3D Cardiomics: An interactive 3D visualisation of the adult cardiac transcriptome — ASN Events
  1. Schedule
  2. Poster Session 2
  3. 3D Cardiomics: An interactive 3D visualisation of the adult cardiac transcriptome

3D Cardiomics: An interactive 3D visualisation of the adult cardiac transcriptome (#246)

Fernando J. Rossello 1 2 , Nathalia M. Tan 1 2 3 , Alex Tokolyi 1 3 , Milena Furtado 1 4 , Mauro W. Costa 1 4 , Jan M. Ruijter 5 , Hieu Nim 1 3 , Nadia Rosenthal 1 4 , Susan K. Nilsson 1 6 , Mirana Ramialison 1 3 , Jose M. Polo 1 2
  1. Australian Regenerative Medicine Institute, Monash University, VIC, Australia
  2. Department of Anatomy and Developmental Biology, Monash University, VIC, Australia
  3. EMBL–Australia Collaborating Group, Systems Biology Institute Australia, Monash University, VIC, Australia
  4. The Jackson Laboratory, Bar Harbor, ME, United States
  5. Department of Anatomy, Embryology & Physiology, Academic Medical Center, Meibergdreef 15, 1100AZ Amsterdam, The Netherlands
  6. CSIRO Manufacturing, Clayton VIC, Australia

The mammalian heart is a complex structure comprised of 4 chambers with several types of specialised cells. Different forms of congenital heart malformations can arise from mutations occurring in these subtypes. To understand how a healthy adult mammalian heart is maintained, knowledge of gene expression at a high resolution in addition to a way to practically view this data is essential. 

In situ hybridisation (ISH) has proven useful to examine gene expression patterns over a whole organism, but is limited by the time taken to analyse many genes and the qualitative nature of the resulting data. High throughput sequencing of mRNA (RNA-seq) allows us to record gene expression at a much finer sensitivity, but few attempts have been made to use this technology in order to understand how gene expression varies over regions of mammalian organs. This is due to the size and complexity of organs leading to vast amounts of data that can be difficult to interpret and analyse.

We performed RNA-sequencing on 18 different regions of the adult murine heart and established a framework: 3D Cardiomics, which for the first time allows anyone to see and compare how any genes are expressed over these regions in three dimensions. 3D Cardiomics is available at 3d-cardiomics.erc.monash.edu. 

Through developing this software, we observed many cases of gene expression gradients traversing the front-back, top-bottom and left-right axis; as well as distinct markers for the atrium and ventricle. Common gene expression patterns were also investigated using Pearson’s correlation which allowed the discovery of genes expressed in similar patterns across the heart. Biological insights were gleaned from the expression levels observed in distinct heart pieces, for example those correlating with the sinoatrial (SA) node. 

Clinicians, researchers and teachers can benefit from this technology, as it gives them an unprecedented view of gene expression throughout the heart. As the first three dimensional visualisation of genome-wide gene expression in an adult mammalian heart, 3D Cardiomics will aid in the understanding of how gene expression differs throughout a healthy heart to allow further understanding of changes to gene expression in heart disease. In the future, our visualisation could be expanded to include additional -omics datasets as well as physiological and electrical measurements tailored in an individual manner.

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