Biology subjects

Beck, J.

Publications and source records attributed to Beck, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Human cortical slices reveal pulse-number-dependent synaptic plasticity during theta-burst magnetic stimulation

Theta-burst transcranial magnetic stimulation is widely used to modulate human brain activity in clinical and experimental settings, yet how clinically relevant stimulation protocols engage synaptic plasticity in human cortical circuits remains poorly understood. Here, we combined controlled magnetic stimulation of viable adult human cortical slices with single-cell electrophysiology to determine whether pulse number constrains synaptic plasticity during intermittent theta-burst stimulation (iTBS). As a functional reference, 10 Hz repetitive magnetic stimulation delivered with 900 pulses robustly potentiated excitatory synaptic transmission in human cortical pyramidal neurons. Similarly, iTBS900 significantly potentiated AMPA receptor-mediated miniature excitatory postsynaptic currents. In contrast, the clinically established 600-pulse iTBS protocol failed to reliably induce detectable synaptic plasticity under otherwise identical stimulation conditions. Paired within-patient experiments confirmed distinct synaptic responses to iTBS600 and iTBS900 in the same human cortical tissue preparations. Together, these findings identify pulse number as an important determinant of theta-burst magnetic stimulation-induced synaptic plasticity in human cortical microcircuits and highlight stimulation dose as a relevant parameter for the design and refinement of therapeutic stimulation protocols.

neuroscience↗

bioRxiv2026

Riboflavin-sensitized UVA collagen crosslinking produced a controllable, dose-dependent increase in the nanomechanical strength of ex vivo bovine dura mater

BackgroundDural defects, either from trauma, tumor resection, surgical approaches, genetics, or spontaneously represent a significant clinical challenge in neurosurgery. Given the established efficacy of riboflavin-sensitized ultraviolet-A (UVA) photo-crosslinking in ophthalmology, this study investigated its feasibility and dose-response characteristics as a novel strategy to biochemically augment the mechanical integrity and strength of ex-vivo bovine dura mater. MethodsForty bovine dura mater specimens were treated ex vivo using riboflavin concentrations of 2, 4, or 8 mM combined with UVA irradiation at 0.3 or 3 mW/cm{superscript 2}. PBS-treated specimens exposed to UVA served as controls. Atomic force microscopy nanoindentation was used to measure the local elastic modulus in matched regions before and after treatment, enabling paired assessment of treatment-induced mechanical changes while minimizing inter-sample variability. Post-treatment stiffness, fold-change from baseline, and riboflavin dose-response relationships were analyzed statistically. ResultsBaseline elastic moduli were equivalent across all groups (mean approximately 52 kPa, p=0.92). While UVA alone caused a modest approximately 2- to 3-fold stiffness increase, riboflavin-UVA treatment produced a dramatic, concentration-dependent effect. The highest treatment (8 mM RF, 3 mW/cm{superscript 2} UVA) increased the elastic modulus 150-fold, from approximately 53 kPa to approximately 8,000 kPa. Post-UV stiffness exhibited a strong linear relationship with riboflavin concentration (R{superscript 2} = 0.994), indicating a precisely titratable crosslinking effect. All treatment conditions were statistically distinguishable (p < 0.001). ConclusionRiboflavin-sensitized UVA crosslinking substantially increases the nanomechanical strength of ex vivo bovine dura mater in a controllable, dose-dependent manner. These findings establish a proof of concept for biochemical reinforcement of dural tissue that might be used clinically. As a next step evaluation using human dura, macroscopic biomechanical testing, penetration-depth analysis, and safety assessment is warranted.

bioengineering↗

bioRxiv2026

Spatially confined niches support hypoxia-associated transcriptional plasticity contributing to malignant progression in IDH-mutant gliomas

