Biology subjects

Fuellen, G.

Publications and source records attributed to Fuellen, G..

14 recordsLinked to original sources

bioRxiv2026

Fertilization offsets the maternal age effect on mouse oocytes provided the oviduct is not itself aged

Advanced maternal age compromises oocyte quality, and it is widely assumed that these deficits are transmitted to embryos. However, because most studies rely on in vivo conception, it has been difficult to separate the effects of oocyte aging from those of an aged fertilization environment. In aging mice, we observed that the fraction of ovulated oocytes forming implantation sites after in vivo conception fell ~3.7-fold, raising the question of whether this was due to reduced fertilization, reduced embryo quality or reduced support from the aged reproductive tract. Therefore we fertilized oocytes of aged and young mice in vitro with a shared young-donor sperm preparation, holding the fertilization environment constant and removing paternal variability. Hallmarks of maternal age were largely offset following fertilization in vitro: aged oocytes produced blastocysts at rates comparable to young controls, with altered - but not deficient - cell-lineage composition and no detectable impairment in development to term (E18.5) after transfer to young oviducts. Proteomic analysis revealed that, unlike the transcriptomic signature, the proteomic age signature of oocytes was not faithfully propagated to the blastocyst: for a subset of proteins, particularly those depleted in aged oocytes, the direction of the age effect reversed between oocyte and blastocyst. Comparison with parthenogenetically activated oocytes showed this divergence to be fertilization-dependent, implicating fertilization - rather than mere embryonic cleavage - as the driver of proteomic change. Stable-isotope labelling in live embryos showed that blastocysts from aged, fertilized oocytes both synthesized more new protein and retained less maternal protein than young counterparts; neither effect was detectable after parthenogenesis. Puromycin labelling, by contrast, showed a maternal-age-associated rise in bulk synthesis regardless of route. Together, these results indicate that the maternal-age effect on the oocyte proteome is labile rather than fixed and can be offset by fertilization itself, provided the maternal environment is not itself aged.

developmental biology↗

bioRxiv2025

A novel and critical role of the intracellular Zona Pellucida protein 2 (ZP2) for blastocyst formation in mice

The zona pellucida (ZP) is the quintessential extracellular structure of mammalian oocytes. Contrary to long-standing view that the synthesis of ZP proteins is specific to oocytes and muted in embryos, we report here that the major zona pellucida protein ZP2 is re-synthesized and functionally required during mouse embryo development. The orthogonal methods of mass spectrometry and monoclonal immunofluorescence revealed an increase of ZP2 abundance at the 8-cell / morula stage, which did not occur when zygotes were microinjected with translation-blocking oligonucleotides (morpholinos). To shed light on the functional significance of embryonic ZP2, we performed protein knockdown using immunodepletion (by Trim-Away) while at the same time preventing replenishment (by translation-blocking morpholino). ZP2 knockdown resulted in morula stage retardation and formation of defective blastocysts, whose cell lineages trophectoderm and primitive endoderm were smaller and less able to support post-implantation development. The transcriptional correlates of these morphological alterations had a gene ontology (biological process) signature that included cell lineage-relevant terms ( endoderm development, gastrulation), while the proteomic correlates had a gene ontology signature related to protein synthesis. Taken together, these results call into question the traditional model that ZP proteins function solely in the extracellular space and accompany embryogenesis as passive bystanders: on the contrary, ZP proteins also participate actively in the intracellular processes of early embryogenesis.

developmental biology↗

bioRxiv2025

Meta-analysis reveals reproducible rapamycin-induced shifts in the mouse gut microbiome

