Biology subjects

Khan, N.

Publications and source records attributed to Khan, N..

At least 19 recordsLinked to original sources

bioRxiv2026

TFAM Dependent Mitochondrial Fitness Limits CD8⁺ T Cell Immunopathology and Sustains Protective Immunity during Viral Pneumonia

During respiratory virus infection, CD8 T cells kill infected cells and establish antigen-specific memory, but mechanisms regulating these functions remain incompletely understood. Here, we identify mitochondrial transcription factor A (TFAM)-dependent mitochondrial fitness as a regulator of CD8 T cell function during influenza infection. Human CD8 T cells exhibited an age-associated decline in TFAM expression and mitochondrial function. To model this physiologically relevant decline and determine its consequences for antiviral immunity, we generated CD8 T cell-specific TFAM-haploinsufficient mice. TFAM insufficiency disrupted mitochondrial integrity and bioenergetics and increased mitochondrial DNA and oxidative stress. During influenza infection, TFAM-insufficient CD8 T cells exhibited increased cytotoxic and inflammatory activity associated with lung immunopathology without improved viral control. This early phenotype was followed by loss of effector function, diminished antigen-specific responses, reduced protection following adoptive transfer, and impaired heterosubtypic recall immunity. Thus, TFAM-dependent mitochondrial fitness is a cell-intrinsic regulator that limits immunopathology while sustaining recall immunity.

immunology↗

bioRxiv2026

VDAC1 regulates stress-associated matrix localization of DJ-1 to support mitochondrial homeostasis and neuronal survival

DJ-1 is a redox-sensitive protein implicated in early-onset Parkinson's disease, and its mitochondrial localization protects against oxidative stress, but the mechanisms regulating its submitochondrial targeting and functional impact on mitochondrial integrity remain poorly understood. We identify voltage-dependent anion channel 1 (VDAC1) as a regulator of the submitochondrial distribution of DJ-1 during stress. Endogenous DJ-1 interacted with VDAC1, and loss of VDAC1 reduced stress-induced DJ-1 accumulation within the mitochondrial matrix. VDAC1-deficient neurons exhibited mitochondrial fragmentation, impaired oxidative phosphorylation, reduced ATP levels, altered reactive oxygen species (ROS) responses, and increased sensitivity to MPP+;. Matrix-targeted, but not outer-membrane-targeted, DJ-1 rescued basal, ATP-linked, and maximal respiration, improved mitochondrial morphology, and enhanced neuronal survival. ATP synthase inhibition also rapidly increased mitochondrial DJ-1, suggesting bioenergetic stress promotes its mitochondrial accumulation. Our findings identify compartment-specific localization as a key determinant of DJ-1 function and establish VDAC1-dependent matrix targeting as a critical mechanism supporting mitochondrial integrity during stress.

neuroscience↗

bioRxiv2026

Myosin 5A mediates membrane-associated periodic skeleton reassembly during axon regeneration in response to ROCK-2 inhibition

The membrane-associated periodic skeleton (MPS) is a submembrane lattice composed of actin rings and spectrin tetramers that repeats every 190 nm along axons and maintains mechanical stability. Loss of the MPS precedes axon fragmentation during degeneration, but during axon regrowth after injury the extent and timing of MPS reformation are not clear. We used stimulated emission depletion (STED) microscopy to track {beta}II-spectrin periodicity in regenerating axons from mouse cortical neurons, human iPSC-derived cortical neurons, and human iPSC-derived motor neurons following mechanical axotomy. Regrowing axons initially lack periodic {beta}II-spectrin organization, particularly near the growth cone. Over 8 to 15 days, periodicity is partially restored in intermediate axonal regions, while distal segments remain disorganized. We found that reducing Rho kinase ROCK-2 activity either pharmacologically or by CRISPRi promotes axon regrowth and accelerates MPS recovery rate five-fold, reaching near-normal levels by 3 days post-injury. To identify the key effectors, we performed co-immunoprecipitation mass spectrometry of the {beta}II-spectrin complex under injury and ROCK-2-inhibited conditions. Myosin 5A (MYO5A) association with spectrin rose sharply upon injury and further increased when ROCK-2 was absent. Functional experiments positioned MYO5A downstream of ROCK-2. Knocking down MYO5A abolished the enhanced regrowth of ROCK-2-deficient neurons, while overexpressing MYO5A increased regrowth in wild-type neurons. Depleting MYO5A also partially disrupted {beta}II-spectrin periodicity in healthy, uninjured axons, indicating a requirement for MYO5A in MPS maintenance under physiological conditions. STED imaging demonstrated that ROCK-2 is arranged periodically along the axon at 190 nm intervals, suggesting it regulates the local lattice. These findings define a ROCK-2/MYO5A pathway linking a targetable kinase to nanoscale cytoskeletal repair and axon regeneration.

