Biology subjects

Khan, A.

Publications and source records attributed to Khan, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Kif2C safeguards radial glial integrity to prevent cortical malformation

Radial glial cells (RGCs) generate cortical neurons and guide radial neuronal migration, yet how microtubule (MT) regulators coordinate progenitor maintenance, mitotic fidelity, and cortical architecture remains unclear. Here, we identify the MT depolymerase Kif2C/MCAK as an essential regulator of RGC integrity with relevance to human neurodevelopmental disorders. Kif2C is enriched in developing cortical RGCs and localizes to radial fibers, basal endfeet, and mitotic structures. Acute Kif2C depletion in embryonic mouse cortices disrupts RG fiber organization, impairs neuronal migration, reduces the RGC pool, and induces mitotic defects, chromosome segregation errors, DNA damage, and cell-cycle arrest. Kif2C-deficient cortices further exhibit focal pial basement membrane disruption and neuronal overmigration, resulting in a cobblestone-like cortical malformation. We identify two individuals with neurodevelopmental disorders carrying rare deleterious KIF2C variants and show that a patient-derived truncating variant fails to rescue Kif2C-deficient cortical phenotypes, implicating KIF2C dysfunction in human neurodevelopmental disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=181 SRC="FIGDIR/small/726143v1_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@1970844org.highwire.dtl.DTLVardef@9fe29eorg.highwire.dtl.DTLVardef@d72ddcorg.highwire.dtl.DTLVardef@103f729_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2026

Does Low Dose Radiation Induced Adaptive Response Influence Initial DNA-DSB formation? Evidence from γH2AX foci Analysis in Human Lymphocytes

PurposeLow-dose radiation-induced adaptive response (LDRIAR) is well documented, but its role in early DNA damage signalling remains unclear. This study aimed to investigate whether adaptive response influences initial DNA double-strand break (DSB) recognition, as reflected by {gamma}H2AX foci formation, and to evaluate its time-dependent expression in human lymphocytes. Materials and MethodsPeripheral blood lymphocytes from three healthy donors were exposed to a priming dose followed by a challenging dose at defined time intervals. DNA damage was assessed using {gamma}H2AX foci analysis, comparing acute and split-dose exposures in both PHA-stimulated (large) and non-stimulated (small) lymphocytes. ResultsA clear time-dependent adaptive response was observed. No significant reduction in {gamma}H2AX foci was detected at 1 h (p > 0.05). At 2 h, a significant decrease was observed ([~]7-8% in large and [~]13% in small lymphocytes; p < 0.01), which increased at 4 h ([~]12% and [~]22%, respectively; p < 0.001). The maximal response occurred at 15 h, with reductions of [~]40- 43% in large and [~]27% in small lymphocytes (p < 0.001). Small lymphocytes exhibited an earlier response, while large lymphocytes showed a greater magnitude at later time points. The temporal trend was consistent across donors, with minor variability at later intervals. ConclusionsThe findings demonstrate that LDRIAR is reflected at the level of DNA damage signalling and follows a defined temporal pattern with cell-type specificity. This suggests that adaptive response may influence early DSB-associated processes, contributing to a better understanding of radiation response mechanisms in radiobiology.

molecular biology↗

bioRxiv2026

Neutrophils rapidly release nucleoli-stored IFNα during infection

Type I interferons (IFN-I) are critical for antiviral defense but can drive severe pathology when dysregulated. Excess IFN-I is associated with prominent neutrophil accumulation; however, the contribution of neutrophils to IFN-I overproduction remains underexplored. In all cell types previously studied, IFN-I is synthesized de novo following sensing of microbial or host-derived inflammatory stimuli. Contrary to this paradigm, we find that neutrophils express IFN during development and store it in the nucleolus, a membrane-less intranuclear condensate classically functioning in ribosome biogenesis. TLR-mediated bacterial sensing induces a nucleolar stress response in neutrophils that triggers rapid release of nucleoli-stored IFN independent of de novo protein synthesis. These findings reveal that neutrophils have repurposed the nucleolus as a cytokine storage and secretory organelle, identify the first naturally occurring immunoregulatory function of nucleolar stress, and provide insight into the relationship between detrimental IFN-I levels and neutrophil accumulation.

