Biology subjects

Kumar, V.

Publications and source records attributed to Kumar, V..

At least 19 recordsLinked to original sources

bioRxiv2026

Identification of TM4SF1 as a novel tumor-associated antigen in biliary tract cancers targetable by CAR-T cell therapy

Background & Aims: Biliary tract cancers (BTCs) are a rare set of genetically heterogenous and aggressive malignancies associated with delayed presentation and poor prognosis. Thus, there is an unmet clinical need for the development of novel therapeutic strategies. Identification of uniquely expressed cell-surface, tumor-associated antigens (TAAs) holds promise in epithelial tumors more generally, as they can serve as ligands for a variety of therapeutics, including CAR-T cell therapy. However, TAA identification in BTCs has been limited by expression in normal liver tissue. Here, we aim to characterize the cell-surface protein transmembrane 4 L six family member 1 (TM4SF1) as a potential BTC TAA targetable by CAR-T therapy. Methods: TM4SF1 expression in BTC relative to normal hepatic/biliary tissue was characterized at the mRNA level by analyzing TCGA datasets and at the protein level by immunohistochemistry of archival primary BTC tissue. Anti-TM4SF1 CAR-T cells were evaluated through in vitro coculture assays against human-derived BTC cell lines and in a cell line-derived xenograft (CDX) model. Results: We find TM4SF1 is significantly upregulated in BTC relative to normal hepatic/biliary tissue and across BTC anatomical subtypes at the mRNA and protein level. To validate TM4SF1 as a targetable TAA in BTC, we show anti-TM4SF1 CAR-T cells demonstrate robust growth inhibition of BTC cell lines in vitro and significant anti-tumor activity against a CDX in vivo. Conclusions: Together, our data provides support for TM4SF1 as a promising TAA in BTCs that can be used for the rational development of targeted therapeutic modalities, including CAR-T cells, in a patient population with significant unmet need.

cancer biology↗

bioRxiv2026

PGC-1α Links Estrogen Receptor Signaling to Japanese Encephalitis Virus Replication in Neuronal cell

Acute encephalitis due to the viral causative agents, such as Japanese Encephalitis Virus (JEV), remains a leading cause of viral encephalitis in Asia, contributing to high mortality and long-term neurological sequelae. The host factors that modulate JEV replication are not well understood. In this study, we investigated the modulation of JEV infection by estrogen in vitro and in vivo. The results demonstrated that estrogen enhances JEV replication in neuronal cells via estrogen receptor alpha (ER) by modulating peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1). Since JEV pathogenesis increases cellular production demands, it results in dysregulation of cellular homeostasis, whereas estrogen treatment helps keep cellular health in check. Also, the mouse model exhibited an increased viral burden with protective antibody titers in response to estrogen. Conclusively, this work highlights the mechanistic link of estrogen-driven mechanisms and identifies the ER-PGC-1-axis as a potential target for sex-specific therapeutic interventions.

microbiology↗

bioRxiv2026

Engineering the NAT-ULT module increases seed number per pod in soybean

Seed number per pod is a major soybean yield-component trait, yet experimentally validated causal modules remain poorly defined. Here, we identify and functionally validate a soybean NAT-ULT regulatory module controlling ovule and seed number per pod. Through a visual screen of a fast-neutron-irradiated Glycine max cv. Williams 82 population, we isolated MO27, which increased four-seeded pod frequency from approximately 2-4% in wild type to 27-30%, without major changes in plant architecture, total pod number, or seed morphology. Comparative genome hybridization mapped the phenotype to a 46.7-kb chromosome 2 deletion containing GmNAT1 and chromosome 6 deletions encompassing GmULT-B1 and GmULT-B3. Ovule-clearing analysis showed that increased seed number originated before fertilization through elevated formation of four-ovule ovaries. CRISPR/Cas9-mediated mutagenesis of GmNAT1, GmULT-B1, and GmULT-B3 increased four-seeded pod frequency without detectable penalties in 100-seed weight, total pod number, or plant height. Tomato SlULT triple mutants also increased floral organ and locule number, supporting conserved ULT-like function in reproductive organ patterning. RNA-seq interaction analysis revealed a chromosome 6-dominant transcriptional state, accompanied by selective non-additive reprogramming of hormone/ovule-number and cell-wall-remodeling modules. Integrated genetic and transcriptomic analyses support a hierarchical model in which NAT-ULT perturbation may enhance meristematic competence and remodel reproductive developmental programs, while additional fast-neutron-background-associated transcriptional changes may further modulate the phenotype. These findings define NAT-ULT as a molecular target for engineering soybean seed number per pod.

