Biology subjects

Zikmund, T.

Publications and source records attributed to Zikmund, T..

9 recordsLinked to original sources

bioRxiv2025

Digital Reprogramming Decodes Epigenetic Barriers of Cell Fate Changes

The fates of differentiated cells in our body can be induced to change by nuclear reprogramming. In this way, cells valuable for therapeutic purposes and disease modeling can be produced. However, the efficiency of this process is low, partly due to properties of somatic donor nuclei which stabilize their differentiated fate but also act as barriers reprogramming-associated cell fate changes. The identity of these reprogramming barriers is not fully understood. Here, we developed an artificial intelligence-based approach to model nuclear reprogramming and used it to identify the chromatin modification H3K27ac as an epigenetic barrier to reprogramming-induced cell fate changes. Using reprogramming by nuclear transfer (NT) to eggs of Xenopus laevis as a model system, we profiled chromatin modifications in differentiated cell types alongside gene expression patterns before and after reprogramming. Our model integrated the data and by leveraging model predictions, we find that genes resisting inactivation during reprogramming display chromatin modification barcodes. This revealed H3K27ac as a novel candidate barrier to NT reprogramming. Reducing H3K27ac levels using p300/CBP inhibitors before reprogramming led to an improved downregulation of genes linked to H3K27ac-modified enhancers after reprogramming. Importantly, these effects were accompanied by improved embryonic development of the resulting nuclear transfer embryos. In summary, our study identified H3K27ac as a safeguarding mechanism of cellular identities and as a reprogramming barrier during NT. Hence, the here-developed Digital Reprogramming" approach is capable of modelling and improving current cell-fate reprogramming strategies.

genomics↗

bioRxiv2024

Pleiotropic function of Dlx5/6 in coordinating the development of mammalian vocal and auditory organs

Acoustic communication, essential for mammalian social interactions, involves both effector (vocal) and receptor (auditory) organs that present a wide variety of morphologies between species. The molecular mechanisms supporting the harmonious diversification of effector and receptor systems along with the evolution of species-specific acoustic communication are still poorly understood. It is conceivable that common genetic pathways determine the parallel morphogenesis of vocal and auditory systems. Here, we investigated this question by generating mutant mice with targeted invalidation of Dlx5/6 genes in the otic placode and cephalic neural crest cells, contributing to the formation of the ear and vocal tract components. We show that Dlx5/6 inactivation provokes simultaneous defects of the outer, middle and inner ear and of the jaw, pharynx and larynx musculoskeletal systems. Our findings support the notion that Dlx5/6 genes played a pleiotropic role in the co-adaptation of vocal and auditory systems in mammals.

developmental biology↗

bioRxiv2024

Somatic Cell Identity Affects Specific Cell Differentiation Programs Upon Reprogramming In Vivo

Nuclear reprogramming can change cellular fates. Yet, reprogramming efficiency is low and the resulting cell types are often not functional. Here, we used nuclear transfer to eggs to follow single cells during reprogramming in vivo. We show that the differentiation success of reprogrammed cells varies across cell types and depends on the expression of genes specific to the previous cellular identity. We find subsets of reprogramming resistant cells that fail to form functional cell types, undergo cell death, or disrupt normal body patterning. Reducing expression levels of genes specific to the cell-type of origin leads to better reprogramming and improved differentiation trajectories. Thus, our work demonstrates that failing to reprogram in vivo is cell-type specific and emphasises the necessity of minimising aberrant transcripts of the previous somatic identity for improving reprogramming.

developmental biology↗

bioRxiv2024

Unveiling Vertebrate Development Dynamics in Frog Xenopus laevis using Micro-CT Imaging

