Biology subjects

Cyganek, L.

Publications and source records attributed to Cyganek, L..

14 recordsLinked to original sources

bioRxiv2026

ATP1A3 E815K Disrupts Sodium Homeostasis and Excitability in Human Alternating Hemiplegia of Childhood Neurons

Alternating hemiplegia of childhood (AHC) is a rare neurodevelopmental disorder primarily caused by heterozygous de novo mutations in the ATP1A3 gene, which encodes the neuron-specific catalytic 3 subunit of the P-type Na/K-ATPase. Among these, the E815K variant is the second most frequent ATP1A3 mutation in AHC and is associated with the most severe clinical phenotypes, characterized by frequent epileptic and dystonic episodes and profound developmental impairment, making it a key target for mechanistic study. Although E815K was shown to disrupt pump function in heterologous systems and animal models, its impact on human neurons remain poorly understood. To investigate its disease-relevant pathophysiology, we generated induced pluripotent stem cells (iPSCs) from an AHC patient carrying the E815K mutation and differentiated them into mature neurons. Patient-derived neurons displayed normal differentiation and synaptogenesis, with preserved evoked synaptic transmission. However, 3-specific Na/K pump currents were nearly abolished, whereas 1 activity remained intact. This selective dysfunction was associated with a depolarized resting membrane potential, reduced input resistance, and diminished intrinsic excitability. Patient neurons generated fewer action potentials in response to depolarizing current steps, displayed altered firing patterns, and showed significantly decreased voltage-gated sodium current densities, while potassium conductance remained unaffected. Taken together, these results indicate that the ATP1A3 E815K mutation disrupts intracellular sodium homeostasis and consequently modifies the excitability of human neurons. Overall, these findings provide mechanistic insight into the molecular pathophysiology underlying this AHC variant and thereby establish a patient-derived neuronal model which serves as a platform for future drug screening approaches and therapeutic investigation.

neuroscience↗

bioRxiv2026

AMPK reinforces mitochondrial metabolism and suppresses pathological remodeling in Complex V-deficient cardiomyocytes

TMEM70 variants represent the most common nuclear cause of mitochondrial ATP synthase (Complex V) deficiency and are associated with particularly severe cardiac manifestations. Yet, how TMEM70 deficiency disrupts cardiomyocyte metabolic maturation and function remains poorly understood, in part because suitable human disease models are lacking. Here, we model TMEM70-related Complex V deficiency using CRISPR-engineered human induced pluripotent stem cells differentiated into cardiomyocytes. While TMEM70-deficient pluripotent cells retain mitochondrial function, differentiated cardiomyocytes develop reduced mitochondrial membrane potential, impaired respiratory capacity, and pathological remodeling, revealing a differentiation-dependent failure of metabolic maturation. Chronic activation of AMP-activated protein kinase (AMPK) restores mitochondrial respiratory capacity despite persistent Complex V deficiency. Proteomic and metabolomic analyses reveal that AMPK activation in TMEM70-deficient cardiomyocytes reinforces mitochondrial and fatty-acid metabolism while suppressing pathological structural remodeling, accompanied by improved cardiac function. Together, these findings identify AMPK-dependent metabolic remodeling as a state-dependent mechanism of functional rescue in mitochondrial cardiomyopathy.

cell biology↗

bioRxiv2026

Distinct mitochondrial DNA single-nucleotide variant signatures in TOP3A-deficient cardiomyocytes

The human heart has a continuous and exceptionally high demand for energy, which is met primarily through mitochondrial oxidative phosphorylation. This dependence places the maintenance and integrity of mitochondrial DNA (mtDNA) for proper mitochondrial function at the center of cardiac health, as mtDNA instability has been shown to cause mitochondrial dysfunction, which can ultimately impair cardiac function leading to cardiomyopathy (CM) and heart failure. However, the contribution of mtDNA instability to cardiac disease remains poorly understood. A growing number of nuclear-encoded proteins have emerged as essential regulators of mtDNA maintenance, organization and segregation. DNA Topoisomerase 3 (TOP3A) is expressed as two isoforms: one is a nuclear-related isoform involved in nuclear genome maintenance while the other localizes to the mitochondria to preserve mtDNA integrity. Recently, individuals bearing biallelic loss-of-function variants in TOP3A manifested phenotypic traits, including CM, typical for mitochondrial dysfunction, supporting a potential mechanistic link between mitochondrial genome instability and TOP3A-related cardiac disease. Here, we investigated the effects of TOP3A deficiency on mtDNA maintenance and stability in the context of TOP3A-associated CM. We employed isogenic wild-type, TOP3A-knockout and BLM-knockout induced pluripotent stem cells (iPSCs) to generate cardiomyocytes (iPSC-CMs) and established a high-throughput, ultra-deep mtDNA sequencing strategy achieving approximately 500,000X coverage to characterize low-frequency mtDNA mutational patterns. Loss of TOP3A triggered an early burst of low-frequency de novo mtDNA single-nucleotide variants during cardiac differentiation, with a striking enrichment within the mitochondrial ribosomal RNA genes, accompanied by a progressive increase in the heteroplasmy of low-frequency mtDNA variants inherited from the common isogenic background. These unique mtDNA signatures were associated with defective mtDNA copy-number expansion and impaired mitochondrial respiration in mature iPSC-CMs. Together, our approach uncovered a previously uncharacterized consequence of TOP3A deficiency and established a link between impaired mtDNA maintenance and mitochondrial dysfunction in TOP3A-associated CM.

