Biology subjects

Streckfuss-Boemeke, K.

Publications and source records attributed to Streckfuss-Boemeke, K..

6 recordsLinked to original sources

bioRxiv2026

Genome-scale modelling and stable isotope tracing reveal dynamic metabolic reprogramming in a human cardiac hypertrophy model

Pathological cardiac hypertrophy is associated with metabolic remodelling; however the temporal dynamics of this remodelling remain poorly defined in human cardiomyocyte systems. Here, we combined transcriptomic profiling, genome-scale metabolic modelling and stable isotope-resolved metabolomics (SIRM) to map the metabolic consequences of endothelin-1 (ET-1) stimulation in human iPSC-derived cardiomyocytes (hiPSC-CMs). Integration of RNA sequencing data obtained after 8 and 48 hours of ET-1 treatment with the Human2.0 genome-scale metabolic model predicted time-dependent remodelling, characterised by progressive increases in glycolytic flux, enhanced glucose carbon entry into the TCA cycle, and a decrease in fatty acid {beta}-oxidation. Computational flux predictions were independently confirmed by extracellular flux analysis and 13C-substrate tracing, with concordance between modelled and measured fluxes. Extracellular flux analysis showed increased glycolytic capacity and mitochondrial respiration after 48 hours, with greater sensitivity to inhibition of mitochondrial pyruvate transport. Glucose tracing revealed increased 13C enrichment of glycolytic, pentose phosphate pathway, serine-glycine and TCA cycle metabolites, consistent with altered glucose-derived carbon allocation. Increased m+3 labelling of selected TCA-related metabolites was compatible with pyruvate anaplerosis, although pathway-specific fluxes were not resolved. In three-dimensional engineered heart tissue (EHTs) treated with ET-1 for 7 days, increased hypertrophic marker expression was accompanied by a blunted inotropic response, and metabolomics showed similar changes in metabolite abundance and glucose-derived labelling to 2D cultures. These findings support hiPSC-CMs and EHTs as complementary platforms for studying early metabolic remodelling in pathological cardiac hypertrophy and provide an integrated framework linking model predictions to functional and isotope-tracing measurements.

cell biology↗

bioRxiv2025

Enhanced iPSC-Cardiomyocyte Maturation via Combined 3D-Culture and Metabolic Cues

Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CM) have become an invaluable tool for disease modelling and drug testing. However, while many etiologies of heart failure involve defects in excitation-contraction coupling, mitochondrial energetics or both, iPSC-CM are limited by the developmental immaturity of these processes. Here, we report a combinatorial strategy to enhance the maturation of human iPSC-CM by integrating three-dimensional (3D) spheroid culture conditions with a defined hormone- and fatty acid-enriched maturation medium (MM). A comprehensive analysis of structural, electrophysiological and Ca2+ handling parameters was performed to evaluate cellular and functional maturation. The iPSC-CM generated under these conditions (3D_MM) exhibit many phenotypic characteristics that resemble those of isolated adult human CM, including (i) a rod-shaped morphology, (ii) cardiac ultrastructural features such as aligned myofilaments, unidirectional organized sarcomeres, and the presence of transverse (t)-tubules, (iii) refined action potential (AP) parameters and Ca2+ handling, and (iv) {beta}-adrenergic responsiveness and a positive force-frequency relationship. Compared with long-term (LT) monolayer cultures of 90 days or the individual cues (3D or MM alone), the 3D_MM protocol achieves mostly superior or at the least non-inferior maturation effects. This systematic investigation further demonstrates that while 3D culturing or MM alone improved specific aspects of maturation, only their synergistic combination produced a comprehensive enhancement of key CM processes, such as excitation-contraction coupling and mitochondrial energetics.

cell biology↗

bioRxiv2025

Peroxisome protein import deficiency causes heart failure in mouse and human

Peroxisomes are ubiquitous cellular organelles with potentially vital roles in lipid and reactive oxygen metabolism. The metabolic demands of the heart are substantial; however, the contribution of peroxisomes to cardiac development, health, and their role in heart failure (HF) remain largely unexplored. We developed and examined a mouse and an engineered human myocardium (EHM) model with a deficiency in cardiac peroxisome biogenesis to investigate the role of peroxisomes in cardiac function and pathology. In the EHM, loss of peroxisome protein import and subsequent peroxisomal metabolic impairment trigger mitochondrial damage and compromise cellular respiration and energy production. Peroxisome dysfunction results in incoherent electrical conduction, defective Ca2+-handling, and ultimately presentation of a HF phenotype with pathological force generation. These phenotypes are mirrored in an orthogonal murine model system with defective cardiac peroxisome biogenesis. Preload-dependent deficits in force generation due to insufficient energy supply are eventually fatal. Thus, peroxisomes play an important role in sustaining normal heart operations. Vice versa, peroxisome maintenance is compromised in pressure overload-induced HF, establishing peroxisomes as potential modulators of pathology and targets of therapy.

cell biology↗

bioRxiv2025

Arrhythpy: An Automated Tool to Quantify and Classify Arrhythmias in Ca2+ Transients of iPSC-Cardiomyocytes

