Biology subjects

Winter, J.

Publications and source records attributed to Winter, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Cortico-cerebellar beta-band dynamics predict flexible motor timing

Flexible motor control requires that movements adapt to changing temporal contexts. Here, we test whether flexible timing is driven by context-dependent encoding across cortico-cerebellar circuits and how neural dynamics within these circuits enable accurate performance. To overcome the signal-to-noise limitations of conventional electro- and magnetoencephalography, we recorded whole-head neural dynamics using optically pumped magnetometer arrays (OPM-MEG). Participants learned a context-dependent task, executing manual button presses at time intervals 800 ms (T1) and 1,600 ms (T2), respectively, to avoid a periocular air puff, which was associated with an implicit conditioned eyeblink. We found that the motor cortex contralateral to the hand and bilateral cerebellar lobule VI dynamically encoded these intervals through beta-band (13-30 Hz) event-related desynchronisation (ERD) that precisely scaled with T1 and T2. The cerebellar trial-by-trial latency of the beta-band ERD predicted the timing of explicit manual actions. Finally, partial directed coherence revealed that baseline bidirectional beta-band coupling across the network transiently weakened from the ipsilateral cerebellum to the contralateral motor cortex during finger movement execution. Our findings show that cortico-cerebellar coupling functions as a gating mechanism and suggest that cerebellar circuits modulate cortical motor activity for flexible, accurate motor timing.

neuroscience↗

bioRxiv2026

Comparative analyses of Gram-negative bacteria isolated from cancer patients with bacteraemia at the Uganda Cancer Institute

Antimicrobial resistance (AMR) exacerbates bacteraemia in cancer patients, particularly in low-resource settings. At the Uganda Cancer Institute, high rates of Enterobacterales producing extended-spectrum {beta}-lactamases (ESBLs) have been reported, with DNA-based detection of bla genes limited to PCR. This study aimed to determine whether bacterial genomic DNA shipped at ambient temperature from Uganda to the UK retained sufficient quality for whole-genome sequencing (WGS), to allow in-depth genomic analyses of isolates. Genomic DNA was extracted from Gram-negative bloodstream isolates (n=77) in Uganda and shipped to the UK at ambient temperature. rpoB gene (77/77, 100%) and WGS data (72/77, 93.5%) were generated for isolates, with 66/72 (91.7%) genomes of high-quality (Escherichia coli n=34; Klebsiella spp. n=32). Bioinformatic analyses included species identification, sequence typing, SNP analysis, AMR and virulence gene profiling, and comparison with publicly available genomes of Ugandan isolates. Phenotypic-genotypic concordance was generally high: 7/77 (9.1%) isolates were misidentified by phenotypic testing, and two showed unexplained carbapenem resistance. E. coli isolates showed diverse sequence types, with high prevalence of blaCTX-M (91.2%) and blaOXA-1 (47.1%); carbapenemase genes were rare. Klebsiella isolates lacked hypermucoidy loci and displayed diverse capsule types, with a high prevalence of ESBLs. Genomic clustering suggested limited within-hospital transmission of strains. Genomic data can provide important insights into the dissemination of bacterial subclades of global concern. The widespread AMR genotypes reported here highlight the need for improved diagnostics and updated treatment guidelines for bacteraemia in Ugandan cancer patients. IMPACT STATEMENTBloodstream infections are a major threat to cancer patients, particularly in low-resource settings where access to advanced diagnostics is limited and infection prevention may be challenging. This study shows that it is feasible to transport bacterial DNA at room temperature from Uganda to the UK for high-quality whole-genome sequencing, helping to overcome a logistical barrier to genomic surveillance. By applying genomic analysis to bacteria that had caused bloodstream infections at the Uganda Cancer Institute, we found that traditional laboratory methods can misidentify some bacteria, and that genomic analyses can provide more accurate and detailed insights into the bacteria causing these serious infections. Our work also highlights gaps in current treatment guidelines and demonstrates how genomic data could help inform updates to these, facilitating more effective antibiotic use in situations where urgent treatment is needed and there is no time to wait for laboratory test results. While there was limited evidence of direct transmission of bacteria between patients in our dataset, the genetic diversity and resistance patterns we observed are concerning and emphasise the need for ongoing monitoring and more extensive future studies.

