Biology subjects

Cross, E.

Publications and source records attributed to Cross, E..

11 recordsLinked to original sources

bioRxiv2026

Semaglutide-induced satiation, nausea, and food reward suppression are mediated by GLP-1 receptors in the area postrema

The GLP-1-based obesity drug semaglutide lowers bodyweight primarily by increasing satiation and satiety, whilst also reducing food reward and commonly causing nausea. The brainstem dorsal vagal complex (DVC) has been identified as a key site of action for these phenotypic components of semaglutides anorectic effect. However, which GLP-1 receptor (GLP-1R) populations within the DVC are recruited to mediate these phenotypic components, and whether they are dissociable, are translationally important but unresolved questions. We addressed these using metabolic and behavioural phenotyping, combined with activity-dependent genetic labelling ( Sema-TRAP) and chemogenetic manipulation of semaglutide-recruited brainstem circuits. Semaglutide potentiated satiation and satiety, caused behavioural proxies of nausea, and suppressed motivation for Western diet, in a largely sex-independent manner. It activated a substantial proportion of GLP-1R-expressing neurons in the brainstem area postrema (AP), but surprisingly most semaglutide-activated neurons in the nucleus tractus solitarius (NTS) did not express GLP-1R. Chemogenetic reactivation of Sema-TRAP neurons in the NTS alone was sufficient to recapitulate the acute effects of semaglutide on satiation, nausea, food reward, and bodyweight. Knockdown of GLP-1R expression in the AP before Sema-TRAPing abolished the recruitment of Sema-TRAPNTS neurons which elicited all these effects, while leaving the effects of semaglutide on satiety and bodyweight intact. These data demonstrate that semaglutide recruits dissociable anorectic circuits to suppress eating via distinct behavioural mechanisms, with non-GLP-1R NTS neurons downstream of GLP-1RAP representing potential therapeutic targets to tune GLP-1-based obesity drugs towards a better-tolerated effect profile.

neuroscience↗

bioRxiv2026

Zinc coordination by the wheat rust effector AvrSr33 provides a structural scaffold required for immune recognition

Abstract/SummaryInteractions between plants and pathogens drive long-term co-evolution through cycles of effector diversification and immune recognition. Effectors play central roles in this molecular interplay, and zinc-binding folds have been identified in a subset of pathogen effectors, yet the contribution of zinc coordination to effector stability and immune recognition remains unclear. Here, we investigated the structure and recognition of the AvrSr33 effector from the wheat stem rust fungus (Puccinia graminis f. sp. tritici, Pgt). Structural and biochemical analyses show that AvrSr33 adopts a fold containing two zinc-binding sites. Transient expression assays in Nicotiana benthamiana show that AvrSr33 directly interacts with Sr33, and comparison of recognised and non-recognised AvrSr33 variants identifies a polymorphic loop associated with recognition. This loop is positioned adjacent to one of the zinc-binding sites with its orientation constrained by zinc coordination. Reciprocal mutations of key surface residues within this region alter recognition, whereas mutation of the zinc-binding site abolishes recognition. Our data suggest that zinc coordination in AvrSr33 provides a structurally constrained scaffold that supports the surface features associated with Sr33 recognition. These findings provide a mechanistic framework for understanding how zinc coordination contributes to effector recognition and may influence the evolutionary trajectories of pathogen effectors.

Plant Biology↗

bioRxiv2026

A complete human pancreatic cancer genome

Cancer genome sequencing is essential for understanding tumor evolution and advancing precision medicine.1 However, reference gaps and germline variants obscure detection of small and large somatic variants and methylation in repetitive regions.1-3 It is common for tumor cells to gain or lose chromosome arms due to somatic structural changes that occur inside highly repetitive satellite DNA sequences in the centromeres.4 To identify the full spectrum of somatic variants, including complex rearrangements, we construct and curate near-complete, haplotype-resolved assemblies of the most recent common ancestor of an early-passage broadly-consented hypodiploid pancreatic cancer cell line and matched normal tissues. The tumor assembly completely recapitulates all 35 tumor chromosomes observed with karyotyping, with multiple translocation-induced hybrid chromosomes. The hybrid chromosomes contain putative functional dicentric and fused centromeres, nested foldback inversions causing 14 breakpoints with a haplotype switch in a single event, and centromeric satellite tandem duplications up to 136 kbp. Direct comparison of tumor and normal assembly haplotypes uncovers >7,000 variants altering >1 Mbp of sequence in repetitive regions that have been hidden by reference gaps and germline variants. 44 % of somatic small variants change representation because they alter germline variants on GRCh38, impacting mutational signatures and kataegis/omikli clusters. Most somatic LINE insertions originate from two hypomethylated non-reference germline LINE insertions, highlighting their impact on insertion mutation burden. These assemblies demonstrate that centromeric, acrocentric, and telomeric regions conventionally excluded from analysis harbor extensive somatic and epigenetic changes. Resolving complete tumor genomes enables a deeper understanding of cancer structural plasticity and the endpoints of breakage-fusion-bridge cycles. These assembled, curated paired normal-tumor benchmarks will serve as a critical foundation for developing future algorithms to characterize the most intractable regions of cancer genomes.

