Biology subjects

Wagner, L.

Publications and source records attributed to Wagner, L..

At least 19 recordsLinked to original sources

bioRxiv2026

A single meiotic product dominates inheritance in Mucor circinelloides

Meiosis is a major source of genetic diversity, yet it remains poorly understood in many pathogenic fungi. In Mucorales, the causative agents of mucormycosis, sexual reproduction has been difficult to study, and reported inheritance patterns have appeared inconsistent with conventional meiosis. Here, meiosis in Mucor circinelloides was demonstrated at genome-wide resolution by generating telomere-to-telomere chromosome assemblies from compatible mating types and analyzing parental markers distributed across the genome. The results reveal meiotic recombination and independent chromosome assortment. However, the outcome of meiosis is strikingly unconventional: all sexual spores derived from a single zygospore share an identical nuclear genotype, even when germination produces distinct sporangia. This pattern suggests that the viable progeny of each zygospore is derived from a single meiotic product, rather than from the four products expected under conventional meiosis. Mitochondrial inheritance is also uniparental, with progeny mitochondria inherited from the (+) mating-type parent. Together, these findings show that sexual reproduction in M. circinelloides entails meiotic recombination, but restricts inheritance to a single viable nuclear product and a single mitochondrial lineage. This decoupling of recombination from equal meiotic contribution reveals a hidden layer of inheritance control in Mucorales, showing how pathogenic fungi can reshuffle chromosomes while producing genetically uniform sibling progeny, an outcome reminiscent of female meiosis in animals.

genetics↗

bioRxiv2026

Catabolism of extracellular glutathione is a driver of metastasis formation

Metastasizing cancer cells require metabolic plasticity to adapt to the microenvironment of the target organ. Analyzing metabolites in interstitial fluids, we found that the liver microenvironment is devoid of cystine but contains high concentrations of glutathione (GSH). Detailed mechanistic analysis revealed that cancer cells degrade extracellular GSH utilizing gamma-glutamyl-transferase (GGT) activity for provision of cysteine to support proliferation and prevent ferroptosis under cystine-free conditions. This was independent of system Xc- but required activity of glutamate-cysteine ligase (GCLC). GGT1 expression was associated with poor survival and upregulated in liver metastases of human breast cancer patients. Overexpression of Ggt1 in murine breast cancer cells enhanced their capacity for liver colonization and promoted lung metastases after orthotopic implantation. This identifies extracellular GSH catabolism as driver of metastasis that supports proliferation and oxidative stress resistance in metabolically challenging microenvironments.

cancer biology↗

bioRxiv2026

M-CSF drives alveolar macrophage plasticity during development and cytomegalovirus infection

Alveolar macrophages (AM), the most frequent resident immune cells of the lung, are at the first line of defence against respiratory pathogens and instruct structural lung cells, e.g. in tissue repair. They are long-lived and receive their terminal phenotypic imprint through signals originating from the unique location at the tissue-air interface, as well as through cytokines like granulocyte-macrophage colony-stimulating factor (GM-CSF) and transforming growth factor-{beta} (TGF-{beta}). However, the regulatory mechanisms governing their phenotypic plasticity, which is conceptually critical for their positioning and differentiation in early life and for their functional adaptation during infection, remain poorly defined. Here we explored respiratory tract infection with cytomegalovirus (CMV), which is closely linked to mammalian immune evolution. Complementary host-pathogen fate-mapping strategies revealed AM to constitute the bottleneck for efficient mouse (M)CMV infection. MCMV infection induced macrophage colony-stimulating factor (M-CSF) in the alveolar space, and culturing of AM in M-CSF led to a profound remodelling of morphology, immunophenotype, and transcriptional identity, e.g. it increased the expression of interferon-stimulated genes (ISG), which modulated susceptibility to infection. Notably, already at baseline recently differentiated neonatal AM across species retained an M-CSF-associated transcriptional program. This was linked to reduced permissiveness to respiratory MCMV infection in vivo. Overall, our findings identify the role of M-CSF-dependent signalling in conferring plasticity to AM, when it is most needed, particularly during early-life establishment and in response to viral infection.

immunology↗

bioRxiv2026

Identification of target genes and regulatory networks for bone mineral density GWAS loci through systematic targeting and inhibition