microbiology↗

bioRxiv2026

Systemic stress states are reversed by NPBWR1 inhibition

Chronic stress is widely studied as a brain-centered driver of depression, yet its effects across the body remain unclear. Here, we define chronic stress as a coordinated molecular state across tissues in mice. Using a whole-body proteomic atlas of 13 tissues, we find that stress effects are strongest in peripheral metabolic and endocrine organs, whereas classical stress-associated brain regions show comparatively modest changes. Cross-organ analyses reveal structured, tissue-specific responses rather than uniform shifts. Inhibition of the stress-regulated receptor NPBWR1 reverses both behavioral deficits and proteomic alterations across organs in both sexes, indicating that this state is dynamically modifiable. Integration with human serum proteomics identifies shared, sex-specific signatures. Across tissues, lipid metabolism emerges as a common stress-responsive pathway, confirmed by hepatic lipid remodeling that is normalized by NPBWR1 inhibition. To facilitate exploration of these data, we provide an interactive cross-organ web-based resource. Together, these findings challenge the brain-centric view of stress pathology and define chronic stress as an organism-wide molecular state.

systems biology↗

bioRxiv2026

16p11.2 Copy Number Variation Alters Genome Architecture and Transcriptional Regulation During Neurodevelopment

Microdeletions and microduplications in 16p11.2 are responsible for a spectrum of neurodevelopmental disorders (NDDs) with partially reciprocal and overlapping symptoms. However, the clinical variability in 16p11.2 microduplication patients is significantly greater than that in patients carrying a microdeletion. Here, we use iPSCs derived from members of a family carrying a 16p11.2 microduplication and model neurodevelopment through in vitro differentiation into neural progenitor cells (NPCs) and neurons. The analysis is complemented by reanalysis of publicly available data from 16p11.2 microdeletion patients. Transcriptome analysis revealed MAPK3-centered hubs of upregulated genes in the microduplication-carrying and downregulated in the microdeletion-carrying cells, indicating that MAPK3 is a central driver of 16p11.2 Copy Number Variation (CNV) pathology. While genes within the 16p11.2 region showed about a two-fold reduction in expression in cells carrying the microdeletion, their expression levels in microduplication-derived NPCs and neurons, but not in iPSCs, were elevated to a degree much higher than expected. This observation was accompanied by a substantial number of dysregulated genes unrelated to the genes in the critical region or their interaction networks. To further investigate whether altered chromatin organization may accompany these transcriptional changes, we generated Hi-C data from patient and control iPSCs and NPCs. This revealed increased chromatin contacts within the duplicated 16p11.2 region in patient-derived iPSCs, while genome-wide compartment analysis showed that increased compartments preferentially co-occurred with upregulated differentially expressed genes, particularly in NPCs. Together, these findings suggest that 16p11.2 microduplication may influence gene expression through both local dosage-dependent mechanisms and broader, differentiation-associated changes in chromatin organization. Our data support a model in which CNV-associated genome architecture changes may modulate transcriptional dysregulation and contribute to the variable neurodevelopmental phenotypes associated with 16p11.2 rearrangements.

pathology↗

bioRxiv2025

Asymmetric mitochondrial trafficking maintains network morphology by balancing perinuclear biogenesis

In functionally polarized cells, mitochondria can form distinct subpopulations, positioned at sites of varying metabolic and energetic demands. Thus far, the potential presence of such subpopulations and implications of their intracellular trafficking in immobile and proliferative cells remains largely undescribed, despite such cells serving as key models. Here, we use substrate micropatterning to create reproducible morphologies of cultured immortalized cells, enabling us to define mitochondrial subpopulations and follow their trafficking by photoactivation. We discovered that mitochondrial material is dispersed asymmetrically throughout the cell via biased anterograde transport from the perinuclear area. Combining quantitative analysis and in silico modeling, we characterize the causes and consequences of unbalanced mitochondrial trafficking. Our findings indicate that this bias is required to distribute new material resulting from perinuclear mitochondrial biosynthesis to sustain mitochondrial mass distribution across the cell, and to maintain normal network connectivity.

