Molecular Cardiology (Zelarayan)

AG Molecular Cardiology (Zelarayán)

The main objective of our research is to understand how molecular and cellular mechanisms govern cardiac function in health and disease, and to translate this knowledge into innovative therapies for cardiomyopathy leading to heart failure. We study how gene regulatory networks, metabolism, and cell-cell communication become dysregulated in the failing heart and how principles of cardiac developmental biology shape regenerative capacity across the lifespan. Using advanced experimental systems ranging from in vivo systems, iPSC derived cardiomyocytes and multicellular organoid models to human myocardial tissue as well as applying systems biology and network based approaches to integrate single cell and functional data into coherent models of cardiac remodeling, we aim to dissect human relevant mechanisms. Building on this mechanistic insight, we develop and test CRISPRa based strategies and other targeted approaches to engineer endogenous protective programs in the myocardium without permanently altering the genome, aiming for precise, durable, and personalized cardiovascular therapies. 

Protocol, Vectors and Cell lines

• Laura Priesmeier, Malte Tiburcy, Laura Cecilia Zelarayán. Protocol for differentiation of vascular smooth muscle cells from human iPSCs and their application in CRISPRa-mediated gene regulation. 
  STAR Protocol 7(1):104345. doi: 10.1016/j.xpro.2025.104345 (2026)
• Kim R, Nagel SH, Liaw NY, Zimmermann WH, Zelarayán LC, Schoger E. Human induced pluripotent stem cells for live cell cycle monitoring and endogenous gene activation. Stem Cell Res. 80:103531. doi: 10.1016/j.scr.2024.103531 (2024) 
  3. Priesmeier L, Schoger E, Cyganek L, Cecilia Zelarayán L. Combining a tetracycline (Tet)-inducible gRNA system and CRISPRa for titratable and timely controlled enhancement of endogenous SHISA3 activation in human induced pluripotent stem cells (hiPSC). Stem Cell Res. 71:103163 (2023)
• Federico Bleckwedel, Giulia Germena, Rabea Hinkel and Laura C. Zelarayán. An optimized protocol for the enrichment of small vesicles from murine and non-human primate heart tissue. Trillium Extracellular Vesicles. doi.org/10.47184/tev.2022.01.03 (2023)
• Schoger E*, Zimmermann WH, Cyganek L, Zelarayán LC*. Establishment of a second generation homozygous CRISPRa human induced pluripotent stem cell (hiPSC) lines for enhanced levels of endogenous gene activation. Stem Cell Res, 56:102518 (2021). *Corresponding authors
• Schoger E*, Zimmermann WH, Cyganek L, Zelarayán LC*. Establishment of two homozygous CRISPR interference (CRISPRi) knock-in human induced pluripotent stem cell (hiPSC) lines for titratable endogenous gene repression. Stem Cell Res. 55:102473 (2021). *Corresponding authors
• Eric Schoger, Loukas Argyriou, Lukas Cyganek and Laura Cecilia Zelarayán. Generation of homozygous CRISPRa human induced pluripotent stem cell (hiPSC) lines for sustained endogenous gene activation. Stem Cell Res 10 14;48:101944 (2020) IF: 2,02
• Noack C, Haupt LP, Zimmermann WH, Streckfuss-Bömeke K, Zelarayán LC. Generation of a KLF15 homozygous knockout human embryonic stem cell line using paired CRISPR/Cas9n, and human cardiomyocytes derivation. Stem Cell Res. 23:127-131 (2017) IF: 3,902
• Maria Patapia Zafeiriou, Claudia Noack and Laura Cecilia Zelarayán Isolation and Primary Culture of Adult Mouse Cardiac Fibroblasts. Bio-Protocols. Vol 6, Iss 13, 7/5/2016 (2016)
• Eric Schoger and Laura C. Zelarayán. Enhancing cardiomyocyte transcription using in vivo CRISPR/Cas9 systems. © Springer International Publishing. Ishikawa, K. (eds) Cardiac Gene Therapy. Methods in Molecular Biology, vol 2573. Humana, New York, NY. 2nd edition. doi.org/10.1007/978-1-0716-2707-5_5. ISBN978-1-0716-2706-8. pp 53–61 (2022)

   

Main research lines

Engineering synthetic transcription to control cell behavior

Engineering synthetic transcription to control cell behavior is a central theme of our work, with the goal of rewiring cardiomyocyte gene regulatory networks in a precise and clinically compatible manner. We established a cardiotropic CRISPR/dCas9 platform in which a heart-specific dCas9 cassette is combined with AAV9-mediated guide RNA delivery, providing a versatile strategy to modulate endogenous gene expression in the postnatal heart. In parallel, we generated CRISPRa/i human induced pluripotent stem cell (hiPSC) lines that enable durable activation or repression of endogenous targets across all hiPSC-derived cardiovascular cell types, forming a scalable discovery and validation platform. To develop therapeutic concepts capable of recovering the damaged heart, we exploit CRISPR for multiplex control of gene regulatory networks

