Biology subjects

Kurtenbach, S.

Publications and source records attributed to Kurtenbach, S..

9 recordsLinked to original sources

bioRxiv2026

LMNA Haploinsufficiency in Human iPSC-Derived Cardiac Organoids Reveals Early Fibrotic Signaling as a Therapeutically Targetable Process

LMNA mutations are a major cause of dilated cardiomyopathy (DCM), with haploinsufficiency representing a common pathogenic mechanism. Yet the earliest disease-initiating events remain poorly defined. Here, we identify a novel intronic splice-site variant, c.937-1G>A, that disrupts pre-mRNA processing and induces nonsense-mediated mRNA decay, resulting in LMNA haploinsufficiency. Using induced pluripotent stem cells (iPSCs) generated from the patients peripheral blood mononuclear cells (PBMCs), we differentiated into self-patterning human cardiac organoids to model early LMNA-DCM in a multicellular human context. Single-nucleus transcriptomics revealed unexpectedly broad remodeling across major cardiac cell types beyond cardiomyocytes. Functionally, LMNA-mutant organoids exhibited impaired contractility, altered calcium handling, and increased arrhythmic activity. These changes were accompanied by early profibrotic activation, including increased reactive oxygen species (ROS), periostin (POSTN) secretion, and CTGF expression. Treatment with the antifibrotic drug nintedanib attenuated this response. Together, these findings show that LMNA haploinsufficiency initiates global pathogenic remodeling at an unexpectedly early developmental stage.

cell biology↗

bioRxiv2025

Cardiomyocyte-specific expression of HIF-1α mediates the cardioprotective effects of Growth Hormone-Releasing Hormone (GHRH)

Heart failure (HF) with preserved ejection fraction (HFpEF) carries a high mortality and remains a major therapeutic challenge. Effective, targeted therapies capable of reversing HFpEF pathophysiology are urgently needed. We previously demonstrated that activation of the cardiac growth hormone-releasing hormone (GHRH) pathway using high potency synthetic agonists of GHRH (GHRH-agonists: MR-356 and MR-409) improves the HFpEF phenotype in both large and small animal models, including in a murine model of cardiometabolic HFpEF (High fat diet + the nitric oxide synthase inhibitor L-NAME [HFD+L-NAME]). Here we sought to define the downstream signaling pathways responsible for this effect. A transcriptomic screen in human iPSC-derived cardiomyocytes (hiPSC-CMs) identified the hypoxia-inducible factor (HIF)-1 pathway as being activated by GHRH receptor (GHRHR) signaling, revealing an oxygen-independent mechanism of HIF-1 activation. Based on this finding, we investigated the interaction between the cardioprotective effects of the GHRH-agonist MR-356 and HIF-1 pathway activation in the murine HFD+L-NAME model of cardiometabolic HFpEF. We generated a cardiomyocyte-specific HIF-1 knockout (HIF-1CMKO) mouse line and demonstrated that our previously reported beneficial effects of GHRH-agonist administration were completely abolished in HIF-1CMKO mice. Together, these findings establish the GHRHR-HIF-1 axis as a central pathway integrating metabolic and contractile remodeling, suggesting that therapeutic targeting of this axis represents a novel disease-modifying approach to treating cardiometabolic HFpEF.

physiology↗

bioRxiv2025

GDF15 reprograms the microenvironment to drive the development of uveal melanoma liver metastases

Uveal melanoma (UM) results in fatal liver metastasis, yet little is known about the interactions between UM and host cells in the tumor microenvironment that promote this distinctive proclivity. Here, we used single cell (sc)-RNA-Seq analysis of UM-hepatic stellate cell (HSC) co-cultures to demonstrate that HSCs enriched for UM cell states that expressed genes implicated in cell survival, metabolic reprogramming and angiogenesis. A lead candidate driver of HSC reprogramming was the TGF-{beta} family member GDF15, which was associated with a metastatic UM phenotype. Silencing of BAP1 in UM cells led to increased GDF15 expression and accumulation of H3K27ac marks at the GDF15 promoter. Treatment of HSCs with GDF15 led to increased expression extracellular matrix proteins, inflammatory cytokines and angiogenic factors, including IL-8. Both exogenous GDF15, IL-8 and conditioned media from UM-HSC co-cultures increased endothelial cell network formation in vitro, an effect that was blocked by anti-GDF15 antibodies. In multiple models of metastatic UM, silencing of GDF15 inhibited the outgrowth of metastatic lesions, associated with reduced deposition of extracellular matrix and recruitment of endothelial cells. UM liver metastasis development is dependent upon GDF15-mediated remodeling of the liver microenvironment leading to an angiogenic response and matrix deposition that supports tumor growth.