cell biology↗

bioRxiv2025

Transcript-Capture sequencing enriches mRNA of Mycobacterium tuberculosis from host samples

Bacterial gene expression from sites of infection are poorly studied due to low levels of bacterial mRNA present in clinical samples. Here, we develop Transcript-Capture Seq, which uses customizable biotinylated probes generated in-house to enrich bacteria-specific RNA from host samples before Next Generation Sequencing (NGS). This method results in a >200-fold increase in bacterial mRNA reads from mixed samples and allows analysis of the complete bacterial transcriptome from clinical samples. We apply Transcript-Capture to models of tuberculosis (TB) infection as well as sputum samples from TB patients. TB patients exhibit unexplained heterogeneity in disease progression, and the activity of Mycobacterium tuberculosis (Mtb) has been proposed to affect treatment response. By applying Transcript-Capture to sputum samples collected from TB patients we generate the first complete in vivo bacterial transcriptome of Mtb via NGS. Mtb from patient sputa shows upregulation of genes involved in host lipid utilization and zinc limitation, as well as a similar gene expression profile to Mtb log phase growth in vitro. Applying Transcript-Capture to clinical sputa provides a snapshot of bacterial activity directly from human patients and can be used to investigate the physiological state of bacteria surviving in vivo. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/685133v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@406294org.highwire.dtl.DTLVardef@1080173org.highwire.dtl.DTLVardef@973909org.highwire.dtl.DTLVardef@21becc_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

An extremophilic Nocardiopsis strain from Great Salt Lake expands the taxonomic range of mycolic acid biosynthesis

Mycolic acids, long-chain fatty acids that form the characteristic and relatively impermeable mycomembrane, have long been considered a defining chemotaxonomic feature of the order Mycobacteriales. Here, we report that Nocardiopsis bonnevillensis, a new type strain isolated from the hypersaline environment of Great Salt Lake, is the first organism outside of this order known to produce mycolic acids. Lipid profiling, acid-fast staining, isoniazid sensitivity, and genome mining confirmed hallmark features of mycolic acid biosynthesis. Evaluation of the strains metabolic capabilities led to the isolation of bonnevanoside, a thiophenyl nonulopyranoside reported here for the first time from a natural source. Moreover, additional Great Salt Lake-derived Nocardiopsis isolates exhibited acid-fast staining, suggesting that this trait may be more widespread than previously recognized. Altogether, these findings expand the taxonomic distribution of mycolic acid biosynthesis, challenge long-standing chemotaxonomic boundaries, and highlight the potential ecological significance of mycolate-containing envelopes in supporting bacterial survival in extreme environments.

microbiology↗

bioRxiv2025

The transcription factor AP-2β defines active enhancers conferring molecular apocrine cell identity in breast cancer

The transcription factor Activating Protein 2{beta} (TFAP2B; AP-2{beta}) is a candidate marker for the molecular apocrine subtype of breast cancer, which lacks expression of the estrogen receptor alpha (ESR1; ER) but sustains a luminal breast cancer phenotype due to the presence of key luminal lineage transcription factors (GATA3, FOXA1) and activity of the androgen receptor (AR). Our objective was to better understand the expression patterns and molecular function of AP-2{beta} in breast cancer. Using multiple clinical cohorts, we show that high TFAP2B expression was associated with low proliferation in ER positive (ER+) breast cancers of ductal and lobular histology, but with enrichment for lobular tumours. High TFAP2B was also evident in high proliferation tumours lacking ER, with no specific enrichment for lobular histology. Restoring AP-2{beta} expression to highly proliferative ER+ breast cancer cell lines that lack it strongly induced apoptosis. Conversely, reducing AP-2{beta} expression in a molecular apocrine breast cancer cell line model potently inhibited proliferation and cell viability associated with downregulation of MYC oncogene expression. To identify genomic determinants of AP-2{beta} function in molecular apocrine cells in relation to other known transcriptional regulators, we performed chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) for AP-2{beta}, AR, GATA3, FOXA1, and acetylated lysine 27 in histone 3 (H3K27ac, a marker of active enhancers and promoters). When present alone, AP-2{beta} was preferentially enriched at active promotors. Enhancers bound by AR, GATA3 and FOXA1 were more active when AP-2{beta} was present and genes that define the molecular apocrine phenotype were significantly more likely to have active enhancers co-occupied by all four transcription factors. We conclude that AP-2{beta} plays a context-dependent role in breast cancer and propose that activation of enhancers defining molecular apocrine identity is a key function of AP-2{beta} in the biology of this subtype of breast cancer.