Pathological tissue remodeling

Cardiomyocyte metabolic reprogramming. 
Heart maturation requires a tightly regulated shift from glycolysis to fatty acid oxidation, and maladaptation of this switch contributes to non-genetic heart failure during stress-induced remodelling. We have shown that CRISPRa-mediated restoration of KLF15 activity in stressed cardiomyocytes normalizes pathological metabolic shifts, prevents maladaptive fetal reprogramming, and improves mitochondrial function, positioning KLF15 as a central node in cardiometabolic control. Emerging data further indicate that KLF15 directly and indirectly influences mitochondrial complexes and broader metabolic gene networks, warranting in-depth investigation in cardiometabolic conditions characterized by reduced KLF15 levels. These studies are expected to broaden the therapeutic potential of KLF15-based CRISPRa strategies to diverse non-genetic cardiomyopathies, and will leverage integrated functional assays, metabolomics, and high-resolution imaging to link transcriptional control to cellular energetics.

Cellular and organ crosstalk.
We investigate how paracrine signalling, via both soluble factors and extracellular vesicles (EVs), shapes the cardiac microenvironment and systemic communication, providing a basis for combinatorial therapies and biomarker discovery. In hypertrophic and failing hearts, we observe upregulation of conventionally secreted proteins and altered EV cargo in cardiomyocytes, which are expected to modulate immune and vascular cell behaviour and to influence distant organs; these mechanisms are dissected using hiPSC-derived 2D/3D cardiac models and in vivo systems.

Mechanisms of vasculogenesis
We investigate how Wnt activation in hypertrophic remodelling re-engages vascular developmental programmes and reveals previously unrecognised crosstalk between cardiomyocytes and vascular lineages. Our work has identified a pool of cardiovascular progenitors arising from the sub epicardial region and progressing toward a vascular cell fate, suggesting that epicardium derived cells contribute to compensatory fetal like reprogramming in the stressed heart. These mechanisms will be dissected using complementary models, including genetically engineered mouse systems, 3D hiPSC derived cardioid tissues, and explanted human hearts, to define context- and species relevant routes of regenerative vasculogenesis with translational potential.

CRISPR-based screening of cardiac transcriptional regulators

Reactivating the regenerative capacity of the adult heart while preserving mature function remains a major unmet clinical need. We leverage CRISPRa/i-based transcriptional screens in hiPSC-derived cardiomyocytes equipped with integrated cell cycle and maturation reporters to identify endogenous, human-relevant factors that drive controlled cardiomyocyte proliferation and promote redifferentiation toward a stable adult state. Using focused transcription factor and pathway libraries, we search for synergistic combinations that induce robust yet reversible cell cycle entry while enhancing sarcomeric organization, electrophysiological maturity, and metabolic competence. Top candidates are validated using AAV9- or lentiviral CRISPR/Cas vectors in vivo and corresponding engineered hiPSC lines to endogenously rewire homeostatic gene networks, establishing a translational pipeline from screen hit to preclinical regenerative and maturation therapy concepts.

Advancing innovative therapeutic strategies and cutting‑edge tools

Our research integrates advanced technologies to dissect cellular and molecular mechanisms and to translate these insights into targeted therapies, with an emphasis on making our CRISPR-based platforms broadly accessible to the scientific community. Building on AAV9-mediated CRISPRa/Cas systems, we are establishing a preclinical pipeline for preventive and disease‑modifying applications, including programmed evaluation in large animal models in collaboration with the German Primate Center (DPZ) and complementary human myocardial slice studies. In parallel, we combine hiPSC‑derived cardiomyocytes with tailored biomaterial scaffolds and defined biophysical cues to generate biologically and mechanically relevant 3D cardiac tissues containing multiple cardiac cell types, providing human‑relevant testbeds for therapeutic development and mechanistic interrogation.

Team

 

Team 

Prof. Dr. rer. nat. Laura Zelarayan

Principal Investigator

Laura.Zelarayan-Behrend

Philipp Peter Stähr

MD Student

Rosa Kim

PhD Student

Tomás Peralta

PhD Student

Shaohan Wang

PhD Student

We are always seeking passionate and driven medical, master and PhD students who are interested in completing a thesis, and joining our translational research team.
If a topic resonates with you, please do not hesitate to reach out via email – we’d be happy to hear from you.