cancer biology↗

bioRxiv2024

Identification of targetable epigenetic vulnerabilities in uveal melanoma

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults, with a strong predilection for hepatic metastasis, occurring in approximately 50% of cases. Metastatic UM remains highly resistant to therapy and is almost invariably fatal. The strongest genetic drivers of UM metastasis are loss-of-function mutations in tumor suppressor BAP1, an epigenetic regulator that serves as the ubiquitin hydrolase subunit of the polycomb repressive deubiquitinase (PR-DUB) complex, and a key player in global epigenetic regulation. Inactivation of BRCA Associated Protein 1 (BAP1) has been shown to induce widespread epigenetic alterations across multiple model systems. To identify novel therapeutic strategies, we investigated whether targeting the epigenome could reveal new vulnerabilities in UM. We performed high-throughput compound screening using a curated epigenetic inhibitor library and identified BET (bromodomain and extra-terminal domain) inhibition as a particularly promising approach. Interestingly, we observed significant heterogeneity in the efficacy of different BET inhibitors in UM. While previous clinical trials with two BET inhibitors have failed to show efficacy in UM, our findings highlight substantial differences in the potency of specific BET inhibitors for this malignancy. Notably, the BET inhibitor mivebresib (ABBV-075) significantly improved survival rates by 50% in a metastatic UM xenograft mouse model and completely prevented detectable metastases in the bones, spinal cord, and brain. Unexpectedly, RNA sequencing revealed a strong transcriptional overlap between BET inhibition and histone deacetylase (HDAC) inhibition--an approach currently under clinical evaluation for UM treatment. Both BET and HDAC inhibitors reversed gene expression signatures associated with high metastatic risk and induced a neuronal differentiation-like phenotype in UM cells. Together, our findings demonstrate that UM cells exhibit a distinct vulnerability to BET inhibition and establish BET inhibitors as promising candidates for further clinical evaluation for metastatic UM.

cancer biology↗

bioRxiv2022

The Growth Hormone Releasing Hormone Signaling Pathway Governs Cardiomyocyte differentiation in human iPS cells.

Here, we present an O2-independent/HIF-1 (Hypoxia inducible factor-1)-dependent mechanism that regulates developmental and regenerative growth of mammalian cardiomyoblasts. An autocrine feedback mechanism of GH/IGF1/SST (Growth hormone/Insulin-like growth factor 1/Somatostatin) signaling, mediated by GHRH/GHRH-R (Growth hormone-releasing hormone/GHRH-Receptor), is established specifically in NKX2-5 (NK2 Homeobox 5) expressing myocardial cells which affects HIF-1 stability through cAMP (cyclic adenosine monophosphate) or cGMP (cyclic guanosine monophosphate) activity. cAMP-mediated HIF-1 stabilization fuels Warburg metabolism and enhances NKX2-5 expression, limiting the developmental and regenerative growth of cardiomyoblasts. In contrast, cGMP-mediated HIF- 1 inhibition (or knock-out of HIF-1) redirects glycolytically derived citrate toward long-chain saturated fatty acid biosynthesis, leading to enhanced developmental and regenerative growth of cardiomyoblasts. These findings suggest that HIF1-mediated glycolysis serves as a rate-limiting, O2-independent sensor of cardiomyogenesis and that targeting GHRH/GHRH-R signaling could be a therapeutic strategy for regenerating the mammalian heart post-injury. O_FIG O_LINKSMALLFIG WIDTH=177 HEIGHT=200 SRC="FIGDIR/small/478572v3_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@16d3f74org.highwire.dtl.DTLVardef@16115edorg.highwire.dtl.DTLVardef@e68dc7org.highwire.dtl.DTLVardef@660861_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSummary Figure.C_FLOATNO Cardiomyoblast proliferative capacity is regulated by HIF1-mediated metabolic profile, through an NKX2-5 lineage-specific, O2-independent feedback mechanism. (A), HIF-1 is aerobically regulated through the intracellular activation of cAMP and cGMP in response to a GH1/IGF1/SST feedback mechanism, which activates the GHRH/GHRH-R signaling pathway in NKX2-5+ cardiomyoblasts. Stabilized HIF-1 (e.g. by CoCl2) promotes Warburg metabolism and cell cycle exit, whereas knockout or inhibition (e.g. YC-1) of HIF-1 or cAMP (low-dose metformin) promotes de novo fatty acid synthesis and enhances cardiomyoblast proliferation. (B), HIF-1 aerobic stabilization switches the metabolism towards glycolysis and restricts cardiomyoblast proliferation. Contrariwise, knockout of HIF-1 promotes oxidative metabolism in the Krebs cycle rather than lactate synthesis, thus stimulating the proliferative and regenerative capacity of cardiomyoblasts. C_FIG