BackgroundWhile hypoxia is a well-established driver of glioblastoma progression, its role in IDH-mutant gliomas, characterized by localized hypoxic microenvironments rather than overt necrosis, remains poorly understood. Here, we investigate how hypoxia and microenvironmental-adaptations shape cellular heterogeneity and transcriptional plasticity in these tumors. MethodsWe integrated bulk, single-cell, and spatial-transcriptomics datasets from IDH-mutant glioma patients (Astrocytomas and Oligodendrogliomas) to characterize cellular-states and map the localization of hypoxic niches. To uncover tumor microenvironment effects, we established co-culture models using primary IDH-mutant glioma cells with human microglia and astrocytes, maintained under hypoxic and normoxic conditions, followed by bulk RNA-sequencing. ResultsWe identified a hypoxia-associated astrocyte-like (AC-like) program that defines a quiescent, non-cycling population with a distinct transcription factor profile indicative of functional plasticity in IDH-mutant gliomas. These cells harbor glioma stem cell (GSC)-like features and are poised for a quiescent-to-activated (Q-to-A) transition that drives tumor progression. Mechanistically, co-culture models reveal that microglia promote this Q-to-A transition by enhancing HBEGF/EGFR paracrine signaling. Spatial transcriptomics uncovers the co-localization of hypoxic niches within quiescent AC-like cells, whereby the activated subpopulation forms discrete niches defined by localized HBEGF/EGFR communication gradients. Notably, tumors exhibiting elevated EGFR-driven activation signatures correlate with higher histological grade and poorer patient survival, implicating the Q-to-A transition as a critical driver of malignant progression. ConclusionQ-to-A transition within the hypoxic niche represents a critical driver of malignant progression in IDH-mutant gliomas, providing a microenvironment-driven mechanism for the transition to higher-grade disease and identifying targetable-vulnerabilities for therapeutic intervention. Key pointsO_LIHypoxic niches spatially confine quiescent, astrocyte-like cellular state characterized by glioma stem cell features in IDH-mutant gliomas. C_LIO_LIMicroglia triggers the quiescent-to-activated (Q-to-A) transition via paracrine EGFR signaling crosstalk. C_LIO_LIEGFR-driven Q-to-A plasticity serves as a microenvironmentally-regulated driver of malignant progression and adverse patient survival. C_LI Importance of the studyWhile high-grade glioblastomas feature well-defined hypoxic and necrotic regions that drive tumor progression and therapy resistance, IDH-mutant gliomas lack these distinct hallmarks, instead exhibiting disorganized hypoxic niches. Consequently, the functional contribution of these niches to tumor progression has remained poorly understood. Although genetic and epigenetic alterations are established drivers of progression in IDH-mutant gliomas, we provide an additional, essential layer of complexity: microenvironment-driven transcriptional plasticity. By uncovering the relationship between tumor hypoxia and heterogeneous glioma cell states, we uncover that these niches are essential for such plasticity. We also show that the tumor microenvironment provides critical molecular cues necessary to initiate a transcriptional shift enabling glioma cells to transition from a quiescent reservoir into an activated state primed for rapid proliferation. By identifying this paracrine mechanism, our work uncovers a targetable vulnerability that dictates how dormant cell reservoirs are mobilized to fuel malignant transformation.

cancer biology↗

bioRxiv2026

Staphylococcus aureus triggers isolate-specific host transcriptional responses alongside TNF-R1 regulated cell death