neuroscience↗

bioRxiv2026

CXCR6⁺ natural killer cell immunotherapy preserves CD4⁺ T helper cells in humanized mice

Human immunodeficiency virus (HIV) persists despite antiretroviral therapy because long-lived viral reservoirs are not eliminated, and ongoing or rebound infection contributes to progressive loss of CD4 T helper cells. Natural killer (NK) cells can acquire adaptive, antigen-experienced functions, including recall responses to HIV envelope protein, suggesting that defined NK-cell subsets may be therapeutically useful against HIV. Because HIV-responsive adaptive NK-cell activity is enriched among CXC chemokine receptor 6-positive (CXCR6) NK cells, we tested whether CXCR6 NK cells provide enhanced antiviral activity and CD4 T-cell protection compared with CXCR6- NK cells. In co-cultures with HIV-infected primary CD4 T cells, PBMC-derived CXCR6 and CXCR6- NK cells both reduced viral replication, but CXCR6 NK cells mediated significantly greater suppression. In HIV-infected humanized mice, weekly infusion of expanded PBMC-derived NK cells lowered plasma viral burden, with CXCR6 NK cells providing stronger preservation of circulating CD4 T cells and significant preservation of splenic CD4 T cells. HIV-Env vaccination further enriched NK cells with enhanced therapeutic activity. CXCR6 NK cells derived from HIV-Env-vaccinated humanized mice produced the strongest suppression of HIV replication and restored CD4 T-cell frequencies in blood and spleen to levels comparable to uninfected controls. Together, these findings identify CXCR6 NK cells as an HIV-responsive adaptive NK-cell subset that combines antiviral activity with preservation of CD4 T-cell immunity in vivo. These data support further development of CXCR6 NK-cell therapy as a vaccine-informed cellular immunotherapy strategy for HIV.

immunology↗

bioRxiv2026

Haplotype-resolved Genome Assemblies of Hybrid Wheatgrass and Bluebunch Wheatgrass Reveal the Stepwise Polyploid Origin and Biased Subgenome Dominance

Concerns over climate change have intensified the demand for stress resistant crops like hybrid wheatgrass (HWG; Elymus hoffmannii, StStStStHH), a perennial forage species known for its exceptional salt and drought tolerance. However, hexaploidy and high heterozygosity have complicated efforts to resolve its genomic structure and evolutionary history. Here, we present high-quality, haplotype-resolved, chromosome-level genome assemblies for HWG (CDC Saltking) and its putative progenitor, bluebunch wheatgrass (Pseudoroegneria spicata, StSt). By integrating PacBio HiFi and ultra-long Oxford Nanopore sequencing with Hi-C scaffolding, we assembled the 10.7 Gb HWG genome into 21 pseudochromosomes per haplotype. Our phylogenomic analysis redefines the origin of the H subgenome, positioning it as an intermediate between Old-World Hordeum marinum (sea barley) and Hordeum brevisubulatum. Notably, we identified significant chromosomal rearrangements, including a unique duplication on St chromosome 4. Transcriptome analysis across multiple tissues revealed a pronounced expression dominance of the H subgenome. This dominance was not associated with reduced LTR density, suggesting that selective pressures for rapid adaptation of the latest subgenome entrant may drive its dominance. Finally, using the f-branch statistic, population genomic analysis of 189 accessions representing eight Elymus and Pseudoroegneria species revealed extensive reticulate evolutionary relationships and identified P. spicata as a major, asymmetric genetic donor within the wheatgrass complex. These resources provide a foundational framework for future genomic research and genetic improvement in grasses and for the introgression of stress-tolerance traits into cereal crops such as wheat. Key MessagesO_LIDevelopment of world-first high-quality chromosomal-level haplotype-resolved genome assemblies of hexaploid HWG and diploid progenitor, Pseudoroegneria spicata, enabled the identification of the subgenome origins. C_LIO_LIThis study resolved the evolutionary placement of the St genome and clarified the history of polyploidization and hybridization in HWG. C_LIO_LIHomeolog expression bias in the H subgenome likely reflects selective pressure favoring greater gene retention and upregulation of functionally important genes, thereby enhancing hybrid fitness. C_LIO_LIPopulation structure analysis distinctly differentiates P. spicata, E. repens, E. hoffmannii from other European Pseudoroegneria species. C_LIO_LIThe findings reveal the complex patterns of interspecific gene flow and population dynamics within the Elymus and Pseudoroegneria species. C_LI

