Biology subjects

Hotz, H.-R.

Publications and source records attributed to Hotz, H.-R..

9 recordsLinked to original sources

bioRxiv2025

Low oxygen promotes extravillous trophoblast progenitor expansion but restrains maturation

Placental development occurs in a low oxygen environment, yet how oxygen tension instructs differentiation of progenitor cytotrophoblasts (CTB) along the extravillous versus villous pathways remains incompletely understood. In particular, the role of low oxygen in early extravillous trophoblast (EVT) progenitor expansion and subsequent maturation has been difficult to assess due to the lack of models allowing sequential, high-resolution characterization. Using human trophoblast organoids and single-cell transcriptomics, we examined the effects of ambient (21%) and physiological (2-3%, 8%) oxygen on EVT and SCT differentiation. We show that low oxygen promotes the initial expansion of column CTB-like progenitors but restricts terminal EVT maturation. Conversely, we show that ambient oxygen drives the formation of EVT and syncytiotrophoblast. Stabilization of HIF-1 partially recapitulates the EVT maturation block but does not contribute to EVT progenitor expansion, indicating HIF-dependent and-independent contributions. These findings clarify how oxygen shapes EVT lineage progression and define HIF-1s role in coordinating progenitor expansion versus maturation.

developmental biology↗

bioRxiv2025

A model of apical-out human first trimester trophoblast organoids to study regeneration after syncytial damage

The villous syncytiotrophoblast in humans is the interface between maternal blood and the placenta and its functions are essential for a successful pregnancy. The syncytium can be damaged in vivo focally by high-velocity and turbulent maternal blood flow, or more globally by oxidative stress. It then quickly regenerates, a process critical for the maintenance of placental functions including nutrient transfer and protection from infections. To investigate this process, we developed apical-out trophoblast organoids from first-trimester placentas and induced mechanical damage to the syncytium. We observed spontaneous regeneration of syncytiotrophoblast both morphologically and functionally. TNFRSF12A, the TWEAK receptor, was identified as a potential enhancer of syncytiotrophoblast regeneration. Supplementation with recombinant TWEAK in organoids increased the expression of cell proliferation and fusion markers, promoting syncytiotrophoblast formation. The source of TWEAK was found to be macrophages derived from maternal blood monocytes that adhere to sites of syncytiotrophoblast damage in vivo. This in vitro model that allows the exploration of syncytial biology has relevance for important pregnancy disorders including pre-eclampsia, where breaks occur more often, and vertical infections, where maternal monocytes could be a source of transmission.

developmental biology↗

bioRxiv2025

An organoid model of the menstrual cycle reveals the role of the luminal epithelium in regeneration of the human endometrium

Menstruation is an unusual physiological process whereby the human endometrium undergoes cyclical shedding yet scarless regeneration. Despite its pivotal role in reproductive health, the cellular states and interactions that coordinate this process are incompletely defined. Here, we establish an in vitro menstrual cycle (IVMC) protocol using human endometrial organoids that faithfully recapitulates the epithelium across the key phases of the menstrual cycle including differentiation, hormonal withdrawal, breakdown and regeneration. This IVMC protocol enables intricate study of the early phases of the cycle, which remain difficult to access in vivo. Using this system, we define transcriptional transitions in ciliated and non-ciliated epithelial cells during regeneration, revealing immediate stress-responsive states followed by wound-responsive ones that precede proliferation. We demonstrate that, in response to breakdown, organoids acquire a transcriptomic signature resembling the in vivo luminal epithelium in the menstrual and proliferative phases of the cycle. Luminal epithelial cells are crucial for this re-epithelialization and express factors such as WNT7A which we show to be required for long-term epithelial maintenance. Moreover, cell-cell communication analyses identify luminal epithelium as a signaling hub, interacting with endothelial and immune cells via pathways including CXCL8, consistent with promotion of angiogenesis and immune recruitment during the regenerative window. Taken together, our study establishes a physiologically relevant paradigm to dissect epithelial renewal and cell-cell interactions during menstruation with potential to extend towards modelling common and distressing conditions such as menstrual disorders and endometriosis.

cell biology↗

bioRxiv2025

The eutherian-specific histone H3.4 promotes germ cell development and reproductive fitness