immunology↗

bioRxiv2026

Fungal Hyphae as Distributed Vapor Sinks

Hygroscopic surfaces act as local vapor sinks that reshape the condensation field around them, but whether distributed biological structures do the same has not been investigated. We have established that hyphae of fungal colonies functionally behave as vapor sinks, creating a dry region of width{delta} around themselves when placed on a cooled substrate. In addition, the radial distribution of droplet sizes steepens during condensation, and the rate at which droplets evaporate locally after chamber drying increases. In order to quantify this behavior, we employed a combination of time-resolved imaging and survival analysis to determine how long individual droplets persist on the surface surrounding the colony. These data were used to derive three quantitative measures of the vapor-sink effect. Each measure was found to be directly proportional to the vapor-sink strength of the substrate, as calibrated against NaCl-agar hydrogels of known water activity (LOOCV RMSE = 0.031 for recovered aw). These findings were consistent across three fungal genera (35 experiments), and all species fell along calibration lines defined by the hydrogel standards. This result is consistent with a diffusion-limited vapor-depletion framework. The measured genus-level{delta} ratios agreed to within 6% of predictions from structural absorbing capacity, and field measurements on Gymnosporangium-infected apple leaves were consistent with the same signatures under natural conditions. These results establish a non-contact method for inferring the material properties of thin hygroscopic biological surfaces from their condensation patterns.

biophysics↗

bioRxiv2026

Natural aging drives a subclinical cardiovascular phenotype in a non-human primate

Aging is an inevitable risk factor for cardiovascular disease. Profound understanding of mechanisms underlying the early stages of cardiovascular aging is essential for the development of novel therapeutics. Therefore, animal models which closely reflect the human condition are highly sought after. Here, we investigated natural cardiovascular aging in a non-human primate, comparing healthy young-adult and aged common marmosets (Callithrix jacchus). Despite preservation of most cardiac functional parameters in aged animals, significant histological alterations were found including fibrosis and microvascular rarefaction. Molecular phenotyping by single-nuclei RNA-sequencing revealed activation of cardiac stress, pro-inflammatory and fibrotic gene programs in aged hearts. Importantly, proteomic analysis of cardiac extracellular vesicles revealed a cardioprotective cargo in young animals while functionally demonstrating pro-angiogenic properties on human cardiac microvascular endothelial cells. Finally, large vessel atherosclerosis was strikingly evident in aged animals and elucidated by bulk RNA-sequencing. Overall, the aging marmoset offers a great potential for translational cardiovascular research.

physiology↗

bioRxiv2026

Epithelial NCAPD3 expression protects against stress-induced intestinal injury in mice

