Biology subjects

Eskeland, R.

Publications and source records attributed to Eskeland, R..

10 recordsLinked to original sources

bioRxiv2026

Proteome-wide multi-omics profiling of osteosarcoma transcription factor networks

Osteosarcoma (OS) is an aggressive bone cancer that most commonly affects children and young adults. OS exhibits a high degree of genomic complexity, as well as cellular plasticity, and dynamic transcriptional regulation is suggested to contribute to treatment resistance and metastasis. Cell lines are well characterized as models to advance our knowledge on OS biology. HOS and U2OS cells have increased invasiveness and higher migratory ability compared with MG63. In this study, we employed a tandem array of consensus transcription factor response elements (catTFREs) proteomic approach to characterize transcription factor (TF) regulatory networks related to OS aggressiveness. We mapped 7,594 proteins and enriched 352 transcription factors and coregulators. When we integrated proteomics with cell line specific gene expression and chromatin accessibility we classified the proteins into different OS cell line dependent sub-clusters and identified TFs and coregulators common for all cell lines and specific for individual cell lines. We demonstrate that RUNX2, MYBL2 and HMGA2 are specifically enriched in HOS and U2OS and may be linked to the cell aggressiveness. ETV5, JUNB, NFIX and ZEB1 were among TFs specific to MG63. Our analysis provides a more comprehensive understanding of the transcriptional drivers that shape OS regulatory landscapes and may have future therapeutic implications.

biochemistry↗

bioRxiv2025

Major waves of H2A.Z incorporation during mouse oogenesis

Mammalian oocytes and embryos have distinct epigenomes that undergo major transitions essential for transmitting life to the next generation. Here, we provide the first genome-wide maps of the histone variant H2A.Z during six different stages of mouse oogenesis. Utilizing picogram- scale chromatin immunoprecipitation and sequencing (picoChIP-seq), we reveal major waves of H2A.Z incorporation occurring early in growing oocytes. We identify distinct patterns of H2A.Z signal at oocyte-specific, embryo-specific, and constant H2A.Z loci. Late oocyte-specific loci precede reduced formation of lamina associated domains and early replication timing in the maternal compared to the paternal genome of 2-cell embryos. While constant H2A.Z is strongly associated with CpG islands (CGIs) and H3K4me3 near transcription start sites (TSS) of active genes, tens of thousands of oocyte- and embryo-specific H2A.Z incorporation sites exist independently of CGIs and TSSs. These TSS-distal H2A.Z sites are frequently enriched at transposable elements (TEs), and an intriguing inverse relationship exists between H2A.Z and H3K4me3 in low CpG environments, such as MTA and MTB retrotransposons (RTs). The existence of changes in H2A.Z distribution that persist across related developmental stages enable preservation of epigenetic information despite major concurrent changes in H3K4me3, H3K27me3, and DNA methylation. Altogether, this reveals new layers of regulation advancing our understanding of how histone variants contribute to the epigenetic landscape during mammalian oogenesis and preimplantation embryo development.

developmental biology↗

bioRxiv2023

ShinyMultiome.UiO: An interactive open-source framework utilizing Seurat Objects for visualizing single-cell Multiomes

MotivationSingle-cell genomics has been revolutionized by the advent of single-cell Multiome sequencing which allows for simultaneous profiling of chromatin accessibility and gene expression in individual nuclei. The analysis and interpretation of large and often complex scMultiome datasets requires in-depth knowledge of computational programming. ResultsWe present ShinyMultiome.UiO, a user-friendly, integrative, and opensource web-based tool that supports Seurat objects for visualization of single-cell Multiome. The ShinyMultiome.UiO facilitates interactive reporting and comprehensive characterization of cellular heterogeneity and regulatory landscapes. With ShinyMultiome.UiO, users can facilitate collaborative efforts for interpre-tation of single-cell Multiome data and make it available to the public. Availability and implementationhttps://github.com/EskelandLab/ShinyMultiomeUiO and demo server, https://cancell.medisin.uio.no/ShinyMultiome.UiO/ set up with a PBMC reference dataset. ContactAnkush.Sharma@medisin.uio.no & Ragnhild.Eskeland@medisin.uio.no

bioinformatics↗

bioRxiv2023

ANDA: An open-source tool for automated image analysis of neuronal differentiation