cancer biology↗

bioRxiv2024

Structural Insights into Broad-Range Polyphosphate Kinase 2 II Enzymes Applicable for Pyrimidine Nucleoside Diphosphate Synthesis

Polyphosphate kinases (PPK) play crucial roles in various biological processes, including energy storage and stress responses, through their interaction with inorganic polyphosphate (polyP) and the intracellular nucleotide pool. Members of the PPK family 2 (PPK2s) catalyse polyP-consuming phosphorylation of nucleotides. In this study, we characterised two PPK2 enzymes from Bacillus cereus (BcPPK2) and Lysinibacillus fusiformis (LfPPK2) to investigate their substrate specificity and potential for selective nucleotide synthesis. Both enzymes exhibited a broad substrate scope, selectively converting over 85% of pyrimidine nucleoside monophosphates (NMPs) to nucleoside diphosphates (NDPs), while nucleoside triphosphate (NTP) formation was observed only with purine NMPs. Preparative enzymatic synthesis of cytidine diphosphate (CDP) was applied to achieve an yield of 49%. Finally, structural analysis of five crystal structures of BcPPK2 and LfPPK2 provided insights into their active sites and substrate interactions. This study highlights PPK2-II enzymes as promising biocatalysts for the efficient and selective synthesis of pyrimidine NDPs.

biochemistry↗

bioRxiv2024

Menadione reduces the expression of virulence- and colonisation-associated genes in Helicobacter pylori

Novel treatment options are needed for the gastric pathogen Helicobacter pylori due to its increasing antibiotic resistance. The vitamin K analogue menadione has been extensively studied due to interest in its antibacterial and anti-cancer properties. Here, we investigated the effects of menadione on H. pylori growth, viability, antibiotic resistance, motility and gene expression using clinical isolates. The minimum inhibitory concentration (MIC) of menadione was 313 {micro}M for 11/13 isolates and 156 {micro}M for 2/13 isolates. The minimum bactericidal concentrations were 1.25-2.5 mM, indicating that concentrations in the micromolar range were bacteriostatic rather than bactericidal. We were not able to experimentally evolve resistance to menadione in vitro. Sub-MIC menadione (16 {micro}M for 24 h) did not significantly inhibit bacterial growth but significantly (p < 0.05) changed the expression of 1291/1615 (79.9 %) genes encoded by strain 322A. Expression of the virulence factor genes cagA and vacA was downregulated in the presence of sub-MIC menadione, while genes involved in stress responses were upregulated. Sub-MIC menadione significantly (p < 0.0001) inhibited the motility of H. pylori, consistent with the predicted effects of the observed significant (p < 0.05) downregulation of cheY, upregulation of rpoN, and changes in expression of flagellar assembly pathway genes seen in the transcriptomic analysis. Through in-depth interrogation of transcriptomics data, we concluded that sub-MIC menadione elicits a general stress response in H. pylori with survival in the stationary phase likely mediated by upregulation of surE and rpoN. Sub-MIC menadione caused some modest increases in H. pylori susceptibility to antibiotics, but the effect was variable with strain and antibiotic type and did not reach statistical significance. Menadione (78 {micro}M) was minimally cytotoxic to human gastric adenocarcinoma (AGS) cells after 4 hours but caused significant loss of cell viability after 24 hours. Given its inhibitory effects on bacterial growth, motility and expression of virulence and colonisation- associated genes, menadione at low micromolar concentrations may have potential utility as a virulence-attenuating agent against H. pylori. Data summaryRNAseq data reported on in this study are available to download from ArrayExpress under accession E-MTAB-14439. Supplementary materials associated with this publication are available from https://figshare.com/projects/Menadione_reduces_the_expression_of_virulence-_and_colonisation-associated_genes_in_Helicobacter_pylori/219631.

microbiology↗

bioRxiv2024

Premature upregulation of miR-92a's target RBFOX2 hijacks PTBP splicing and impairs cortical neuronal differentiation.