plant biology↗

bioRxiv2026

Anti-target chemical-space coverage of Indian medicinal plant phytochemicals

Computational safety evaluation of phytochemical libraries commonly relies on models trained on experimentally tested compounds and applied to much larger and chemically diverse collections. An important but often overlooked question is whether predicted compounds are adequately represented within the experimental chemical space underlying these models. Here, we examined this question for the Indian Medicinal Plants, Phytochemistry and Therapeutics (IMPPAT) database using experimentally characterized datasets for three anti-target endpoints: hERG blockade, cytochrome P450 (CYP) inhibition, and pregnane X receptor (PXR) induction. After structure standardization, 14,956 unique IMPPAT compounds were compared with 8,877 hERG, 4,905 CYP, and 4,138 PXR reference compounds using consensus nearest-neighbor similarity based on Morgan and atom-pair fingerprints. At a Tanimoto similarity threshold of 0.80, only 0.92%, 0.30%, and 0.46% of IMPPAT compounds had close measured analogs in the hERG, CYP, and PXR datasets, respectively. Relative to the internal nearest-neighbor distributions of the reference datasets, a typical IMPPAT compound lay near the 1st percentile, indicating substantial chemical-space separation. Compounds with close experimental analogs also showed distinct molecular characteristics, with descriptor-based logistic regression yielding cross-validated AUC values of 0.77-0.80. Plant-level enrichment was markedly reduced after excluding widely distributed metabolites and was further restricted when the nearest measured analog was required to have pIC50 or pEC50 [≥] 5. The remaining signals were concentrated in a limited number of taxa, including Rauvolfia, Sinopodophyllum/Dysosma, Cinchona, and Catharanthus roseus. Overall, most IMPPAT phytochemicals lack close structural representation among currently measured anti-target compounds. Computational safety predictions for these molecules should therefore be interpreted as extrapolations and accompanied by explicit measures of structural support. Absence of a close experimental analog should be regarded as a gap in available evidence rather than evidence of safety.

bioinformatics↗

bioRxiv2026

Genetically distinct neurodegenerative proteinopathies engage overlapping proteostasis components

Neurodegenerative proteinopathies are defined by distinct proteins whose folding, trafficking and clearance depend on shared proteostasis machinery. Whether these disorders engage common components or only common processes has been unresolved. We mapped 16 disease proteins from 12 disorders onto a fixed 990-protein proteostasis network. Across the 12 disorders, the neighborhoods of these proteins shared specific proteins beyond expectations from process composition and connectivity. The same held for the two disorders defined by more than one protein. Nine proteins contributed disproportionately, and only autophagys removal significantly reduced similarity. Removing PRKN, HSPA8 or UBQLN2 in silico reduced path efficiency, marking them candidate shared network vulnerabilities. In human brain proteomes, Alzheimers disease-zone proteins showed greater abundance remodeling in the insoluble fraction; recurrence across disorders showed no such association. The result is a component-level architecture prioritizing network-derived candidates for cross-disease functional testing.

neuroscience↗

bioRxiv2026

Genotype-dependent behavioral signatures of opioid withdrawal revealed by automated behavioral quantification