BackgroundStaphylococcus aureus (S. aureus) is an increasingly recognized intracellular pathogen, yet infection outcomes vary with bacterial isolate and host cell type. The mechanisms underlying these differences remain poorly understood. This study investigates how distinct intracellular S. aureus isolates influence host signaling programs and infection outcomes by modulating cell death pathways and TNF-R1 dependent regulation of host cell fates across different human cell lines. MethodsFour S. aureus isolates were analyzed for intracellular localization using transmission electron microscopy (TEM), structured illumination microscopy (SIM), serial block-face scanning electron microscopy (SBF-SEM), and imaging flow cytometry. Transcriptional reprogramming of infected U937 monocytes was examined by mRNA sequencing. Infection outcomes were characterized and compared to A549 and SaOS-2 cell lines employing Luminex cytokine assays, flow cytometry and Western blot analysis to characterize host cell death mechanisms in both wild-type and TNF-R1 deficient backgrounds. ResultsAll S. aureus isolates localized to endolysosomal and cytosolic compartments but also peri and putatively intranuclearly, revealing an unexpected intracellular niche. In U937 monocytes, infection induced a conserved stress signature alongside isolatespecific transcriptional programs divergently affecting inflammation, metabolism, and cell fate, which was markedly attenuated in response to the chronicinfection isolate EDCC 5464. Cell death outcomes were likewise isolatedependent, involving intrinsic and extrinsic apoptosis, mitochondrial depolarization, and caspase-1 activation at distinct temporal dynamics. TNFR1 loss initially delayed but exacerbated late, isolate-independent cytotoxicity, identifying TNFR1 as a key regulator of U937 infection outcome. SaOS2 and A549 cell death was far less affected by isolate or TNF-R1 deficiency. ConclusionsThese results highlight the multilayered determinants governing intracellular S. aureus survival, non-canonical intracellular localization, and host cell susceptibility. The TNF/TNF-R1 axis is identified to critically determine regulated host defense during early infection stages in a tissue-specific manner. Together with distinct isolate-driven gene expression profiles, infection risks under TNF-targeted therapies and the contribution of S. aureus heterogeneity should be considered in the design of future host-directed treatment strategies. Plain English summaryThe bacterium Staphylococcus aureus (S. aureus) often lives harmlessly in humans but can cause severe or recurrent infections when the skin barrier is broken or the immune system is weakened. A major reason for its persistence is its ability to hide inside human cells, where it is shielded from immune attacks and antibiotics. To effectively target such bacteria, it is crucial to understand that infections vary depending on both the bacterial strain and the infected cell type. Many reasons behind these differences are still puzzling. We explored how different types of S. aureus (collected from different disease types) change how human cells respond to infection. We focused on how the different strains influence the way immune cells adjust their gene activity during infection, and how a receptor called TNF-R1 is involved in managing cell death responses. Bacteria were found not only in compartments meant to destroy them but also near and even inside the cell nucleus, an unexpected location. All strains triggered a similar stress response but also distinct patterns influencing inflammation, metabolism, and cell survival. A strain linked to chronic infection caused weaker responses, suggesting greater stealth. Cells lacking TNF-R1 initially survived longer but later showed greater damage, indicating this receptors role in infection control. In lung and bone cells, these effects were less pronounced. Concludingly, S. aureus occupies unexpected niches inside human cells and uses varying survival strategies. TNF-R1 is a key regulator of host infection responses in the analyzed immune cells, highlighting that both bacterial diversity and host factors must be considered when developing targeted treatments. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/723175v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1b4214org.highwire.dtl.DTLVardef@18f4ee6org.highwire.dtl.DTLVardef@1851742org.highwire.dtl.DTLVardef@ba0359_HPS_FORMAT_FIGEXP M_FIG Peri- and intranuclear localization early after S. aureus uptake across host cell lines, with isolate-specific modulation of host fates and a critical role for TNF-R1 to mediate regulated death responses of U937 cells. At 2 hpi, intracellular S. aureus not only localizes in (LAMP-1 decorated) membrane-enclosed compartments or directly in the cytosol, but within invaginations of the nuclear surface and intranuclearly with or without being surrounded by a vesicular membrane in U937wt, SaOS-2wt, and A549wt cells. At 4 hpi, S. aureus triggers differential gene expression in (A) U937wt cells to an isolate-specific extent, with both unique and shared transcriptomic signatures across the four isolates, that is muted for the chronic infection isolate EDCC 5464. Apoptotic cell death is induced to an isolate-dependent extent involving extrinsic initiator caspase-8, intrinsic initiator caspase-9 (EDCC 5055 only), and variable effector caspase-3/-7 activity in the earlier stages of infection (6 hpi), which then barely increases (24 hpi) in U937wt cells. S. aureus-induced cell death and caspase activation is abolished in (B) U937{Delta}TNF-R1 at 6 hpi, but is significantly reinforced at 24 hpi with diminished isolate-specificity. Correspondingly, mitochondrial trans-membrane potential ({Delta}{Psi}m) is disrupted for all isolates upon TNF-R1 knockout, as well as caspase-1 activity, suggesting pyroptotic pathway activation at later stages of infection. (C) SaOS-2 wt cells show moderate caspase-3/-7 and -1 activation, while infection induces detachment of (D) A549wt cells with minimal caspase activation. Infection induces an isolate- and cell line-dependent cytokine release. Coloured arrows indicate the mean proportion of effector-positive cells ({uparrow} [~]20-40%, {uparrow} {uparrow} 40-60%, {uparrow} {uparrow} {uparrow} >60%) representing each S. aureus isolate. Grayed signaling arrows indicate the hypothesis by which TNF-R1 activation and internalization is required to kill lysosomal S. aureus via activation of anti-microbial enzymes and downstream regulated death pathway activation. Created with BioRender.com. C_FIG

microbiology↗

bioRxiv2026

Neuronal precursor cell persistence in Ganglioglioma is associated with ECM remodeling and immune cell infiltration