genomics↗

bioRxiv2026

Impact of Aging, Sex, and Species on the mRNA Expression of Matrix Metalloproteinases Following Ischemic Stroke

Matrix metalloproteinase (MMP) expression and function are highly context dependent, varying across physiological and pathological conditions. We previously documented the expression profiles of select MMPs in the ischemic brains of young male rodents. However, aging is a major risk factor for stroke in humans and is associated with vasculature alterations, increased oxidative stress, and elevated inflammation. In addition, sex differences have been reported in stroke incidence and severity. Despite this, the effects of age, sex, and species on brain MMP gene expression after cerebral ischemia/reperfusion (I/R) has not been systematically examined. Therefore, we investigated how age, sex, and species influence the mRNA expression of all known MMPs (22 total) in the brain following cerebral I/R. Moderate-to-severe neurological deficits were induced by transient middle cerebral artery occlusion (MCAO) followed by reperfusion in young and aged male and female C57BL/6 mice and in young male Sprague-Dawley rats. Brain tissue from the ipsilateral (ischemic) hemisphere was collected on post-MCAO day 1, and MMP mRNA levels were quantified by real-time PCR and expressed as fold change relative to the sham control group. Across species, MMP-3, MMP-8, MMP-12, MMP-13, MMP-19, MMP-20, and MMP-27 were upregulated in both rats and mice. Species-specific increases were also observed: MMP-1, MMP-7, MMP-9, MMP-14, MMP-21, and MMP-25 were upregulated only in rats, whereas MMP-10 was upregulated only in mice. The most strongly upregulated MMPs were MMP-12 in rats and MMP-3, MMP-10, and MMP-12 in mice. By contrast, MMP-15 and MMP-17 were downregulated in both species, whereas MMP-23 and MMP-24 were downregulated only in rats and mice, respectively. Within mice, MMP-3, MMP-10, MMP-12, MMP-19, MMP-20, and MMP-21 increased in both sexes and age groups, except for MMP-19 in aged males and MMP-21 in young males. MMP-14 increased only in females (young and aged), whereas MMP-27 increased only in males (young and aged). Notably, MMP-3, MMP-10, and MMP-12 were the three most highly upregulated MMPs in both male and female mice regardless of age. Overall MMP mRNA expression levels were higher in aged male mice and lower in aged female mice relative to sex-matched young mice. Among all MMPs examined, MMP-12 showed the most marked upregulation across species and, within mice, across age groups and sexes. Collectively, these findings demonstrate that brain MMP gene expression after cerebral I/R is modulated by age, sex, and species, underscoring the importance of incorporating these biological variables when targeting MMPs individually or in combination in preclinical rodent stroke models.

neuroscience↗

bioRxiv2025

Integrative metagenomics and structural bioinformatics identify explainable gut microbial variants associated with Crohns disease