cell biology↗

bioRxiv2021

RB1 loss triggers dependence on ESRRG in retinoblastoma

Retinoblastoma (Rb) is a deadly childhood eye cancer that is classically initiated by inactivation of the RB1 tumor suppressor. Clinical management continues to rely on nonspecific chemotherapeutic agents that are associated with treatment resistance and toxicity. Here, we analyzed 103 whole exomes, 16 whole transcriptomes, 5 single-cell transcriptomes, and 4 whole genomes from primary Rb tumors to identify novel Rb dependencies. Several recurrent genomic aberrations implicate estrogen-related receptor gamma (ESRRG) in Rb pathogenesis. RB1 directly interacts with and inhibits ESRRG, and RB1 loss uncouples ESRRG from negative regulation. ESRRG regulates genes involved in retinogenesis and oxygen metabolism in Rb cells. ESRRG is preferentially expressed in hypoxic Rb cells in vivo. Depletion or inhibition of ESRRG causes marked Rb cell death which is exacerbated in hypoxia. These findings reveal a novel dependency of Rb cells on ESRRG, and they implicate ESRRG as a potential therapeutic vulnerability in Rb.

cancer biology↗

bioRxiv2020

PieParty: Visualizing cells from scRNA-seq data as pie charts

Single cell RNA sequencing (scRNA-seq) has been a transformative technology in many research fields. Dimensional reduction techniques such as UMAP and tSNE are used to visualize scRNA-seq data in two or three dimensions in order for cells to be clustered in biologically meaningful ways. Subsequently, gene expression is frequently mapped onto these plots to show the distribution of gene expression across the plots, for instance to distinguish cell types. However, plotting each cell with only one color leads to repetitive and unintuitive representations. Here, we present Pie Party, which allows scRNA-seq data to be plotted such that every cell is represented as a pie chart, and every slice in the pie charts corresponds to the gene expression of individual genes. This allows for the simultaneous visualization of the expression of multiple genes and gene networks. The resulting figures are information dense, space efficient and highly intuitive. PieParty is publicly available on GitHub at https://github.com/harbourlab/PieParty.

bioinformatics↗

bioRxiv2020

UPhyloplot2: Visualizing Phylogenetic Trees from Single-Cell RNA-seq Data

Recent advances in single cell sequencing technologies allow for greater resolution in assessing tumor clonality using chromosome copy number variations (CNVs), which can be inferred from single cell RNA-seq (scRNA-seq) data using applications such as inferCNV. Inferences regarding tumor clonality are frequently visualized using phylogenetic plots, which previously required time-consuming and tedious manual analysis. Here, we present UPhyloplot2, a python script that generates phylogenetic plots directly from inferCNV output files. The tool is publicly available at https://github.com/harbourlab/UPhyloplot2/.

bioinformatics↗

bioRxiv2019

SparK: A Publication-quality NGS Visualization Tool

While there are sophisticated resources available for displaying NGS data, including the Integrative Genomics Viewer (IGV) and the UCSC genome browser, exporting regions and assembling figures for publication remains challenging. In particular, customizing track appearance and overlaying track replicates is a manual and time-consuming process. Here, we present SparK, a tool which auto-generates publication-ready, high-resolution, true vector graphic figures from any NGS-based tracks, including RNA-seq, ChIP-seq, and ATAC-seq. Novel functions of SparK include averaging of replicates, plotting standard deviation tracks, and highlighting significantly changed areas. SparK is written in Python 3, making it executable on any major OS platform. Using command line prompts to generate figures allows later changes to be made very easy. For instance, if the genomic region of the plot needs to be changed, or tracks need to be added or removed, the figure can easily be re-generated within seconds without the manual process of re-exporting and re-assembling everything. After plotting with SparK, changes to the output SVG vector graphic files are simple to make, including text, lines, and colors. SparK is publicly available on GitHub: https://github.com/harbourlab/SparK.

bioinformatics↗