Intestinal epithelial cells are central players in mucosal barrier integrity and host-microbe interactions. Genetic studies have revealed that epithelial dysfunction is a key contributor to the pathogenesis of inflammatory bowel disease. Non-SMC condensin II complex subunit D3 (NCAPD3) is essential for chromatin organization and stability. NCAPD3 also promotes antimicrobial defense and autophagy responses in vitro. NCAPD3 expression is decreased in intestinal epithelial cells from patients with ulcerative colitis; however, it is not known whether loss of NCAPD3 expression drives intestinal barrier dysfunction or is a result of disease-associated inflammation. To investigate this relationship in vivo, a tissue-specific approach was required, as global constitutive knockout of NCAPD3 is embryonic lethal. Therefore, a transgenic mouse line with doxycycline-inducible expression of a short hairpin RNA targeting NCAPD3 restricted to villin-expressing cells was generated (NCAPD3KD mice) to enable the study of NCAPD3 function in the intestinal epithelium. Treatment of NCAPD3KD mice with 9-tert-butyl doxycycline resulted in [~]75% reduction of NCAPD3 protein in EpCAM+ intestinal cells. Short-term epithelial NCAPD3 knockdown did not induce spontaneous colitis but was associated with increased serum amyloid A and a trend towards increased intestinal permeability. Upon dextran sodium sulfate or Salmonella enterica serovar Typhimurium {Delta}AroA challenge, NCAPD3KD mice exhibited exacerbated weight loss, higher disease activity, increased histopathological damage, abnormal colonic cytokines and chemokines, and significantly increased intestinal permeability. These results indicate that NCAPD3 expression in the intestinal epithelium is required for optimal barrier maintenance and antimicrobial defense under chemical or microbial stress. These findings support prior in vitro observations and solidify NCAPD3 as a regulator of intestinal epithelial barrier function and mucosal host defense. Author SummaryNCAPD3 is a multifunctional protein with established roles in chromatin organization, genome stability, mitochondrial function, and antimicrobial defense. Dysregulated NCAPD3 is implicated in human diseases, such as inflammatory bowel disease (IBD) and microcephaly; however, due to its essential role in cellular division, determination of whether NCAPD3 loss drives these pathologies in vivo has been lacking. Using a new transgenic mouse model that selectively reduces NCAPD3 expression in intestinal epithelial cells, our study establishes NCAPD3 as an epithelial regulator of the mammalian intestine that enhances epithelial barrier resilience and antimicrobial defense during stress. Although dispensable for short-term basal homeostasis, NCAPD3 function becomes critical during epithelial injury and enteric infection. Reduced NCAPD3 expression may therefore lower the threshold for inflammatory disease by weakening barrier integrity, amplifying inflammatory cascades, and impairing antimicrobial defenses. These findings position NCAPD3 as a potential modulator of IBD susceptibility and highlight chromatin organization as an important, previously underappreciated layer of intestinal epithelial regulation.

cell biology↗

bioRxiv2026

Neurometabolic correlates of accelerated aging and neurocognitive late effects in long-term survivors of pediatric hodgkin lymphoma and acute lymphoblastic leukemia

Adult survivors of pediatric cancers are at elevated risk for neurocognitive late effects, but how these effects relate to metabolic perturbations in the brain remains unclear. To address this knowledge gap, the present study explored associations between neurometabolite levels and neurocognitive function in adult survivors of Hodgkin lymphoma (HL) and acute lymphocytic leukemia (ALL). Data were collected from a single-center observational study conducted at St. Jude Childrens Research Hospital (SJCRH) between October 2022 and November 2024. Adult survivors of HL (N=11 [5 females]; [≥]5 years post-diagnosis; mean [SD] current age 34 [9.5] years) and ALL (N=24 [16 females]; [≥]5 years post-diagnosis; current age 40 [12.6] years) and community controls (N=35 [17 females]; current age 40 [11] years) completed standardized neurocognitive tests of memory, attention, executive function, and processing speed. Participants also underwent proton magnetic resonance spectroscopy (1H MRS) to quantify neurometabolite levels in the left dorsolateral prefrontal cortex (dlPFC), left hippocampus, and left cerebellum. Analyses used regression models to examine differences in the slope of the relationship between neurometabolite and neurocognitive function or between neurometabolite and age. When comparing HL survivors vs controls, significant interactions were identified for group x age on the ratio of myo-inositol to N-Acetyl aspartic acid (mI/NAA; p=0.007) and group x Gamma-Aminobutyric Acid (GABA) on processing speed (p=0.04) in the left dlPFC. When comparing ALL survivors vs controls, significant interactions were identified for group x myo-inositol on verbal fluency in the left hippocampus (p=0.01) and group x GABA on cognitive flexibility in the left cerebellum (p=0.01). These preliminary findings suggest that neuroinflammation may be a mechanistic underpinning of age-associated neurocognitive impairment in pediatric cancer survivors.

neuroscience↗

bioRxiv2026

Microtubules sustain the fidelity of cellularization in a coenocytic relative of animals

