FCT/DAAD Transnational cooperation

From Petri Dish to the living heart: A systems biology approach to identify and validate key genes and processes driving cardiogenesis


Regenerative medicine promises to replace damaged tissues/organs. An attractive approach is the propagation and differentiation of pluripotent cells towards desired cell types. Of great biomedical interest is generation of functional cardiac muscle cells or their progenitor cells. However, cardiomyogenesis involves complex temporally ordered genetic events, which are still not fully understood, hindering such approach. We expect to clarify the cardiomyogenesis process applying systems biology approaches with experimental tools.

In collaboration with the group led by Agapios Sachinidis at the Institute of Neurophysiology of the University of Cologne (Germany), we will analyze and compare existing complementary transcriptome datasets, in vitro and in vivo data, integrating them within molecular interaction networks, identify novel genetic regulators and validate them experimentally using techniques such as knockdown and overexpression, leading to the development of an in silico model for cardiogenesis. The funding serves for the training and research visits especially of young scientists involved this project.

One of the results of this collaboration is the study of gene expression during murine heart development (Molecular Therapy - Nucleic Acids 2018). To identify the underlying regulation, we carried out the first transcriptomic monitoring of microRNA and polyadenylated RNAs in parallel of the embryonic murine heart. This unique dataset allowed us to assess role of microRNAs and their regulatory effects on target genes. We found that more than 200 microRNAs were differentially expressed during embryonic heart development and of those, we could identified 28 microRNAs as potential novel regulators through integrative analysis of expression data, functional annotation and known or predicted regulatory interactions. This represents a considerable expansion of the current repertoire of known cardiac microRNAs.Currently, we are undertaken experimental follow up studies to validate and characterise the role of these microRNAs. Additionally, we detected 25 long non-coding RNAs as differentially expressed. Long non-coding RNAs are known to play a role in the regulation of gene expression through a variety of mechanisms on transcriptional, post-transcriptional, and epigenetic levels. Therefore, the set of detected long non-coding RNAs provides an additional list of potential regulators for future study. The discovery of novel regulators in the developing heart is important, as it is well established that the embryonic and neo-natal murine heart has the capacity to regenerate upon damage, whereas this healing process is absent in the mature heart. Thus, insights how this remarkable regenerative program is regulated on molecular level might provide us with important cues for the development of regenerative therapies for the adult heart.

As a companion tool of our study, we implemented HeartmiR database. It is is based on the integration of our transcriptomic data and a set of over 100 000 experimentally detected or computationally predicted interactions between 386 miRNAs and 9,211 target genes. In creating an open access database and interactive visualization tools implemented in HeartmiR, we hope provide a computational resource that will contribute to identification of microRNAs involved in regulating heart development.

CCMAR/UAlg Participants

Matthias E. Futschik, CCMAR/CBMR, UAlg

José Bragança, CBMR/DCBM, UAlg

Daniel Oliveira, CBMR, UAlg

Susana Machado, CBMR, UAlg

Rui Machado, CBMR, UAlg

José P. Pinto, CBMR, UAlg

João Santos, CBMR, UAlg

8 - 17 August 2016: Kick-off meeting at the University of Algarve
Agapios visited the SysBioLab to discuss the results of the bioinformatic analysis carried out by Rui, to draft a first manuscript, and to enjoy (of course) the hospitality of the sunny Algarve. We had a productive and joyful time and are looking forward to visit your lab in Cologne, Agapios!
Work Farewell


Rui Machado, Agapios Sachinidis and Matthias E. Futschik (2021) Detection of Novel Potential Regulators of Stem Cell Differentiation and Cardiogenesis through Combined Genome-Wide Profiling of Protein-Coding Transcripts and microRNAs. Cells, 10(9), 2477 (pdf+html)

Davood Sabour, Rui S.R. Machado, José P. Pinto, Susan Rohani, Raja G.A. Sahito, Jürgen Hescheler, Matthias E. Futschik and Agapios Sachinidis (2018) Parallel Genome-wide Profiling of Coding and Non-coding RNAs to Identify Novel Regulatory Elements in Embryonic and Maturated Heart, Molecular Therapy - Nucleic Acids, 12, 158-173 (pdf+html)


Rui S. R. Machado, José P. Pinto, Davood Sabour, José Bragança, , A. Sachinidis and Matthias E. Futschik (2017) HEARTI ToolBox: An online platform for the analysis in silico of cardiomyogenesis, Poster presentation, 9th International Meeting of the Stem Cell Network NRW, Münster, Germany

Matthias Futschik: The many faces of stem cells: Meta-analysis of stemness signatures, Contributed talk, 7th Bioinformatics and Stem Cells Satellite Meeting, Münster, Germany

PhD theses

João Santos: Cited2 in cardiac development: an inside and outside job. Universidade do Algarve (2020)

Rui Machado: Identification of key factors of heart regeneration using a systems biology approach. Universidade do Algarve (2021)


A webserver enabling the querying of microRNAs and mRNAs to identify relevant miRNA-mRNA interactions for late heart development.

A web-based platform for the analysis of integrated expression datasets associated with cardiomyogenesis. The latest version of HeartEXpress contains over 120 microarray measurements that were analysed and compared in various ways.