Biology subjects

Khan, R.

Publications and source records attributed to Khan, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Molecular MRI of Neuroinflammation in Alzheimer's Disease using a Folate-targeted Nanoprobe

Background: Neuroinflammation, driven by activated microglia, plays a central role in the pathogenesis of Alzheimer's disease (AD). Non-invasive imaging of neuroinflammation holds promise for advancing our understanding of disease mechanisms and evaluating anti-inflammatory therapeutic strategies. The folate receptor (FR), specifically its {beta} isoform, has been identified as a marker of pro-inflammatory myeloid cells in peripheral inflammatory diseases; however, its association with AD neuroinflammation remains unknown. In this work, we first determined FR expression in microglia in mouse models of AD and subsequently evaluated molecular MRI (mMRI) using a folate-targeted nanoprobe for in vivo imaging of the folate receptor expression. Methods and results: Microglial activation and FR expression in APP/PS1 and P301S transgenic mouse models of AD was measured using flow cytometry. A FR-targeted nanoprobe for mMRI was prepared by functionalizing high T1-relaxivity liposomal gadolinium nanoparticle with folic acid. Following intravenous injection, localization of the nanoprobe in the brains of aged transgenic and wild-type mice was measured using T1-weighted MRI. Post-mortem microscopy measured nanoprobe localization relative to microglia and amyloid pathology. In both mouse models, FR{beta} was significantly (p < 0.05) upregulated in pro-inflammatory microglia expressing TNF and IL-1{beta}. The folate-targeted nanoprobe demonstrated MR signal enhancement in the cortical and hippocampal regions of transgenic mice but not in wild type mice; non-targeted nanoprobe control did not demonstrate signal enhancement in brain of transgenic mice. Microscopy confirmed colocalization of FR-targeted nanoprobe with IBA1-positive microglia/macrophages and amyloid plaques. Conclusions: Pro-inflammatory microglia exhibit elevated levels of FR, and its measurement by non-invasive mMRI is a promising marker of neuroinflammation in AD.

neuroscience↗

bioRxiv2026

TGFB1-Engineered Induced Mesenchymal Stromal Cells Exhibit High Immunomodulatory Potency and Durably Reprogram Synovial Macrophages in Osteoarthritis

Clinical translation of mesenchymal stromal cell (MSC) therapies derived from primary tissue sources is limited by manufacturing inconsistencies driven by donor-to-donor variability, which reduces predictability of clinical response. Induced pluripotent stem cell (iPSC)-derived MSCs (iMSCs) offer a promising donor-independent, clonal alternative strategy that is also more amenable to engineering, but whether engineered iMSCs reproduce the potency attributes of primary MSCs remains unclear. Here, we benchmarked a doxycycline-inducible, hTERT-immortalized iMSC line engineered to overexpress TGFB1 (TGFB1-iMSCs), a key regulator of macrophage polarization, against multiple adipose tissue-derived MSC (MSC(AT)) donors across predefined immunomodulatory and angiogenic potency attributes. TGFB1-iMSCs were smaller and more circular with comparable or higher proliferative rates than primary MSC(AT) donors. Interestingly, they had a distinct angiogenic signature (EDIL3, EDN1, PDGFA), and nine differentially expressed microRNAs were predicted to target secretory trafficking and growth factor receptor signalling. Functionally, however, TGFB1-iMSCs secreted less VEGF and showed intermediate HUVEC tube formation, but matched or exceeded all primary MSC(AT) donors in a monocyte-macrophage transwell immunomodulatory assay. Notably, in a murine destabilization of the medial meniscus (DMM) model of post-traumatic osteoarthritis, a single intra-articular injection of TGFB1-iMSCs, but not MSC(AT), reduced total synovial macrophage numbers and lowered the MHCII/CD206 ratio at eight weeks, although it did not reduce cartilage degeneration, synovitis, or fibrosis. Together, these findings show that TGFB1-engineered iMSCs have a macrophage-directed potency profile distinct from that of primary MSC(AT). Immortalized iMSCs therefore provide a reproducible platform for mechanistically dissecting engineered MSC potency and its effects on the immune environment.

immunology↗

bioRxiv2026

The phage shock protein A (PspA) maintains membrane potential and supports NADH dehydrogenase function in mycobacteria

