Biology subjects

Seidel, T.

Publications and source records attributed to Seidel, T..

5 recordsLinked to original sources

bioRxiv2026

Polyploid cardiomyocytes define disease-specific transcriptional states in the mammalian heart

The adult mammalian heart has a limited regenerative capacity. Following injury, cardiomyocytes undergo a hypertrophic response accompanied by polyploidization, which has been described as a barrier to proliferation and regeneration of the heart1,2. However, the unique molecular programs of polyploidy, or genome multiplied cardiomyocytes, and their influence on the disease-related myocardial remodelling process remains unclear. Here, we integrate single-nuclei and high-resolution spatial multi-omics across human, rat, and mouse hearts to define novel cardiac cell states and their tissue niches in ischemic and non-ischemic heart disease. Computational analysis across scales allowed us to generate detailed networks of the cardiac tissue remodelling process as well as tissue and sub-cellular environments uniquely enriched in polyploid cardiomyocytes or their diploid origins. We identify a conserved, dichotomous transcriptional program distinguishing diploid from polyploid cardiomyocytes. Polyploid cardiomyocytes demonstrated rewired metabolic and chromatin-remodeling transcriptional programs and recapitulate the gene signature of immature human fetal cardiomyocytes. Notably, we observe that polyploid cardiomyocytes--rather than the general myocyte population--are the primary sites of enrichment for major heart-failure drug targets, including the mineralocorticoid, {beta}1-adrenergic, and glucagon-like peptide-1 receptors. Based on our cross-species dataset we further identified TNIK, a Wnt-pathway regulator expressed in polyploid cardiomyocytes across species, as a potential therapeutic target and demonstrate that pharmacological TNIK inhibition improves cardiac function after myocardial infarction in rats. Together, this species-spanning, disease-resolved study redefines cardiomyocyte heterogeneity in heart disease and suggests a therapeutic path to heart failure treatment by targeting polyploid cardiomyocytes.

genomics↗

bioRxiv2026

Cross-species architecture of the cardiac transverse-axial tubular system in mammals

Cardiac excitation-contraction coupling relies on a pancellular network of regular cardiomyocyte surface membrane invaginations, termed the transverse-axial tubular system (TATS). The TATS is ubiquitously present in adult mammalian cardiomyocytes, enabling efficient structural and functional coupling of sarcolemma and intracellular Ca2+ stores. However, TATS ultrastructural characteristics across species, and their relation to cardiomyocyte morphology and physiological parameters such as heart rate, remain largely unexplored. Here, we quantified TATS and cardiomyocyte features in a large confocal microscopy dataset (78 3D volumes) obtained from tissue slices across eight species (mouse, rat, rabbit, pig, horse, elephant, whale, and human). We developed and applied a semi-automated image analysis pipeline to quantify mean cytosolic distances to the nearest TATS (Cyto-TATSmin, a measure inversely related to TATS density), transverse-to-axial tubule ratio, and cardiomyocyte dimensions. Cyto-TATSmin and transverse tubule fraction differed substantially between species, with the lowest Cyto-TATSmin in mouse and highest in human. Within species, except mouse, rat, and horse, Cyto-TATSmin was positively correlated with cardiomyocyte cross-sectional area. Across all species, Cyto-TATSmin correlated with species life span and body weight, and was inversely correlated with average resting heart rate. Our findings reveal structural scaling principles within species differences in cardiac cellular ultrastructure and provide a resource for studying TATS organisation in health and disease. As TATS remodelling is a common hallmark of cardiac pathology, awareness of species-differences is needed to guide the design and interpretation of translational research.

