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

Monika Mohenska; Nathalia M Tan; Alex Tokolyi; Milena B Furtado; Mauro W Costa; Andrew J Perry; Jessica Hatwell-Humble; Karel van Duijvenboden; Hieu T Nim; Yuan M M Ji; Natalie Charitakis; Denis Bienroth; Francesca Bolk; Celine Vivien; Anja S Knaupp; David R Powell; David A Elliott; Enzo R Porrello; Susan K Nilsson; Gonzalo Del Monte-Nieto; Nadia A Rosenthal; Fernando J Rossello; Jose M Polo; Mirana Ramialison

doi:10.1016/j.yjmcc.2021.09.011

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

J Mol Cell Cardiol. 2022 Feb:163:20-32. doi: 10.1016/j.yjmcc.2021.09.011. Epub 2021 Oct 5.

Authors

Monika Mohenska¹, Nathalia M Tan¹, Alex Tokolyi², Milena B Furtado³, Mauro W Costa³, Andrew J Perry⁴, Jessica Hatwell-Humble⁵, Karel van Duijvenboden⁶, Hieu T Nim⁷, Yuan M M Ji², Natalie Charitakis⁸, Denis Bienroth⁹, Francesca Bolk¹⁰, Celine Vivien⁹, Anja S Knaupp¹, David R Powell⁴, David A Elliott¹¹, Enzo R Porrello¹², Susan K Nilsson⁵, Gonzalo Del Monte-Nieto², Nadia A Rosenthal¹³, Fernando J Rossello¹⁴, Jose M Polo¹⁵, Mirana Ramialison¹⁶

Affiliations

¹ Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, Victoria, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia.
² Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia.
³ Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; The Jackson Laboratory, Bar Harbor, ME, USA.
⁴ Monash Bioinformatics Platform, Monash University, Wellington Road, Clayton, Victoria, Australia.
⁵ Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; Biomedical Manufacturing, CSIRO Manufacturing, Bag 10, Clayton South, Australia.
⁶ Department of Medical Biology, Academic Medical Centre, Amsterdam, the Netherlands.
⁷ Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; Faculty of Information Technology, Monash University, Clayton, Victoria, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne 3052, VIC, Australia; Systems Biology Institute Australia, Clayton, Victoria, Australia.
⁸ Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne 3052, VIC, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.
⁹ Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne 3052, VIC, Australia.
¹⁰ Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne 3052, VIC, Australia; Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Melbourne 3052, VIC, Australia.
¹¹ Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne 3052, VIC, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.
¹² Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne 3052, VIC, Australia; Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Melbourne 3052, VIC, Australia; Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne 3010, VIC, Australia.
¹³ Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; The Jackson Laboratory, Bar Harbor, ME, USA; National Heart and Lung Institute, Imperial College London, London, United Kingdom.
¹⁴ Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, Victoria, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia. Electronic address: [email protected].
¹⁵ Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, Victoria, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia. Electronic address: [email protected].
¹⁶ Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; The Jackson Laboratory, Bar Harbor, ME, USA; Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne 3052, VIC, Australia; Systems Biology Institute Australia, Clayton, Victoria, Australia. Electronic address: [email protected].

PMID: 34624332
DOI: 10.1016/j.yjmcc.2021.09.011

Abstract

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/.

Keywords: 3D organ; Bioinformatics; Cardiac model; Cardiac systems; Data visualization; Spatial transcriptomics; Systems biology.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Gene Expression Profiling / methods
Heart*
Mammals
Mice
Transcriptome*