Maintenance of membrane integrity and proton motive force (PMF) is critical for bacterial survival. The phage shock protein (Psp) system, conserved across bacterial species, stabilizes the membrane, maintains PMF, and protects against envelope damage. However, how the conserved effector PspA contributes to PMF maintenance remains unclear. Here, using the mycobacterial Psp system as a genetically tractable model, we provide mechanistic insight into this process. We show that PspA and the accessory protein PspM jointly sustain membrane potential, with PspM required to maintain a ~70 kDa PspA isoform at the membrane during envelope stress. Loss of PspA increases susceptibility to thioridazine, which targets type II NADH dehydrogenase (NDH-2), and to Ro 48-8071, an inhibitor of menaquinone biosynthesis. Notably, hypersusceptibility to thioridazine is rescued by exogenous menaquinone. Consistent with these phenotypes, a pspA-deficient mutant exhibits impaired NADH dehydrogenase activity despite unchanged abundance of NDH-2 and menaquinone (MK-9). Together, these findings identify a functional link between PspA and NADH dehydrogenase-dependent respiration and suggest that PspA contributes to PMF maintenance by supporting respiratory electron transfer.

molecular biology↗

bioRxiv2026

Multiple roads to swarming: divergent molecular machineries drive the repeated evolution of locusts

Locust swarming, one of nature's most spectacular examples of a repeated emergent polyphenism, has long been suspected to rely on conserved "swarming genes" or shared genomic features. By applying a model-clade approach comparing six species that vary in their degrees of plasticity and collective behavior, we show that the evolution of swarming locusts is not driven by shared genomic features or a universal set of swarming genes. In contrast, we find that this phenomenon evolved through flexible regulatory architectures, in which the degree of behavioral plasticity directly correlates with the total scale of density-responsive gene expression. While different locust species recruit largely non-overlapping gene sets to achieve the same syndrome, these divergent molecular machineries converge on similar higher-level biological functions. Thus, multiple molecular pathways achieve locust swarming, challenging the preconceived notion about the genetic prerequisites to transition from solitary to collective states. Further, we establish that a complex syndrome such as locust swarming emerges through modular regulatory systems that can be amplified, modified, or attenuated across the tree of life.

evolutionary biology↗

bioRxiv2026

Hv1 proton channel is essential for splenic antibacterial defense and immune homeostasis during the chronic phase of traumatic brain injury in male mice

BackgroundTraumatic brain injury (TBI) is increasingly recognized as a chronic condition with lasting systemic consequences. Beyond persistent neuroinflammation, long-term TBI disrupts peripheral immune homeostasis, increasing susceptibility to infection and organ dysfunction, particularly in older patients. The voltage-gated proton channel Hv1, expressed in microglia and peripheral immune cells, regulates oxidative injury via modulation of NADPH oxidase activity. Yet few animal studies extend long enough to recapitulate the lifelong trajectory of human TBI, leaving the long-term effects of Hv1 deficiency on systemic immune homeostasis unresolved. MethodsYoung adult (3-month-old) male wild-type (WT) and Hv1 knockout (Hv1KO) mice were subjected to a moderate controlled cortical impact (CCI), and survival was monitored for up to 18 months post-injury, with endpoint analyses performed at 21 months of age. After neurological behavioral assessments, spleen, lung, liver, gut, ipsilateral cortex, and blood samples were collected for flow cytometry, qPCR, NanoString nCounter Panels, and in vivo plasma transfer studies. ResultsHv1 deficiency resulted in significantly increased mortality following TBI, starting at 14 months post-injury, compared with WT/TBI mice. No significant difference in survival was observed between the two sham groups. At 18 months post-injury, Hv1KO mice exhibited significant weight loss and splenomegaly. qPCR revealed an approximately 30-fold increase of pan-bacterial 16S rRNA levels in the spleens of Hv1KO/TBI mice, but not in the lungs or liver. Furthermore, chronic TBI in the Hv1KO mice led to a compromised intestinal tight junction and mucus barrier integrity, accompanied by aberrant activation of the cyclic GMP-AMP synthase-stimulator of interferon genes pathway in the spleen. Transcriptomic profiling of the spleen, liver, and lung revealed distinct post-injury immune signatures in Hv1KO mice. In contrast, surviving Hv1KO/TBI mice showed modest behavioral resilience and a partially neuroprotective cortical transcriptomic profile. Lastly, systemic transfer of plasma from WT/TBI or Hv1KO donors into naive young adult mice altered immune responses in the spleen, lung, and brain. ConclusionsHv1 plays a critical role in maintaining peripheral immune integrity and antibacterial defense throughout the chronic course of TBI. Despite conferring modest neuroprotection through attenuation of microglial-mediated oxidative stress, Hv1 deficiency exacerbated systemic phagocyte dysfunction and significantly reduced long-term survival.