Opioid withdrawal drives continued opioid use in opioid use disorder (OUD), which affected an estimated 4 million Americans in 2024. However, only one non-opioid medication is FDA-approved for withdrawal treatment, and there is great need for more diverse treatment options. Mice are powerful models to study opioid withdrawal because they allow for controlled drug and environmental exposure, express OUD-relevant phenotypes, and provide access to withdrawal-relevant tissue at exact time points. However, mouse models are hindered by their over reliance on a single genetic background (C57BL/6J). Using a single background risks limiting the translatability of preclinical studies as they are projected into genetically diverse human populations. Inferring withdrawal intensity in mice typically relies on single behaviors or indexes of behaviors, and applying these approaches across mouse genetic diversity faces a critical challenge: differing withdrawal responses could either encode differences in withdrawal severity, or differences in withdrawal-evoked behaviors independent of severity. To overcome this limitation, a more comprehensive assessment of opioid withdrawal behaviors across mouse genetic diversity is needed. Here we leverage computer vision and machine learning to automate the simultaneous quantification of many mouse behaviors during opioid withdrawal in eight diverse strains of mice. We reveal that all eight strains exhibit withdrawal-evoked behaviors, and these behaviors are sufficient to identify the withdrawal state of the mouse. However, the effect of withdrawal on individual behaviors or indexes of behaviors is not uniform across genetic diversity, and extending methods tuned in one strain risks misclassifying withdrawal in others. Finally our approach was able to distinguish graded withdrawal intensity, as defined by opioid exposurewithin3of4strainstested. We therefore conclude that opioid withdrawal behavior is profoundly shaped by genetic background, but withdrawal severity can nonetheless be established within a background. Combining automated computer-vision phenotyping with genotype-aware modeling provides a scalable path toward genetically informed withdrawal assessment in diverse mouse populations, with the ultimate goal of identifying the genetic and biological networks that modulate opioid withdrawal and may represent new targets for treating opioid use disorder.

animal behavior and cognition↗

bioRxiv2026

An automated machine vision-based index for Rett Syndrome provides a generalizable framework for modeling rare disease therapeutics

Rare diseases collectively affect millions of people, yet therapeutic development remains limited by preclinical phenotyping which is often dependent on subjective, low-resolution manual behavioral assessment. Rett syndrome (RTT), a rare disease affecting 1 in 10,000 female births, is caused by a MeCP2 deficiency. In mouse models for this disease, symptom severity is measured primarily with the observational Bird score. This subjective six-item ordinal scale was used to demonstrate that MeCP2 deficiency is reversible, but offers limited resolution for ranking candidate therapies or detecting partial rescue. We applied an automated machine learning (ML) pipeline to a humanized Mecp2 R270X mouse model. We conducted weekly Bird scoring and recorded one-hour open-field trials from 3 to 10 weeks of age in 24 hemizygous (Mecp2-/Y) males and 24 wild-type littermates, then extracted over 400 behavioral features spanning gait kinematics, open-field activity, body morphometrics, and trained behavior classifiers. Manual Bird scoring tracked overall disease trajectory, but most of its dynamic range derived from two of six items. In contrast, ML features separated genotypes as early as three weeks and identified disease-relevant behaviors not captured by the Bird protocol, including increased tail-tip amplitude, repetitive wall-directed jumping, and prolonged behavioral arrest. Sparse PLS-DA separated genotypes at every age tested. A composite score modeled from the ML features reproduced the temporal pattern of the total Bird score with substantially less variability. Subsampling analyses showed that the ML feature set reached 5% cross-validated genotype misclassification error with only 12 to 16 animals, whereas the Bird score did not reach the 5% threshold even with 44 animals before week 6, a reduction in animal use consistent with the 3Rs. Applied to a Mecp2 minigene rescue study, the composite score reproduced genotype separation in an independent cohort and detected both a partial shift of treated hemizygous survivors toward wild-type values and adverse effects of the construct in wild-type mice. These results establish an objective, high-resolution severity index for RTT and a generalizable framework for preclinical phenotyping in a rare disease.

neuroscience↗

bioRxiv2026

MyoAssist 1.0: An Open-Source Framework for Neuromechanical Simulation of Physical Human-Device Interaction