Metagenomics has revealed disease-associated shifts in microbial taxa and functions in inflammatory bowel disease (IBD) patients. However, the role of genomic variation in gut commensals remains poorly understood. Here, we integrated metagenomic profiling, variant calling, and structural bioinformatics to identify disease-associated variants in the gut microbes. Crohns disease (CD) and ulcerative colitis (UC) showed significant negative associations with Bacteroides uniformis, Bacteroides vulgatus, and Eubacterium rectale. These bacteria exhibited 190,712 single-nucleotide polymorphisms, including 479 CD-specific and 235 UC-specific variants. Variant prioritization identified a CD-specific Val170Leu substitution in the conserved starch-binding domain of the Starch Utilization System D (SusD) protein in B. uniformis. Structural modeling and cyclodextrin docking indicated reduced binding affinity in the mutant, while 200-ns molecular dynamics simulations showed stable ligand retention only in the wild type. These findings suggest that impaired starch metabolism driven by SusD variation may contribute to B. uniformis depletion in CD and demonstrate the value of integrating metagenomics with structural analyses to identify functionally relevant microbial variants.

bioinformatics↗

bioRxiv2025

Neonatal BCG Vaccination Engages the Vasculature to Elicit γδ T Cell-Mediated Protection against Tuberculosis

The Bacillus Calmette-Guerin (BCG) vaccine remains the only approved vaccine against tuber-culosis (TB). Although its efficacy against pulmonary TB in adults is limited, BCG provides re-markable protection against miliary TB when administered during infancy. Despite more than 100 million infants worldwide receiving BCG annually, the mechanisms underlying its neonatal protective effects remain poorly defined. Here, we demonstrate that subcutaneous neonatal BCG vaccination (BCG-sc) induces a marked expansion of {gamma}{delta} T cells producing IL-17 and IL-22, which mediated protection against subsequent Mycobacterium tuberculosis (Mtb) experimental infection. A similar expansion of {gamma}{delta} T cells was observed in a longitudinal cohort of infants, from birth to three months of infants followed after intradermal BCG vaccination. Mechanistical-ly, BCG-mediated protection in neonates was linked to its early vascular dissemination through the distinct structure of neonatal skin, resembling the protective effects of intravenous BCG in adults. Moreover, neonatal BCG-sc vaccination generated a distinct BCG-induced microbiome signature, characterized by enrichment of Prevotellaceae, Tannerellaceae, and Bifidobacteriaceae, which was associated with protection. Together, these findings identify {gamma}{delta} T cells as key mediators of early-life BCG-induced immunity and highlight the role of the gut-lung axis in long-term protection against TB from infancy into adulthood.

immunology↗

bioRxiv2025

B7-H3 upregulation in ischemic stroke: friend or foe?

B7-H3 (CD276) is an immune checkpoint co-signaling molecule expressed on immune and non-immune cells. It is best known for suppressing T-cell responses but can also promote inflammation depending on the microenvironment. In neuroinflammatory models such as experimental autoimmune encephalomyelitis, B7H3 expression increases concomitantly with the inflammatory response, and its inhibition is associated with reduced disease progression. Although its role in ischemic stroke remains unclear, we hypothesized that cerebral ischemia/reperfusion (I/R) would upregulate B7-H3 expression in the ischemic brain and that increased B7-H3 expression would positively correlate with pro-inflammatory cytokine expression. Young and aged male and female rodents, including normotensive and spontaneously hypertensive rats to model comorbid hypertension, underwent transient middle cerebral artery occlusion (MCAO) followed by reperfusion. Brain tissue was collected on post-ischemic days 1, 3, 5, or 7. B7-H3 mRNA was analyzed by real-time PCR, whereas protein expression was assessed by Western blotting and immunohistochemistry at selected time points. B7-H3 expression was significantly upregulated in the ischemic brain across sexes, age groups, and species. The extent of B7-H3 degradation in the ischemic brain was influenced by species, sex, age, and time after cerebral I/R. Upregulation of B7-H3 was observed at both the mRNA and protein levels, and increased expression was localized primarily to the somatosensory cortex and caudate putamen in the ipsilateral hemisphere, the main regions affected in this MCAO model. Elevated B7-H3 expression in the ischemic brain positively correlated with the pro-inflammatory mediator TNF. The temporal profile of B7-H3 expression observed in rats paralleled the early inflammatory phase associated with secondary tissue damage following ischemic stroke. These findings identify B7-H3 as an ischemia-induced immune checkpoint molecule in the brain that may modulate post-stroke immune responses and support further investigation into its beneficial versus detrimental roles in neuroinflammation, as well as its potential as a therapeutic target following cerebral I/R.