neuroscience↗

bioRxiv2026

Experimental characterization of chicken OSX/SP7 and embryonic expression analysis reveal skeletal and neural expression domains

The specificity protein 7 (SP7), also known as Osterix (OSX), is a zinc-finger transcription factor essential for osteoblast differentiation and skeletal development. Hereafter, the protein is referred to as OSX/SP7 throughout the manuscript. Although OSX/SP7 has been extensively studied in mammals and teleost fish, its developmental expression pattern in chicken (Gallus gallus) has not been described. Using an experimentally isolated chicken OSX/SP7 sequence, we examined OSX/SP7 mRNA expression during embryogenesis by in situ hybridization. As expected, OSX/SP7 expression was detected in developing skeletal elements undergoing ossification. Unexpectedly, transcripts were also observed in the neuroepithelium, retina, central nervous system, embryonic muscles and integument. Notably, OSX/SP7 expression was present in the neural tube from Hamburger and Hamilton stage 9 and persisted in the developing central nervous system until at least HH40, suggesting that OSX/SP7 functions during avian development may extend beyond osteogenesis. In addition, we reconstructed the chicken OSX/SP7 coding sequence and inferred its associated untranslated regions. The reconstructed ORF was independently supported by maternal and paternal haplotype-resolved chicken genome assemblies and retained the characteristic domain architecture of vertebrate OSX/SP7 proteins despite substantial divergence outside the DNA-binding domain. Taken together, these findings broaden the developmental landscape of OSX/SP7 expression in birds and provide new molecular resources for future studies of OSX/SP7 regulation and function during vertebrate development.

developmental biology↗

bioRxiv2026

A Single Lipid Nanoparticle Formulation Enables Delivery of Diverse RNA Therapeutics to Human Muscle Models of Duchenne Muscular Dystrophy

Duchenne muscular dystrophy is a lethal neuromuscular disorder caused by the absence of dystrophin, for which no curative treatment is available. RNA-based approaches have shown promising results; however, their evaluation is hindered by the lack of robust and rapid delivery methods for differentiated human muscle cells, which represent the most physiologically relevant in vitro models for assessing therapeutic strategies. Here, we establish a versatile lipid nanoparticle platform enabling efficient delivery of diverse RNA therapeutics across a range of human muscle models, including myotubes, induced pluripotent stem cell-derived myotubes, myoblasts, cardiomyocytes, and 3D engineered skeletal muscle tissues. Remarkably, a single commercially available lipid nanoparticle formulation supports delivery of cargos spanning more than 300-fold in size, from short antisense oligonucleotides ([~]20 nt) to complex CRISPR-based editors (up to [~]6.7 kb), including Cas9 nucleases, adenine base editors, and CRISPRa systems. This enables efficient gene correction and transcriptional modulation, resulting in dystrophin restoration or compensatory utrophin upregulation in relevant Duchenne muscular dystrophy models. Together, our results establish a single lipid nanoparticle formulation as a versatile platform for RNA delivery in human muscle systems and provide a practical framework for the rapid preclinical assessment of emerging therapies for Duchenne muscular dystrophy and other neuromuscular disorders. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/741396v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@a18d71org.highwire.dtl.DTLVardef@4d0faforg.highwire.dtl.DTLVardef@140b078org.highwire.dtl.DTLVardef@1a235_HPS_FORMAT_FIGEXP M_FIG C_FIG Created in BioRender. Leclerc, D. (2026) https://BioRender.com/90h0fme

molecular biology↗

bioRxiv2026

Pyridoxine supplementation confers protection against SGPL1R222Q variant sphingosine phosphate lyase insufficiency syndrome

