Single-cell mapping of microRNA expression during cardiac development

Stefanos Leptidis1, Eleni Papakonstantinou1, Katerina Pierouli1, Athanasios Mitsis1, Sarantis Chlamydas2, Aspasia Efthimiadou3, George P. Chrousos4,5, Elias Eliopoulos1, Emil Hansson6, Dimitrios Vlachakis1,7,8

1 Laboratory of Genetics, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece

2 Active Motif, Office park Nysdam, Avenue Reine Astrid 92, La Hulpe, Belgium

3 Hellenic Agricultural Organization-Demeter, Institute of Soil and Water Resources, Department of Soil Science, Lycovrisi, Greece

4 Laboratory of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece

5 Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, Athens, Greece

6 Karolinska Institutet/AstraZeneca Integrated Cardio Metabolic Centre, Huddinge, Sweden

7 Laboratory of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece

8 School of Informatics, Faculty of Natural & Mathematical Sciences, King’s College London, London, United Kingdom

Competing interests: SL none; EP none; KP none; AM none; SC none; AE none; GPC none; EE none; DV none

Leptidis et al. (2021) EMBnet.journal 26(Suppl A), e958 http://dx.doi.org/10.14806/ej.26.A.958


The heart is an exceptionally complex tissue comprised of a variety of different cell types. Understanding physiological cardiac development and its relationship to the development of pathological cardiac diseases require the careful investigation of their related developmental pathways. A highly significant regulatory layer during cellular differentiation is the post-transcriptional regulation via non-coding RNAs and, more specifically, microRNAs (Liu et al., 2010). Previous microRNA transcriptomic studies in the heart lacked in the identification of their differential expression per cell-type (Leptidis et al., 2013). Since microRNAs can target many mRNAs, identifying their cell-type-specific expression is necessary to elucidate the intricate cellular interactions and regulatory pathways and the development of targeted therapeutic approaches.

This study uses data from single-cell small RNA sequencing (small-seq) (Faridani et al., 2016) from early embryonic cardiac progenitor murine cells. We aim to identify the transcriptional profile of small RNAs, mainly microRNAs, during cardiac development. Unlike single-cell RNA sequencing (scRNAseq), there are no established cell-type markers nor data analysis methods in the case of small-seq. Thus, we develop a methodology for identifying cell-types using their microRNA profile, coupled to their predicted targets stemming from various miRNA target prediction algorithms. These data are then cross-referenced with preliminary scRNAseq data in the same tissue, with established cell-types. Deciphering the transcriptomic landscape of microRNAs during cardiac development, along with identifying cell-types based on the relationship between their RNA and microRNA fingerprint, enables the in-depth study of the intricate regulatory interactions between cells, cell-types and different embryonic days.


This research is co-financed by Greece and the European Union (European Social Fund- ESF) through the Operational Programme «Human Resources Development, Education and Lifelong Learning» in the context of the project “Reinforcement of Postdoctoral Researchers - 2nd Cycle” (MIS-5033021), implemented by the State Scholarships Foundation (ΙΚΥ).



1. Wang J, Chen Y, Hao S, Feng W, Shen Z (2017) Balanced Faridani OR et al. (2016) Single-cell sequencing of the small-RNA transcriptome. Nat Biotechnol 34:1264-1266. http://dx.doi.org/10.1038/nbt.3701

2. Leptidis S et al. (2013) A deep sequencing approach to uncover the miRNOME in the human heart. PLoS One 8:e57800. http://dx.doi.org/10.1371/journal.pone.0057800

3. Liu N, Olson EN (2010) MicroRNA regulatory networks in cardiovascular development. Dev Cell 18:510-525. http://dx.doi.org/10.1016/j.devcel.2010.03.010


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