BackgroundGangliogliomas (GGs) are low-grade glioneuronal tumors that frequently present with drug-resistant epilepsy. Although their indolent course contrasts with their high epileptogenic potential, the oncogenic mechanisms sustaining neuronal precursor-like populations within the tumor microenvironment remain poorly defined. MethodsWe performed spatial transcriptomic profiling on eight histologically confirmed GGs and matched healthy cortex to map the cellular and molecular architecture of the tumor microenvironment. Integrated analysis with weighted gene correlation network analysis (WGCNA) defined recurrent oncogenic programs and spatially resolved tumor-stroma interactions. ResultsEight conserved gene modules emerged, encompassing physiological cortical, reactive glial, and oncopathological programs. The latter captured extracellular matrix (ECM) remodeling, vascular-immune signaling, and persistence of immature, proliferative neuronal-like states. Spatial modeling revealed that these oncopathological programs form structured niches at the tumor-brain interface, where radial glia-derived neuronal-like tumor cells coexist with immune and stromal elements engaged in ECM turnover and cytokine signaling. ConclusionsGanglioglioma represents a hybrid glioneuronal neoplasm in which developmental neuronal programs are co-opted by tumor-associated stromal and immune cues. This convergence establishes a permissive oncogenic niche that sustains precursor-like tumor cells and provides a mechanistic basis for both the tumors benign growth and its intrinsic epileptogenicity. Key PointsO_LISpatial transcriptomics identifies reproducible transcriptional programs that define the ganglioglioma microenvironment. C_LIO_LITumor-associated regions show transcriptional programs consistent with immature neuronal states together with ECM remodelling and immune activity. C_LIO_LISingle-cell reference data indicate that immature neuronal programs in ganglioglioma resemble radial glia-derived developmental states. C_LI Importance of the StudyGanglioglioma is a low-grade glioneuronal tumor that combines benign growth with pronounced epileptogenicity, yet the molecular basis of this dual behavior remains poorly understood. Through spatial transcriptomics integrated with single-cell analysis, we reveal that ganglioglioma architecture is defined by two interacting transcriptional axes: a residual glioneuronal network and a tumoral niche enriched for extracellular-matrix, vascular, and immune programs. Within these niches, immature neuronal-like tumor cells persist in a developmentally arrested state maintained by ECM-immune signaling. This spatially organized interplay between physiological and pathological programs explains both the low oncologic aggressiveness and high excitability of these lesions. Our findings provide molecular signatures that may refine diagnostic classification within the LEAT spectrum, delineate epileptogenic zones, and identify candidate pathways for therapeutic modulation of the ganglioglioma microenvironment.

neuroscience↗

bioRxiv2026

Spatial analysis reveals the evolving organization of low-grade and high-grade IDH-mutant glioma

Adult diffuse gliomas are comprised of malignant cell states interwoven with the non-malignant brain microenvironment. Here we combine spatial transcriptomics and spatial proteomics of IDH-mutant gliomas to define organizational principles across histological grades. In low-grade tumors, spatial organization arises from underlying nonmalignant brain structures. For example, we classify low-grade tumor regions as embedded into white matter and identify a sharp white-grey matter junction that restricts cortical invasion and is associated with marked changes in tumor composition and cellular phenotypes. This junction is preferentially traversed by oligodendrocyte progenitor (OPC)-like malignant cells, which may drive tumor expansion. In contrast, intermediate-grade tumors are largely disorganized, with few recurring pairwise interactions between cancer cell states and TME cell types. In high-grade tumors, hypoxia/necrosis-associated global structure begins to emerge, reminiscent of IDH-wildtype glioblastoma. Together, these findings reveal two independent axes of glioma spatial organization--from brain anatomy-driven organization in low-grade tumors to hypoxia-associated structure in high-grade tumors--and establishes a framework that links tumor grade to recurrent spatial associations between cell states and cell types.

cancer biology↗

bioRxiv2026

Hypoxia and Associated Acidosis Generate Cell-Type Specific Myeloid Responses in Glioblastoma

Hypoxia is a defining feature of glioblastoma (GBM), yet how it cooperates with hypoxia-associated acidosis to shape microglia and infiltrating monocyte-derived macrophages (MDM) remains poorly understood. We integrated cyclic immunohistochemistry, single-cell RNA sequencing, spatial transcriptomics, in vitro cell cultures, and DNA methylation profiling to outline hypoxia-driven responses in up to 136 GBMs. These hypoxic niches were selectively enriched for MDMs that activated carbonic anhydrase (CA) mediated pH buffering and other metabolic adaptation programs, enabling survival in acidic hypoxia, increasingly interacted with cancer cells, and show polarization toward immunosuppressive myeloid-derived suppressor cell (MDSC)-like states. In contrast, microglia were depleted in hypoxic areas, lacked compensatory CA isoenzymes, and developed TNF-linked stress responses and loss of homeostatic identity in acidic hypoxia. These findings identify metabolic adaptation to hypoxia-associated microenvironmental stress as a key determinant of GBM immune architecture, driving myeloid cell fates, spatial TME reorganization and the emergence of immunosuppressive tumor ecosystems.