Physical human-device interaction is central to many emerging technologies in neurorehabilitation and assistive robotics, but simulation-based research in this area remains fragmented across musculoskeletal models, assistive-device representations, task definitions, and controller-development workflows. This fragmentation limits the accessibility, reproducibility, and extensibility of studies on prostheses, exoskeletons, wearable rehabilitation devices, and related human-device systems. Here we introduce MyoAssist 1.0, an open-source framework for neuromechanical simulation of physical human-device interaction built within the MyoSuite ecosystem. MyoAssist organizes each simulation environment as a composed human-device-task system that combines compatible musculoskeletal, assistive-device, and task-scenario components through a shared composition pipeline. The current release includes 15 assistive-device models spanning gait assistance, upper-body support, manipulation, and seated mobility and supports compatible musculoskeletal models ranging from reduced lower-limb models to a 416-muscle full-body model. These human-device systems can be simulated within the broad task scenarios provided by MyoSuite, while MyoAssist adds locomotion-specific task scenarios with configurable terrain and target-velocity conditions for gait-assistive studies. MyoAssist also provides two complementary controller-development frameworks: a reinforcement-learning framework for training adaptive policies and a controller-optimization framework for tuning structured, interpretable human and device controllers. Both frameworks operate on the same simulation environments and provide standardized evaluation outputs for inspecting, comparing, reusing, and extending learned and structured control strategies. By integrating modular human models, assistive-device models, task scenarios, and training workflows under a shared open-source interface, MyoAssist aims to lower the barrier to reproducible simulation-based research and to support collaborative development of assistive technologies for neurorehabilitation and physical human-device interaction.

bioengineering↗

bioRxiv2026

Comparative co-expression reveals a regulatory core shared by angiosperm and conifer roots under cold

* Climate change is reducing the boreal snowpack that insulates soils, exposing tree roots to more frequent freezing. The molecular cold response of roots is poorly characterised, and its conservation across the angiosperm-gymnosperm divide is unknown. We asked how much of the root cold response is shared among divergent boreal trees. * We profiled fine-root transcriptomes of four boreal trees (Picea abies, Pinus sylvestris, Betula pendula and Populus tremula) and two Arabidopsis thaliana ecotypes during a ten-day 5 {degrees}C treatment by RNA sequencing, and used comparative co-expression to detect conserved regulation independently of response timing. * Expressed genes were largely shared, but the genes differentially expressed, and the timing of their response, diverged between species. Despite this, a core of orthologues retained conserved co-expression neighbourhoods across more than 300 million years, enriched for growth regulation, metabolism and stress signalling, including a gibberellin-related metabolic component of the growth response. * The root cold response is therefore species specific in identity and timing, yet underlain by a conserved co-expression core.

plant biology↗

bioRxiv2026

An extended N-terminus restrains the plant cell death-inducing ability of the catalytically competent ribonuclease domain in a pea powdery mildew RALPH effector

RALPH (RNase-like proteins associated with haustoria) effectors, which are preferentially expressed in haustoria and structurally resemble fungal T1/F1 RNases, constitute one of the largest effector families in powdery mildew (PM) fungi, yet their functions in dicot-adapted PM species remain poorly understood. Unlike cereal PM RALPHs, which lack the catalytic residues required for RNase activity, some dicot PM RALPHs retain these residues. Here, we performed a comprehensive structural and expression-based characterization of the pea PM Erysiphe pisi RALPH (EpRALPH) repertoire and functionally characterized EpRALPH11, a RALPH effector with partial conservation of the catalytic residues of T1/F1 fungal RNases. Comparative analyses identified multi-RNase-domain RALPHs as a conserved feature of the Erysiphe lineage, while expression profiling showed that many EpRALPHs are preferentially expressed in haustoria during early host colonization. AlphaFold 3-based structural analyses revealed a conserved T1/F1 RNase-like fold despite substantial sequence and surface charge divergence, indicating functional diversification among EpRALPHs. EpRALPH11 enhanced susceptibility to E. pisi in Medicago truncatula, localized to the nucleolus, and induced nucleolar fragmentation when heterologously expressed in Nicotiana benthamiana leaves. Its RNase domain exhibited T1 RNase activity in vitro, supporting the retention of a catalytically competent RNase domain and, together with its nucleolar localization, suggesting that EpRALPH11 targets plant rRNA and disrupts nucleolar functions. The RNase domain induced cell death in N. benthamiana, whereas the full-length protein and catalytic mutants did not. Cell death induction required exclusive nucleolar localization of the RNase domain, and an extended N-terminal intrinsically disordered region suppressed this activity in the full-length protein. Together, our findings reveal a previously unrecognized mechanis regulating RNase activity in a dicot PM RALPH effector and provide new insights into the functional diversification of RALPHs and their adaptation to obligate biotrophy.