neuroscience↗

bioRxiv2025

NF-κB driven inflammation mediates loss of upper airway epithelial tolerance to Streptococcus pneumoniae during influenza co-infection

Streptococcus pneumoniae asymptomatically colonizes the human nasopharynx, where epithelial tolerance maintains mucosal homeostasis. However, influenza A virus (IAV) co-infection transforms this tolerogenic state into an inflammatory environment that promotes bacterial outgrowth and invasion. Here, we identify a TGF-{beta}1 dependent epithelial program that sustains mucosal tolerance during Spn colonization and demonstrate that IAV co-infection disrupts this pathway through IL-17RA-NF-{kappa}B driven inflammation in the nasopharynx. In a murine colonization model, TGF-{beta}1 blockade enhanced pro-inflammatory cytokine production and neutrophil recruitment, resulting in inflammation-driven Spn clearance. IAV co-infection suppressed epithelial TGF-{beta}1 signaling, increased TRAF6/NF-{kappa}B activation, and impaired tight junction integrity, leading to Spn dissemination. Mechanistically, IL-17RA signaling contributed to the hyperactivation of the TRAF6/NF-{kappa}B axis. Pharmacologic inhibition of TRAF6 or NF-{kappa}B restored epithelial barrier function and reduced Spn translocation in a human air-liquid interface nasopharyngeal epithelial model. These findings reveal a conserved epithelial signaling axis through which influenza disrupts mucosal tolerance and promotes Spn invasion, highlighting the canonical TRAF6-NF-{kappa}B pathway as a potential therapeutic target to preserve epithelial integrity and mitigate Spn infection during viral-bacterial co-infection of the upper respiratory tract.

immunology↗

bioRxiv2025

Oral administration of engineered recombinant outer membrane vesicles-based nano-vaccine formulation triggers robust mucosal and systemic humoral immunity against poultry pathogens

Although vaccination is an integral part of poultry health management, affordable, scalable, and easily administrable new-generation vaccine discovery platforms are required to combat emerging infectious diseases. Oral vaccines offer an alternative to injectable options owing to their ease of administration; however, existing platforms fail to confer robust protective systemic and mucosal immunity. Here, we used engineered outer membrane vesicles (rOMVs) displaying the desired vaccine antigens, and derived from hypervesiculating probiotic E coli Nissle 1917 (EcN) [36], which elicits both mucosal and systemic immunity when administered orally. Using such approach, we attempted to formulate rOMV based single Oral vaccine against Newcastle Disease Virus (NDV) and Infectious Bursal Disease Virus (IBDV), which pose significant risks to the poultry sector. We engineered rOMVs to display the antigenic regions of immunodominant Hemagglutinin-Neuraminidase (HN) and Viral Protein 2 (VP2) of NDV and IBDV, respectively, on their surface, with sizes less than 150 nm and considerable polydispersity. The Oral administration of these rOMVs expressing the HN and VP2 induced a robust immune response which shows enhanced production of high-titer antigen-specific sIgA and IgG, which were able to neutralize the virus effectively in an in-vitro infection model system. While the poultry pathogens such as NDV and IBDV served as a model, the rOMV-based platforms hold considerable potential for the development of a multivalent oral biotherapeutic agent, including vaccines against a wide range of emerging human and animal pathogens by engineering rOMVs to display immunodominant antigenic portions, demonstrating its capability as a next-generation oral vaccine discovery platform.