cell biology↗

bioRxiv2025

PKC Promotes T-Tubule Membrane Loss by Activating a PKD-NFκB Endocytic Pathway

BackgroundIn heart disease, the membrane of the cardiomyocyte transverse-axial tubular system (TATS) deteriorates. This impairs contractility, hinders recovery and predisposes to arrhythmia. However, the key signals and cellular processes driving TATS loss are not understood. We investigated protein kinase C (PKC) and its downstream signals in animal and human cardiomyocytes. MethodsVentricular cardiomyocytes were isolated from healthy adult rat, rabbit and failing human hearts and treated with the PKC activator phorbol 12-myristat 13-acetat (PMA) or receptor-mediated agonists, alongside inhibitors targeting PKC, PKD, NF{kappa}B, MKK1-ERK1/2, NFAT, or endocytic pathways. TATS density was analyzed by confocal microscopy using lipophilic membrane dyes. Signaling pathway activation was determined by Western blotting and RNA sequencing. Ca2+ signals and contractility were assessed in rat cells. Mechanisms of TATS loss were studied using endocytosis assays involving fixable dextran. ResultsPMA induced severe TATS loss, which was prevented by inhibiting PKC, PKD, NF{kappa}B or MKK1, but not by blocking NFAT or p38 MAPK. Receptor-mediated PKC activation also decreased TATS density. All effective inhibitors suppressed I{kappa}B expression. RNA sequencing indicated PMA-mediated activation of the NF{kappa}B and MAPK/ERK pathways and genes related to endocytosis. NF{kappa}B inhibition did not suppress the MAPK pathway, but MKK inhibition suppressed NF{kappa}B. PMA decreased Ca2+ transient amplitudes and contractility, whereas NF{kappa}B inhibitors preserved both. Dextran assays revealed that TATS membranes were internalized via a macropinocytic process that followed saturation kinetics was upregulated by PMA, downregulated by NF{kappa}B inhibition, and required PI3K, myosin I, and clathrin-independent endocytosis and correlated with the rate of TATS loss. Key findings were consistent in human cardiomyocytes and in ex-vivo rat and rabbit myocardial slice culture. ConclusionsPKC activation drives TATS loss in human and animal myocytes via PKC-PKD-NF{kappa}B, T-tubules are degraded by endocytic internalization, offering a new perspective on how cardiomyocyte membranes may deteriorate in heart disease.

cell biology↗

bioRxiv2024

Spatio-temporal dynamics of the fibrotic niche in cardiac repair

The heart is one of the least regenerative organs in humans, and ischemic heart disease is the leading cause of death worldwide. Understanding the cellular and molecular processes that occur during cardiac wound healing is an essential prerequisite to reducing health burden and improve cardiac function after myocardial tissue damage. By integrating single-cell RNA-sequencing with imaging-based spatial transcriptomics, we reconstructed the spatio-temporal dynamics of the fibrotic niche after ventricular injury in adult mice. Our analysis reveals dynamic regulation of local cell communication niches over time. We identified interactions that regulate cardiac repair, including fibroblast proliferation silencing by Trem2high macrophages that prevents excessive fibrosis. Moreover, we discovered a rare population of dedifferentiating cardiomyocytes during early post-lesion stages, which was sustained by signals from myeloid and lymphoid cells. Culturing non-regenerative mouse cardiomyocytes or human heart tissue with these niche factors reactivated progenitor gene expression and cell cycle activity. In summary, this spatio-temporal cell type atlas provides valuable insights into the heterocellular interactions that control cardiac repair. HighlightsO_LIscRNA-seq and in situ sequencing reveal spatio-temporal dynamics of heart repair C_LIO_LILocal heterocellular communication niches coordinate overall wound response C_LIO_LIFibroblast cell cycle silencing by Trem2high macrophages suppresses excessive fibrosis C_LIO_LICardiomyocyte plasticity is promoted by myeloid and lymphoid cells C_LI

systems biology↗

bioRxiv2021

Retrograde Control of Cytosolic Translation Targets Synthesis of Plastid Localized Proteins and Nuclear Responses for Efficient Light Acclimation.

Canonical retrograde signalling comprises information transmission from organelles to the nucleus and in particular controls gene expression for organellar proteins. The need to re-assess this paradigm was suggested by discrepancies between de novo protein synthesis and transcript abundance in response to excess light. Here we uncover major components of a translation-dependent retrograde signalling pathway that first impacts translation and then transcription. The response realization depends on the kinases Mitogen-activated protein kinase 6 (MPK6) and Sucrose non-fermenting 1-related kinase (SnRK1) subunit, AKIN10. Global ribosome foot-printing revealed differential ribosome association of 951 transcripts within 10 min after transfer from low to high light. Despite predominant translational repression, 15 % of transcripts were increased in translation and enriched for chloroplast-localized photosynthetic proteins. About one third of these transcripts, including Stress associated proteins (SAP) 2 and 3, share regulatory motifs in their 5'-UTR that act as binding sites for glyceraldehyde-3-phosphate dehydrogenase (GAPC) and light responsive RNA binding proteins (RBPs). SAP2 and 3 are both translationally regulated and interact with the calcium sensor Calmodulin-like 49 (CML49), which promotes relocation to the nucleus inducing a translation-dependent nuclear stress response. Thus, translation-dependent retrograde signalling bifurcates to directly regulate a translational circuit of chloroplast proteins and simultaneously initiate a nuclear circuit synchronizing retrograde and anterograde response pathways, serving as a rapid mechanism for functional acclimation of the chloroplast.

plant biology↗