genetics↗

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

Variant U1 snRNAs contribute to cell cycle and differentiation control of human iPS cells

Maintenance of stem cell identity as well as differentiation of stem cells into the various lineages requires intricate regulation of gene expression. Despite intensive research, our understanding of these regulatory networks remains incomplete. Here, we focus on the understudied paralogs of the U1 small nuclear RNA (snRNA) gene known as variant U1 (vU1) snRNAs. By generating isogenic knockout lines of human induced pluripotent stem cells for two different vU1s, we show that their loss profoundly changes both hiPSC gene expression and cell cycle profiles. These changes appear to manifest at the level of alternative splicing choices, including those at recursive splicing sites, and lead to the differential availability of stem cell regulators. Together, our results shed new light on the function of vU1 snRNAs and further our understanding of the programs controlling human pluripotency.

genomics↗

bioRxiv2025

SarcAsM: AI-based multiscale analysis of sarcomere organization and contractility in cardiomyocytes

Cardiomyocyte function critically depends on sarcomere dynamics and their organization in myofibrils. To uncover how cardiomyocyte function emerges from individual sarcomere dynamics, comprehensive analysis of Z-bands (nanometer scale), sarcomeres ([~]2 {micro}m scale), and myofibrils ([~]10 to 100 {micro}m scale) is required. Tools for such multiscale analyses are presently lacking. Here we introduce the Sarcomere Analysis Multitool (SarcAsM), which combines deep learning and graph-based methods for automated, fast, and unbiased structural assessment of sarcomeric Z-bands, sarcomeres, and myofibrils as well as their organization in larger myofibril domains. SarcAsM features a generalist deep learning model, pre-trained on a broad range of experimental and published images, ensuring its versatile application and immediate usability across diverse datasets. Finally, we demonstrate the versatile utility of SarcAsM in analyzing sarcomere structure and dynamics under acute and chronic drug exposure in hiPSC-derived cardiomyocytes with fluorescently tagged Z-bands. SarcAsM is available as open-source Python package and stand-alone application.

bioinformatics↗

bioRxiv2025

BTRR complex deficiency is a driver for genomic instability in Bloom syndrome

Biallelic loss-of-function (LoF) variants in the BTRR complex members BLM, TOP3A, RMI1, and RMI2 cause Bloom syndrome (BSyn). The BTRR complex mainly acts on DNA replication and DNA repair processes, and dysfunction of this complex underlies the increased genomic instability and cancer predisposition associated with the BSyn phenotype. Here, we report CRISPR/Cas9-based genome-edited isogenic induced pluripotent stem cell (iPSC) models with compound heterozygous LoF variants in BLM, TOP3A, and RMI1. The cellular phenotype of all three BTRR-deficient iPSC lines included chromosome segregation defects, increased sister chromatid exchange rates, and impaired DNA single-strand template repair. Using single-cell whole genome sequencing, we showed that BTRR complex deficiency causes increased genome copy number alterations (CNAs) and, therefore, is a driver for genomic instability. CNA load was further induced by applying replication stress, and we observed that BTRRKO iPSCs acquired fewer de novo CNA events compared to wild-type cells, suggesting a possible selection loss against cells with high levels of DNA damage. Importantly, stress-induced and non-stress-induced CNAs in single-cell genomes were not stochastically distributed throughout the genome, but instead enriched at fragile sites. This finding might offer an opportunity for the development of novel NGS-based approaches to measure rates of genomic instability in disease conditions.