Rapamycin is a geroprotective compound that extends lifespan and is well characterised in systemic physiology. However, due to heterogeneous methodologies, its effects on the gut microbiome, an emerging regulator of ageing and health, remain poorly defined. Here, we systematically assessed these effects in mice using a harmonised meta-analysis workflow, reprocessing raw sequence data end-to-end. We conducted a harmonised meta-analysis of the gut microbiome using 16S rRNA gene amplicon data from three independent mouse studies (n = 54) spanning dietary and intraperitoneal rapamycin interventions with matched controls. All samples were uniformly processed using a standardised 16S rRNA bioinformatics workflow. Genus-level abundances were modelled using two complementary approaches: a per-study zero-inflated beta modelling framework with random-effects meta-analysis, and a batch-corrected linear modelling framework incorporating correction prior to meta-analysis. Dose-response meta-regression assessed whether rapamycin-associated changes scaled with dose (42-990 mg/kg), integrating presence and magnitude of effects across heterogeneous study designs. Rapamycin treatment induced reproducible shifts in specific taxa across studies, with a subset of core responders consistently altered regardless of dose. Among the core responders, Bacteroides increased (OR = 1.59, q = 0.042) and Muribaculum decreased (OR = 0.55, q = 0.042), each significant in both frameworks. Whereas Ruminococcus decreased (OR = 0.60, q = 0.089), it was significant in the batch-corrected framework, but only a trend in zero-inflated modelling. Dose-sensitivity analyses highlighted Lachnospiraceae as the most consistent dose-sensitive taxon, with other associations largely restricted to extreme doses. Functional pathway analysis revealed alterations in energy metabolism and microbial stress response. This harmonised meta-analysis highlights notable shifts in the gut microbiome connected to rapamycin across the examined studies, outlining potential core microbial signatures. These findings were observed within heterogeneous experimental contexts, and further validation in additional studies will be needed to confirm their generality.

microbiology↗

bioRxiv2023

First cleavage is a manifestation of the geometry of the unfertilized oocyte: implications for monozygotic twinning in mice.

A long-standing question in mammalian embryology is whether regional differences of oocyte composition matter for the properties of blastomeres receiving those regions after fertilization. A hitherto untested hypothesis is that allocation depends on the orientation of 1st cleavage. However, the orientation is influenced by the site of sperm entry, which can be almost anywhere on the membrane of oocytes when these are inseminated. This variability undermines consistency and reproducibility of studies. Therefore, we harnessed the intracytoplasmic sperm injection to impose the site of fertilization in three specific ooplasmic regions (animal pole, vegetal pole, equator) in mice. Notwithstanding this categorical distinction, after 1st cleavage, the sister blastomeres differed from each other nearly the same way, as measured by gene expression and twin blastocysts formation following 2-cell embryo splitting. We reasoned that either the oocyte territories did not matter, or their effect was obscured by other factors. To shed light on these possibilities, we immobilized the oocytes on the micromanipulation stage during sperm injection and for 24 h thereafter. Imaging revealed that the orientation of 1st cleavage, instead of varying with the fertilization site, followed the shorter diameter of the unfertilized oocyte. This led in most cases to the segregation of animal and vegetal hemispheres into the sister blastomeres of 2-cell embryos. Since one blastomere received more of the animal materials and the other blastomere more of the vegetal materials, this offers a rationale to explain the distinct properties of monozygotic twins derived from 2-cell embryos in mice.

developmental biology↗

bioRxiv2022

Intracellular fraction of zona pellucida protein 3 is required for the oocyte to embryo transition in mice

In oocyte biology the zona pellucida has long been known to operate three extracellular functions, namely, encasing the oocytes in ovarian follicles, mediating sperm-oocyte interaction and preventing premature embryo contact with maternal epithelia. The present study uncovers a fourth function that is fundamentally distinct from the other three, being critical for embryonic cell survival. Intriguingly, the three proteins of the mouse zona pellucida (ZP1, ZP2, ZP3) were found abundantly present also inside the embryo four days after fertilization, as shown by mass spectrometry, immunoblotting and immunofluorescence. Trim-away-mediated knockdown of ZPs in fertilized oocytes resulted in various grades of embryopathy: knockdown of ZP1 impeded blastocyst expansion, knockdown of ZP2 hampered the 2nd zygotic cleavage, while knockdown of ZP3 hampered the 1st zygotic cleavage - unlike the overexpression. Transcriptome analysis of ZP3-knockdown embryos pointed at defects of cytoplasmic translation in the context of embryonic genome activation. This conclusion was supported by reduced protein synthesis in the ZP3-knockdown and by the lack of cleavage arrest when knockdown was postponed from the 1-cell to the late 2-cell stage. These data place constraints on the long-standing notion that the zona pellucida proteins only operate in the extracellular space. We postulate that such noncanonical localization of ZP3 reflect novel roles in the embryos interior during the oocyte-to-embryo transition in mice. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/521410v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@18c0ca2org.highwire.dtl.DTLVardef@19168aeorg.highwire.dtl.DTLVardef@16f784forg.highwire.dtl.DTLVardef@143c4b7_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2022

Computational identification of natural senotherapeutic compounds that mimic dasatinib based on gene expression data