BackgroundImaging of in vitro neuronal differentiation and measurements of cell morphologies has led to novel insights into neuronal development. Live-cell imaging techniques and large datasets of images has increased the demand for automated pipelines for quantitative analysis of neuronal morphological metrics. ResultsWe present ANDA, an analysis workflow for quantification of various aspects of neuronal morphology from high-throughput live-cell imaging screens. This tool automates the analysis of neuronal cell numbers, neurite lengths and neurite attachment points. We used rat, chicken and human in vitro models for neuronal differentiation and have demonstrated the accuracy, versatility, and efficiency of the tool. ConclusionsANDA is an open-source tool that is easy to use and capable of automated processing from time-course measurements of neuronal cells. The strength of this pipeline is the capability to analyse high-throughput imaging screens.

cell biology↗

bioRxiv2022

Multi-omics analysis of paracetamol exposure identifies dysregulated genes involved in neurotoxicity and neuronal differentiation of human embryonic stem cells

Prenatal paracetamol exposure has been associated with neurodevelopmental outcomes in childhood. Pharmacoepigenetic studies show differences in cord blood DNA methylation between paracetamol exposed and unexposed neonates. However, causal implications and impact of long-term prenatal long-term paracetamol exposure on brain development remain unclear. Using a multi-omics approach, we investigated the effects of paracetamol on a model of early human brain development. We exposed human embryonic stem cells undergoing in vitro neuronal differentiation to daily media changes with paracetamol concentrations corresponding to maternal therapeutic doses. Single-cell RNA-seq and ATAC-seq integration identified paracetamol-induced chromatin-opening changes linked to gene expression. Differentially methylated and/or expressed genes were involved in signalling, neurotransmission, and cell fate-determination trajectories. Some genes involved in neuronal injury and development-specific pathways, such as KCNE3, overlapped with differentially methylated genes previously identified in cord blood associated with prenatal paracetamol exposure. Our data suggest that paracetamol may play a causal role in impaired neurodevelopment. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/519620v2_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@e1a75forg.highwire.dtl.DTLVardef@b36a1forg.highwire.dtl.DTLVardef@fc25e4org.highwire.dtl.DTLVardef@1bb1c8_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2022

A multi-omics approach to visualize early neuronal differentiation in 4D

Neuronal differentiation of pluripotent stem cells is an established method to study physiology, disease and medication safety. However, the sequence of events in human neuronal differentiation and the ability of in vitro models to recapitulate early brain development are poorly understood. We developed a protocol optimized for the study of early human brain development and neuropharmacological applications. We comprehensively characterized gene expression and epigenetic profiles at four timepoints, as the cells differentiate from embryonic stem cells towards a heterogenous population of progenitors, immature and mature neurons bearing telencephalic signatures. A multi-omics roadmap of neuronal differentiation, combined with searchable interactive gene analysis tools, allows for extensive exploration of early neuronal development and the effect of medications. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=178 SRC="FIGDIR/small/478732v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@163539forg.highwire.dtl.DTLVardef@72c09org.highwire.dtl.DTLVardef@dc04eforg.highwire.dtl.DTLVardef@c821d2_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMulti-omics charting a new neuronal differentiation protocol for human ES cells C_LIO_LISingle-cell analyses reveals marker genes during neuronal differentiation C_LIO_LIIdentified transcriptional waves similar to early human brain development C_LIO_LISearchable tools to visualize single-cell gene expression and chromatin state C_LI In BriefWe have developed a novel protocol for human embryonic stem cells to study neural induction and early neuronal differentiation. Multi-omics analyses uncovered cell populations, genes and transcriptional waves defining cell fate commitment. We comprehensively describe epigenetic landscapes and gene expression and provide searchable analysis tools for exploration of the data.

cell biology↗

bioRxiv2022

Robust and reproducible neuronal differentiation of human embryonic stem cells for neurotoxicology

Neuronal differentiation from pluripotent cells is commonly used to recapitulate events in early brain development. Neuronal precursors and developing neurons cultured in vivo, rely on attachment, density and cell-to-cell communication, and cell-passaging steps should be minimised to avert disruption of network cross-connectivity. This is crucial both for viability and maturation, and the former also applies to human embryonic stem cells (hESCs). Neuronal differentiation protocols from hESCs for neurotoxicology assessment studies should therefore provide standardized cell density requirements, and optimised coating matrix conditions. The effect of drug treatments may be masked by compound instability and degradation in cell culture medium but performing daily media changes can circumvent these issues. Here, we describe a robust neuronal differentiation protocol using dual SMAD/WNT signalling inhibitors LDN193189, SB431542 and XAV939 (LSX) for neural induction of hESCs, followed by self-patterning and cell maturation stages, for the generation of ventral telencephalic progenitors and neurons. We provide critical information on the optimized cell culture parameters and standardized methods of stage-specific validation. Using cell counts, immunofluorescence, qRT-PCR, and a proof of principle treatment with valproic acid to showcase issues with drug-induced cell toxicity, we facilitate reproducibility of the protocol. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/477818v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@19f0f89org.highwire.dtl.DTLVardef@1b4feaaorg.highwire.dtl.DTLVardef@1bb832borg.highwire.dtl.DTLVardef@1a07efd_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2021