Cellularization is the coordinated division of a multinucleate cytoplasm into many cells.1-3 Multinucleation is a common life cycle strategy observed across eukaryotic lineages, including in microbial eukaryotes, fungi, plants and animals, and is associated with the ability to transition to a unicellular state through cellularization.4 In the best-studied model for this process, Drosophila melanogaster, cellularization requires the coordinated action of actin and microtubule (MT) networks to bring about the synchronous invagination of plasma membrane furrows, but the extent of conservation of these mechanisms across eukaryotes remains unknown.1,5,6 Here we investigate cellularization in the ichthyosporean Sphaeroforma arctica, a close relative of animals with a multinucleate life cycle stage.7-9 Using live cell imaging, ultrastructure expansion microscopy (U-ExM) and volume electron microscopy, we define the membrane, MT and actin dynamics that accompany cellularization in S. arctica. Using pharmacological inhibitors and centrifugation, we show that MTs, in addition to positioning nuclei, play a role in guiding nascent furrows to sustain equi-partitioning of nuclei and cytoplasm between daughter cells. Our findings indicate that cellularization is regulated through crosstalk between actin and MT networks, exhibiting mechanistic parallels with canonical cytokinesis, and establish S. arctica as a valuable model for investigating general principles of cellularization.

cell biology↗

bioRxiv2026

FRAPPe - a novel FRET-based biosensor to detect inorganic polyphosphates

Inorganic polyphosphate (polyP), a linear polymer of orthophosphate residues, is involved in a range of cellular processes, including phosphate storage, blood clotting, chromatin remodeling, RNA processing, and mitochondrial function. Despite its significance, tools for monitoring polyP with specificity and in real time are lacking, limiting insights into its dynamics. Here, we present FRAPPe (FRET-based Ratiometric Analysis of Polyphosphate), a FRET-based sensor for polyP. FRAPPe consists of an eCFP-eYFP FRET pair flanking CHAD, a polyP-binding domain. The sensor remains unresponsive to nucleic acids and other polyanions, while polyP binding induces a significant decrease in FRET, allowing quantitative estimation of polyP. We further show that FRAPPe can qualitatively estimate polyP levels from crude cell extracts, supporting its utility in high-throughput genetic and pharmacological screens to identify regulators of polyP metabolism and signaling.

biochemistry↗

bioRxiv2026

Functional recruitment of astrocyte-derived neurons into the mouse visual cortex

Inducing neurogenesis from glia could permit circuit remodeling and neuron replacement in the brain. Indirect evidence suggests that glia-to-neuron reprogramming is feasible, but the dynamics of conversion have not been directly observed, and it remains unclear whether glia-derived cortical neurons can functionally integrate into brain circuits. Here, we use two-photon imaging to visualize the reprogramming of astroglia into induced neurons in the mouse cortex in vivo. We track the emergence of spontaneous neuron-like calcium transients in astrocyte-derived induced neurons, demonstrating their functional activity in vivo. Importantly, these induced neurons exhibit orientation tuned, visually evoked calcium responses, demonstrating their functional integration into cortical circuitry - a prerequisite for their utility in circuit repair. Thus, astrocytes can be recruited to generate functional neurons in the postnatal cortex, enabling circuit remodeling in perinatal injury or neurodevelopmental disorders without relying on external cellular sources.

neuroscience↗

bioRxiv2026

Motor Intention Drives Corticospinal Facilitation during Interception Planning

Intercepting a moving target requires integrating visual motion information with motor preparation, yet how active motor preparation and gaze strategy jointly shape corticospinal excitability during interception planning remains unclear. We applied single-pulse transcranial magnetic stimulation over primary motor cortex to probe corticospinal excitability while participants either prepared to intercept a moving target or passively viewed its motion. Targets moved at one of two speeds, and participants judged target speed relative to a reference after each trial. Across blocks, participants were instructed to either smoothly pursue the target or fixate their eyes on the interception zone. Motor-evoked potentials were elicited at baseline, after task instruction, early during target motion, or shortly before target arrival. Task and gaze strategy interacted to influence both perceptual judgments and corticospinal excitability. Preparing to intercept produced a robust facilitation of corticospinal excitability immediately before movement onset, regardless of gaze strategy. In contrast, corticospinal excitability during passive viewing did not differ from baseline. Smooth pursuit improved perceptual accuracy and reduced interception timing error compared with fixation but did not independently influence corticospinal facilitation. These findings demonstrate that active motor preparation is the primary determinant of the transition to a state of facilitated excitability during interception planning, whereas eye movements modulate perceptual estimates and support behavioral performance. New & NoteworthyThis study dissociates the contributions of visual tracking, eye movements, and active motor preparation to corticospinal excitability during interception. Here, we show that corticospinal facilitation emerges primarily when an action is planned, whereas passive viewing remains at baseline despite identical visual input. Smooth pursuit enhanced perceptual accuracy and interception timing but had a limited effect on corticospinal excitability, highlighting active motor preparation as the key driver of corticospinal output.