immunology↗

bioRxiv2025

Paraquat Licences α-Synuclein to Trigger NLRP3-Dependent Pyroptosis in Microglia

Parkinsons disease (PD) is characterized by dopaminergic neurodegeneration and the pathological accumulation of -synuclein (Syn) aggregates. While its etiology is multifactorial, environmental toxicants such as paraquat, a widely used herbicide banned in over 70 countries but still permitted in some regions, including Australia, are strongly implicated. We previously showed that Syn activates the NLRP3 inflammasome in microglia, inducing interleukin-1{beta} (IL-1{beta}) release without triggering pyroptosis. Here, we examine how paraquat modulates microglial NLRP3 activation by Syn. Using primary microglia from wild-type (WT) and Nlrp3 knockout (Nlrp3-/-) mice, alongside human monocyte-derived microglia, we demonstrate that paraquat induces dose-dependent NLRP3 activation in LPS-primed WT microglia via NADPH oxidase-mediated reactive oxygen species (ROS) generation. This results in ASC speck formation and IL-1{beta} release, which is absent in Nlrp3-/- microglia and blocked by the selective NLRP3 inhibitor MCC950. While Syn alone fails to induce pyroptosis, co-treatment with paraquat resulted in caspase-1-dependent lactate dehydrogenase (LDH) release and gasdermin-D cleavage, hallmarks of pyroptotic cell death. This response was also suppressed by NLRP3 inhibition. Our findings reveal that paraquat acts as a critical second hit to license Syn-induced inflammasome-dependent pyroptosis in microglia, highlighting a mechanistic link between environmental toxin exposure and innate immune activation in PD pathogenesis. Targeting this axis with brain-penetrant NLRP3 inhibitors may offer an alternative therapeutic avenue for synucleinopathies associated with environmental toxins.

neuroscience↗

bioRxiv2025

mGluR4-Npdc1 complex mediates α-synuclein fibril-induced neurodegeneration

Fibrils of misfolded -synuclein (-syn) accumulate in Parkinsons disease and other synucleinopathies, spreading between cells to template further misfolding and drive neurodegeneration. -syn fibril entry into healthy neurons is recognized as a key step in the disease process but remains ill-defined mechanistically. Here, we comprehensively assessed the membrane proteome for binding of -syn fibrils. Expression cloning identified mGluR4 and Npdc1 as plasma membrane proteins expressed by substantia nigra neurons capable of supporting high affinity -syn fibril binding. Moreover, mGluR4 and Npdc1 cellular signaling functions were titrated by the presence of extracellular fibrillary -syn. While striatal -syn fibril injection led to nigral dopamine neuron loss in wild type mice, deletion of either Grm4 or Npdc1 provided protection of dopamine neurons. We observed mGluR4 and Npdc1 to form a complex that regulates mGluR4 signaling. Cultured neurons lacking both Grm4 and Npdc1 fail to bind -syn fibrils, to accumulate phosphorylated -syn and to lose synapses. Transheterozygous Grm4, Npdc1 mice showed protection from nigral neuron loss after striatal -syn injection, demonstrating genetic interaction between the two binding proteins. On a transgenic -syn A53T background, double Grm4, Npdc1 heterozygosity robustly increased mouse survival, motor function and spinal motoneuron number. Thus, a cell surface mGluR4-Npdc1 complex participates in -syn neurodegeneration.

neuroscience↗

bioRxiv2025

ALOX12B overexpression in the skin drives inflammasome/Th17 signaling axis to promote inflammation in the mouse model and human patients