Alternative splicing is a crucial component of neuronal differentiation, yet the mechanisms that regulate splicing transitions during embryonic brain development remain incompletely understood. Here, we identify a post-transcriptional mechanism that times the expression of the splicing factor Rbfox2 during neurogenesis. RBFOX2 is normally expressed at low levels in neural progenitor cells (NPCs) and becomes upregulated in newborn neurons where it promotes neuronal differentiation. Unexpectedly, premature expression of Rbfox2 in NPCs of the embryonic mouse neocortex blocked their differentiation into neurons rather than promoting it. Genome-wide analysis revealed widespread alternative splicing changes enriched for NDD genes and associated with a hybrid NPC- and neuron-like splicing pattern that significantly deviates from the normal splicing developmental trajectory. Remarkably, premature Rbfox2 expression induced the inclusion of validated target exons that are otherwise repressed by PTBP2 pointing to an antagonistic splicing relationship. Integrative scRNA-seq analysis confirmed a negatively correlated expression between these two RNA-binding proteins (RBP) along differentiation pseudotime. Strikingly, we identified the NPC-specific miRNA 92a-3p as a regulator of the Rbfox2 expression switch: expression of miR-92a reduced RBFOX2 levels and reversed splicing patterns of target genes in vitro, while silencing miR-92a in vivo increased RBFOX2 expression in the embryonic cortex. Together, these findings reveal a previously unrecognized miRNA-RBP regulatory axis that ensures the proper timing of NPC-to-neuron splicing transitions in the developing cortex and provide new insights into splicing dysregulation as a contributing factor to the emergence of neurodevelopmental disorders. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=152 HEIGHT=200 SRC="FIGDIR/small/614071v3_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@16248caorg.highwire.dtl.DTLVardef@198dd0dorg.highwire.dtl.DTLVardef@d8887aorg.highwire.dtl.DTLVardef@1e8419e_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical Abstract Schematic representation of the proposed splicing regulation for the transition of undifferentiated NPCs to neurons in the developing cerebral cortex.

genomics↗

bioRxiv2024

Improved vectors for retron-mediated CRISPR-Cas9 genome editing in Saccharomyces cerevisiae

In vivo site-directed mutagenesis is a powerful genetic tool for testing the effects of specific alleles in their normal genomic context. While the budding yeast Saccharomyces cerevisiae possesses classical tools for site-directed mutagenesis, more efficient recent CRISPR-based approaches use Cas cutting combined with homologous recombination of a repair template that introduces the desired edit. However, current approaches are limited for fully prototrophic yeast strains, and rely on relatively low efficiency cloning of short gRNAs. We were thus motivated to simplify the process by combining the gRNA and its cognate repair template in cis on a single oligonucleotide. Moreover, we wished to take advantage of a new approach that uses an E. coli retron (EcRT) to amplify repair templates as multi-copy single-stranded (ms)DNA in vivo, which are more efficient templates for homologous recombination. To this end, we have created a set of plasmids that express Cas9-EcRT, allowing for co-transformation with the gRNA-repair template plasmid in a single step. Our suite of plasmids contains different antibiotic (Nat, Hyg, Kan) or auxotrophic (HIS3, URA3) selectable markers, allowing for editing of fully prototrophic wild yeast strains. In addition to classic galactose induction, we generated a {beta}-estradiol-inducible version of each plasmid to facilitate editing in yeast strains that grow poorly on galactose. The plasmid-based system results in >95% editing efficiencies for point mutations and >50% efficiencies for markerless deletions, in a minimum number of steps and time. We provide a detailed step-by-step guide for how to use this system.