neuroscience↗

bioRxiv2025

Insights into the AAV packaging mechanism: Cryo-EM Structure of the AAV2 Rep-Capsid Packaging Complex

The Adeno-associated virus (AAV) has become the most used viral vector for gene therapy applications to treat monogenic diseases, with over 250 clinical trials and six FDA-approved biologics. AAV has a single-stranded DNA genome encapsulated in a 60-subunit icosahedral protein shell. Assembly of empty capsids occurs in the nucleus, and in a subsequent step, the genome is packaged by the motor activity of the AAV Rep proteins. The translocation of ssDNA has been suggested to occur through one of the twelve channels at the fivefold symmetry axis. While there is substantial evidence that Rep proteins directly interact with the capsid, the specific molecular determinants, stoichiometry, and translocation mechanism remain unknown. To understand how Rep proteins assemble on the capsid, we examined Rep-capsid complexes using cryo-electron microscopy with single-particle reconstruction. Our results show that Rep proteins can assemble into the capsid fivefold pore as either pentameric or hexameric rings. The different ring complexes dock into the pore similarly, using the post-sensor1 {beta}-hairpin motif (pos1{beta}h2) as a capsid interaction module. This interaction induces the folding of a segment in the capsid HI loop, resulting in an expansion of the pos1{beta}h2 {beta}-sheet. Our structures show that any of the AAV Rep proteins can interact with the capsid, and this mode of interaction may be a conserved mechanism across all parvoviruses. Collectively, our results provide insights into the mechanism of AAV genome encapsidation and could inform strategies to improve recombinant AAV packaging efficiency.

biochemistry↗

bioRxiv2025

Pairing extinction training with vagus nerve stimulation (VNS) reduces drug-seeking by altering activity in afferents to the medial prefrontal cortex

Relapse triggered by drug-associated cues or stress remains a major challenge in treating substance use disorders (SUDs), as re-exposure reliably provokes craving and reinstatement of drug seeking. Extinction-based interventions can reduce cue reactivity, yet extinction learning is often weak or context-dependent, limiting its clinical impact. Vagus nerve stimulation (VNS) enhances learning-related plasticity via widespread engagement of neuromodulatory systems and cortical circuits. Recent preclinical work shows that pairing extinction with VNS facilitates extinction learning and reduces cue-induced reinstatement of cocaine seeking, suggesting translational potential as an adjunct to exposure-based therapies. However, the circuit-level mechanisms underlying these effects remain unclear. To address this gap, we examined how VNS paired with extinction alters activity in medial prefrontal cortex (mPFC) networks that regulate drug seeking, focusing specifically on afferent projections from the basolateral amygdala (BLA) and ventral hippocampus (vHPC). Male rats received retrograde AAV-eGFP infusions into either the prelimbic (PL) or infralimbic (IL) cortex to label upstream projections, followed by cocaine self-administration, extinction training with VNS or sham stimulation, and cue-induced reinstatement. cFos immunolabeling in the BLA and vHPC revealed pathwayspecific modulation: VNS decreased overall BLA activity and reduced activation of BLA to IL projections, but increased activation of BLA to PL projections. In the vHPC, VNS selectively decreased activation of vHPC to IL projections without affecting PL-projecting neurons. Because these pathways synapse onto parvalbumin interneurons (PVIs) in the mPFC, we quantified PVI activation and found that VNS decreased overall prefrontal cFos expression, but increased PVI activity in the PL, and decreased PVI activity in the IL. Together, these results demonstrate that VNS paired with extinction reshapes prefrontal-amygdala-hippocampal circuits in a pathway-specific manner, potentially modulating feed-forward inhibition to reduce relapse-like behavior. These findings support VNS as a promising strategy to strengthen extinction learning and improve treatment outcomes in SUD.

