TY - JOUR
T1 - Single-cell, whole-embryo phenotyping of mammalian developmental disorders
AU - Huang, Xingfan
AU - Henck, Jana
AU - Qiu, Chengxiang
AU - Sreenivasan, Varun K.A.
AU - Balachandran, Saranya
AU - Amarie, Oana V.
AU - Hrabě de Angelis, Martin
AU - Behncke, Rose Yinghan
AU - Chan, Wing Lee
AU - Despang, Alexandra
AU - Dickel, Diane E.
AU - Duran, Madeleine
AU - Feuchtinger, Annette
AU - Fuchs, Helmut
AU - Gailus-Durner, Valerie
AU - Haag, Natja
AU - Hägerling, Rene
AU - Hansmeier, Nils
AU - Hennig, Friederike
AU - Marshall, Cooper
AU - Rajderkar, Sudha
AU - Ringel, Alessa
AU - Robson, Michael
AU - Saunders, Lauren M.
AU - da Silva-Buttkus, Patricia
AU - Spielmann, Nadine
AU - Srivatsan, Sanjay R.
AU - Ulferts, Sascha
AU - Wittler, Lars
AU - Zhu, Yiwen
AU - Kalscheuer, Vera M.
AU - Ibrahim, Daniel M.
AU - Kurth, Ingo
AU - Kornak, Uwe
AU - Visel, Axel
AU - Pennacchio, Len A.
AU - Beier, David R.
AU - Trapnell, Cole
AU - Cao, Junyue
AU - Shendure, Jay
AU - Spielmann, Malte
N1 - Publisher Copyright:
© 2023, The Author(s).
PY - 2023/11/23
Y1 - 2023/11/23
N2 - Mouse models are a critical tool for studying human diseases, particularly developmental disorders1. However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse2. 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 sequencing3 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 regions4,5. 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.
AB - Mouse models are a critical tool for studying human diseases, particularly developmental disorders1. However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse2. 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 sequencing3 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 regions4,5. 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.
UR - http://www.scopus.com/inward/record.url?scp=85176552712&partnerID=8YFLogxK
U2 - 10.1038/s41586-023-06548-w
DO - 10.1038/s41586-023-06548-w
M3 - Journal articles
C2 - 37968388
AN - SCOPUS:85176552712
SN - 0028-0836
VL - 623
SP - 772
EP - 781
JO - Nature
JF - Nature
IS - 7988
ER -