De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks

Marco Salas, SergioStockholms universitet,Science for Life Laboratory (SciLifeLab),Institutionen för biokemi och biofysik,Stockholm Univ, Sci Life Lab, Dept Biochem & Biophys, Solna, Sweden (författare)

With the emergence of high throughput single cell techniques, the understanding of the molecular and cellular diversity of mammalian organs have rapidly increased. In order to understand the spatial organization of this diversity, single cell data is often integrated with spatial data to create probabilistic cell maps. However, targeted cell typing approaches relying on existing single cell data achieve incomplete and biased maps that could mask the true diversity present in a tissue slide. Here we applied a de novo technique to spatially resolve and characterize cellular diversity of in situ sequencing data during human heart development. We obtained and made accessible well defined spatial cell-type maps of fetal hearts from 4.5 to 9 post conception weeks, not biased by probabilistic cell typing approaches. With our analysis, we could characterize previously unreported molecular diversity within cardiomyocytes and epicardial cells and identified their characteristic expression signatures, comparing them with specific subpopulations found in single cell RNA sequencing datasets. We further characterized the differentiation trajectories of epicardial cells, identifying a clear spatial component on it. All in all, our study provides a novel technique for conducting de novo spatial-temporal analyses in developmental tissue samples and a useful resource for online exploration of cell-type differentiation during heart development at sub-cellular image resolution.

MEDICIN OCH HÄLSOVETENSKAP Medicinska och farmaceutiska grundvetenskaper Cell- och molekylärbiologi hsv//swe
MEDICAL AND HEALTH SCIENCES Basic Medicine Cell and Molecular Biology hsv//eng
NATURVETENSKAP Biologi Biokemi och molekylärbiologi hsv//swe
NATURAL SCIENCES Biological Sciences Biochemistry and Molecular Biology hsv//eng
NATURVETENSKAP Matematik Matematisk analys hsv//swe
NATURAL SCIENCES Mathematics Mathematical Analysis hsv//eng
NATURVETENSKAP Data- och informationsvetenskap Bioinformatik hsv//swe
NATURAL SCIENCES Computer and Information Sciences Bioinformatics hsv//eng
Convolutional neural networks
Cytology
Image resolution
Mammals
Tissue
Cell data
Cell types
Cell typing
Cellular diversity
Heart development
Human heart
Molecular diversity
Probabilistics
Single cells
Spatio-temporal models
Cells
article
cardiac muscle cell
cell differentiation
conception
convolutional neural network
fetus heart
human
human tissue
single cell RNA seq
spatiotemporal analysis
animal
genetics
mammal
metabolism
Animals
Humans
Myocytes
Cardiac
Neural Networks
Computer

Yuan, XiaoUppsala universitet,Institutionen för informationsteknologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)xiayu170 (författare)
Sylven, ChristerKarolinska Inst, Dept Med, Stockholm, Sweden (författare)
Nilsson, MatsStockholms universitet,Science for Life Laboratory (SciLifeLab),Institutionen för biokemi och biofysik,Stockholm Univ, Sci Life Lab, Dept Biochem & Biophys, Solna, Sweden(Swepub:su)matsn (författare)
Wählby, Carolina,professor,1974-Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för informationsteknologi(Swepub:uu)cli05194 (författare)
Partel, Gabriele,1988-Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för informationsteknologi,Katholieke Univ Leuven, Lab Multiom Integrat Bioinformat, Dept Human Genet, Leuven, Belgium.;VIB KU Leuven Ctr Brain & Dis Res, Lab Computat Biol, Dept Human Genet, Leuven, Belgium(Swepub:uu)gabpa510 (författare)
Stockholms universitetScience for Life Laboratory (SciLifeLab) (creator_code:org_t)

Ingår i:PloS Computational Biology: Public Library of Science (PLoS)18:81553-734X1553-7358

Av författaren/redakt...: Marco Salas, Ser ...; Yuan, Xiao; Sylven, Christer; Nilsson, Mats; Wählby, Carolina ...; Partel, Gabriele ...

Om ämnet

MEDICIN OCH HÄLSOVETENSKAP: MEDICIN OCH HÄLS ...; och Medicinska och f ...; och Cell och molekyl ...

Av lärosätet: Stockholms universitet; Uppsala universitet; Karolinska Institutet

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