neuroscience↗

bioRxiv2025

Evolutionary fingerprinting of protein-coding genes in RNA viruses

RNA viruses evolve rapidly to adapt to changing host environments. Much of this adaptation occurs at the level of protein-coding genes. Thus, some of the most well-characterized examples of rapid adaptation have been found in virus proteins that are exposed on the surface of the viral particle, where they mediate host receptor binding and cell entry. To investigate whether surface-exposed proteins and other proteins encoded by viruses exhibit different patterns of evolution under selection, we analyzed 244 protein-coding genes from 28 species of RNA viruses representing 15 taxonomic families. First, we show that gene-wide rates of non-synonymous (dN) and synonymous (dS) substitutions do not differentiate between categories of proteins. To provide a more detailed comparison between genes, we inferred for each alignment the bivariate posterior distribution over a fixed grid of codon site-specific dN and dS values. This distribution is the genes evolutionary fingerprint. Next, we computed the Wasserstein distance for every pair of fingerprints, which is analogous to amount of work required to reshape one distribution to another. After compensating for differences in genetic variation among viruses and proteins, we found that surface-exposed proteins could not be distinguished from non-exposed proteins in the space induced by the Wasserstein distance matrix. However, surface-exposed proteins from enveloped viruses were significantly clustered apart from their counterparts in non-enveloped viruses. In contrast, there was no significant separation between these categories of viruses for proteins with polymerase activity. We show that this pattern is more consistent with relaxed purifying selection than adaptive evolution in proteins associated with viral envelopes.

evolutionary biology↗

bioRxiv2025

High-confidence structural predictions of extrachromosomal DNA with ecDNAInspector

Extrachromosomal DNA (ecDNA) are circularized genomic elements that reside outside canonical chromosomes. ecDNA amplify oncogene copy number, enhance chromatin accessibility, and act as mobile enhancers through cis- and trans-regulatory interactions, collectively boosting oncogene expression. ecDNA has been implicated in tumor progression, intratumoral heterogeneity, and poor patient prognosis. Despite various lines of evidence that ecDNA promotes aggressive disease, the mechanisms and selective pressures leading to ecDNA formation and propagation remain poorly understood as are their structures. While several computational tools have been developed to infer ecDNA presence or absence from short read sequencing data, accurate identification of large or complex ecDNA structures remains challenging. Here we introduce ecDNAInspector, a novel computational framework to systematically assess the confidence of ecDNA predictions from existing inference tools. Leveraging abundant short-read whole genome sequencing (WGS) data from population-scale cohorts, we demonstrate that ecDNAInspector accurately identifies high-confidence ecDNA calls, improving interpretability and facilitating the association with clinical features. As an illustrative example, applied to a cohort of 250 breast cancers, ecDNAInspector identifies associations between ecDNA structure and molecular subgroups of disease. These findings are supported by orthogonal omic data and experimental characterization of ecDNA captured in representative cell lines. ecDNAInspector provides a scalable, data-driven approach to characterize ecDNA structure, enabling integrative studies of the clinical and biological impact of this non-mendelian mode of oncogene amplification and inheritance.

cancer biology↗

bioRxiv2025

Colorectal cancer relies on an immunosuppressive cellular topography and genomic adaptations for establishing brain metastases