Osteoporosis is characterized by low bone mineral density (BMD) and elevated fracture risk. Most BMD-associated GWAS variants lie in noncoding regions, complicating efforts to identify causal genes and mechanisms. To overcome this variant-to-function challenge, we previously developed STING-seq, a framework integrating biobank-scale GWAS with single-cell CRISPR inhibition (CRISPRi) screening to directly connect noncoding cis-regulatory elements (CREs) to their target genes. Applied to human fetal osteoblast (hFOB) cells across osteogenic differentiation, STING-seq linked 76 CREs to 75 target genes at BMD loci. Arrayed CRISPRi and activation validated key CRE-gene relationships, including long-range enhancers regulating CXCL12 (over 500 kb apart). We further uncovered trans-regulatory networks and characterized the DAP3-YY1AP1 bidirectional promoter, demonstrating a role for DAP3 in mineralization via mitochondrial pathways. Together, these findings provide mechanistic insight into how noncoding GWAS variants shape osteoblast activity and highlight the genes and pathways that mediate genetic effects on BMD.

genomics↗

bioRxiv2026

Crosstalk between Stromal cells and Macrophages Shapes Host Immunity to Mycobacteria

Granulomas are disease-defining heterocellular tissue structures in mycobacterial infections. They play a multifaceted role ranging from containing the pathogen to causing tissue destruction. Here, we established a mature peritoneal granuloma model in C57BL/6 mice to investigate the dynamic cell-cell interactions during mycobacterial infection, including long-term immune alterations in serous cavities as important sites of disease manifestation. We found that mycobacteria reside in stromal cells, which actively modulate the local tissue environment and shape macrophage responses, particularly through formation of chemokines and colony-stimulating factor 1. Chronic infection induces sustained reprogramming and diversification of stromal cells toward specialized, immune-like states, including active transfer of mycobacteria to macrophages and a pronounced interferon response. Consequently, stromal cells acquire immunoregulatory properties and support pathogen handling, monocyte recruitment and macrophage maturation, thereby playing a decisive role in granuloma formation and thus in the immune response to mycobacteria. HIGHLIGHTSO_LIA novel peritoneal mycobacterial infection model reveals heterocellular crosstalk in mature granulomas. C_LIO_LIMycobacterial infections persistently reshape immune architecture of serous cavities as important disease sites. C_LIO_LIStromal cells act as mycobacterial host cells and acquire immune effector functions. C_LIO_LIStromal cells co-organize the tissue host-pathogen interface by recruiting and directly communicating with bone marrow-derived monocytes. C_LI

immunology↗

bioRxiv2026

Human basal radial glia morphotypes are transcriptionally distinct and exhibit different cell fate determination

Basal radial glia (bRG) are key neural progenitors driving human neocortical expansion. They exhibit remarkable morphological heterogeneity, yet the stability and functional significance of their distinct morphotypes remains unclear. Using human cortical brain organoids combined with long-term live imaging and morphology-resolved spatial transcriptomics (CellShape-seq), we show that bRG morphotypes display distinct morphodynamic behaviors, proliferative capacities and transcriptional profiles. While bifurcated bRG remodel extensively during mitosis to produce morphologically diverse progeny, multipolar cells are most morphologically flexible during interphase. Multipolar bRG further show the greatest proliferative capacity and the transcriptional signature related to progenitor state. Bifurcated bRG are least proliferative and are enriched for the multifunctional gene expression regulator YBX1. Pharmacological inhibition of YBX1 depletes bifurcated bRG, reduces neurogenesis, and promotes glial commitment. Our findings link progenitor morphology, gene expression and fate, providing a framework for understanding the cellular logic of human cortical development.

neuroscience↗

bioRxiv2025

Insular error network enables self-correcting intracranial brain-computer interface

Error recognition is fundamental to adaptive behavior, enabling rapid compensatory action when outcomes deviate from expectations. Central to this function are neural circuits for performance monitoring, encoding cognitive signals that could support more reliable neural interfaces. Here, we recorded intracranial electroencephalography (iEEG) in epilepsy patients to enable a motor brain-computer interface (BCI) while sampling error-related activity across a distributed network. Our work reveals high-frequency population dynamics emerging in the anterior insula and propagating to the prefrontal cortex as the interface fails to follow the users intention. We identify spatially organized insular responses to error processing and movement feedback, highlighting it as a heterogeneous hub linking action and outcome. Real-time integration of error responses enables a self-correcting neural interface that enhances usability by reducing the need for manual user intervention. Together, our work demonstrates a human intracranial BCI harnessing insular brain activity, integrating cognitive processes directly into device control.

neuroscience↗

bioRxiv2025

Language network functional connectivity in infancy predicts developmental language trajectories