Inflammation plays a pivotal role in the etiopathogenesis of chronic inflammatory skin diseases. However, the underlying mechanism remains unclear. Here, we employed Gene expression meta-analysis and clinical validation strategy to dissect the global architecture of immune dysregulation responsible for inflammatory conditions in the skin. Using such approaches, we identified a gene signature comprising of ALOX12B, which is significantly upregulated in psoriatic and atopic dermatitis patient skin samples, and correlates with increased levels of pathological IL-1{beta} and Th17 responses. Surprisingly, ALOX12B is predominantly expressed in the skin. Furthermore, skin-specific overexpression of human ALOX12B in transgenic mice resulted in psoriasis-like inflammatory symptoms, including epidermal hyperplasia, immune cell infiltration, and elevated IL-1{beta}/Th17 responses. ALOX12B is a non-heme iron-containing enzyme that catalyses the production of 12R-HETE from polyunsaturated fatty acids such as arachidonic acid. Mechanistically, we found that ALOX12B/12R-HETE accumulation in the skin acts as an intrinsic danger signal that triggers enhanced IL-1{beta} processing and secretion via ROS generation and NLRP3 inflammasome activation. Increased IL-1{beta} levels in turn drive IL-17 producing T-cell polarization. We further designed a novel first-in-class, potent ALOX12B inhibitor, 6a, which exhibited favorable topical pharmacokinetic and safety profiles. The topical application of 6a reduced inflammation-associated pathologies in Tg-hALOX12B mice by suppressing 12R-HETE-induced IL-1{beta} production and ROS generation. These findings revealed a novel mechanism mediated by ALOX12B/12R-HETE overexpression that controls skin inflammation, thereby providing a promising therapeutic target for treating inflammatory skin diseases. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/658245v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@13cdf3forg.highwire.dtl.DTLVardef@164cac3org.highwire.dtl.DTLVardef@3c0364org.highwire.dtl.DTLVardef@2ca91_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO The proposed mechanism through which ALOX12B modulates the inflammatory pathway in psoriasiform-like inflammatory conditions in the skin. The study provides insight into the role of ALOX12B in skin inflammation. Increased levels of ALOX12B expression in the skin result in 12R-HETE accumulation, which subsequently triggers the IL-1/Th17 inflammatory cascade through ROS generation and inflammasome activation. IL-1 produced by the activated inflammasome leads to the polarization of naive T-cells to activated IL-17 producing CD4+ T-cells, which are involved in the skin-inflammation related pathologies such as keratinocyte proliferation, and cellular infiltration. Hence, we propose ALOX12B as a novel potential therapeutic target for psoriasis-like inflammatory skin disorders. Additionally, we designed a novel first-in-class ALOX12B inhibitor, 6a; which shows a substantial alleviation in ALOX12B enzymatic activity, thereby reducing cellular ROS, which in turn results in reduced levels of IL-1, as a result inhibiting IL-1/Th17 inflammatory pathway and subsequent reduction in pathological inflammatory skin conditions. A portion of the image was created using Biorender.com C_FIG HighlightsO_LIALOX12B is a key gene upregulated in the skin during psoriasis and atopic dermatitis. C_LIO_LITransgenic mice overexpressing ALOX12B in the skin developed Psoriasis-like inflammatory symptoms. C_LIO_LIMechanistically, ALOX12B, through 12R-HETE, enhanced IL-1{beta} production via ROS generation and NLRP3 inflammasome activation. Further elevated IL-1{beta} production promotes Th17 cell polarization. C_LIO_LINovel first-in-class ALOX12B inhibitor alleviates inflammatory symptoms in a transgenic mouse model. C_LIO_LIStudy reveals a crucial ALOX12B/12R-HETE-inflammasome-IL-17 axis involvement in inflammatory skin diseases. C_LI

immunology↗

bioRxiv2025

Genomic Analysis Reveals Genetic Diversity, Population Structure and Evolutionary Dynamics in Bluebunch wheatgrass (Pseudoroegneria species)

Bluebunch wheatgrass (BBWG: Pseudoroegneria species) is an outcrossing perennial grass of considerable ecological and agricultural importance due to its resilience in adverse environmental conditions. To gain a deeper understanding of the diversity, population structure, and genetic relationship within the Pseudoroegneria genus, we analyzed genomic variations of 145 genotypes representing seven species (P. spicata, P. tauri, P. geniculata, P. libanotica, P. strigosa, P. stipifolia, and P. cognata) from major global lineages, using genotyping-by-sequencing. Our results identify six distinct genetic clusters, with P. spicata (a North America species) clearly separated from the other six species underscoring its unique genetic identity. In contrast, the Eurasian species exhibit mixed ancestry, indicating intricate genetic relationships and widespread exchange of genetic material. Furthermore, no single species tree fully captures the relationships among them, implying interactions such as hybridization or gene flows between closely related species. To investigate the evolutional history of Eurasian BBWG species, we reconstructed the species tree topology based on the SNV (single nucleotide variants) matrix, which revealed potential gene flow events. Our findings suggest that the Eurasian BBWG species have undergone reticulate evolution, characterized by substantial gene flow.

