molecular Genetics, Berlin (Germany); German Centre for Cardiovascular Research (DZHK), Lübeck (Germany)

Mouse models are a critical tool for studying human diseases, particularly developmental disorders. However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse. Here we set out to establish single-cell RNA sequencing of the whole embryo as a scalable platform for the systematic phenotyping of mouse genetic models. We applied combinatorial indexing-based single-cell RNA sequencing to profile 101 embryos of 22 mutant and 4 wild-type genotypes at embryonic day 13.5, altogether profiling more than 1.6 million nuclei. The 22 mutants represent a range of anticipated phenotypic severities, from established multisystem disorders to deletions of individual regulatory regions. We developed and applied several analytical frameworks for detecting differences in composition and/or gene expression across 52 cell types or trajectories. Some mutants exhibit changes in dozens of trajectories whereas others exhibit changes in only a few cell types. We also identify differences between widely used wild-type strains, compare phenotyping of gain- versus loss-of-function mutants and characterize deletions of topological associating domain boundaries. Notably, some changes are shared among mutants, suggesting that developmental pleiotropy might be ‘decomposable’ through further scaling of this approach. Overall, our findings show how single-cell profiling of whole embryos can enable the systematic molecular and cellular phenotypic characterization of mouse mutants with unprecedented breadth and resolution.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2349056

Journal Information:: Nature (London), Journal Name: Nature (London) Journal Issue: 7988 Vol. 623; ISSN 0028-0836

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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