ShinyArchR.UiO: User-friendly, integrative and open-source tool for visualisation of single-cell ATAC-seq data using ArchR

MotivationMapping of chromatin accessibility landscapes in single-cells and the integration with gene expression enables a better understanding of gene regulatory mechanisms defining cell identities and cell-fate determination in development and disease. Generally, raw data generated from single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) are deposited in repositories that are inaccessible due to lack of in-depth knowledge of computational programming. ResultsWe have developed ShinyArchR.UiO, an R-based shiny app, that facilitates scATAC-seq data accessibility and visualisation in a user-friendly, interactive, and open-source web interface. ShinyArchR.UiO is a tool that can streamline collaborative efforts for interpretation of massive chromatin accessible data and promotes open access data sharing for wider audiences. Availability and implementationShinyArchR.UiO is available at https://Github.com/EskelandLab/ShinyArchRUiO and a demo server set up with a haematopoietic tutorial dataset: https://cancell.medisin.uio.no/ShinyArchR.UiO ContactAnkush.Sharma@medisin.uio.no & Ragnhild.Eskeland@medisin.uio.no

bioinformatics↗

bioRxiv2021

Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers

Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked to dysregulation of the regulatory program in cancer cells. To shed light on the underlying molecular mechanism driving this process, we hypothesized that aberrant methylation patterns could be controlled by the binding of specific transcription factors (TFs) across cancer types. By combining DNA methylation arrays and gene expression data with TF binding sites (TFBSs), we explored the interplay between TF binding and DNA methylation in 19 cancer types. We performed emQTL (expression-methylation quantitative trait loci) analyses independently in each cancer type and identified 13 TFs whose expression levels are correlated with local DNA methylation patterns around their binding sites in at least 2 cancer types. The 13 TFs are mainly associated with local demethylation and are enriched for pioneer function, suggesting a specific role for these TFs in modulating chromatin structure and transcription in cancer patients. Furthermore, we confirmed that de novo methylation is precluded across cancers at CpGs lying in genomic regions enriched for TF-binding signatures associated with SP1, CTCF, NRF1, GABPA, KLF9, and/or YY1. The modulation of DNA methylation associated with TF binding was observed at cis-regulatory regions controlling immune- and cancer-associated pathways, corroborating that the emQTL signals were derived from both cancer and tumor-infiltrating cells. As a case example, we experimentally confirmed that FOXA1 knock-down is associated with higher methylation in regions bound by FOXA1 in breast cancer MCF-7 cells. Finally, we reported physical interactions between FOXA1 with TET1 and TET2 both in an in vitro setup and in vivo at physiological levels in MCF-7 cells, adding further support for FOXA1 attracting TET1 and TET2 to induce local demethylation in cancer cells.

cancer biology↗

bioRxiv2017

Tex19.1 Restricts LINE-1 Mobilisation in Mouse Embryonic Stem Cells

Mobilisation of retrotransposons to new genomic locations is a significant driver of mammalian genome evolution. In humans, retrotransposon mobilisation is mediated primarily by proteins encoded by LINE-1 (L1) retrotransposons, which mobilise in pluripotent cells early in development. Here we show that TEX19.1, which is induced by developmentally programmed DNA hypomethylation, can directly interact with the L1-encoded protein L1-ORF1p, stimulate its polyubiquitylation and degradation, and restrict L1 mobilisation. We also show that TEX19.1 likely acts, at least in part, through promoting the activity of the E3 ubiquitin ligase UBR2 towards L1-ORF1p. Moreover, we show that loss of Tex19.1 increases L1-ORF1p levels and mobilisation of L1 reporters in pluripotent mouse embryonic stem cells implying that Tex19.1 prevents new retrotransposition-mediated mutations from arising in the germline genome. These data show that post-translational regulation of L1 retrotransposons plays a key role in maintaining trans-generational genome stability in the epigenetically dynamic developing mammalian germline.

genetics↗