Although developmental language delays affect approximately 10% of children in the general population, the neurodevelopmental mechanisms that support normative language acquisition, and atypicalities that may predict later language delay, across the first year of life are poorly understood. Here, resting-state fMRI data from the Baby Connectome Project was used to evaluate age-related changes in language network functional connectivity and alterations associated with suboptimal language development. Additionally, a data-driven machine learning algorithm was used to partition our sample into three groups who showed Delayed, Typical, and Advanced trajectories of language development. These groups reliably differed on several assessments of language ability during infancy and toddlerhood. Using a priori brain regions involved in adult language processing, a seed-based functional connectivity analysis showed broad age-related increases in functional synchrony and specialization throughout the infant language network. Additionally, the Delayed group showed several atypical patterns of functional connectivity with language regions. Importantly, the magnitude of connectivity differences consistently predicted later language scores at two-year outcome across several different language assessments. These findings add to our understanding of normative neurodevelopmental patterns underlying language acquisition, and identify several potential biomarkers associated with language delay that could serve as future targets to inform diagnoses and clinical interventions. HighlightsO_LIThe language network undergoes significant maturational changes during infancy C_LIO_LIWith age, functionally similar nodes integrate, while dissimilar nodes segregate C_LIO_LILanguage-delayed infants show atypical connectivity in the language network C_LIO_LIThese early atypicalities predict later language development at two-year outcome C_LIO_LIWe identify several neural signatures associated with early language delay C_LI

neuroscience↗

bioRxiv2025

A confound-free method to manipulate pupil size in psychological experiments

Those who study visual perception and visuo-spatial attention are increasingly paying interest to the ways in which these processes are influenced by the size of the pupil. However, this realm of research is complicated by the pupils notorious susceptibility to confounders and difficulties in disentangling cause and effect. Recent studies have sought a solution in the exploitation of intrinsically photosensitive retinal ganglion cells (ipRGCs), which trigger pupil constrictions upon detecting blue light. Experiments typically present stimuli against blue versus red backgrounds of equal perceived luminance, to effectuate systematically smaller pupils in the former than in the latter condition. Here we provide a further validation of this method, by testing a scenario of potential concern. Via retino-hypothalamic pathways, ipRGC activation modulates alertness and arousal. Blue and red backgrounds may therefore differentially impact behavior in addition to the pupil, potentially confounding inferences about the pupils impact on cognition. This was investigated with an auditory task in which participants responded as quickly as possible to sequences of randomly timed beeps while looking at blue versus red displays. Each participant was tested with an easy and a difficult version of the auditory task. Results suggest that the ipRGC method is good to go: in the presence of effects of task difficulty on both pupil size and task performance, the display color exclusively influenced pupil size without affecting task performance.

neuroscience↗

bioRxiv2025

Cell-free genome-wide transcriptomics through machine learning optimization

1Despite advances in transcriptomics, understanding of genome regulation remains limited by the complex interactions within living cells. To address this, we performed cell-free transcriptomics by developing a platform using an active learning workflow to explore over 1,000,000 buffer conditions. This enabled us to identify a buffer that increased mRNA yield by 20-fold, enabling cell-free transcriptomics. By employing increasingly complex conditions, our approach untangles the regulatory layers controlling genome expression.

synthetic biology↗

bioRxiv2025

Spontaneous eye movements reveal that premotor cortex is involved in human thinking

Non-visual saccades (NVS) are spontaneous eye movements humans make while thinking. Their role is puzzling and there is no framework to explain them in terms of underlying neural systems. Here we studied neural activity preceding NVS when subjects performed standardized abstract thinking tasks. We used high-density EEG and focused on frontal and parietal channels representing oculomotor cortical areas. We found that NVS are distinctively preceded by neural activity changes in frontal and parietal EEG channels qualitatively different to that for voluntary saccades. However, only the ERP amplitude changes in frontal channels, but not in parietal channels, were different from saccadic preparation. A source reconstruction analysis additionally revealed that presaccadic neural activity originated mainly in the premotor cortex. Frequency spectrum analyses showed increased synchronization in alpha to low gamma bands suggesting complex top-down and bottom-up processing. We propose that this presaccadic activity while thinking represents evidence accumulation and attentional shifts, as shown before in the premotor cortex during sensorimotor tasks. Our findings suggest that human thinking appears to function similarly to human actions and engages premotor areas responsible for evaluating and manipulating objects also when evaluating and manipulating concepts.

neuroscience↗

bioRxiv2025

Evolutionary hotspots of structural variation drive inter-individual differences in the expression of fusion transcripts in the human brain