genomics↗

bioRxiv2026

Physiologically relevant media are associated with overlapping metabolic responses in primary human hepatocytes and Huh7 cells

BackgroundMetabolic dysfunction-associated steatotic liver disease (MASLD) is challenging to study in vivo in humans and in vitro models are limited. Although primary human hepatocytes (PHHs) are considered the gold-standard, immortalized hepatic cell lines are utilised due to scalability. This study compared the metabolic responses of PHHs with our Huh7-based model cultured in physiologically-relevant fatty acid (FA) mixtures. MethodsPHH and Huh7 cells were treated with 2% human serum, sugars and FAs enriched in either unsaturated (OPLA) or saturated (POLA) FAs for 4 or 7 days, respectively. Stable isotope tracers investigated basal metabolic changes in response to treatment. Cell viability, media biochemistry, intracellular metabolism, lipid droplet morphology and gene expression were quantified. ResultsHuh7 cells had greater viability than PHHs, while NEFA uptake and triglyceride secretion were similar. OPLA and POLA increased large lipid droplets in Huh7 cells, whereas only OPLA produced comparable effects in PHHs. Despite higher baseline TG in PHHs, both models showed similar lipid composition, de novo lipogenic responses, and glycogen levels. Compared to Huh7 cells, PHHs exhibited higher 3-hydroxybutyrate, lower lactate, reduced glucose uptake, and donor-dependent transcriptomic variability. ConclusionsHuh7 cells are metabolically adaptable and when cultured in physiologically-relevant media, produce metabolic readouts similar PHH cells.

cell biology↗

bioRxiv2025

Quantifying Conformational Heterogeneity of 3D Genome Organization in Fruit Fly

The three-dimensional (3D) organization of interphase chromatin in eukaryotes is complex; details of the corresponding genome structures vary stochastically from cell to cell. Here, we propose a metric to quantify the cell-to-cell heterogeneity of the 3D chromatin conformations in ensembles of single cells: Conformational Heterogeneity (C.H.) is defined as the standard deviation of the ensemble distribution of the per cell average Euclidean inter-loci distances [<]Rs[>], for a given genomic separation s between the loci. We have used the metric to examine and quantify in detail the cell-to-cell heterogeneity of conformations of the interphase X chromosome in fruit fly generated via three distinctly different modeling approaches, which take experimental Hi-C data as input. Two of the approaches use bulk Hi-C and lamina-DamID data, while the third relies on single-cell Hi-C maps. An algorithm is proposed to facilitate comparison of C.H. of models constructed at different resolutions, and to examine the behavior of conformational heterogeneity with increasing model resolution. Higher resolution models show a greater C.H., in general. The impact of the model resolution is strongest near the genomic distance s corresponding to the resolution limit of the model, and diminishes for larger genomic distances: extrapolating the resolution from approximately 14 kb to 2 kb has little effect on the C.H. beyond [~]100 kb. All chromatin models examined in this work show a very similar trend of monotonically increasing structural heterogeneity with s, up to the genomic TAD size; beyond that, significant differences arise, with the model based on single-cell Hi-C showing nearly opposite trend compared to the two models that use bulk Hi-C data. We attribute these major differences to relatively subtle differences in the modeling approaches, which we discuss. Based on the analysis, we propose to explore the possibility of inclusion of bulk Hi-C data into training of chromatin models that are based on necessarily limited single-cell Hi-C data. Within our computational approach, depletion of nuclear lamins leads to increased structural heterogeneity at nearly all genomic separations, with the potential implication that cell functions that depend on chromatin structure might be more variable within lamins depleted nuclei compared to the wild type.

genomics↗

bioRxiv2024

Mitochondrial leakage and mtDNA damage trigger early immune response in Inclusion Body Myositis.