Many genes encoding chromatin proteins are subject to evolutionary selection driving reproductive fitness. In mice and men, the histone H3.4 variant is essential to spermatogenesis. Here we define the evolutionary origin and molecular-physiological roles of sequence variation in H3f4 for male germ cell development in mice. Our phylogenetic analyses indicate that eutherian H3f4 orthologs originate from an ancestral H3.2 gene existing prior to the divergence of eutherian and marsupial mammals over 100 million years ago. Positioned in truncated histone gene clusters, eutherian H3f4 orthologs show increased non-synonymous and synonymous substitution rates compared to orthologous marsupial H3.2 loci located in typically large histone clusters. To determine the impact of sequence divergence on reproductive fitness, we reverted non-synonymously substituted residues in H3f4 to those present in canonical H3.1 (H3f4V24A, H3f4H42R, H3f4S98A). Hemizygous expression of such triply reverted H3f4H3.1 allele on a H3f4-deficiency background caused an >40% reduction in testis weight associated with impaired meiotic DNA double strand break repair, death of pachytene spermatocytes, impaired differentiation of spermatids and aberrant expression of thousands of genes during spermatid elongation. Hemizygous expression of individual residue substitution alleles revealed residues V24 and H42 of H3.4 to promote spermatogenesis, while residue S98 is neutral. Together, our study shows that H3f4 has been subject to positive evolutionary selection, promoting male reproductive fitness.

genetics↗

bioRxiv2023

Molecular logic of neuromodulatory systems in the zebrafish telencephalon

The function of neuronal networks is determined not only by synaptic connectivity but also by neuromodulatory systems that broadcast information via distributed connections and volume transmission. To understand the molecular constraints that organize neuromodulatory signaling in the telencephalon of adult zebrafish we used transcriptomics and additional approaches to delineate cell types, to determine their phylogenetic conservation, and to map the expression of marker genes at high granularity. The combinatorial expression of GPCRs and cell type markers indicates that all neuronal cell types are subject to modulation by multiple monoaminergic systems and distinct combinations of neuropeptides. Individual cell types were associated with multiple (typically >30) neuromodulatory signaling networks but expressed only a few diagnostic GPCRs at high levels, suggesting that different neuromodulatory systems act in combination albeit with unequal weights. These results provide a detailed map of cell types and brain areas in the zebrafish telencephalon, identify core components of neuromodulatory networks, highlight the cell type-specificity of neuropeptides and GPCRs, and begin to decipher the logic of combinatorial neuromodulation.

neuroscience↗

bioRxiv2022

Galaxy Training: A Powerful Framework for Teaching!

There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis and stewardship are still rarely taught in life science educational programs [1], resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org); an open access, community-driven framework for the collection of FAIR training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform [2]. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments.

bioinformatics↗

bioRxiv2020

Expanding the Galaxy's reference data

SummaryProperly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows to easily organize, retrieve, and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. Additionally, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenies remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS repository from GalaxyProject.org, with mirrors across the United States, Canada, Europe, and Australia, enabling easy use outside of Galaxy. Availability and implementationThe ability of Galaxy to use refgenie assets was added to the core Galaxy framework in version 20.05, which is available from https://github.com/galaxyproject/galaxy under the Academic Free License version 3.0. The refgenie Data Manager tool can be installed via the Galaxy ToolShed, with source code managed at https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull and released using an MIT license.

bioinformatics↗

bioRxiv2020

A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework

BackgroundThe vast ecosystem of single-cell RNA-seq tools has until recently been plagued by an excess of diverging analysis strategies, inconsistent file formats, and compatibility issues between different software suites. The uptake of 10x Genomics datasets has begun to calm this diversity, and the bioinformatics community leans once more towards the large computing requirements and the statistically-driven methods needed to process and understand these ever-growing datasets. ResultsHere we outline several Galaxy workflows and learning resources for scRNA-seq, with the aim of providing a comprehensive analysis environment paired with a thorough user learning experience that bridges the knowledge gap between the computational methods and the underlying cell biology. The Galaxy reproducible bioinformatics framework provides tools, workflows and trainings that not only enable users to perform one-click 10x preprocessing, but also empowers them to demultiplex raw sequencing from custom tagged and full-length sequencing protocols. The downstream analysis supports a wide range of high-quality interoperable suites separated into common stages of analysis: inspection, filtering, normalization, confounder removal and clustering. The teaching resources cover an assortment of different concepts from computer science to cell biology. Access to all resources is provided at the singlecell.usegalaxy.eu portal. ConclusionsThe reproducible and training-oriented Galaxy framework provides a sustainable HPC environment for users to run flexible analyses on both 10x and alternative platforms. The tutorials from the Galaxy Training Network along with the frequent training workshops hosted by the Galaxy Community provide a means for users to learn, publish and teach scRNA-seq analysis. Key PointsO_LISingle-cell RNA-seq has stabilised towards 10x Genomics datasets. C_LIO_LIGalaxy provides rich and reproducible scRNA-seq workflows with a wide range of robust tools. C_LIO_LIThe Galaxy Training Network provides tutorials for the processing of both 10x and non-10x datasets. C_LI

bioinformatics↗

bioRxiv2017

Community-driven data analysis training for biology

The primary problem with the explosion of biomedical datasets is not the data itself, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web-browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences.

bioinformatics↗