Sphingosine-1-phosphate lyase insufficiency syndrome (SPLIS) is a rare condition causing nephrotic syndrome, neuropathy, and other manifestations. SPLIS is caused by mutations in SGPL1, which encodes sphingosine-1-phosphate lyase (SPL), a pyridoxal 5-phosphate (PLP)-dependent enzyme needed to degrade the bioactive sphingolipid sphingosine-1-phosphate (S1P). Supplementation with the PLP precursor pyridoxine benefits some individuals with PLP-dependent enzymopathies. We sought to establish whether pyridoxine has therapeutic activity in SPLIS. Neurological improvement, plasma S1P normalization, and increased SPL activity in patient-derived fibroblasts were observed after pyridoxine supplementation in a patient with R222Q-variant SPLIS. Additionally, PLP dose-dependently augmented recombinant R222Q-variant SPL activity. To further explore pyridoxines effects, gene editing was employed to create an R222Q-variant SPLIS mouse model. SPLR222Q mice fed pyridoxine-enriched chow lacked obvious phenotypes. However, SPL inactivation, S1P accumulation, wasting, anemia, proteinuria, and glomerulosclerosis developed in SPLR222Q but not WT mice fed chow with reduced pyridoxine. Ultrastructural analysis and super-resolution microscopy showed podocyte loss and foot process effacement. Transcriptional profiling revealed a pattern of cytokine upregulation and extracellular matrix remodeling. Inhibiting S1P production prevented nephrosis in SPLR222Q mice fed chow lacking pyridoxine. Our findings establish a novel SPLIS mouse model that recapitulates R222Q-variant SPLIS, demonstrates its responsiveness to pyridoxine, and implicates S1P in its pathophysiology.

molecular biology↗

bioRxiv2026

Rotating Letters in the Mind's Eye: Behavioral and electro-cortical associations with 3D Mental-Rotation Ability

Mental rotation in 3D is a key cognitive skill involving dynamic spatial transformations, for which pronounced individual differences have been documented. Here we ask whether individual differences in 3D abilities can be explained by analogous differences in 2D abilities. 3D mental-rotation was assessed by the Vandenberg & Kruse Mental Rotation Test (3D-MRT) and examined for association with performance and underlying electrocortical mechanisms during a 2D letter rotation task. Participants (N=40) first completed the MRT and then performed a computerized 2-D letter rotation task in which they had to identify whether letters were oriented in a standard or a mirrored direction (parity judgment) when rotated at 0{degrees}, 60{degrees}, 120{degrees}, and 180{degrees} while EEG was recorded. Reaction times (RTs) and error rates increased with angular disparity. The angular disparity effect on RT was smaller for mirrored letters. Low, relative to high, 3D-MRT scoring participants showed more pronounced accuracy declines at higher rotation angles. An EEG Event Related Potential (ERP) known as the Rotation-Related Negativity (RRN) became more pronounced with increasing angular disparity. High 3D-MRT scores were associated with a stronger RRN response at central-parietal sites. In addition, the ERP-P3b wave was more pronounced at central-parietal sites for low 3D-MRT scorers, independent of angular disparity. It is concluded that 3D rotational ability is positively associated with 2D mental rotation performance, and more strongly with enhanced recruitment of neural visual-spatial cortical representations than with enhanced recruitment of more general cognitive resources.

neuroscience↗

bioRxiv2026

Interpreting Omics Data Analysis with Large Language Models for Disease Target and Drug Discovery

In biomedical scientific discovery, synthesizing prior knowledge from the literature is an essential component of interpreting numerical omics data analyses for disease target identification and drug discovery. Large language models (LLMs) alone can rapidly retrieve disease mechanisms from biomedical text, but text-only outputs are general and unreliable for target and drug prioritization without cohort-specific quantitative evidence. Herein, we propose a provenance-aware Text-to-Target framework that couples schema-constrained multi-model LLM retrieval with numeric omics data analysis. The key design is a modality-aware fusion step: candidates are partitioned into overlap-supported anchors, retrieval-only hidden hubs, and network-emergent novelty nodes, then propagated into staged hypothesis and strategy generation under topology constraints. We evaluate the model in Alzheimers disease (AD) and pancreatic ductal adenocarcinoma (PDAC). In PDAC, the workflow produced a balanced 75-gene candidate universe and a 23-strategy portfolio, with significant DepMap support at both target level and strategy level. In AD, stricter candidate controls yielded a compact 34-gene universe and 14 strategies; under an expanded CRISPRbrain registry, both target-level axes were significant, with strong strategy-level enrichment. Across both diseases, final strategies preserved full provenance closure to the candidate pool, enabling end-to-end auditability from retrieval artifacts to validation outputs. These results support a transferable discovery architecture in which omics evidence constrains biological activity, LLM retrieval expands mechanistic search space, and network-aware fusion preserves interpretability. The framework provides a reproducible basis for dual-disease target prioritization and motivates continuous literature-mechanism concordance with agentic evidence-refresh loops.