Polymyositis with mitochondrial pathology (PM-Mito) was first identified in 1997 as a subtype of idiopathic inflammatory myopathy. Recent findings demonstrated significant molecular similarities between PM-Mito and Inclusion Body Myositis (IBM), suggesting a trajectory from early to late IBM and prompting the inclusion of PM-Mito as an IBM precursor (early IBM) within the IBM spectrum. Both PM-Mito and IBM show mitochondrial abnormalities, suggesting mitochondrial disturbance is a critical element of IBM pathogenesis. The primary objective of this cross-sectional study was to characterize the mitochondrial phenotype in PM-Mito at histological, ultrastructural, and molecular levels and to study the interplay between mitochondrial dysfunction and inflammation. Skeletal muscle biopsies of 27 patients with PM-Mito and 27 with typical IBM were included for morphological and ultrastructural analysis. Mitochondrial DNA (mtDNA) copy number and deletions were assessed by qPCR and long-range PCR, respectively. In addition, full-length single-molecule sequencing of the mtDNA enabled precise mapping of deletions. Protein and RNA levels were studied using unbiased proteomic profiling, immunoblotting, and bulk RNA sequencing. Cell-free mtDNA (cfmtDNA) was measured in the serum of IBM patients. We found widespread mitochondrial abnormalities in both PM-Mito and IBM, illustrated by elevated numbers of COX-negative and SDH-positive fibers and prominent ultrastructural abnormalities with disorganized and concentric cristae within enlarged and dysmorphic mitochondria. MtDNA copy numbers were significantly reduced, and multiple large-scale mtDNA deletions were already evident in PM-Mito, compared to healthy age-matched controls, similar to the IBM group. The activation of the canonical cGAS/STING inflammatory pathway, possibly triggered by the intracellular leakage of mitochondrial DNA, was evident in PM-Mito and IBM. Elevated levels of circulating cfmtDNA also indicated leakage of mtDNA as a likely inflammatory trigger. In PM-Mito and IBM, these findings were accompanied by dysregulation of proteins and transcripts linked to the mitochondrial membranes. In summary, we identified that mitochondrial dysfunction with multiple mtDNA deletions and depletion, disturbed mitochondrial ultrastructure, and defects of the inner mitochondrial membrane are features of PM-Mito and IBM, underlining the concept of an IBM-spectrum disease (IBM-SD). The activation of inflammatory pathways related to mtDNA release indicates a significant role of mitochondria-associated inflammation in the pathogenesis of IBM-SD. Thus, mitochondrial abnormalities precede tissue remodeling and infiltration by specific T-cell subpopulations (e.g., KLRG1+) characteristic of late IBM. This study highlights the critical role of early mitochondrial abnormalities in the pathomechanism of IBM, which may lead to new approaches to therapy.

neuroscience↗

bioRxiv2021

A reference induced pluripotent stem cell line for large-scale collaborative studies

Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate iPSC lines and deeply characterised their genetic properties using whole genome sequencing, their genomic stability upon CRISPR/Cas9-based gene editing, and their phenotypic properties including differentiation to commonly-used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and hundreds of its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field. SummaryThe authors of this collaborative study deeply characterized human induced pluripotent stem cell (iPSC) lines to rationally select a clonally-derived cell line that performs well across multiple modalities. KOLF2.1J was identified as a candidate reference cell line based on single-cell analysis of its gene expression in the pluripotent state, whole genome sequencing, genomic stability after highly efficient CRISPR-mediated gene editing, integrity of the p53 pathway, and the efficiency with which it differentiated into multiple target cell populations. Since it is deeply characterized and can be readily acquired, KOLF2.1J is an attractive reference cell line for groups working with iPSCs. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/472643v6_ufig1.gif" ALT="Figure 1"> View larger version (84K): org.highwire.dtl.DTLVardef@cef106org.highwire.dtl.DTLVardef@31d5d8org.highwire.dtl.DTLVardef@1ce6d8corg.highwire.dtl.DTLVardef@17a19d2_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2021

Qualification of ELISA and neutralization methodologies to measure SARS-CoV-2 humoral immunity using human clinical samples

In response to the SARS-CoV-2 pandemic many vaccines have been developed and evaluated in human clinical trials. The humoral immune response magnitude, composition and efficacy of neutralizing SARS-CoV-2 are essential endpoints for these trials. Robust assays that are reproducibly precise, linear, and specific for SARS-CoV-2 antigens would be beneficial for the vaccine pipeline. In this work we describe the methodologies and clinical qualification of three SARS-CoV-2 endpoint assays. We developed and qualified Endpoint titer ELISAs for total IgG, IgG1, IgG3, IgG4, IgM and IgA to evaluate the magnitude of specific responses to the trimeric spike (S) antigen and total IgG specific to the spike receptor binding domain (RBD) of SARS-CoV-2. We also qualified a pseudovirus neutralization assay which evaluates functional antibody titers capable of inhibiting the entry and replication of a lentivirus containing the Spike antigen of SARS-CoV-2. To complete the suite of assays we qualified a plaque reduction neutralization test (PRNT) methodology using the 2019-nCoV/USA-WA1/2020 isolate of SARS-CoV-2 to assess neutralizing titers of antibodies in plasma from normal healthy donors and convalescent COVID-19 individuals.