BackgroundXenopus laevis, the African clawed frog, is a versatile vertebrate model organism employed across various biological disciplines, prominently in developmental biology to elucidate the intricate processes underpinning body plan reorganization during metamorphosis. Despite its widespread utility, a notable gap exists in the availability of comprehensive datasets encompassing Xenopus late developmental stages. FindingsIn the present study, we harnessed micro-computed tomography (micro-CT), a non-invasive 3D imaging technique utilizing X-rays to examine structures at a micrometer scale, to investigate the developmental dynamics and morphological changes of this crucial vertebrate model. Our approach involved generating high-resolution images and computed 3D models of developing Xenopus specimens, spanning from premetamorphosis tadpoles to fully mature adult frogs. This extensive dataset enhances our understanding of vertebrate development and is adaptable for various analyses. For instance, we conducted a thorough examination, analyzing body size, shape, and morphological features, with a specific emphasis on skeletogenesis, teeth, and organs like the brain at different stages. Our analysis yielded valuable insights into the morphological changes and structure dynamics in 3D space during Xenopus development, some of which were not previously documented in such meticulous detail. This implies that our datasets effectively capture and thoroughly examine Xenopus specimens. Thus, these datasets hold the solid potential for additional morphological and morphometric analyses, including individual segmentation of both hard and soft tissue elements within Xenopus. ConclusionsOur repository of micro-CT scans represents a significant resource that can enhance our understanding of Xenopus development and the associated morphological changes. The widespread utility of this amphibian species, coupled with the exceptional quality of our scans, which encompass a comprehensive series of developmental stages, opens up extensive opportunities for their broader research application. Moreover, these scans have the potential for use in virtual reality, 3D printing, and educational contexts, further expanding their value and impact. Graphical abstract & lay summary3D images of selected developmental stages of X. laevis in a comparison (scale bar = 10 mm). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=67 SRC="FIGDIR/small/598452v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@1bc4664org.highwire.dtl.DTLVardef@1b1750dorg.highwire.dtl.DTLVardef@17bddaaorg.highwire.dtl.DTLVardef@115de4e_HPS_FORMAT_FIGEXP M_FIG C_FIG Lay summaryX-ray tomography was used to examine the African clawed frog (Xenopus laevis). An extensive data set of specimens from tadpoles to adult frogs provides novel insights into the changes and developmental dynamics of selected structures, which opens avenues to an improved understanding of this crucial animal model.

developmental biology↗

bioRxiv2022

High resolution micro-CT imaging in mice stroke models: from 3D detailed infarct characterization to automatic area segmentation

Characterization of brain infarct lesion in rodent models of stroke is crucial to assess the outcome of stroke therapies and to study the disease pathophysiology. However, so far it has been mostly performed by: 1) histological methods, a time-consuming process that lead to significant flaws and tissue distortion; or 2) via MRI imaging, which is faster, yielding 3D information but at high costs. High-resolution micro-CT imaging became, in the last decade, a simple, fast, and cheaper solution, allowing 3D analysis of samples. Here, we describe that high-resolution micro-CT, either using iodine/OsO4 as contrast agents, can be successfully applied for fine quantification and localization of lesion size and edema volume in preclinical stroke models. We successfully correlated this new approach with the standard histological method TTC. In transient MCAO mouse stroke model, we were able to identify/quantify large lesioned areas (segmented in core and penumbra), up to degenerated finer striatal myelinated fibers in a transient ischemic attack (TIA) mouse model, at different timepoints post-ischemia, through manual and automatic segmentation approaches (deep learning). Furthermore, 3D reconstructions of the whole brain allow for brain atlas co-registration of the specific affected brain areas. Hence, the presented methodology, through iodine/OsO4 micro-CT imaging, constitutes a valuable advance in tools for precise and detailed assessment of stroke outcomes in preclinical animal studies.

neuroscience↗

bioRxiv2021

Bleeding in patients and mice with Alagille syndrome: sex differences and risk factors

Spontaneous lethal bleeds are major cause of death in the pediatric liver disease Alagille syndrome (ALGS), yet risk factors and screening methods have not been established. We performed a systematic review and identified significantly more female than male patients with idiopathic intracranial hemorrhage (10:1). We investigated bleeding and vasculature in patients and a mouse model for ALGS (Jag1Ndr/Ndr mice) and asked whether phenotypes identified in mice could be detected in patients non-invasively. Jag1Ndr/Ndr mice bled spontaneously, exhibiting a thin skull and vascular defects including artery-vein crossings, tortuous vessels, capillary breakdown and CADASIL-like sparse vascular smooth muscle cell coverage which was aggravated by hypertension. Retinographs from patients confirmed tortuous blood vessels and artery-vein crossings in ALGS. In conclusion, Jag1Ndr/Ndr mice could be used to develop interventions for vascular defects in ALGS, and retinography could provide a non-invasive method for vascular analysis in these pediatric patients.

