Mirjana Novković1*, Aleksandra Vitkovac1, Andjela Milicevic1, Emilija Milosevic1, Jovana Jasnic1, Vladimir Jovanovic2 and Snezana Kojic1
1Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Serbia
2Human Biology and Primate Evolution Group, Department for Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
mirjana.novkovic [at] imgge.bg.ac.rs
Abstract
Zebrafish possess a remarkable capacity to regenerate both cardiac and skeletal muscle tissues, whereas most higher vertebrates, including humans, have largely lost the ability to regenerate the heart, while retaining the capacity for skeletal muscle repair. Thus, the key for unlocking the endogenous regenerative potential of human heart may be hidden in common genes involved in both processes. Zebrafish regenerate heart through coordinated tissue remodeling and regenerative signaling processes which induce cardiomyocyte dedifferentiation and proliferation, enabling restoration of lost myocardium instead of forming a permanent fibrotic scar as in humans. On the other hand, zebrafish repair skeletal muscle through an evolutionarily conserved multistep process that relies on activation and proliferation of tissue-resident stem (satellite-like) cells, which differentiate into muscle cell progenitors and finally to myofibers, leading to functional muscle recovery. To gain deeper insight into common genes and pathways involved in heart regeneration and skeletal muscle repair, and the role of ankrd1a gene, we performed Weighted Gene Co-expression Network Analysis on RNA sequencing data from injured tissues of wild type and ankrd1a-/- zebrafish (GSE285387, GSE277480). Regarding injury, the heart showed 3 positive and 3 negative, while skeletal muscle showed 2 positive and 1 negative correlated modules. Independent network analysis revealed that injury in both cardiac and skeletal muscle tissues induces highly coordinated transcriptional programs enriched for extracellular matrix organization, inflammatory pathways, and cell cycle, while suppressing muscle contraction, oxidative phosphorylation and other metabolic processes. Despite tissue-specific module structures, functional convergence was observed at the pathway level, supported by sharing more than 40% of central genes across the tissues. We further investigated the role of ankrd1a, a well-established stress-responsive mechanosensor and transcription cofactor that is rapidly and consistently upregulated during cardiac and skeletal muscle healing in zebrafish. Genotype-associated transcriptomic changes were reflected in independent co-expression networks by 3 positively and 1 negatively correlated module in both heart and skeletal muscle. Enrichment analyses showed upregulation of pathways associated with spliceosome, transcription, and post-translational protein modification, suggesting activation of compensatory mechanisms that may help zebrafish adapt to the loss of functional ankrd1a protein.
Keywords: heart, regeneration, muscle, WGCNA, ankrd1a