cancer biology↗

bioRxiv2025

Iron-Associated Mesenchymal Plasticity and Tumor Invasion in Glioblastoma

Glioblastoma (GBM) recurrence is driven by tumor cells that infiltrate surrounding brain tissue and evade surgical and therapeutic eradication. Although dysregulated iron handling is a recognized feature of the necrotic and hemorrhagic GBM tumor core, its relationship to invasive tumor cell states remains incompletely defined. Here, we investigated how iron-associated microenvironments relate to transcriptional programs of invasion in human GBM. Using multi-regional single-nucleus RNA sequencing of human GBM specimens encompassing tumor core, invasive front, and infiltrated cortex, we found that malignant cells from the tumor core exhibit coordinated upregulation of iron uptake and storage pathways together with invasion-associated gene programs. At the single-cell level, iron metabolism and invasion signatures were strongly correlated, defining a distinct core-enriched malignant subpopulation with mesenchymal-like transcriptional identity, stress-adaptive features, and angiogenic signaling. These iron-high/invasion-high cells aligned with mesenchymal-and astrocyte-like GBM states and were associated with unfavorable patient survival. Despite elevated oxidative stress and ferroptosis-associated transcriptional pressure, this population concurrently expressed anti-apoptotic and anti-ferroptotic regulators, consistent with an iron-tolerant invasive state. To assess functional consequences of iron exposure, we modeled iron-rich conditions using non-cytotoxic particulate iron in patient-derived GBM cell lines and human organotypic cortical slice cultures. Iron exposure induced intracellular iron accumulation, oxidative stress responses, increased tumor cell motility in vitro, and enhanced invasion within intact human brain tissue. Collectively, these findings demonstrate that iron-rich tumor core niches are closely associated with mesenchymal plasticity and invasive behavior in GBM and support a role for iron-associated microenvironmental pressure in shaping invasive tumor cell states. Key PointsO_LITranscriptional profiling reveals that the GBM tumor core harbors malignant cells that strictly couple active iron metabolism with invasive programs. C_LIO_LIThis iron-accumulating, Mesenchymal-like subpopulation is distinctively characterized by angiogenesis and stress resistance. C_LIO_LIIron supplementation in vitro and human ex vivo models are sufficient to drive mesenchymal transition and significantly enhance tumor migration and tissue invasion. C_LI Importance of the StudyGlioblastoma (GBM) recurrence is driven by highly invasive tumor cells that evade resection and resist therapy. Yet the microenvironmental pressures that push GBM cells into an invasive, therapy-resistant state remain poorly defined. Although iron dysregulation has been implicated across cancers, its role as a microenvironmental determinant of GBM invasion has never been demonstrated in physiologically relevant human systems. By integrating multi-regional single-nucleus RNA sequencing with functional validation in patient-derived GBM lines and human organotypic cortical slice cultures, we uncover a core-enriched, iron-associated mesenchymal program that co-segregates with invasion, stress adaptation, and angiogenic signaling. We further show that physiologically relevant iron exposure is sufficient to induce mesenchymal transition, enhance motility, and accelerate tissue invasion within human cortical architecture. These findings position iron as a selective driver that links the hemorrhagic, necrotic GBM core to the emergence of invasive subpopulations that seed recurrence. The data identify iron handling and stress-response pathways as actionable therapeutic vulnerabilities, providing a foundation for strategies that target metabolic resilience and iron-dependent invasive states in GBM. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/695920v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@141cc11org.highwire.dtl.DTLVardef@bcb055org.highwire.dtl.DTLVardef@1dcd332org.highwire.dtl.DTLVardef@ad7cad_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

A data and task-constrained mechanistic model of the mouse outer retina shows robustness to contrast variations

Visual processing starts in the outer retina where photoreceptors transform light into electrochemical signals. These signals are modulated by inhibition from horizontal cells and sent to the inner retina via excitatory bipolar cells. The outer retina is thought to play an important role in contrast invariant coding of visual information, but how the different cell types implement this computation together remains incompletely understood. To understand the role of each cell type, we developed a fully-differentiable biophysical model of a circular patch of mouse outer retina. The model includes 200 cone photoreceptors with a realistic phototransduction cascade and ribbon synapses as well as horizontal and bipolar cells, all with cell-type specific ion channels. Going beyond decades of work constraining biophysical models of neurons only by experimental data, we used a dual approach, constraining some parameters of the model with available measurements and others by a visual task: (1) We fit the parameters of the cone models to whole cell patch-clamp measurements of photocurrents and two-photon glutamate imaging measurements of synaptic release. (2) We then trained the spatiotemporal outer retina model with photoreceptors and the other cell types to perform a visual classification task with varying contrast and luminance levels. We found that our outer retina model could learn to solve the classification task despite contrast and luminance variance in the stimuli. Testing different cell type compositions and connectivity patterns, we found that feedback from horizontal cells did not further improve task performance beyond that of excitatory photoreceptors and bipolar cells. This is surprising given that horizontal cells are positioned to mediate communication across cones and that they add to the models number of trainable parameters. Finally, we found that our model generalized better to out of distribution contrast levels than a linear classifier. Our work shows how the nonlinearities found in the outer retina can accomplish contrast invariant classification and teases apart the contributions of different cell types.

