bioRxiv preprint doi: https://doi.org/10.1101/302802; this version posted April 23, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Talman, Teppo, Pöhö et al. Molecular atlas of postnatal mouse heart development Virpi Talman PhD1*, Jaakko Teppo MSc2,3*, Päivi Pöhö MSc2*, Parisa Movahedi MSc4, Anu Vaikkinen PhD2, S. Tuuli Karhu MSc1, Kajetan Trošt PhD5, Tommi Suvitaival PhD5, Jukka Heikkonen PhD4, Tapio Pahikkala PhD4, Tapio Kotiaho PhD2,6, Risto Kostiainen PhD2#, Markku Varjosalo PhD3#, Heikki Ruskoaho MD, PhD1# 1Drug Research Program and Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, FI-00014 Helsinki, FINLAND 2 Drug Research Program and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI-00014 Helsinki, FINLAND 3 Institute of Biotechnology and HiLIFE Helsinki Institute of Life Science, University of Helsinki, FI-00014 Helsinki, FINLAND 4 Department of Future Technologies, Faculty of Mathematics and Natural Sciences, University of Turku, FI-20500 Turku, FINLAND 5 Steno Diabetes Center Copenhagen, DK-2820 Gentofte, DENMARK 6 Department of Chemistry, Faculty of Science, University of Helsinki, FI-00014 Helsinki, FINLAND * Equal contribution # Correspondence to: Heikki Ruskoaho, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, FINLAND. [email protected] or Markku Varjosalo PhD, Institute of Biotechnology and HiLIFE Helsinki Institute of Life Science, University of Helsinki, P.O. Box 65, FI-00014 Helsinki, FINLAND [email protected] or Risto Kostiainen PhD, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, FINLAND, [email protected]. Word count: 7881 1 bioRxiv preprint doi: https://doi.org/10.1101/302802; this version posted April 23, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Molecular atlas of postnatal mouse heart development Abstract Rationale: Mammals lose the ability to regenerate their hearts within one week after birth. During this regenerative window, cardiac energy metabolism shifts from glycolysis to fatty acid oxidation, and recent evidence suggests that metabolism may participate in controlling cardiomyocyte cell cycle. However, the molecular mechanisms mediating the loss of postnatal cardiac regeneration are not fully understood. Objective: This study aims at providing an integrated resource of mRNA, protein and metabolite changes in the neonatal heart to identify metabolism-related mechanisms associated with the postnatal loss of regenerative capacity. Methods and Results: Mouse ventricular tissue samples taken on postnatal days 1, 4, 9 and 23 (P01, P04, P09 and P23, respectively) were analyzed with RNA sequencing (RNAseq) and global proteomics and metabolomics. Differential expression was observed for 8547 mRNAs and for 1199 of the 2285 quantified proteins. Furthermore, 151 metabolites with significant changes were identified. Gene ontology analysis, KEGG pathway analysis and fuzzy c-means clustering were used to identify biological processes and metabolic pathways either up- or downregulated on all three levels. Among these were branched chain amino acid degradation (upregulated at P23) and production of free saturated and monounsaturated medium- to long-chain fatty acids (upregulated at P04 and P09; downregulated at P23). Moreover, the HMG-CoA synthase (HMGCS)-mediated mevalonate pathway and ketogenesis were transiently activated. Pharmacological inhibition of HMGCS in primary neonatal rat ventricular cardiomyocytes reduced the percentage of BrdU+ cardiomyocytes, providing evidence that the mevalonate and ketogenesis routes may participate in regulating cardiomyocyte cell cycle. Conclusions: This is the first systems-level resource combining data from genome-wide transcriptomics with global quantitative proteomics and untargeted metabolomics analyses of the mouse heart throughout the early postnatal period. This integrated multi-level data of molecular changes associated with the loss of cardiac regeneration may open up new possibilities for the development of regenerative therapies. Keywords: heart regeneration; heart development; neonatal mouse cardiomyocyte; proteomics; metabolomics; transcriptomics Non-standard Abbreviations and Acronyms All gene symbols are available in the Supplemental Dataset S1. BCAA, branched chain amino acid; BrdU, bromodeoxyuridine; GCxGC-MS, two-dimensional gas chromatography-mass spectrometry; hPSC, human pluripotent stem cell; LC-MS, liquid chromatography-mass spectrometry; LME, linear mixed effect; MSEA, metabolite set enrichment analysis; RNAseq, RNA