immunology↗

bioRxiv2021

AusTraits: a curated plant trait database for the Australian flora

We introduce the AusTraits database - a compilation of measurements of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 375 traits across 29230 taxa from field campaigns, published literature, taxonomic monographs, and individual taxa descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological parameters (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual-, species- and genus-level observations coupled to, where available, contextual information on site properties. This data descriptor provides information on version 2.1.0 of AusTraits which contains data for 937243 trait-by-taxa combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data to increase our collective understanding of the Australian flora.

ecology↗

bioRxiv2018

Observing action sequences elicits sequence-specific neural representations in frontoparietal brain regions

Learning new skills by watching others is important for social and motor development throughout the lifespan. Prior research has suggested that observational learning shares common substrates with physical practice at both cognitive and brain levels. In addition, neuroimaging studies have used multivariate analysis techniques to understand neural representations in a variety of domains including vision, audition, memory and action, but few studies have investigated neural plasticity in representational space. As such, although movement sequences can be learned by observing other peoples actions, a largely unanswered question in neuroscience is how experience shapes the representational space of neural systems. Here we combined pre- and post-training fMRI sessions with six days of observational practice to examine whether the observation of action sequences elicits sequence-specific representations in frontoparietal brain regions and the extent to which these representations become more pronounced with observational practice. Our results showed that observed action sequences are modelled by distinct patterns of activity in frontoparietal cortex and that such representations largely generalise to very similar, but untrained, sequences. These findings advance our understanding of what is modelled during observational learning (sequence-specific information), as well as how it is modelled (reorganisation of frontoparietal cortex is similar manner to that of physical practice). Thus, on a more fine-grained neural level than demonstrated previously, we show the representational structure of how frontoparietal cortex maps visual information onto motor circuits to order to enhance motor performance.\n\nSignificance statementLearning by watching others is a cornerstone in the development of expertise and skilled behaviour. However, it remains unclear how visual signals are mapped onto motor circuits for such learning to occur. Here we show that observed action sequences are modelled by distinct patterns of activity in frontoparietal cortex and that such representations largely generalise to very similar, but untrained, sequences. These findings advance our understanding of what is modelled during observational learning (sequence-specific information), as well as how it is modelled (reorganisation of frontoparietal cortex is similar manner to that of physical practice). More generally, these findings demonstrate how motor circuit involvement in the perception of action sequences shows high fidelity to the physical performance of action sequences.

neuroscience↗

bioRxiv2018

Protein pheromone MUP20/Darcin is a vector and target of indirect genetic effects in mice.

Social behavior in animals is an adaptive process influenced by environmental factors and direct and indirect genetic effects. Indirect genetic effects (IGEs) include mechanisms by which individuals of particular genotypes can influence the behavioral phenotypes and genotypes (via modulated patterns of gene expression) of other individuals with different genotypes. In groups of adult mice, IGEs can be unidirectional, from one genotype to the other, or bidirectional, resulting in a homogenization of the behavioral phenotypes within the group. Critically, it has been theorized that IGEs constitute a large fitness target on which deleterious mutations can have pleiotropic effects, meaning that individuals carrying certain behavior-altering mutations can impose the fitness costs of those mutations on others comprising the broader social genome. Experimental data involving a mouse model support the existence of these IGE-amplified fitness losses; however, the underlying biological mechanisms that facilitate these remain unknown. In a mouse model of IGEs, we demonstrate that the Major Urinary Protein 20 pheromone, also called Darcin, produced by mice lacking the adhesion protein Neuroligin-3 acts as a vector to deleteriously modify the social behavior of wild-type mice. Additionally, we showed that lack of social interest on the part of Neuroligin-3 knockout mice is independent of their environment. These findings reveal a new role for mammalian pheromones in mediating the externalization of social deficits from one individual to others comprising the population through IGEs.\n\nAuthor SummaryIndirect genetic effects (IGEs) are mechanisms by which individuals of particular genotypes can influence the behavioral phenotype of individuals of different genotypes, sometimes disruptively, in instances where one member of the population carriers a deleterious behavior altering variant. Although disruptive IGEs have been demonstrated in mice, its underlying molecular and genetic mechanisms remain unknown. Using an IGEs mouse model, we demonstrated that the pheromone protein Major Urinary Protein 20, also named Darcin, is as a vector and target of social epistasis a specific type of IGEs. This finding reveals a new function for mammalian pheromones in mediating social epistasis to degrade group social behavior.

animal behavior and cognition↗