genetics↗

bioRxiv2025

Guiding G protein signaling by target enhancement of GPCRs

Activation of G protein coupled receptors coupling to the Gi/o pathway leads to the activation of G protein-activated inward rectifier potassium channels (GIRK) in a fast membrane-delimited manner in excitable cells. Activation of GIRK causes the hyperpolarization of the cell membrane, where hyperpolarization is dependent on te availability of Gi/o coupled GPCRs and GIRK. In particular, in optogenetic and chemogenetic experiments neuronal silencing depends on downstream targets of Gi/o-coupled GPCRs. To selectively enhance Gi/o mediated GIRK currents, we created expression cassettes consisting of a homomer forming GIRK subunit and various light-activated Gi/o-coupled GPCRs (Melanopsin, Long-wave-sensitive opsin 1, Parapinopsin or Opsin 7b). We demonstrate that light-activation of the GIRK/GPCR constructs induces robust GIRK currents in human embryonic kidney 293 cells, cardiomyocytes and cerebellar Purkinje cells and changes the net effect of G protein signaling of the promiscuous Opn4L from a Gq/11 mediated excitation towards an Gi/o mediated inhibition. Thus, our tools enhance target selectivity and improve optogenetic control of the Gi/o pathway by light in excitable cells.

neuroscience↗

bioRxiv2024

CardioMEA: Comprehensive Data Analysis Platform for Studying Cardiac Diseases and Drug Responses

In recent years, high-density microelectrode arrays (HD-MEAs) have emerged as a valuable tool in preclinical research for characterizing the electrophysiology of human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). HD-MEAs enable the capturing of both extracellular and intracellular signals on a large scale, while minimizing potential damage to the cell. However, a gap exists between technological advancements of HD-MEAs and the availability of effective data-analysis platforms. To address this need, we introduce CardioMEA, a comprehensive data-analysis platform designed specifically for HD-MEA data that have been obtained from iPSC-CMs. CardioMEA features scalable data processing pipelines and an interactive web-based dashboard for advanced visualization and analysis. In addition to its core functionalities, CardioMEA incorporates modules designed to discern crucial electrophysiological features between diseased and healthy iPSC-CMs. Notably, CardioMEA has the unique capability to analyze both extracellular and intracellular signals, thereby facilitating customized analyses for specific research tasks. We demonstrate the practical application of CardioMEA by analyzing electrophysiological signals from iPSC-CM cultures exposed to seven antiarrhythmic drugs. CardioMEA holds great potential as an intuitive, user-friendly platform for studying cardiac diseases and assessing drug effects.

bioengineering↗

bioRxiv2023

LZTR1 polymerization provokes cardiac pathology in recessive Noonan syndrome

Noonan syndrome patients harboring causative variants in LZTR1 are particularly at risk to develop severe and early-onset hypertrophic cardiomyopathy. However, the underling disease mechanisms of LZTR1 missense variants driving the cardiac pathology are poorly understood. Hence, therapeutic options for Noonan syndrome patients are limited. In this study, we investigated the mechanistic consequences of a novel homozygous causative variant LZTR1L580Pby using patient-specific and CRISPR/Cas9-corrected iPSC-cardiomyocytes. Molecular, cellular, and functional phenotyping in combination with in silico prediction of protein complexes uncovered a unique LZTR1L580P-specific disease mechanism provoking the cardiac hypertrophy. The homozygous variant was predicted to alter the binding affinity of the dimerization domains facilitating the formation of linear LZTR1 polymer chains. The altered polymerization resulted in dysfunction of the LZTR1-cullin 3 ubiquitin ligase complexes and subsequently, in accumulation of RAS GTPases, thereby provoking global pathological changes of the proteomic landscape ultimately leading to cellular hypertrophy. Furthermore, our data showed that cardiomyocyte-specific MRAS degradation is mediated by LZTR1 via the autophagosome, whereas RIT1 degradation is mediated by both LZTR1-dependent and LZTR1-independent proteasomal pathways. Importantly, uni-or biallelic genetic correction of the LZTR1L580P missense variant rescued the molecular and cellular disease-associated phenotype, providing proof-of-concept for CRISPR-based gene therapies.

cell biology↗

bioRxiv2022

Alteration of myocardial structure and function in RAF1associated Noonan syndrome: Insights from cardiac disease modeling based on patient-derived iPSCs