bioinformatics↗

bioRxiv2026

Phylogenomic analyses of the Austral podocarps (Podocarpus: Podocarpaceae) reveals unlikely hybrid ancestry of a New Zealand species

Hybridisation is ubiquitous amongst plants and has important evolutionary consequences ranging from the collapse of distinct lineages through to the generation of new species. Here, we develop a phylogenetic hypothesis for the Austral podocarps (Podocarpus), a monophyletic group of six species distributed in Tasmania, mainland Australia, New Zealand and New Caledonia, and identify a putative hybrid lineage. Using a targeted capture approach to generate DNA sequence data, we find discordance between nuclear and plastid derived phylogenetic estimates and in particular, the relationships of the New Zealand species Podocarpus nivalis and Australian P. lawrencei are significantly discordant. Species network analyses largely resolve this incongruence and indicate that P. nivalis is a hybrid lineage, with P. laetus (New Zealand) and P. lawrencei as parents. We hypothesise that P. nivalis has arisen following trans-Tasman dispersal of P. lawrencei, and shows eco-geographic divergence from P. laetus, which could facilitate reproductive isolation. We suggest that introgression from P. laetus to colonising P. lawrencei could significantly reduce founder effects while cold tolerance inherited from P. lawrencei has enabled P. nivalis to occupy alpine environments. Our findings highlight the importance of reticulate evolution in Southern Hemisphere conifers and demonstrate the value of phylogenomic network approaches for resolving recent and complex radiations.

evolutionary biology↗

bioRxiv2026

A distal CTCF-binding site drives MYC expression plasticity in a negative feed-forward loop

Oncogene expression heterogeneity systemically diversifies cancer cell phenotypes, enabling selection and cancer evolution. Here we document that the level of MYC expression variation is coordinated by a negative feed-forward loop involving the non-coding CCAT1 eRNA and the MYC gating process. While CCAT1 eRNA indirectly antagonizes MYC gating by promoting MYC transcriptional initiation and elongation, the MYC protein promotes gated MYC expression in a feedback loop by inhibiting both MYC transcription and CCAT1 expression. This entire process is coordinated by a CTCF binding site positioned within CCAT1 at a distal, oncogenic super-enhancer, which functions as a master switch by coordinating both CCAT1 and gated MYC expression to diversify cells toward both low and high MYC levels, as determined by heterogeneity metrics. As hallmarks of this principle are frequent in breast cancer and colorectal tumors, the dynamics of this new principle may underlie transitions between therapy-resistant low-MYC, and proliferative high-MYC tumor cells. Highlights- Transcriptional rate regulates MYC gating frequency - CCAT1 expression indirectly inhibits MYC gating by promoting MYC transcription - High MYC protein levels promote gated expression by inhibiting both MYC transcription and CCAT1 expression - These features are controlled by a single CTCF binding in the distant super-enhancer to drive expression plasticity in colorectal cancer cells

cancer biology↗

bioRxiv2026

Repeated Mild Head Injury Establishes a Senescent Cranial Bone Marrow Niche that Impairs Brain Metabolism

