Biology subjects

Nadel, A.

Publications and source records attributed to Nadel, A..

3 recordsLinked to original sources

bioRxiv2025

Human Engineered Heart Tissue Models for Pharmacological Studies- Inhibition of Small-Conductance Ca2+-activated K+ (KCa2) channel

Atrial fibrillation (AF) is a common cardiac arrhythmia increasing stroke risk. Current treatments show limited effectiveness and can cause serious side effects. At the moment there is a lack of well-established human models recapitulating complex cardiac microenvironment for studying potential AF therapies. To address the limitations of existing models we developed 3D in vitro human Engineered Heart Tissue (EHT) model using atrial and ventricular human-induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) with either human atrial fibroblasts (HAF) or human ventricular fibroblasts (HVF).These chamber-specific EHTs exhibit differences in gene expression, ion channels and physiological responses, enabling studying Frank-Starling mechanisms and Ca2+ response. Using KCa2 channel inhibitor AP14145, we observed increased contraction force and prolonged relaxation time, suggesting negative modulation of KCa2.2/KCa2.3 channels and increased atrial-effective refractory period (AERP). The EHT model provides a valuable platform for examining KCa2 channel inhibitors impact and evaluating chamber-specific drug effects in controlled in vitro settings.

developmental biology↗

bioRxiv2025

Multi-omic screening identifies RBMXL3 as a primate-specific RNA-binding protein and candidate regulator of RNA metabolism in human spermatogenesis

BackgroundRBMXL3 is a primate-specific gene localized on the X chromosome, which expression is detectable mainly in the male gonad. So far, very little is known about the RBMXL3 protein function and its molecular interactions. However, recent reports mention the RBMXL3 gene in the context of human spermatogenesis, cancer, and a breathing disorder that affects newborns. In this study, we investigate the RBMXL3s molecular network on a genome-wide scale using the human seminoma cell line (TCam-2) as a male germline in vitro model. MethodsBy using transcriptomic (RNA sequencing (RNA-seq) and enhanced crosslinking and immunoprecipitation (eCLIP)) and proteomic (Co-immunoprecipitation coupled with Mass Spectrometry, (Co-IP-MS)) approaches we show RBMXL3 importance in RNA metabolism. Additionally, Western Blot, qRT-PCR, immunostaining, and confocal imaging were used in order to investigate the function of RBMXL3. Finally, we used a plasmid-based L1 retrotransposition assay to demonstrate the suppressive effect of RBMXL3 on human Long Interspersed Nuclear Element-1 (LINE-1, L1) retrotransposition. ResultsOur RNA-seq data show that RBMXL3 expression drives gene expression changes and influence alternative splicing in human cells. Moreover, by performing eCLIP we provide a proof that RBMXL3 binds to a wide range of RNA transcripts. Additionally, we confirmed the nuclear localization of RBMXL3 in TCam-2 cells and its presence in spermatogonia and spermatocytes within the human testis. Finally, we report for the first time that RBMXL3 restricts human LINE-1 retrotransposition. ConclusionsOur findings for the first time identify primate-specific RBMXL3 protein as a new upstream regulator of RNA metabolism, characterized by broad RNA-binding activity in human TCam-2 cells. Finally, we show that RBMXL3 expression heavily reduces LINE-1 retrotransposition in human cells, underlying RBMXL3 importance in maintaining genome integrity. Our data suggest that RBMXL3 may contribute to the regulation of transcriptome dynamics in male germ cells, while its broader functional implications remain to be determined. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=56 SRC="FIGDIR/small/677621v3_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@8bf116org.highwire.dtl.DTLVardef@180fe82org.highwire.dtl.DTLVardef@1c52960org.highwire.dtl.DTLVardef@11f7519_HPS_FORMAT_FIGEXP M_FIG C_FIG Created with BioRender.com

cell biology↗

bioRxiv2017

OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer

Accurate quantification of cellular and mitochondrial bioenergetic activity is of great interest in medicine and biology. Mitochondrial stress tests performed with Seahorse Bioscience XF Analyzers allow estimating different bioenergetic measures by monitoring oxygen consumption rates (OCR) of living cells in multi-well plates. However, studies of statistical best practices for determining OCR measurements and comparisons have been lacking so far. Therefore, we performed mitochondrial stress tests in 126 96-well plates involving 203 fibroblast cell lines to understand how OCR behaves across different biosamples, wells, and plates. We show that the noise of OCR is multiplicative, that outlier data points can concern individual measurements or all measurements of a well, and that the inter-plate variation is greater than intra-plate variation. Based on these insights, we developed a novel statistical method, OCR-Stats, that: i) robustly estimates OCR levels modeling multiplicative noise and automatically identifying outlier data points and outlier wells; and ii) performs statistical testing between samples, taking into account the different magnitudes of the between- and within-plates variations. This led to a significant reduction of the coefficient of variation across plates of basal respiration by 36% and of maximal respiration by 32%. Moreover, using positive and negative controls, we show that our statistical test outperforms existing methods, which either suffer from an excess of false positives (within-plates methods), or of false negatives (between-plates methods). Altogether, the aim of this study is to propose statistical good practices to support experimentalists in designing, analyzing, testing and reporting results of mitochondrial stress tests using this high throughput platform.

bioinformatics↗