neuroscience↗

bioRxiv2025

Association between Cortical Thickness and Functional Response to Linguistic Processing in the Occipital Cortex of Early Blind Individuals

Blindness has been shown to induce changes in the structural and functional organization of the brain. However, few studies have investigated the relationship between these structural and functional changes. In this study, we examined cortical thickness within occipital regions of interest in 38 early blind individuals and explored its relationship to functional activation during linguistic processing. Participants engaged in tactile Braille reading and auditory processing tasks involving words, pseudowords, and control conditions to assess various aspects of linguistic processing. Linear mixed models revealed a significant association between cortical thickness and functional activation in the occipital cortex during linguistic tasks. Specifically, lower cortical thickness in the middle occipital gyrus, the calcarine sulcus, and the parieto-occipital sulcus were linked to increased activation during orthographic processing in blind participants (Braille pseudowords vs. Braille nonsense-symbols). Similarly, lower cortical thickness in the calcarine sulcus and parieto-occipital sulcus was associated with greater functional activation during phonological processing (auditory pseudowords vs. auditory control). These findings align with prior research suggesting that structural and functional adaptations in the visual cortex of blind individuals may be influenced by developmental mechanisms such as pruning or myelination. This study highlights the interplay between cortical structure and functional reorganization in the blind brain.

neuroscience↗

bioRxiv2025

Customizing the Structure of a Minimal TIM Barrel to Craft a De Novo Enzyme

The TIM barrel is the most prevalent fold in natural enzymes, supporting efficient catalysis of diverse chemical reactions. While de novo TIM barrels have been successfully designed, their minimalistic architecture lacks structural elements essential for substrate binding and catalysis. Here, we present CANVAS, a computational workflow that introduces a structural lid into a minimal de novo TIM barrel to anchor catalytic residues and form an active-site pocket for enzymatic function. Starting from two de novo TIM barrels, we designed nine variants with distinct lids to form active sites for the Kemp elimination. Four designs showed measurable activity, with the most active reaching a catalytic efficiency of 21,000 M-{superscript 1} s-{superscript 1} at its optimal pH. A co-crystal structure of this variant bound to a transition-state analogue confirmed the accuracy of the designed lid and active site. Using the X-ray structure of a lower-activity variant (19 M-{superscript 1} s-{superscript 1}), we applied ensemble-based design to optimize its active site, increasing catalytic efficiency by >1,600-fold to 32,000 M-{superscript 1} s-{superscript 1}. These results demonstrate that de novo TIM barrels can be endowed with substrate binding pockets supporting efficient catalytic function, establishing a platform for building enzymes on demand from minimal protein scaffolds.

biochemistry↗

bioRxiv2024

Human microRNA-153-3p targets specific neuronal genes and is associated with the risk of Alzheimer's disease.

Alzheimers disease (AD) is a progressive degenerative disease characterized by a significant loss of neurons and synapses in cognitive brain regions and is the leading cause of dementia worldwide. AD pathology comprises extracellular amyloid plaques and intracellular neurofibrillary tangles. However, the triggers of this pathology are still poorly understood. Repressor element 1-silencing transcription/neuron-restrictive silencer factor (REST/NRSF), a transcription repressor of neuronal genes, is dysregulated during AD pathogenesis. How REST is dysregulated is still poorly understood, especially at the post-transcriptional level. MicroRNAs (miRNAs), a group of short non-coding RNAs, typically regulate protein expression by interacting with target mRNA transcript 3-untranslated region (UTR) and play essential roles in AD pathogenesis. Herein, we demonstrate that miR-153-3p reduces REST 3-UTR activities, mRNA, and protein levels in human cell lines, along with downregulating amyloid-{beta} precursor protein (APP) and -synuclein (SNCA). We determine by mutational analyses that miR-153-3p interacts with specific targets via the seed sequence present within the respective mRNA 3UTR. We show that miR-153-3p treatment alters the expression of these specific proteins in human neuronally differentiated cell lines and human induced pluripotent stem cells and that miR-153-3p is itself dysregulated in AD. We further find that single nucleotide polymorphisms (SNPs) within 5kb of the MIR153-1 and MIR153-2 genes are associated with AD-related endophenotypes. Elevation of miR-153-3p is associated with a reduced probability of AD, while elevated REST may associate with a greater probability of AD. Our work suggests that a supplement of miR-153-3p would reduce levels of toxic protein aggregates by reduced expression of APP, SNCA and REST expression, all pointing towards a therapeutic and biomarker potential of miR-153-3p in AD and related dementias.