Noonan syndrome (NS), the most common among the RASopathies, is caused by germline variants in genes encoding components of the RAS-MAPK pathway. Distinct variants, including the recurrent Ser257Leu substitution in RAF1, are associated with severe hypertrophic cardiomyopathy (HCM). Here, we investigated the elusive mechanistic link between NS-associated RAF1S257L and HCM using three-dimensional cardiac bodies and bioartificial cardiac tissues generated from patient-derived induced pluripotent stem cells (iPSCs) harboring the pathogenic RAF1 c.770C>T missense change. We characterize the molecular, structural and functional consequences of aberrant RAF1 -associated signaling on the cardiac models. Ultrastructural assessment of the sarcomere revealed a shortening of the I-bands along the Z disc area in both iPSC-derived RAF1S257L cardiomyocytes, and myocardial tissue biopsies. The disease phenotype was partly reverted by using both MEK inhibition, and a gene-corrected isogenic RAF1L257S cell line. Collectively, our findings uncovered a direct link between a RASopathy gene variant and the abnormal sarcomere structure resulting in a cardiac dysfunction that remarkably recapitulates the human disease. These insights represent a basis to develop future targeted therapeutic approaches.

cell biology↗

bioRxiv2021

Single-cell transcription profiles in Bloom syndrome patients link BLM deficiency with altered condensin complex expression signatures

Bloom syndrome (BS) is an autosomal recessive disease clinically characterized by primary microcephaly, growth deficiency, immunodeficiency, and predisposition to cancer. It is mainly caused by biallelic loss-of-function mutations in the BLM gene, which encodes the BLM helicase, acting in DNA replication and repair processes. Here, we describe the gene expression profiles of three BS fibroblast cell lines harboring causative, biallelic truncating mutations obtained by single-cell (sc) transcriptome analysis. We compared the scRNA transcription profiles from three BS patient cell lines to two age-matched wild-type controls and observed specific deregulation of gene sets related to the molecular processes characteristically affected in BS, such as mitosis, chromosome segregation, cell cycle regulation, and genomic instability. We also found specific upregulation of genes of the Fanconi anemia pathway, in particular FANCM, FANCD2, and FANCI, which encode known interaction partners of BLM. The significant deregulation of genes associated with inherited forms of primary microcephaly observed in our study might explain in part the molecular pathogenesis of microcephaly in BS, one of the main clinical characteristics in patients. Finally, our data provide first evidence of a novel link between BLM dysfunction and transcriptional changes in condensin complex I and II genes. Overall, our study provides novel insights into gene expression profiles in BS on a single-cell level, linking specific genes and pathways to BLM dysfunction.

genetics↗

bioRxiv2021

Effects of Hydroxychloroquine and Azithromycin on iPSC-derived Cardiomyocytes: Considerations for the Treatment of COVID-19 Patients

Despite known adverse effects of hydroxychloroquine (HCQ) and azithromycin (AZM) on cardiac function, HCQ and AZM have been used as combination therapy in the treatment of COVID-19 patients. Recent clinical data indicate higher complication rates with HCQ/AZM combination treatment in comparison to monotherapy. Here, we used human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) to systematically investigate the effects of HCQ and AZM individually and in combination. The clinically observed QT prolongation caused by treatment with HCQ could be recapitulated in iPSC-CMs based on prolonged field potential duration (FPDc). Interestingly, HCQ-induced FPDc prolongation was strongly enhanced by combined treatment with AZM, although AZM alone slightly shortened FPDc in iPSC-CMs. Furthermore, combined treatment with AZM and HCQ leads to higher cardiotoxicity, more severe structural disarrangement, and more pronounced contractile and electrophysiological dysfunctions, compared to respective mono-treatments. First mechanistic insights underlying the synergistic effects of AZM and HCQ on iPSC-CM functionality are provided based on increased Cx43- and Nav1.5-protein levels. Taken together, our results highlight that combined treatment with HCQ and AZM strongly enhances the adverse effects on cardiomyocytes, providing mechanistic evidence for the high mortality in patients receiving HCQ/AZM combination treatment.

pharmacology and toxicology↗

bioRxiv2020

Local translation in synaptic mitochondria influences synaptic transmission

Mitochondria possess a small genome that codes for core subunits of the oxidative phosphorylation system, and whose expression is essential for energy production. Information on the regulation and spatial organization of mitochondrial gene expression in the cellular context has been difficult to obtain. Here we addressed this by devising an imaging approach to analyze mitochondrial translation, by following the incorporation of clickable non-canonical amino acids. We applied this method to multiple cell types, including hippocampal neurons, where we found ample evidence for mitochondrial translation in both dendrites and axons. Translation levels were surprisingly heterogeneous, were typically stronger in axons, and were independent of their distance from the cell soma, where mitochondria presumably descent from. Presynaptic mitochondrial translation correlated with local synaptic activity, and blocking mitochondria translation reduced synaptic function. Overall, these findings demonstrate that mitochondrial gene expression in neurons is intimately linked to neuronal function.

biochemistry↗