The highest risk factor for chronic diseases is chronological age, and age-related chronic diseases account for the majority of deaths worldwide. Targeting senescent cells that accumulate in disease-related tissues presents a strategy to reduce disease burden and to increase healthspan. Our goal was the computational identification of senotherapeutic repurposing candidates that potentially eliminate senescent cells, based on their similarity in gene expression effects to dasatinib, a tyrosine-kinase inhibitor that induces apoptosis in certain senescent cell types, and that is frequently used as a senolytic together with quercetin. The natural senolytic piperlongumine (a compound found in long pepper), and the natural senomorphics parthenolide, phloretin and curcumin (found in various edible plants) were identified as potential substitutes of dasatinib. The gene expression changes underlying the repositioning highlight apoptosis-related genes and pathways. The four compounds, and in particular the top-runner piperlongumine, may be combined with quercetin to obtain natural formulas emulating the dasatinib + quercetin (D+Q) formula that is frequently used in clinical trials targeting senescent cells.

bioinformatics↗

bioRxiv2021

Gene co-expression analyses of health(span) across multiple species

Health(span)-related gene clusters/modules were recently identified based on knowledge about the cross-species genetic basis of health, to interpret transcriptomic datasets describing health-related interventions. However, the cross-species comparison of health-related observations reveals a lot of heterogeneity, not least due to widely varying health(span) definitions and study designs, posing a challenge for the exploration of conserved healthspan modules and, specifically, their transfer across species. To improve the identification and exploration of conserved/transferable healthspan modules, here we apply an established workflow based on gene co-expression network analyses employing GEO/ArrayExpress data for human and animal models, and perform a comprehensive meta-analysis of the resulting modules related to health(span), yielding a small set of health(span) candidate genes, backed by the literature. For each experiment, WGCNA (weighted gene correlation network analysis) was thus used to infer modules of genes which correlate in their expression with a "health phenotype score" and to determine the most-connected (hub) genes for each such module, and their interactions. After mapping these hub genes to their human orthologs, 12 health(span) genes were identified in at least two species (ACTN3, ANK1, MRPL18, MYL1, PAXIP1, PPP1CA, SCN3B, SDCBP, SKIV2L, TUBG1, TYROBP, WIPF1), for which enrichment analysis by g:profiler finds an association with actin filament-based movement and associated organelles as well as muscular structures. We conclude that a meta-study of hub genes from co-expression network analyses for the complex phenotype health(span), across multiple species, can yield molecular-mechanistic insights and can direct experimentalists to further investigate the contribution of individual genes and their interactions to health(span).

genomics↗

bioRxiv2019

Unraveling the heterogeneous mutational signature of spontaneously developing tumors in MLH1-/- mice

MLH1 knock out mice represent a preclinical model that resembles features of the human counterpart. As these mice develop mismatch repair deficient (MMR-D) neoplasias in a sequential twin-peaked manner (first lymphomas, then gastrointestinal tumors) we aimed at identification of the underlying molecular mechanisms. Using whole-exome sequencing, we focused on (I) shared and (II) mutually exclusive mutations and described the processes of ongoing mutational events in tumor-derived cultures.\n\nA heterogeneous genetic landscape was found, with few mutations shared among different neoplasias (ARID1A and IDH2). Mutations in tumor suppressor genes SMAD4 and POLE were mutually exclusive in lymphomas, most likely contributing to a more aggressive in vivo phenotype. Comparing the mutational profile of selected primary tumors and their corresponding cell line upon in vitro culture revealed continuous increased numbers of somatic gene mutations. The same was true for coding microsatellite mutations in selected MMR-D target genes, showing a gradual increase during in vitro passage. With respect to this latter type of mutations, partial overlap was detectable, yet recognizing shared vaccination antigens. The two most promising candidates are AKT3, a RAC-gamma serine/threonine-protein kinase with relevance in maintenance of cellular homeostasis and the endonuclease ERCC5 (Excision Repair 5), involved in DNA excision repair.\n\nNovel results of a comparison between spontaneously developing lymphomas and gastrointestinal tumors as models for MMR-D driven tumorigenesis are reported. In addition to identification of ARID1A as a potentially causative mutation hotspot, our comprehensive characterization of the mutational signature is a starting point for immune-based approaches to therapy.\n\nAuthor SummaryThis study describes the mutational spectrum of MLH1-/--associated tumors, spontaneously developing in mice. While these tumors arise at the bottom of the same germline mutation, the clinical presentations as well as resulting molecular alterations are heterogeneous, and thus likely being directly linked. Highly aggressive lymphomas, developing early in life are ultra-hypermutated and harbor mutations in tumor suppressor genes SMAD4 and POLE. Gastrointestinal tumors develop later in life and show different mutations. By performing in-depth whole exome sequencing analysis, we here identified for the first time a common mutational hotspot. ARID1A constitutes a potentially causative mutation, shared among different MLH1-/--associated tumors and thus irrespective of the origin. Additional interesting and identified candidate genes include AKT3, a RAC-gamma serine/threonine-protein kinase and the endonuclease ERCC5. Both genes are bona fide tumor suppressors with significant relevance in DNA excision repair and maintenance of cellular homeostasis. This finding is of particular relevance for subsequent therapeutic and - even more important - prophylactic vaccination approaches aiming at entity-overlapping treatment of MLH1-/--related tumors.