plant biology↗

bioRxiv2026

Comparative genomics of abiotic stress response in Norway spruce and Scots pine

Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) are dominant boreal forest species with globally important contributions to carbon capture and storage and sustain an extensive forestry industry. Both species have adapted to cold and episodic drought, yet each occupies a distinct ecological niche. How conserved their stress responses are, which features are lineage-specific, and how far mechanisms known from herbaceous angiosperms apply, remain open questions of importance in the face of ongoing climate change. We profiled roots and needles of both species under drought and cold, combining differential expression with an orthology-aware comparative co-expression framework that places each gene on a conservation-divergence gradient. Differential expression was largely organ- and stress-specific, yet cross-species overlap at the orthogroup level was extensive and increased with stress intensity. Comparative co-expression recovered a further conserved regulatory backbone that per-timepoint differential expression did not resolve, enriched for abscisic-acid-centred signalling, oxidative and osmotic-stress responses and growth suppression, and containing canonical stress response transcription-factor families including NAC, WRKY and bZIP/ABF. The breadth of co-expression conservation for a gene was coupled to purifying selection on its coding sequence and to network connectivity. Additionally, segmental duplicates shared between the species were enriched among conserved drought circuits, whereas lineage-specific duplicates were enriched among genes lacking conserved co-expression. Regulatory conservation and genome architecture thus describe a single conservation-divergence axis, providing an evolution-anchored criterion that helps separate candidate core regulators (which are conserved, network-central and constrained) from reactive change that differential expression alone cannot resolve. Significance statementCold and drought are recurring threats to boreal forests, yet how conifers coordinate their responses, and how much of that response is evolutionarily conserved, has been difficult to establish. Comparing Norway spruce and Scots pine, two species separated by a deep evolutionary divergence, we show that the genes whose co-expression is most broadly conserved between the species are also those under the strongest purifying selection on their protein-coding sequences. As these two species diverged so long ago, this conserved regulatory core stands out as an evolutionary signal that simple comparisons of differentially expressed genes fail to capture. The approach provides an evolution-anchored way to distinguish genes central to the stress response from lineage-specific or reactive change.

plant biology↗

bioRxiv2026

A uniform tissue-clearing framework and mesoSPIM-ultra enable cm-scale single-neuron tracing

Tissue-clearing and light-sheet microscopy have transformed volumetric imaging of intact organs, yet limited mechanistic understanding of dehydration-based clearing continues to constrain rational protocol design and broader applicability. Here, we define the cardinal chemical and physical principles underlying dehydration-based tissue-clearing and establish a new pipeline for large-volume imaging. To maximize imaging performance, we developed the "mesoSPIM-ultra", an upgraded mesoSPIM platform with a temperature-controlled sample chamber, a large field-of-view (FoV) camera and specialized optics to achieve long-working-distance, high-resolution imaging of cleared samples. We applied this approach to investigate the projectome of Chx10+ neurons, a cell population with complex axonal morphologies along the entire mouse spinal-cord and brain, and implicated in ipsilateral orienting behaviors. By combining behavioral analysis with post-hoc single-neuron reconstructions, we revealed previously inaccessible branching architectures and long-range projections extending from the brainstem to the spinal cord. Together, our work establishes a mechanistic foundation for tissue-clearing and scalable imaging.

neuroscience↗

bioRxiv2026

A rapid, field-deployable paper-based biosensor for the detection of African swine fever virus in whole blood

African swine fever virus (ASFV) poses a major transboundary threat to global swine production, underscoring the need for rapid and field-deployable diagnostic tools. Although quantitative polymerase chain reaction (qPCR)-based assays are the standard molecular assay for ASFV detection, their reliance on centralized laboratory infrastructure, multi-step sample preparation, and trained personnel limit their utility for timely decision-making at the point of need (PON). Here, we report a portable molecular diagnostic platform that enables colorimetric quantitative loop-mediated isothermal amplification (qLAMP) directly from diluted whole blood on microfluidic paper-based analytical devices ({micro}PADs). The assay targets the conserved ASFV viral protein 72 (VP72) and topoisomerase II (TOPII) genes and incorporates objective image-based colorimetric signal analysis to reduce user-dependent interpretation. Using plasmid DNA spiked into whole blood diluted to 5% (v/v) in 5% D-mannitol, the {micro}PAD-LAMP assay achieved a limit of detection (LOD) of 25 copies per reaction (67 copies/{micro}L of whole blood sample) for VP72 targets with no observed cross-reactivity against nine common swine pathogens, demonstrating 100% analytical sensitivity and specificity during in-house testing and 90% and 92% analytical sensitivity and specificity respectively in an external laboratory evaluation. The complete assay was performed within 60 minutes using a portable heating and imaging platform. Together, these results demonstrate a simple, DNA extraction-free molecular diagnostic approach that enables rapid and reliable ASFV detection from whole blood applicable to field-relevant conditions.