genetics↗

bioRxiv2024

In vivo CRISPR base editing for treatment of Huntington's disease

Huntingtons disease (HD) is an inherited and ultimately fatal neurodegenerative disorder caused by an expanded polyglutamine-encoding CAG repeat within exon 1 of the huntingtin (HTT) gene, which produces a mutant protein that destroys striatal and cortical neurons. Importantly, a critical event in the pathogenesis of HD is the proteolytic cleavage of the mutant HTT protein by caspase-6, which generates fragments of the N-terminal domain of the protein that form highly toxic aggregates. Given the role that proteolysis of the mutant HTT protein plays in HD, strategies for preventing this process hold potential for treating the disorder. By screening 141 CRISPR base editor variants targeting splice elements in the HTT gene, we identified platforms capable of producing HTT protein isoforms resistant to caspase-6-mediated proteolysis via editing of the splice acceptor sequence for exon 13. When delivered to the striatum of a rodent HD model, these base editors induced efficient exon skipping and decreased the formation of the N-terminal fragments, which in turn reduced HTT protein aggregation and attenuated striatal and cortical atrophy. Collectively, these results illustrate the potential for CRISPR base editing to decrease the toxicity of the mutant HTT protein for HD.

bioengineering↗

bioRxiv2024

SPLICER: A Highly Efficient Base Editing Toolbox That Enables In Vivo Therapeutic Exon Skipping

Exon skipping technologies enable exclusion of targeted exons from mature mRNA transcripts, which has broad applications in molecular biology, medicine, and biotechnology. Existing exon skipping techniques include antisense oligonucleotides, targetable nucleases, and base editors, which, while effective for specific applications at some target exons, remain hindered by shortcomings, including transient effects for oligonucleotides, genotoxicity for nucleases and inconsistent exon skipping for base editors. To overcome these limitations, we created SPLICER, a toolbox of next-generation base editors consisting of near-PAMless Cas9 nickase variants fused to adenosine or cytosine deaminases for the simultaneous editing of splice acceptor (SA) and splice donor (SD) sequences. Synchronized SA and SD editing with SPLICER improves exon skipping, reduces aberrant outcomes, including cryptic splicing and intron retention, and enables skipping of exons refractory to single splice-site editing. To demonstrate the therapeutic potential of SPLICER, we targeted APP exon 17, which encodes the amino acid residues that are cleaved to form the A{beta} plaques in Alzheimers disease. SPLICER reduced the formation of A{beta}42 peptides in vitro and enabled efficient exon skipping in a mouse model of Alzheimers disease. Overall, SPLICER is a widely applicable and efficient toolbox for exon skipping with broad therapeutic applications.

bioengineering↗

bioRxiv2024

Spatiotemporal Modeling of Mitochondrial Network Architecture

In many cell types, mitochondria undergo extensive fusion and fission to form dynamic, responsive network structures that contribute to a number of homeostatic, metabolic, and signaling functions. The relationship between the dynamic interactions of individual mitochondrial units and the cell-scale network architecture remains an open area of study. In this work, we use coarse-grained simulations and approximate analytic models to establish how the network morphology is governed by local mechanical and kinetic parameters. The transition between fragmented structures and extensive networks is controlled by local fusion-to-fission ratios, network density, and geometric constraints. Similar fusion rate constants are found to account for the very different structures formed by mammalian networks (poised at the percolation transition) and well-connected budding yeast networks. Over a broad parameter range, the simulated network structures can be described by effective mean-field association constants that exhibit a non-linear dependence on the microscopic non-equilibrium fusion, fission, and transport rates. Intermediate fusion rates are shown to result in the highest rates of network remodeling, with mammalian mitochondrial networks situated in a regime of high turnover. Our modeling framework helps to elucidate how local parameters that govern mitochondrial interactions give rise to spatially resolved dynamic network structures at the cellular scale.