While most protein-coding regions in our genome are highly conserved, phenotypic variation largely arises from differences in gene transcription, splicing, and translation. Intra-gene splicing variations are a known source of inter-individual differences. However, inter-gene splicing events, which generate fusion transcripts--RNA molecules combining exons from multiple distinct genes--are less explored. Fusion transcripts are well-studied in cancer, but their expression and inter-individual variability in normal human tissues has not been thoroughly investigated. We conducted a genome-wide fusion transcript analysis in postmortem human brain tissues from 276 individuals, identifying 717 distinct fusion transcripts. Many had protein coding potential, further supported in some cases by ribosome profiling data. Fusion transcripts that were present in only part of the human population were predominantly located within segmental duplication (SD) "hotspots"; highly copy number-variable genomic regions linked to neurodevelopmental and neurodegenerative diseases. None of these variable fusion transcripts were present in chimpanzee or rhesus macaque, suggesting they are human-specific. We confirmed that SD-derived fusion transcripts arise from structural genomic rearrangements in the human population, previously associated with neurodevelopmental and neurodegenerative disease risk. Inter-individual variation in fusion transcript expression represents an overlooked source of genetic diversity, with potential to contribute to differences in disease susceptibility.

molecular biology↗

bioRxiv2024

Gαolf Regulates Biochemical Signaling in Neurons Associated with Movement Control and Initiation

The heterotrimeric G-protein subunit, Golf, acts to transduce extracellular signals through G-protein coupled receptors (GPCRs) and stimulates adenylyl cyclase mediated production of the second messenger cyclic adenosine monophosphate. Numerous mutations in the GNAL gene, which encodes Golf, have been identified as causative for an adult-onset dystonia. These mutations disrupt GPCR signaling cascades in in vitro assays through several mechanisms, and this disrupted signaling is hypothesized to lead to dystonic motor symptoms in patients. However, the cells and circuits that mutations in GNAL corrupt are not well understood. Published patterns of Golf expression outside the context of the striatum are sparse, conflicting, often lack cell type specificity, and may be confounded by expression of the close GNAL homolog of GNAS. Here, we use RNAScope in-situ hybridization to quantitatively characterize Gnal mRNA expression in brain tissue from wildtype C57BL/6J adult mice. We observed widespread expression of Gnal puncta throughout the brain, suggesting Golf is expressed in more brain structures and neuron types than previously accounted for. We quantify transcripts at a single cell level, and use neuron type specific markers to further classify and understand patterns of GNAL expression. Our data suggests that brain regions classically associated with motor control, initiation, and regulation show the highest expression of GNAL, with Purkinje Cells of the cerebellum showing the highest expression of any neuron type examined. Subsequent conditional Gnal knockout in Purkinje cells led to markedly decreased intracellular cAMP levels and downstream cAMP-dependent enzyme activation. Our work provides a detailed characterization of Gnal expression throughout the brain and the biochemical consequences of loss of Golf signaling in vivo in neurons that highly express Gnal.

neuroscience↗

bioRxiv2024

Autophagosome turnover requires Arp2/3 complex-mediated maintenance of lysosomal integrity

Autophagy is an intracellular degradation process that maintains homeostasis, responds to stress, and plays key roles in the prevention of aging and disease. Autophagosome biogenesis, vesicle rocketing, and autolysosome tubulation are controlled by multiple actin nucleation factors, but the impact of actin assembly on completion of the autophagic pathway is not well understood. Here we studied autophagosome and lysosome remodeling in fibroblasts harboring an inducible knockout (iKO) of the Arp2/3 complex, an essential actin nucleator. Arp2/3 complex ablation resulted in increased basal levels of autophagy receptors and lipidated membrane proteins from the LC3 and GABARAP families. Under both steady-state and starvation conditions, Arp2/3 iKO cells accumulated abnormally high numbers of autolysosomes, suggesting a defect in autophagic flux. The inability of Arp2/3 complex-deficient cells to complete autolysosome degradation and turnover is explained by the presence of damaged, leaky lysosomes. In cells treated with an acute lysosomal membrane-damaging agent, the Arp2/3-activating protein WHAMM is recruited to lysosomes, where Arp2/3 complex-dependent actin assembly is crucial for restoring intact lysosomal structure. These results establish the Arp2/3 complex as a central player late in the canonical autophagy pathway and reveal a new role for the actin nucleation machinery in maintaining lysosomal integrity.