sequencing 2 bioRxiv preprint doi: https://doi.org/10.1101/302802; this version posted April 23, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Talman, Teppo, Pöhö et al. Introduction production in the postnatal heart. Moreover, the peroxisome proliferator-activated receptor (PPAR) Adult human hearts possess a negligible regen- signaling plays an important role in activating erative capacity and therefore cell loss in response lipid metabolism.17 to myocardial infarction (MI) leads to scar forma- The profound changes in the energy metabo- tion, remodeling of the surrounding myocar- lism of cardiomyocytes are associated with altera- dium, progressive impairment of cardiac function tions in mitochondria: the fetal type mitochondria and eventually to heart failure (reviewed in 1, 2). undergo mitophagy and are replaced with mature Approximately only 0.5-1% of human cardiomyo- adult-type mitochondria in a Parkin-dependent cytes are renewed annually through proliferation process to allow more efficient ATP produc- of existing cardiomyocytes.3, 4 This is insufficient tion.18 Increased oxidative metabolism promotes for regeneration after MI, which can cause a loss reactive oxygen species (ROS) production and of up to 25% (~1 billion) of cardiomyocytes.5 The thereby induces a DNA damage response, which is renewal rate is higher in infants and adolescents believed to contribute to cardiomyocyte cell cycle than in the elderly, indicating higher regenera- arrest.19 However, oxidative DNA damage does tive potential in children.3, 6 Remarkably, certain not fully correlate with cardiomyocyte cell cycle amphibians and fish, as well as neonatal rodents withdrawal in humans and is thus insufficient to can fully regenerate their hearts after an injury.7-9 explain the loss of regenerative capacity.20 On This occurs predominantly through proliferation molecular level, endogenous mechanisms known of remaining cardiomyocytes in the areas adja- to regulate cardiomyocyte proliferation include cent to the injury.8, 10 However, rodents lose this neuregulin-ERBB2 signaling, Hippo-YAP pathway, regenerative capacity within 7 days after birth due and the transcription factor GATA4, among to cardiomyocyte cell cycle withdrawal,8 which is others.11, 21-23 However, even though metabolic considered to represent a major hurdle for the pathways are controlled by the same signals that development of regeneration-inducing thera- regulate cell proliferation,24 their significance in pies.11-13 In line with cardiac regeneration in neona- cardiac regeneration and cardiomyocyte prolifera- tal rodents, full functional recovery of a newborn tion is yet uncovered. baby with a massive MI suggests that humans pos- In search of regenerative therapies, a number sess a similar intrinsic capacity to regenerate their of studies have utilized transcriptomics to identify hearts at birth.14 It is therefore crucially important mechanisms regulating cardiac regeneration (for to elucidate the molecular mechanisms mediating recent examples, see25-27). However, proteomic the postnatal loss of cardiac regeneration. and metabolomic changes have not been thor- Upon birth, the resistance of pulmonary circu- oughly investigated. Here we report the first lation drops dramatically due to the expansion integrated study combining genome-wide RNA of lung alveoli, causing an increase in systemic sequencing (RNASeq), global proteomics and blood pressure and shunt closure. This in turn untargeted metabolomics to characterize in detail induces a steep increase in arterial blood oxygen the metabolic changes occurring during the content. Increased cardiac workload and altered postnatal heart development. metabolic environment induce a switch from anaerobic glycolysis, which is the main source of energy in the embryonic heart, to mitochon- Materials & Methods 15 drial fatty acid β-oxidation soon after birth. This The experimental design is summarized in Figure switch is controlled by signaling that involves 1. Two separate sets of mouse ventricular tissue 16 hypoxia-inducible factor 1α (HIF1α) and HAND1. samples were used. Set 1 encompassed samples Upon birth, HAND1 expression is rapidly down- from postnatal days 1, 4 and 9 (P01, P04 and P09, regulated, allowing cardiomyocytes to shut down respectively) representing hearts with full regen- glycolysis and initiate lipid oxidation. Failure to erative capacity (P01), partial regenerative capac- downregulate HAND1 and thereby initiate