3D-cardiomics: A spatial transcriptional atlas of the mammalian heart

Understanding the spatial gene expression and regulation in the heart is key to uncovering its developmental and physiological processes, during homeostasis and disease. Numerous techniques exist to gain gene expression and regulation information in organs such as the heart, but few utilize intuitiv...

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Published in:Journal of molecular and cellular cardiology 2022-02, Vol.163, p.20-32
Main Authors: Mohenska, Monika, Tan, Nathalia M., Tokolyi, Alex, Furtado, Milena B., Costa, Mauro W., Perry, Andrew J., Hatwell-Humble, Jessica, van Duijvenboden, Karel, Nim, Hieu T., Ji, Yuan M.M., Charitakis, Natalie, Bienroth, Denis, Bolk, Francesca, Vivien, Celine, Knaupp, Anja S., Powell, David R., Elliott, David A., Porrello, Enzo R., Nilsson, Susan K., del Monte-Nieto, Gonzalo, Rosenthal, Nadia A., Rossello, Fernando J., Polo, Jose M., Ramialison, Mirana
Format: Article
Language:English
Subjects:
3D organ
Bioinformatics
Cardiac model
Cardiac systems
Data visualization
Spatial transcriptomics
Systems biology
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Summary:Understanding the spatial gene expression and regulation in the heart is key to uncovering its developmental and physiological processes, during homeostasis and disease. Numerous techniques exist to gain gene expression and regulation information in organs such as the heart, but few utilize intuitive true-to-life three-dimensional representations to analyze and visualise results. Here we combined transcriptomics with 3D-modelling to interrogate spatial gene expression in the mammalian heart. For this, we microdissected and sequenced transcriptome-wide 18 anatomical sections of the adult mouse heart. Our study has unveiled known and novel genes that display complex spatial expression in the heart sub-compartments. We have also created 3D-cardiomics, an interface for spatial transcriptome analysis and visualization that allows the easy exploration of these data in a 3D model of the heart. 3D-cardiomics is accessible from http://3d-cardiomics.erc.monash.edu/. [Display omitted] •Transcriptome-wide profiling of the murine heart reveals complex spatial patterns.•Identification of novel markers for cardiac subsections.•3D-cardiomics allows for interrogation of gene expression in the adult heart. See https://3d-cardiomics.erc.monash.edu.au/.•Users can run a standalone 3D-cardiomics version for custom visualization. See https://github.com/Ramialison-Lab/3DCardiomics.
ISSN:0022-2828
1095-8584
DOI:10.1016/j.yjmcc.2021.09.011