cancer biology↗

bioRxiv2018

An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo

Early mouse embryos have an atypical translational machinery comprised of cytoplasmic lattices, poorly competent for translation. Thus, the impact of transcriptomic changes on the operational levels of proteins has likely been overestimated in the past. To find out, we used liquid chromatography-tandem mass spectrometry to detect and quantify 6,550 proteins in the oocyte and in six developmental stages (from zygote to blastocyst) collected in triplicates, and we also performed mRNA sequencing.\n\nIn contrast to the known split between the 2-cell and 4-cell stages at the transcript level, on the protein level the oocyte-to-embryo transition appeared to last until the morula stage. In general, protein abundance profiles were weakly correlated with those of their cognate mRNAs and we found little or no concordance between changes in protein and transcript expression relative to the oocyte at early stages. However, concordance increased towards morula and blastocyst, hinting at a more direct coupling of proteins with transcripts at these stages, in agreement with the increase in free ribosome abundance. Independent validation by immunofluorescence and qPCR confirmed the existence of genes featuring strongly positively and negatively correlated protein and transcript. Moreover, consistent coverage of most known protein complexes indicates that our dataset represents a large fraction of the expressed proteome. Finally, we identified 20 markers, including members of the endoplasmic reticulum pathway, for discriminating between early and late stages.\n\nThis resource contributes towards closing the gap between the predicted phenotype, based on mRNA, and the actual phenotype, based on protein, of the mouse embryo.

developmental biology↗

bioRxiv2018

Maternally inherited differences within mitochondrial Complex I control murine healthspan.

Mitochondrial complex I, the largest enzyme complex of the mitochondrial oxidative phosphorylation machinery, has been proposed to contribute to a variety of age-related pathological alterations as well as longevity. The enzyme complex-consisting proteins are encoded by both nuclear (nDNA) and mitochondrial DNA (mtDNA). While some association studies of mtDNA-encoded complex I genes and lifespan in humans have been reported, experimental evidence and the functional consequence of such variants is limited to studies using invertebrate models. Here, we present experimental evidence that a homoplasmic mutation in the mitochondrially encoded complex I gene mt-Nd2 modulates lifespan by altering cellular tryptophan levels and, consequently, ageing-related pathways in mice. A conplastic mouse strain carrying a mutation at m.4738C>A in mt-Nd2 lived significantly shorter than the controls did. The same mutation led to a higher susceptibility to glucose intolerance induced by high-fat diet feeding. These phenotypes were not observed in mice carrying a mutation in another mtDNA-encoded complex I gene, mt-Nd5, suggesting the functional relevance of particular mutations in complex I to ageing and age-related diseases.

genetics↗

bioRxiv2018

Pathway maps enable straightforward yet customized and semi-automated yet insightful analyses of omics data

To explore the molecular processes underlying some biological theme of interest based on public data, gene lists are used herein as input for the construction of annotated pathway maps, employing Cytoscape apps, and then high-throughput (\"omics\") gene expression data are overlaid onto these maps. Seeded with a published set of marker genes of the senescence-associated secretory phenotype and the genes of the cellular senescence KEGG pathway, a gene/protein interaction network and annotated clusters (a \"pathway map\") of cellular senescence are derived. The map can be amended, by adding some application-specific genes, and overlaid with gene expression data describing cellular senescence of fibroblasts and with disease-related gene expression data associated with prostate and pancreatic cancer, and with ischemic stroke, allowing insights into the role of cellular senescence in disease. Some gene expression data are derived from the \"Biomarker Benchmark repository\". The pathway map approach can be followed in principle for any biological theme of interest, fostering much-needed independence from the investigator-biased expert networks usually used for overlaying gene expression data.

genomics↗

bioRxiv2018

Healthspan pathway maps in C. elegans and humans highlight transcription, prolifera-tion/biosynthesis and lipids