cell biology↗

bioRxiv2024

Somatic gene delivery for flexible in vivo modeling of high-risk sarcoma

A particular challenge hampering therapeutic advancements for high-risk sarcoma patients is the broad spectrum of molecularly distinct sarcoma entities and the corresponding lack of suitable model systems to recapitulate and study these diseases. To overcome this predicament, we developed a novel genetically-controlled, yet versatile mouse modeling platform allowing delivery of different genetic lesions by electroporation (EPO) of the thigh muscle wildtype mice. This optimized sarcoma EPO-GEMM (EPO-based genetically engineered mouse model) platform allowed the generation of ten biologically distinct sarcoma entities, including Synovial Sarcoma (SS), fusion-positive and fusion-negative Rhabdomyosarcoma (RMS), Alveolar Soft Part Sarcoma (ASPS), Undifferentiated Pleomorphic Sarcoma (UPS) and Infantile Fibrosarcoma (IFS). Comprehensive molecular profiling and cross-species analyses confirmed faithful recapitulation of the human disease, including the expression of relevant immunotherapy targets. Syngeneic allografting enabled reliable preservation and scalability of Sarcoma-EPO-GEMMs for treatment trials, such as B7-H3-directed CAR-T cell therapy in an immunocompetent background.

cancer biology↗

bioRxiv2024

Loss of STIM1 and STIM2 in salivary glands disrupts ANO1 function but does not induce Sjogren's disease

Sjogrens disease (SjD) is an autoimmune disease characterized by xerostomia (dry mouth), lymphocytic infiltration into salivary glands and the presence of SSA and SSB autoantibodies. Xerostomia is caused by hypofunction of the salivary glands and has been involved in the development of SjD. Saliva production is regulated by parasympathetic input into the glands initiating intracellular Ca2+ signals that activate the store operated Ca2+ entry (SOCE) pathway eliciting sustained Ca2+ influx. SOCE is mediated by the STIM1 and STIM2 proteins and the ORAI1 Ca2+ channel. However, there are no studies on the effects of lack of STIM1/2 function in salivary acini in animal models and its impact on SjD. Here we report that male and female mice lacking Stim1 and Stim2 (Stim1/2K14Cre) in salivary glands showed reduced intracellular Ca2+ levels via SOCE in parotid acini and hyposalivate upon pilocarpine stimulation. Bulk RNASeq of the parotid glands of Stim1/2K14Cre mice showed a decrease in the expression of Stim1/2 but no other Ca2+ associated genes mediating saliva fluid secretion. SOCE was however functionally required for the activation of the Ca2+ activated chloride channel ANO1. Despite hyposalivation, ageing Stim1/2K14Cre mice showed no evidence of lymphocytic infiltration in the glands or elevated levels of SSA or SSB autoantibodies in the serum, which may be linked to the downregulation of the toll-like receptor 8 (Tlr8). By contrast, salivary gland biopsies of SjD patients showed increased STIM1 and TLR8 expression, and induction of SOCE in a salivary gland cell line increased the expression of TLR8. Our data demonstrate that SOCE is an important activator of ANO1 function and saliva fluid secretion in salivary glands. They also provide a novel link between SOCE and TLR8 signaling which may explain why loss of SOCE does not result in SjD.

physiology↗

bioRxiv2023

Global motor dynamics - Invariant neural representations of motor behavior in distributed brain-wide recordings

Neural activity is presumed to be correlated with motor behavior almost everywhere in the brain, implying that many different brain processes are involved in generating a behavioral output. Recent studies in multiple non-human species have observed pervasive brain-wide neural activity directly related to motor output. However, similar brain-wide investigations in humans with high-temporal resolution are lacking to date. Here, we recorded invasive data from brain-wide distributed electrodes in humans and reveal global neural dynamics that are predictive of movement across tasks and across participants. The dynamics are remarkably stable between participants with substantially varying electrode configurations and to loss of information. We demonstrate that these global neural dynamics are near brain-wide and present in all participants. Uncovering these global neural dynamics may allow for a more holistic and network-based perspective on motor-related neural activity.

neuroscience↗

bioRxiv2023

Rapid and sensitive detection of genome contamination at scale with FCS-GX

Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBIs Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequences in new genomes. FCS-GX screens most genomes in 0.1-10 minutes. Testing FCS-GX on artificially fragmented genomes demonstrates sensitivity >95% for diverse contaminant species and specificity >99.93%. We used FCS-GX to screen 1.6 million GenBank assemblies and identified 36.8 Gbp of contamination (0.16% of total bases), with half from 161 assemblies. We updated assemblies in NCBI RefSeq to reduce detected contamination to 0.01% of bases. FCS-GX is available at https://github.com/ncbi/fcs/.

bioinformatics↗