Selected Publications

1. Schoger E, Kim R, Bleckwedel F, Peralta T, Priesmeier L, Fischer J, Stengel L, Rocha C, Santos GL, Lutz S, Boileau E, Baumgarten N, Schulz MH, Dieterich C, Müller OJ, Cyganek L, Cabrera-Orefice A, Eberl H, Maack C, Streckfuss-Bömeke K, Pavez-Giani M, Doroudgar S, Sosalla ST, Zelarayán LC. Enhancing KLF15 Activity in Cardiomyocytes: A Novel Approach to Prevent Pathological Reprogramming and Fibrosis via Nuclease-Deficient dCas9VPR. Signal Transduct Target Ther. 11, doi:10.1038/s41392-026-02593-9 (2026) 
2. Jost ME, Schweizer M, Henning P, Gorzelanny C, Lehners M, Ellinger B, Boix-Campos J, Kux JM, Singh S, Fachinger A, Martinez Pomier K, VanSchouwen B, Billing AM, Biedenweg D, Schweizer M, Siegel S, Reimer R, Brandt M, Priesmeier L, Fuchs U, Pflaumenbaum J, Nikolaev VO, Newbury-Ecob R, Wilsdon A, Rybczynski M, Gehle P, Zelarayán LC, Stafforst T, Feil R, Rinschen MM, Pless O, Eaton P, Sáez PJ, Otto O, Melacini G, Demal TJ, Eschenhagen T, Herberg FW, Cuello F. Activating PRKG1 Variant Enhances Smooth Muscle Cell Deformability To Cause Aortopathy. JACC Basic Transl Sci. 11(2):101452. doi: 10.1016/j.jacbts.2025.101452 (2026)
3. Bolesani E, Bornhorst D, Iyer LM, Zawada D, Friese N, Morgan M, Lange L, Gonzalez DM, Schrode N, Leffler A, Wunder J, Franke A, Drakhlis L, Sebra R, Schambach A, Goedel A, Dubois NC, Dobreva G, Moretti A, Zelaráyan LC, Abdelilah-Seyfried S, Zweigerdt R. Transient stabilization of human cardiovascular progenitor cells from human pluripotent stem cells in vitro reflects stage-specific heart development in vivo. Cardiovasc Res. 120(11):1295-1311. doi: 10.1093/cvr/cvae118. (2024) 
4. Eric Schoger*, Federico Bleckwedel*, Giulia Germena, Cheila Rocha, Petra Tucholla, Izzatullo Sobitov, Wiebke Möbius, Maren Sitte, Christof Lenz, Mostafa Samak, Rabea Hinkel, Zoltán V. Varga, Zoltán Giricz, Gabriela Salinas, Julia C. Gross and Laura C. Zelarayán. Single-cell transcriptomics reveal extracellular vesicles secretion with a cardiomyocyte proteostasis signature during pathological remodeling. Communication Biology 21;6(1):79 (2023) (*contributed equally)
5. Yanpu Chen, Felipe F. Lüttmann, Eric Schoger, Hans R. Schöler, Laura C. Zelarayán, Kee-Pyo Kim, Jody J. Haigh, Johnny Kim,* and Thomas Braun. Reversible reprogramming of cardiomyocytes to a fetal state drives adult heart regeneration in mice. Science 373(6562):1537-1540 (2021)
6. Franziska S. Rathjens, Lavanya M. Iyer, Anke Renger, Fahima Syeda, Claudia Noack, Andreas Jungmann, Matthias Dewenter, Karl Toischer, Ali El-Armouche, Oliver J. Müller, Larissa Fabritz, Wolfram-Hubertus Zimmermann, Laura C. Zelarayán* and Maria-Patapia Zafeiriou*. Preclinical evidence for the therapeutic value of TBX5 normalization in arrhythmia control. Cardiovascular Research cvaa239 (2020) (*corresponding authors)
7. Elif Levent, Claudia Noack, Laura C. Zelarayán, Dörthe Katschinski, Wolfram Zimmermann, and Malte Tiburcy. Inhibition of PHD enzymes protects from reoxygenation injury in engineered human myocardium. Circulation, 142:1694–1696 (2020)
8. Schoger E, Carroll KJ, Iyer LM, McAnally JR, Tan W, Liu N, Noack C, Shomroni O, Salinas G, Groß J, Herzog N, Doroudgar S, Bassel-Duby R, Zimmermann WH, Zelarayán LC. CRISPR-mediated activation of endogenous gene expression in the postnatal heart. Circ Res 3;126(1):6-24 (2020)
9. Claudia Noack*, Lavanya M. Iyer*, Norman Y. Liaw, Eric Schoger, Sara Khadjeh, Eva Wagner, Monique Woelfer, Maria-Patapia Zafiriou, Hendrik Milting, Samuel Sossalla, Katrin Streckfuss-Boemeke, Gerd Hasenfuss, Wolfram-Hubertus Zimmermann, and Laura C. Zelarayán. KLF15-Wnt-dependent cardiac reprograming reveals a novel vascular player, SHISA3 in the mammalian heart. Journal of the American College of Cardiology 74(14):1804-1819 (*contributed equally) (2019)
10. Lavanya M. Iyer, Sankari Nagarajan, Monique Woelfer, Eric Schoger, Sara Khadjeh, Maria Patapia Zafiriou, Vijayalakshmi Kari, Jonas Herting, Sze Ting Pang, Tobias Weber, Franziska S. Rathjens, Thomas H. Fischer, Karl Toischer, Gerd Hasenfuss, Claudia Noack, Steven A. Johnsen and Laura C. Zelarayán. A context-specific cardiac Beta-catenin and GATA4 interaction influences TCF7L2 occupancy and remodels chromatin driving disease progression in the adult heart. Nucleic Acids Research 46(6):2850-2867 (2018)