Colorectal cancer (CRC) brain metastases have a poor prognosis and limited treatment options, including resistance to radiation therapy. Little is known about the molecular and cellular mechanisms that enable CRC tumor cells to adapt to the brain and establish a supportive tumor microenvironment. To address this gap we used spatial transcriptomics to analyze 51 CRC brain metastases. A subset had matched primary colon tumors and longitudinally paired metastatic resections before and after radiation treatment. We identified the critical spatial cellular features of the tumor epithelium and the surrounding tumor microenvironment that support metastatic growth in the brain. CRC brain metastases developed a stromal microenvironment with abundant fibroblasts and tumor-associated macrophages. A fibroblast-macrophage cellular neighborhood promoted angiogenesis, extracellular matrix remodeling, and immune suppression. Tumor cells showed local adaptations. In endothelial-rich regions, they were proliferative whereas in macrophage-rich regions, they were more differentiated and immune evasive. Compared with paired primary tumors, CRC brain metastases showed increased chromosomal instability, with activation of RNA-processing, stress response, and junctional remodeling pathways. After radiation treatment, resistant clones had increased epithelial-mesenchymal transition, while the immunosuppressive stroma remained intact. We identified tumor-derived MIF, GDF15, PRSS3 and SEMA3C ligands and macrophage-derived SPP1 that have the potential to affect multiple cell types in the metastatic niche. These ligand-receptor interactions drive angiogenesis, stromal activation and immune suppression. In a macrophage-tumor-fibroblast co-culture model, knockout of SPP1 in macrophages led to reduced expression of lipid-metabolism related genes and disrupted tumor-promoting interactions. Together, these results indicate that CRC growth in the brain is sustained by a specific cellular organization with immunosuppressive multicellular interactions.

cancer biology↗

bioRxiv2025

Cannabidiol as a Prophylactic Agent Against Glioblastoma Growth: A Preclinical Investigation

PurposeGlioblastoma (GBM) is one of the most aggressive brain tumors, with limited treatment options and poor outcomes due to frequent relapse after surgery. This study aims to investigate whether pretreatment with inhaled cannabidiol (CBD) can inhibit GBM growth in a preclinical murine model. Specifically, we hypothesize that CBD pretreatment may reduce tumor progression and modulate the tumor microenvironment. MethodsC57BL/6 mice were pretreated with inhaled CBD for either 3 or 14 days, or a placebo, followed by intracranial implantation of glioblastoma cells. Tumor growth, immune checkpoint expression (IDO, PD-L1), and key biomarkers (MGMT, Ki67) were assessed to determine the impact of CBD pretreatment on tumor progression and the immune microenvironment. ResultsThe 14-day CBD pretreatment significantly reduced tumor growth compared to both the placebo and 3-day CBD groups. Additionally, this group showed lower expression of immune checkpoints (IDO, PD-L1) and reduced levels of MGMT and Ki67, suggesting enhanced tumor suppression. These results indicate that prolonged CBD pretreatment modulates the tumor microenvironment and may improve tumor control and reduce relapse risk. ConclusionThis study demonstrates that inhaled CBD pretreatment significantly inhibits GBM growth in a preclinical model. CBDs ability to reduce immune checkpoint expression and key biomarkers associated with tumor progression suggests that it could be an effective strategy for enhancing the efficacy of GBM therapies and potentially improving post-surgical outcomes. Further research is required to investigate its clinical potential and mechanisms of action.

cancer biology↗

bioRxiv2025

CREation of an expanded plant memory gene circuit toolkit

Genetic circuits rely on modular, well-characterized genetic parts to achieve predictable cellular behaviour. Despite their widespread adoption, biological parts are complex and when used in a new molecular context can result in unexpected outcomes. Site-specific recombinases have been widely used due to their unique ability to induce precise, irreversible changes to a DNA sequence, making them ideal tools for memory logic operations. However, unexpected context-specific failures of even the most widely used recombinase, Cre, has limited the expansion and complexity of synthetic gene circuits in diverse species. Here, through a systematic analysis of Cre failure in plant gene circuits, we uncovered multiple unexpected post-recombination interactions within the transcriptional unit between the promoter region, recombinase, and their cognate recognition sites. These significantly inhibit transcriptional activity, preventing circuit functionality. Specifically, post-recombination Cre recombinase exhibits an inhibitory property by binding to lox sites, with the remaining lox site repressing transcription. By thoroughly characterizing these dynamics, we restored Cre functionality and expanded the plant-based recombinase toolkit for Cre-related recombinases, developing combinations of recombinases and cognate sites with different activation levels for constructing logic gates with stable memory functions. We further developed multiple functional split-recombinase systems for simultaneous logic using a range of dimerization domains and constructed complex logic gates, including 3-input and 6-input AND gates. Together, this exploration of component context dependency in genetic circuits, even with commonly used parts like the Cre/lox system, has implications extending beyond plant systems, and significantly expands plant memory circuit capabilities.

synthetic biology↗