The molecular basis of aging and of aging-associated diseases is being unraveled at an increasing pace. An extended healthspan, and not merely an extension of lifespan, has become the aim of medical practice. However, a precise definition of health and healthspan is not straightforward, and the causal molecular basis of health \"per se\" is largely unknown. Here, we define health based on the absence of diseases and dysfunctions. Based on an extensive review of the literature, in particular for humans and C. elegans, we compile a list of features of health and of the genes associated with them. Clusters of these genes based on molecular interaction data give rise to maps of healthspan pathways for humans, featuring the themes transcription initiation, proliferation and cholesterol/lipid processing, and for C. elegans, featuring the themes immune response, mitochondrion and biosynthesis based on genetic and compound intervention data, and lipids, biosynthesis and transcription based on WormBase compound intervention data. Overlaying healthspan-related gene expression data (describing effects of metabolic intervention associated with improvements in health) onto the aforementioned healthspan pathway maps, we observe the downregulation of Notch signalling in humans and of proliferation/cell-cycle in C. elegans. The former reflects the proinflammatory role of the Notch pathway. We identify transcription, proliferation/biosynthesis and lipids as a common theme on the annotation level, and proliferation-related kinases on the gene/protein level. Our literature-based data corpus, including visualization, is available as a reference for future investigations, at http://www.h2020awe.eu/index.php/pathways/.

bioinformatics↗

bioRxiv2017

Combination of mitochondrial tRNA and OXPHOS mutation reduces lifespan and physical condition in aged mice

Mutations in the mitochondrial DNA (mtDNA) are widely known to impact on lifespan and tissue integrity. For example, more than 250 pathogenic mtDNA mutations are known, many of which lead to neurological symptoms. In addition, major neurodegenerative diseases share key components of their etiopathogenesis with regard to mtDNA mutations, mitochondrial dysfunction and oxidative stress. In our study we used a set of conplastic mouse models carrying stable point mutations in mitochondrial genes of transfer RNA (tRNA) and oxidative phosphorylation (OXPHOS)-proteins. We analyzed the impact of these mutations on complex traits like lifespan, learning and memory in the ageing process. The combination of both point mutations in the OXPHOS complex IV gene and adenine insertions in the mitochondrially encoded tRNA arginine (tRNA-Arg) gene (mt-Tr) leads to an age-dependent phenotype with elevated mitochondrial superoxide production in the neocortex. Mice with this combination of tRNA and OXPHOS mutations show significantly reduced lifespan and poor physical constitution at the age of 24 months, whereas single point mutations in OXPHOS or mt-tRNA(Arg) do not have this impact. Therefore, we suggest a synergistic effect of these mutations.

developmental biology↗

bioRxiv2017

Low-level mitochondrial heteroplasmy modulates DNA replication, glucose metabolism and lifespan in mice

Mutations in mitochondrial DNA (mtDNA) lead to heteroplasmy, i.e. the intracellular coexistence of wild-type and mutant mtDNA strands, which impact a wide spectrum of diseases but also physiological processes, including endurance exercise performance in athletes. However, the phenotypic consequences of limited levels of naturally-arising heteroplasmy have not been experimentally studied to date. We hence generated a conplastic mouse strain carrying the mitochondrial genome of a AKR/J mouse strain (B6-mtAKR) together with a C57BL/6J nuclear genomic background, leading to >20% heteroplasmy in the origin of light-strand DNA replication (OriL). These conplastic mice demonstrate a shorter lifespan as well as dysregulation of multiple metabolic pathways, culminating in impaired glucose metabolism, compared to wild-type C57BL/6J mice carrying lower levels of heteroplasmy. Our results indicate that physiologically relevant differences in mtDNA heteroplasmy levels at a single, functionally important site impair metabolic health and lifespan in mice.\n\nHighlightsO_LIWe identify heteroplasmy of the adenine-repeat variation (9 to 13A) in nt5172 in the origin of light-strand DNA replication (OriL) in inbred mice.\nC_LIO_LIB6-mtAKR mice carry >20% 12A heteroplasmy in the OriL, while B6 mice carry only [~] 10% heteroplasmy.\nC_LIO_LIThe level of 12A heteroplasmy correlates to mtDNA copy number, glucose metabolism, and lifespan in mice.\nC_LIO_LIGiven the established role of mtDNA heteroplasmy in regards to endurance exercise performance in athletes, these findings may impact our understanding of metabolism and aging in humans.\nC_LI

genetics↗