developmental biology↗

bioRxiv2020

Local retinoic acid directs emergence of the extraocular muscle functional unit

Coordinated development of muscles, tendons, and their attachment sites ensures emergence of functional musculoskeletal units that are adapted to diverse anatomical demands among different species. How these different tissues are patterned and functionally assembled during embryogenesis is poorly understood. Here, we investigated the morphogenesis of extraocular muscles (EOMs), an evolutionary conserved cranial muscle group that is crucial for the coordinated movement of the eyeballs and for visual acuity. By means of lineage analysis, we redefined the cellular origins of periocular connective tissues interacting with the EOMs, which do not arise exclusively from neural crest mesenchyme as previously thought. Using 3D imaging approaches, we established an integrative blueprint for the EOM functional unit. By doing so, we identified a developmental time window where individual EOMs emerge from a unique muscle anlage and establish insertions in the sclera, which sets these muscles apart from classical muscle-to-bone type of insertions. Further, we demonstrate that the eyeballs are a source of diffusible retinoic acid that allow their targeting by the EOMs in a temporal and dose dependent manner. Using genetically modified mice and inhibitor treatments, we find that endogenous local variations in the concentration of retinoids contribute to the establishment of tendon condensations and attachment sites that precede the initiation of muscle patterning. Collectively, our results highlight how global and site-specific programs are deployed for the assembly of muscle functional units with precise definition of muscle shapes and topographical wiring of their tendon attachments.

developmental biology↗

bioRxiv2019

DoUble resin Casting micro computed Tomography (DUCT) reveals biliary and vascular pathology in a mouse model of Alagille syndrome

BACKGROUND AND AIMSAlagille syndrome, like several other liver diseases, is characterized by malformation of lumenized structures, such as the circulatory or biliary systems. Liver architecture has typically been studied through 2D sections and, more recently, using thick tissue sections combined with immunofluorescence. We aimed to develop a robust method to image, digitalize and quantify 3D architecture of the biliary and vascular systems in tandem. METHODSThe biliary and portal vein trees of the mouse liver were injected with Microfil resin, followed by microCT scanning. Tomographic data was segmented and analyzed using a MATLAB script we wrote to investigate length, volume, tortuosity, branching, and the relation between the vascular and biliary systems. Double resin casting micro computed tomography (DUCT) was applied to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), in which the biliary system is absent at postnatal stages, but regenerates by adulthood. Phenotypes discovered using DUCT were validated with cumbersome consecutive liver sections from mouse and human liver including patients with Alagille syndrome. RESULTSDUCT revealed tortuous bile ducts either placed further from portal veins, or ectopically traversing the parenchyma and connecting two portal areas, in Jag1Ndr/Ndr mice. Furthermore, bile ducts either ended abruptly, or branched independently of portal vein branching, with bifurcations placed hilar or peripheral to portal vein branches. The branching defects, parenchymal bile ducts, and blunt endings were confirmed in patient samples. CONCLUSIONDUCT is a powerful technique, which provides computerized 3D reconstruction of casted networks. It exposes and quantifies previously unknown vascular and biliary phenotypes in mouse models, revealing new phenotypes in patients. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/848481v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1565121org.highwire.dtl.DTLVardef@1e86cfcorg.highwire.dtl.DTLVardef@4b4cc3org.highwire.dtl.DTLVardef@19cb20e_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2018

Unique morphogenetic signatures define mammalian neck muscles and associated connective tissues

In vertebrates, head and trunk muscles develop from different mesodermal populations and are regulated by distinct genetic networks. Neck muscles at the head-trunk interface remain poorly defined due to their complex morphogenesis and dual mesodermal origins. Here, we use genetically modified mice to establish a 3D model that integrates regulatory genes, cell populations and morphogenetic events that define this transition zone. We show that the evolutionary conserved cucullaris-derived muscles originate from posterior cardiopharyngeal mesoderm, not lateral plate mesoderm, and we define new boundaries for neural crest and mesodermal contributions to neck connective tissue. Furthermore, lineage studies and functional analysis of Tbx1- and Pax3-null mice reveal a unique genetic program for somitic neck muscles that is distinct from that of somitic trunk muscles. Our findings unveil the embryological and developmental requirements underlying tetrapod neck myogenesis and provide a blueprint to investigate how muscle subsets are selectively affected in some human myopathies.

developmental biology↗