genomics↗

bioRxiv2025

DEK::NUP214 acts as an XPO1-dependent transcriptional activator of essential leukemia genes

The t(6;9)(p22.3;q34.1) translocation/DEK::NUP214 fusion protein defines a distinct subgroup of younger AML patients classified as a separate disease entity by the World Health Organization. DEK is a nuclear factor with multifunctional roles, including gene regulation, while its fusion partner, NUP214, plays a pivotal role in nuclear export by interacting with transport receptors such as XPO1. However, the precise mechanism by which DEK::NUP214 drives leukemia remains unclear. A comprehensive multi-omics comparison of 57 AML primary samples (including whole genome sequencing, targeted sequencing, transcriptomics, and drug screening with > 500 compounds) revealed that t(6;9) cases display a selective response to XPO1 inhibitors (Selinexor & Eltanexor) and a distinct transcriptomic signature characterized by the overexpression of FOXC1 and HOX genes that are key leukemia mediators. CUT&RUN experiments demonstrated the direct binding of DEK::NUP214 to the promoters of FOXC1 and HOXA/B clusters. Strikingly, the expression of these genes and the binding of DEK::NUP214 to their regulatory regions were selectively reduced upon XPO1 inhibition in t(6;9) cells. Altogether, these results identified a novel function of DEK::NUP214 as an XPO1-dependent transcriptional activator of key leukemia drivers and provide a rationale to explore the use of XPO1 inhibitors in this patient population.

cancer biology↗

bioRxiv2025

Programing Immunogenicity of Dengue EDIII Vaccine Antigens Using Engineered Outer Membrane Vesicles (OMVs)

Dengue is a mosquito-borne viral infection and is more prevalent in the world with no therapeutics and suboptimal vaccine performance against all four serotypes of the dengue virus. Hence, there is an urgent requirement for a non-infectious and non-replicative vaccine candidate that can elicit a balanced and serotype-specific immune response. In this study, we have engineered bacterial outer membrane vesicles (rOMVs) that display EDIII antigens (EDIII rOMVs). The current formulation modulates the expression of costimulatory molecules on antigen-presenting cells (APCs) as well as enhances the uptake and presentation. Subsequently, the EDIII rOMVs elicited a strong antigen-specific polyfunctional response from CD4+ and CD8+ T cells. The robust antibody response was facilitated by a germinal center reaction characterized by high T follicular helper (Tfh) and B cell response levels in the mice that received EDIII rOMVs. Notably, the produced antibodies demonstrated the ability to neutralize all four dengue virus serotypes in an in vitro infection model, indicating its potential role in protective immunity. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/640071v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@689d81org.highwire.dtl.DTLVardef@3c878aorg.highwire.dtl.DTLVardef@1e6b1aaorg.highwire.dtl.DTLVardef@9a5180_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

Apparent digestibility and nutritional performance of bakery waste produced in Punjab Pakistan for Labeo rohita fingerlings

This study aimed to examine the impact of bakery waste supplementation on the nutrient digestibility and performance metrics of rohu (Labeo rohita) juveniles. Fish were fed with seven different diets containing bakery waste products (biscuits, cream cake, bread, and dry rusk) in combination with rice polish and wheat flour. Chromic oxide (1%) was added to the diet as an inert marker to measure nutrient digestibility. The results indicated a significant difference (p < 0.05) in the digestibility of crude protein, lipid, gross energy, and dry matter among the dietary groups. Fish fed with rice polish had the lowest apparent digestibility value of protein (16.13 {+/-} 1.86), whereas fish fed wheat flour had the highest (77.70 {+/-} 0.05). Moreover, it was shown that fish fed rusk waste had better growth. It has been concluded that bakery wastes could be used as a cheaper fish feed ingredient source for the manufacturing of cost-effective feed for L. rohita. This investigation was discussed within the context of providing cost effective ingredients for sustainable aquaculture production in Pakistan.

zoology↗