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

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-NietoNadia A. Rosenthal, Fernando J. Rossello, Jose M. Polo, Mirana Ramialison

Research output: Contribution to journal › Article › Research › peer-review

13 Citations (Scopus)

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/.

Original language	English
Pages (from-to)	20-32
Number of pages	13
Journal	Journal of Molecular and Cellular Cardiology
Volume	163
DOIs	https://doi.org/10.1016/j.yjmcc.2021.09.011
Publication status	Published - Feb 2022

Keywords

3D organ
Bioinformatics
Cardiac model
Cardiac systems
Data visualization
Spatial transcriptomics
Systems biology

Access to Document

10.1016/j.yjmcc.2021.09.011

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Mohenska, M., Tan, N. M., Tokolyi, A., Furtado, M. B., Costa, M. W., Perry, A. J., Hatwell-Humble, J., van Duijvenboden, K., Nim, H. T., Ji, Y. M. M., Charitakis, N., Bienroth, D., Bolk, F., Vivien, C., Knaupp, A. S., Powell, D. R., Elliott, D. A., Porrello, E. R., Nilsson, S. K., ... Ramialison, M. (2022). 3D-cardiomics: A spatial transcriptional atlas of the mammalian heart. Journal of Molecular and Cellular Cardiology, 163, 20-32. https://doi.org/10.1016/j.yjmcc.2021.09.011

@article{5086981d6bfd4b3f95e17d963ffe43d4,

title = "3D-cardiomics: A spatial transcriptional atlas of the mammalian heart",

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",

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

note = "Funding Information: J.M.P. was funded by a Sylvia-Charles Viertel Fellowship and an ARC Future Fellowship. M.R. was funded by the Sun Foundation, an NHMRC/Heart Foundation Career Development Fellowship (1049980), ARC Discovery Project Grant (DP190102771) and an NHMRC Ideas Grant (APP1180905). A.T. was supported by a Biomedical Research Victoria UROP/CSL scholarship. G.dM.N. was funded by a Heart Foundation Future Leader Fellowship (102036) and ARC Discovery Project Grant (DP190101475). E.R.P. and D.A.E. acknowledge grant and fellowship support from The Stafford Fox Medical Research Foundation and the Royal Children's Hospital Foundation . MCRI is supported by the Victorian Government's Operational Infrastructure Support Program . The Australian Regenerative Medicine Institute is supported by grants from the State Government of Victoria and the Australian Government. Publisher Copyright: {\textcopyright} 2021 Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",

year = "2022",

month = feb,

doi = "10.1016/j.yjmcc.2021.09.011",

language = "English",

volume = "163",

pages = "20--32",

journal = "Journal of Molecular and Cellular Cardiology",

issn = "0022-2828",

publisher = "Elsevier",

}

Mohenska, M, Tan, NM, Tokolyi, A, Furtado, MB, Costa, MW, Perry, AJ, Hatwell-Humble, J, van Duijvenboden, K, Nim, HT, Ji, YMM, Charitakis, N, Bienroth, D, Bolk, F, Vivien, C, Knaupp, AS , Powell, DR, Elliott, DA, Porrello, ER, Nilsson, SK , del Monte-Nieto, G, Rosenthal, NA, Rossello, FJ, Polo, JM & Ramialison, M 2022, '3D-cardiomics: A spatial transcriptional atlas of the mammalian heart', Journal of Molecular and Cellular Cardiology, vol. 163, pp. 20-32. https://doi.org/10.1016/j.yjmcc.2021.09.011

TY - JOUR

T1 - 3D-cardiomics

T2 - A spatial transcriptional atlas of the mammalian heart

AU - Mohenska, Monika

AU - Tan, Nathalia M.

AU - Tokolyi, Alex

AU - Furtado, Milena B.

AU - Costa, Mauro W.

AU - Perry, Andrew J.

AU - Hatwell-Humble, Jessica

AU - van Duijvenboden, Karel

AU - Nim, Hieu T.

AU - Ji, Yuan M.M.

AU - Charitakis, Natalie

AU - Bienroth, Denis

AU - Bolk, Francesca

AU - Vivien, Celine

AU - Knaupp, Anja S.

AU - Powell, David R.

AU - Elliott, David A.

AU - Porrello, Enzo R.

AU - Nilsson, Susan K.

AU - del Monte-Nieto, Gonzalo

AU - Rosenthal, Nadia A.

AU - Rossello, Fernando J.

AU - Polo, Jose M.

AU - Ramialison, Mirana

N1 - Funding Information: J.M.P. was funded by a Sylvia-Charles Viertel Fellowship and an ARC Future Fellowship. M.R. was funded by the Sun Foundation, an NHMRC/Heart Foundation Career Development Fellowship (1049980), ARC Discovery Project Grant (DP190102771) and an NHMRC Ideas Grant (APP1180905). A.T. was supported by a Biomedical Research Victoria UROP/CSL scholarship. G.dM.N. was funded by a Heart Foundation Future Leader Fellowship (102036) and ARC Discovery Project Grant (DP190101475). E.R.P. and D.A.E. acknowledge grant and fellowship support from The Stafford Fox Medical Research Foundation and the Royal Children's Hospital Foundation . MCRI is supported by the Victorian Government's Operational Infrastructure Support Program . The Australian Regenerative Medicine Institute is supported by grants from the State Government of Victoria and the Australian Government. Publisher Copyright: © 2021 Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2022/2

Y1 - 2022/2

N2 - 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/.

AB - 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/.

KW - 3D organ

KW - Bioinformatics

KW - Cardiac model

KW - Cardiac systems

KW - Data visualization

KW - Spatial transcriptomics

KW - Systems biology

UR - http://www.scopus.com/inward/record.url?scp=85116929932&partnerID=8YFLogxK

U2 - 10.1016/j.yjmcc.2021.09.011

DO - 10.1016/j.yjmcc.2021.09.011

M3 - Article

C2 - 34624332

AN - SCOPUS:85116929932

SN - 0022-2828

VL - 163

SP - 20

EP - 32

JO - Journal of Molecular and Cellular Cardiology

JF - Journal of Molecular and Cellular Cardiology

ER -

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

Abstract

Keywords

Access to Document

Other files and links

Role of human non-coding DNA regulatory elements (REs) in heart development and disease

Formation of boundaries in the developing embryo

Endocardial sprouting and mechano-signalling in heart trabeculation

Cite this

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

Abstract

Keywords

Access to Document

Other files and links

Projects

Role of human non-coding DNA regulatory elements (REs) in heart development and disease

Formation of boundaries in the developing embryo

Endocardial sprouting and mechano-signalling in heart trabeculation

Cite this