bioengineering↗

bioRxiv2026

The CYP27A1 - VDR Feedback Rheostat Controls Mitochondrial Protein Homeostasis and Preserves Hippocampal - Striatal Network Integrity to rescue Cognitive impairment in HD condition

Emerging evidence links vitamin D (VD) deficiency to cognitive and motor dysfunction in Huntingtons disease (HD), yet the underlying mechanism remains unclear. Here, we combine in vitro genetic and 3-nitropropionic acid (3-NP)-induced in vivo models of HD to define the mechanistic basis of VD-mediated neuroprotection. We demonstrate that VD supplementation restores cognitive and motor deficits while improving mitochondrial function and cellular survival. Mechanistically, VD enhances mitochondrial fusion and rescues complex II expression, a key defect in HD pathology. We identify the mitochondrial enzyme CYP27A1 as a critical mediator of this effect, as its expression is reduced in HD models but restored upon VD treatment. Overexpression of CYP27A1 recapitulates the protective effects of VD, confirming its central role in maintaining mitochondrial integrity. Furthermore, VD promotes vitamin D receptor (VDR)-dependent transcriptional activation of CYP27A1 and additional nuclear- and mitochondrial-encoded genes, establishing a regulatory feedback loop that supports mitochondrial biogenesis and function. VD supplementation also improves proteostasis via attenuating endoplasmic reticulum stress. Together, our findings uncover a previously unrecognized VD-CYP27A1 axis that links mitochondrial dysfunction to HD pathology and highlight CYP27A1 as a potential therapeutic target.

neuroscience↗

bioRxiv2026

Cognitive function depends upon Satb2 gene dosage in cortical projection neurons

SATB2-associated syndrome (SAS) is a severe neurodevelopmental disorder caused by de novo heterozygous SATB2 mutations, yet how haploinsufficiency disrupts brain development remains poorly understood. While homozygous Satb2 loss causes profound embryonic cell-fate defects, we demonstrate using a heterozygous mouse model that SAS phenotypes emerge primarily during postnatal circuit maturation. Integrating chromatin profiling, transcriptomics, electrophysiology, and behavior, we show that SATB2 acts as a dose-sensitive chromatin regulator that binds conserved enhancer-promoter landscapes to orchestrate networks linked to human intelligence. Although excitatory neuron subtype specification is preserved, Satb2 heterozygotes adopt an intermediate epigenetic state that drives cell-type-specific dysregulation of genes enriched for intellectual disability risk variants. Consequently, mutant neurons exhibit simplified dendritic arborization, reduced intrinsic excitability, and weakened layer 2/3-to-layer 5 intracortical connectivity. These circuit deficits culminate in the disorganization of the somatosensory barrel cortex and severe impairments in whisker-dependent texture discrimination. Finally, by restricting Satb2 heterozygosity to the cortex, we decouple these cortical sensory deficits from subcortical vocalization phenotypes. Together, our work links SATB2 dosage to chromatin architecture and postnatal circuit maturation, revealing a critical, post-mitotic therapeutic window for intervention in SAS.

neuroscience↗

bioRxiv2026

SCD1 inhibition synergizes with TMZ to improve IDH1 MUT glioma survival of mice via lipotoxic stress