neuroscience↗

bioRxiv2024

Differentiable simulation enables large-scale training of detailed biophysical models of neural dynamics

Biophysiscal neuron models provide insights into cellular mechanisms underlying neural computations. However, a central challenge has been the question of how to identify the parameters of detailed biophysical models such that they match physiological measurements at scale or such that they perform computational tasks. Here, we describe a framework for simulation of detailed biophysical models in neuroscience--JO_SCPLOWAXLEYC_SCPLOW--which addresses this challenge. By making use of automatic differentiation and GPU acceleration, JO_SCPLOWAXLEYC_SCPLOW opens up the possibility to efficiently optimize large-scale biophysical models with gradient descent. We show that JO_SCPLOWAXLEYC_SCPLOW can learn parameters of biophysical neuron models with several hundreds of parameters to match voltage or two photon calcium recordings, sometimes orders of magnitude more efficiently than previous methods. We then demonstrate that JO_SCPLOWAXLEYC_SCPLOW makes it possible to train biophysical neuron models to perform computational tasks. We train a recurrent neural network to perform working memory tasks, and a feedforward network of morphologically detailed neurons with 100,000 parameters to solve a computer vision task. Our analyses show that JO_SCPLOWAXLEYC_SCPLOW dramatically improves the ability to build large-scale data- or task-constrained biophysical models, creating unprecedented opportunities for investigating the mechanisms underlying neural computations across multiple scales.

neuroscience↗

bioRxiv2024

Weber's law and natural inference

For most extensive sensory variables such as speed or numerosity, the discrimination thresholds of human subjects are proportional to the value around which the discrimination is performed, a scaling known as Webers law. Many theories have been proposed for this law, which all rely on the assumption that neurons are noisy. By contrast, we argue here that noisy neurons are not required to explain Webers law. Instead, we propose that it is the unavoidable consequence of the statistics of natural sensory inputs. In natural environments, sensory measurements are typically scaled by global variables such as contrast in vision or loudness in audition. These global scaling parameters induce positive correlations among measurements which in turn lead to Webers scaling. This theory makes testable experimental predictions and accounts for the fact that tuning curves to speed and numerosity in vivo are approximately log normal.

animal behavior and cognition↗

bioRxiv2024

Focal cortical dysplasia type II-dependent maladaptive myelination in the human frontal lobe

Focal cortical dysplasias (FCDs) are local malformations of the human neocortex and a leading cause of intractable epilepsy. FCDs are classified into different subtypes including FCD IIa and IIb, characterized by a blurred gray-white matter boundary or a transmantle sign indicating abnormal white matter myelination. Recently, we have shown that myelination is also compromised in the gray matter of FCD IIa of the temporal lobe. Since myelination is key for brain function which is imbalanced in epilepsy, in the current study we investigated myelination in the gray matter of FCD IIa and IIb from the frontal lobe. We found that in particular FCD IIb showed myelination disturbances such as increased numbers of myelinating oligodendrocytes (OLs) and an irregular and disorganized myelination pattern covering an enlarged area in comparison to FCD IIa and controls. Interestingly, both FCD types presented with larger axon diameters when compared to controls. A significant correlation of axon diameter and myelin sheath thickness was found for FCD IIb and controls, whereas in FCD IIa large caliber axons were less myelinated. On the level of gene expression, FCD IIb presented with a significant up-regulation of myelin-associated mRNA synthesis in comparison to FCD IIa and by enhanced binding-capacities of the transcription factor MYRF to promoters of myelin-associated genes reflecting the need for more myelin due to increased axon diameters. These data show that FCD IIa and IIb are characterized by divergent signs of maladaptive myelination which may contribute to the epileptic phenotype. Main pointsO_LIIn the gray matter of the frontal lobe, FCD IIa and FCD IIb are characterized by divergent signs of maladaptive myelination. C_LIO_LIFCD IIa presents with an ordinary radial fiber pattern, but with a reduced thickness of the myelin sheath around large diameter axons and with an attenuation of the myelin synthesis machinery. C_LIO_LIFCD IIb is characterized by an irregular and disorganized myelin fiber pattern, a higher density of myelinating oligodendrocytes and an elevated transcriptional turnover of myelin-associated genes. C_LI

neuroscience↗

bioRxiv2023

Antiepileptic medication strengthens excitatory neurotransmission in pyramidal neurons of the adult human neocortex