biophysics↗

bioRxiv2023

Stage-specific expression patterns and co-targeting relationships among miRNAs in the developing mouse cerebral cortex

microRNAs are particularly important during brain development, however, the composition and temporal dynamics of miRNA regulatory networks are not sufficiently characterized. Here, we performed small RNA sequencing of mouse embryonic cortical samples at E14, E17, and P0 as well as in neural progenitor cells differentiated in vitro into neurons. Using co-expression network analysis, we detected clusters of miRNAs that were co-regulated at distinct developmental stages. miRNAs such as miR-92a/b acted as hubs during early, and miR-124 and miR-137 during late neurogenesis. Notably, validated targets of P0 hub miRNAs were enriched for down-regulated genes related to stem cell proliferation, negative regulation of neuronal differentiation and RNA splicing, among others, suggesting that miRNAs are particularly important for modulating transcriptional programs of crucial factors that guide the switch to neuronal differentiation. As most genes contain binding sites for more than one miRNA, we furthermore constructed a co-targeting network where numerous miRNAs shared more targets than expected by chance. Using luciferase reporter assays, we demonstrated that simultaneous binding of miRNA pairs to neurodevelopmentally relevant genes exerted an enhanced transcriptional silencing effect compared to single miRNAs. Taken together, our study provides a comprehensive resource of miRNA longitudinal expression changes during corticogenesis. Furthermore, we highlight several potential mechanisms through which miRNA regulatory networks can shape embryonic brain development.

developmental biology↗

bioRxiv2023

Dynamic X-chromosomal reactivation enhances female brain resilience

While random X-chromosome inactivation in female cells of placental mammalians silences one allele of the majority of X-chromosomal genes, a considerable fraction is only incompletely and variably inactivated resulting in a tissue-specific pattern of mono- and biallelic expression. Here we used clonal human female induced pluripotent stem cells (iPSCs) allowing to trace the (in)activation status of the two X-chromosomes individually along neural differentiation trajectories. We discovered X-chromosome-wide locus- and lineage-specific dynamic usage of the two X-chromosomal alleles in female cells induced by differentiation. Leveraging iPSCs derived from patients with an X-linked neurodevelopmental disorder, we demonstrate that activation of alleles on the inactive X-chromosome can exert protective effects on the manifestation of disease phenotypes in female neural cells and tissue. Taken together, our data demonstrate that alleles on the inactive X-chromosome can serve as a critical reservoir reactivated during differentiation, thereby enhancing resilience of female neural tissue.

neuroscience↗

bioRxiv2022

Liver Endothelium Microenvironment Promotes HER3-mediated Cell Growth in Pancreatic ductal adenocarcinoma

[~]90% metastatic pancreatic ductal adenocarcinoma (mPDAC) occurs in the liver, and the 5-year survival rate for patients with mPDAC is only at 3%. We previously reported that liver endothelial cells (ECs) secreted soluble factors to promote colorectal cancer cell survival in a paracrine fashion. However, the effects of liver ECs on mPDAC have not been elucidated. In this study, we used primary ECs from non-neoplastic liver tissues. We treated PDAC cells with conditioned medium (CM) from liver ECs, with CM from PDAC as controls, and determined that liver EC-secreted factors increased PDAC cell growth. Using an unbiased receptor tyrosine kinase array, we identified human epidermal growth factor receptor 3 (HER3, also known as ErbB3) as a key mediator in EC-induced growth in PDAC cells that have HER3 expression (HER3 +ve). We found that EC-secreted neuregulins activated the HER3-AKT signaling axis, and that depleting neuregulins from EC CM or blocking HER3 with an antibody, seribantumab, attenuated EC-induced proliferation in HER3 +ve PDAC cells, but not in cells without HER3 expression. Furthermore, we determined that EC CM increased PDAC xenograft growth in vivo, and that seribantumab blocked EC-induced growth in xenografts with HER3 expression. These findings elucidated a paracrine role of liver ECs in promoting PDAC cell growth, and identified the HER3-AKT axis as a key mediator in EC-induced functions in PDAC cells with HER3 expression. Implicationsover 70% mPDAC express HER3. This study suggests the potential of using HER3-targeted therapies for treating patients with HER3 +ve mPDAC.

cancer biology↗