Arrhythmias constitute an intricate and clinically significant phenomenon of great importance in various research areas. Ca2+ homeostasis plays a pivotal role in forming rhythmic contractions in the heart, and its dysregulation has emerged as a critical component in developing arrhythmias. Until now, however, the quantification of arrhythmias has been limited to indirect measurements via Ca2+ sparks, electrophysiological parameters, or manual classification, which can lead to human bias. We aimed to develop an analysis platform that directly and automatically analyzes arrhythmias in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). Here, we present Arrhythpy, a robust and automated open-source program to quantify and classify confocal microscopy-based Fluo-4 Ca2+ transients to generate a measure of arrhythmia. In contrast to other automated and semi-automated analysis tools, that measure established parameters such as time-to-peak, Arrhythpy directly analyzes the degree of arrhythmia in a Ca2+ transient. We demonstrate its utility in monitoring Ca2+ transient-based arrhythmias in atrial and ventricular iPSC-CMs of healthy individual and cardiac disease patients, including dilated cardiomyopathy (DCM) and Takotsubo syndrome (TTS). Arrhythpy was validated by analyzing drug-treated iPSC-CMs, confirming the beating frequency effects of compounds that directly activate (Isoprenaline) or inhibit (Metoprolol) beta-adrenergic signaling. Arrhythpy analysis of iPSC-CMs of TTS patients recapitulated TTS phenotypes, including atrial arrhythmia that could be normalized with beta-blocker treatment. The programs adaptable framework enables arrhythmic pattern analysis in various cell types using periodic dye-based line scan measurement techniques, applicable to single cells or layered cultures.

pharmacology and toxicology↗

bioRxiv2025

RBM20-variants induce distinct calcium handling and metabolic phenotypes in patient-specific stem cell models of dilated and non-compaction cardiomyopathy

Background and aimMutations in the splice regulator RBM20 account for [~]3 % of genetic cardiomyopathies. In particular, the highly conserved RS domain is a hotspot for disease-associated mutations. Previously, mutations at same amino acid position 634 in the hotspot RS-domain were found to cause dilated cardiomyopathy (DCM) with left ventricular non-compaction (R634L) or without (R634W), but the pathophysiological mechanisms that govern the heterogeneity in phenotype presentation remained unknown. Here, we identify the molecular events caused by the distinct RBM20 mutations from DCM and left-ventricular non-compaction (LVNC) using patient-specific stem cell models. MethodsWe generated induced pluripotent stem cell-derived cardiomyocytes (iPSC-CM) of one LVNC- and two DCM-patients harboring the RBM20-mutations R634L (LVNC) or R634W (DCM). We investigated alternative splicing activity, RBM20 localization, sarcomeric regularity, cAMP level, kinase-specific phosphorylation of key Ca2+ handling enzymes, physiological cardiac functions as Ca2+ homeostasis, and metabolic activity on a patient-specific cardiomyocyte level. Force generation was analyzed in patient-specific engineered myocardial tissues. Isogenic rescue and mutation insertion lines were generated by CRISPR/Cas9 technology to analyze the direct impact of the RBM20 mutations on the cardiac phenotype. ResultsWe observed common splicing aberrations for LVNC- and DCM-CM in TTN and RYR2, RBM20 cytoplasmatic accumulation and irregular sarcomeric structure. LVNC-CM harboring the RBM20-p.R634L variant show distinct molecular, cellular and functional impairments that manifest in CAMK2D, TRDN and IMMT mis-splicing. Splicing defects in LVNC-CM correlate with elevated systolic Ca2+ and faster Ca2+ kinetics with elevated cAMP levels and PLN-hyperphosphorylation. An increased metabolic activity and mitochondrial membrane potential support the hyperactive LVNC-CM. By contrast, DCM-CM (RBM20-p.R634W) distinctly present with decreased systolic Ca2+ and increased SR Ca2+leak but unchanged Ca2+ kinetics and metabolic activity. Both mutations lead to severely reduced force of contraction in engineered myocardium. CRISPR/Cas9 gene-edited isogenic control lines of both described RBM20 mutations in LVNC and DCM demonstrated the causative nature of the two mutations and their diverging effects. Further, L-type Ca2+ channel blockade by verapamil ameliorates the Ca2+ cycling and leakage phenotypes in LVNC- and DCM-CM. ConclusionWe show the first comparative iPSC-model of splice-defect-associated RBM20-dependent LVNC-p.R634L and DCM-p.R634W. We found shared and variant-specific phenotypes on a patient-specific level. Our data demonstrate that the different RBM20 mutations manifest in distinct molecular aberrations in alternative splicing and RBM20 cytoplasmic accumulation that convey various physiological impairments in structure, Ca2+ handling, metabolism and contractile force.

molecular biology↗

bioRxiv2020

A roadmap for the characterization of energy metabolism in human cardiomyocytes derived from induced pluripotent stem cells

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) are an increasingly employed model in cardiac research and drug discovery. A significant limitation with respect to clinical translation is their immature structural and functional phenotype. Cellular metabolism plays an integral role in determining phenotype but the metabolic profile of hiPSC-CM during maturation is poorly characterized. In this study we employ a combination of methods including extracellular flux and 13C-glucose flux analyses to study the metabolic profile of hiPSC-CM over a 12 week maturation period. Results show a progressive remodeling of pathways involved in energy metabolism and substrate utilization. The oxidative capacity of hiPSC-CM and particularly their ability to utilize fatty acids increased with time. In parallel, relative glucose oxidation was reduced while glutamine oxidation was maintained at similar levels. Anaerobic glycolysis as assessed by lactate production was maintained throughout the 12 week period but with significant alterations in proximal glycolytic enzymes such as hexokinase and phosphofructokinase. We also observed a progressive maturation of mitochondrial oxidative capacity at comparable levels of mitochondrial content between timepoints. The time-dependent restructuring of the hiPSC-CM metabolic profile indicates their potential to overcome the lack of full maturation previously reported and enhance their applicability for pharmacological studies and cardiac disease modeling.

cell biology↗