Homeostatic synaptic plasticity serves to maintain neuronal function within a dynamic range upon perturbations in network activity. While coordinated structural and functional changes at synaptic sites play a crucial role in adaptive processes, the specific regulatory mechanisms and biological relevance of homeostatic plasticity in the human brain warrant further investigation. In this study, we investigated the effects of neural network silencing, achieved through pharmacological inhibition of voltage-gated sodium channels or glutamatergic neurotransmission - common targets of antiepileptic medication - on functional and structural properties of murine and human cortical tissue. Using mouse entorhino-hippocampal tissue cultures, acute neocortical slices of adult mice, and human brain tissue, we characterize homeostatic synaptic plasticity across models, brain regions, and species. Our findings demonstrate local homeostatic synaptic plasticity in the adult human neocortex, highlighting the potential effects of antiepileptic medication in brain regions unaffected by the primary diseases, which might represent a mechanism for neuropsychiatric effects linked to these medications and increased seizure susceptibility upon discontinuation of antiepileptic medication.

neuroscience↗

bioRxiv2023

Large Scale Comparative Deconvolution Analysis of the Canine and Human Osteosarcoma Tumor Microenvironment Uncovers Conserved Clinically Relevant Subtypes

Osteosarcoma is a relatively rare but aggressive cancer of the bones with a shortage of effective biomarkers. Although less common in humans, Osteosarcomas are fairly common in adult pet dogs and have been shown to share many similarities with their human analogs. In this work, we analyze bulk transcriptomic data of 213 primary and 100 metastatic Osteosarcoma samples from 210 pet dogs enrolled in nation-wide clinical trials to uncover three Tumor Microenvironment (TME)-based subtypes: Immune Enriched (IE), Immune Enriched Dense Extra-Cellular Matrix-like (IE-ECM) and Immune Desert (ID) with distinct cell type compositions, oncogenic pathway activity and chromosomal instability. Furthermore, leveraging bulk transcriptomic data of canine primary tumors and their matched metastases from different sites, we characterize how the Osteosarcoma TME evolves from primary to metastatic disease in a standard of care clinical setting and assess its overall impact on clinical outcomes of canines. Most importantly, we find that TME-based subtypes of canine Osteosarcomas are conserved in humans and predictive of progression free survival outcomes of human patients, independently of known prognostic biomarkers such as presence of metastatic disease at diagnosis and percent necrosis following chemotherapy. In summary, these results demonstrate the power of using canines to model the human Osteosarcoma TME and discover novel biomarkers for clinical translation.

cancer biology↗

bioRxiv2023

Attraction of female house mice to male ultrasonic courtship vocalizations depends on their social experience and estrous

Male house mice (Mus musculus) produce complex ultrasonic vocalizations (USVs), especially during courtship and mating. Playback experiments suggest that female attraction towards recordings of male USVs depends on their social experience, paternal exposure, and estrous stage. We conducted a playback experiment with wild-derived female house mice (M. musculus musculus) and compared their attraction to male USVs versus the same recording without USVs (background noise). We tested whether female attraction to USVs is influenced by the following factors: (1) social housing (two versus one female per cage); (2) neonatal paternal exposure (rearing females with versus without father); and (3) sexual receptivity (pro-estrous and estrous stages versus non-receptive metestrous and diestrous stages). We found that females showed a significant attraction to male USVs but only if females were housed with another female. Individually housed females showed the opposite response. We found no evidence that pre-weaning exposure to a father influenced females preferences, whereas sexual receptivity influenced females attraction to male USVs: non-receptive females showed preferences towards male USVs but receptive females did not. Finally, we found that individually housed females were more likely to be in sexually receptive estrous stages than those housed socially, and that attraction to male USVs was most pronounced amongst non-receptive females that were socially housed. Our findings indicate that the attraction of female mice to male USVs depends upon their social experience and estrous stage, though not paternal exposure. They contribute to the growing number of studies showing that social housing and estrous stage influence the behavior of house mice and we show how such unreported variables can contribute to the replication crisis.

animal behavior and cognition↗