Mutations in the isocitrate dehydrogenase enzyme (IDH1) are prevalent in low-grade gliomas, such as oligodendrogliomas. Other than surgery, radiation, and chemotherapy, few options for treatment exist. The standard of care for patients currently consists of maximal safe resection, as well as the potential use of radiation and chemotherapy, typically followed by radiographic surveillance. Although significant advances have been achieved, these have not translated into meaningful improvements in overall survival, warranting the development of novel therapies. Herein, we demonstrate that the inhibition of SCD1 in vitro leads to decreased colony formation and is more specific to IDH1MUT glioma than the IDH1WT cells, We further identified MF-438 as an active inhibitor of this enzyme and showed that this inhibitor is linked with iron transport and ferroptosis. MF438 depleted oleic (C18:1) and palmitoleic acid (C16:1) levels, driving saturated phosphatidylcholine (PC) accumulation and ER stress (INSIG1, SEL1L upregulation). TS603 exhibited selective polyunsaturated phosphatidylcholine reduction with downregulation of GPX4, FTH1, and KEAP1, and upregulation of NCOA4, SLC11A2, ALDH7A1, and DPP4, consistent with ferroptosis priming via ferritinophagy-driven expansion of the labile iron pool, as confirmed by FerroOrange flow cytometry. Neutral lipid metabolism genes (LPIN1, LDLR, PNPLA3, ACSL1), intracellular lipid transport genes (TMEM41B, OSBP, STARD4), and lipid droplet organization genes (SQLE, CHKA, AUP1) were coordinately upregulated in TS603 after treatment with MF-438. MF438+TMZ activated the integrated stress response (ATF3, DDIT3, IRF1, CDKN1A, GADD45B) and synergistically suppressed TS603 neurosphere growth (p=0.0326). In vivo combination between MF-438 and TMZ showed improved survival versus the TMZ-alone group, in an IDH1-mutant oligodendroglioma model. Tissue analyses showed significant reduced Ki67 expression, a marker of cellular proliferation, in the combination treatment. Collectively, these findings suggest that targeting lipid metabolism may enhance the efficacy of standard-of-care therapy in IDH1-mutant oligodendroglioma.

Cancer Biology↗

bioRxiv2026

Atomistic Simulation of Blood Brain Barrier Permeability of Propolis Derived Natural Compounds

The ability of small molecules to cross the blood-brain barrier (BBB) remains a major bottleneck in neurotherapeutic development. While experimental assays and machine learning approaches provide approximate permeability estimates, they lack atomistic insight into the underlying transport mechanisms. Here, we employ all-atom molecular dynamics simulations of a compositionally realistic BBB lipid bilayer to characterize the passive permeation of two bioactive propolis-derived compounds, Caffeic Acid Phenethyl Ester (CAPE) and Artepillin-C (ARC). Using steered molecular dynamics and umbrella sampling, we computed free energy profiles, diffusion coefficients, and permeability metrics across the membrane. CAPE encounters a modest barrier at the lipid headgroup region but minimal resistance within the hydrophobic core, resulting in a low free energy barrier ([~]2-3 kcal/mol) and favorable permeability (logP_eff {approx} 0.28). In contrast, ARC exhibits a substantial energetic barrier within the membrane core, leading to high resistivity and strongly unfavorable permeability (logP_eff {approx} -10.91). The heterogeneous lipid model reproduces experimentally consistent membrane properties and reveals how lipid composition modulates transport energetics. These findings provide mechanistic insight into BBB permeability and demonstrate the utility of atomistic simulations for guiding the design of neuroactive therapeutics.

biophysics↗

bioRxiv2026

Membrane proteomics of the Drosophila circadian neural network

Circadian behaviors are controlled by dedicated brain pacemaker neurons, whose activity oscillate during the day and the night. The Drosophila brain contains ca. 240 such neurons. Their molecular clock is synchronized, but the phase of their rhythmic neural activity differs dramatically between functional groups. This explains how specific circadian neurons can for example promote morning or evening locomotor activity. To understand in depth how the circadian network functions, we surveyed its membrane proteome in the morning and evening, using in situ protein labeling and mass spectrometry. In addition to detecting known regulators of circadian behavior, we identified novel membrane or membrane-associated proteins present in circadian neurons. Through genetic screens, we found that many of these proteins regulate circadian behavior. In particular, Piezo regulates morning activity specifically under short photoperiod, and its loss compromises the structural plasticity of the clock neurons controlling locomotion at dawn. Our work thus illustrates the power of proteome-guided genetic screens to understand the mechanisms underlying circadian behavior.

neuroscience↗