Traumatic brain injury (TBI) of any severity is associated with long-term systemic inflammation and increased risk of peripheral comorbidities, yet the mechanisms driving immune dysregulation and accelerated aging after repeated mild head impacts remain poorly defined. Here, we investigated the acute and chronic effects of repeated mild TBI (rmTBI) on distal and proximal bone marrow compartments in the femur and calvaria, respectively. Using a modified weight-drop mouse model delivering rotational and acceleration-deceleration forces (3 hits/week for up to 16 weeks), rmTBI produced no mortality, skull fracture, hemorrhage, or brain leukocyte infiltration. One day after three consecutive impacts, rmTBI induced robust proliferation of LSK stem/progenitor cells in both femoral and calvarial marrow, evidenced by Ki67 expression, BrdU incorporation, and increased monocyte output. By 8 weeks (24 impacts), injury-induced proliferation subsided and LSK cells exhibited increased senescence-associated {beta}-galactosidase activity and upregulation of tumor suppressor genes. At 16 weeks (48 impacts), LSK populations were depleted at both sites, displaying reduced proliferative capacity, telomere shortening, and pancytopenia in otherwise young adult mice. Calvarial bone marrow cells exposed to rmTBI released a distinct cytokine and proteomic secretome marked by elevated IL-6, suppressed mitochondrial and metabolic signaling, and enhanced DNA repair pathways. Notably, skull-derived secretome factors impaired cortical and hippocampal mitochondrial metabolism, and reduced microglial mitochondrial membrane potential. Together, these findings identify replicative senescence of the brain-adjacent bone marrow niche as an early and progressive consequence of repeated mild head injury, linking rmTBI to long-lasting metabolic dysfunction, impaired immunity, and accelerated aging. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/699107v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@683c8eorg.highwire.dtl.DTLVardef@15fc42forg.highwire.dtl.DTLVardef@48f398org.highwire.dtl.DTLVardef@170bbcc_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Global phylogeography of Amrasca biguttula (Hemiptera: Cicadellidae) across eight countries reveals a single-haplotype incursion into the United States beyond its putative native range

Amrasca biguttula is a pest of cotton, ornamentals, and vegetables, and is invading the southeastern United States. We addressed five questions: (1) Are US populations genetically identical to those in the putative native range? (2) Does the southeastern US outbreak extend the recent Puerto Rico and Florida invasion or represent separate introductions? (3) Does the lineage infesting ornamentals match that on other crops? (4) What is the mitochondrial cytochrome oxidase subunit 1 (mtCOI) diversity of A. biguttula? (5) Which regions constitute its native versus invaded range? Adults were collected from Florida, Georgia, South Carolina, Texas, and Puerto Rico. Species identity was confirmed morphologically and by sequencing mtCOI, where possible, from five individuals per site, yielding consensus haplotypes. We analyzed 11 US, 20 Puerto Rican, and 342 sequences originating from publicly available databases (n = 373). Phylogenetic analysis confirmed monophyly of this species. A haplotype network recovered 70 unique haplotypes, including a star-like core of 68 radiating from Hap01 and two divergent singletons. The mainland US and Chinese populations were fixed for Hap01, indicating recent introductions. Puerto Rico exhibited Hap01, Hap52, and Hap70, reflecting multiple introductions, but could also result from haplotype diversity carried within a single introduction involving many individuals. Furthermore, southeastern US sites were fixed for Hap01, indicating extension from Puerto Rico and Florida. No haplotype was host-specific, confirming a lineage across crops. Diversity metrics indicate recent expansion in Iraq, Hong Kong, and Puerto Rico. South Asia, particularly Bangladesh, India, and Pakistan, showed the highest haplotype diversity, supporting its role as the putative native range. In contrast, low diversity in China and the US is consistent with recent invasion. Curation yielded 373 high-quality sequences, providing a unified database to support quarantine and management strategies.

genetics↗

bioRxiv2025

A Comparative Evaluation of Adjuvants for Enhancing Antibody Responses to a Nanoparticle-Based Malaria Vaccine

Effective pre-erythrocytic Plasmodium falciparum vaccines targeting circumsporozoite protein (CSP) must elicit strong and durable antibody responses. We assessed the ability of different classes of adjuvants to enhance immunity of a promising CSP-epitope-targeted virus-like particle (VLP)-based vaccine. Five formulations significantly increased anti-CSP IgG titers and several also enhanced antibody durability. This study identifies promising adjuvants that enhance both the magnitude and longevity of VLP-induced immunity.

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

Propionate metabolism dysregulation promotes drug-tolerant persister cell survival in non-small cell lung cancer

Recent studies show that genetic sequencing can not fully explain drug resistance in non-small cell lung cancer (NSCLC), suggesting undiscovered non-genetic mechanisms that can enable cancer cell survival. Propionate metabolism is the pathway by which odd-chain fatty acids, branched chain amino acids, and cholesterol are metabolized. We have previously shown that methylmalonic acid (MMA), a byproduct of propionate metabolism that accumulates when the pathway is disrupted, can activate epithelial-to-mesenchymal transition (EMT) in cell lines. But the clinical significance of propionate metabolism in cancer patients is not known. Here we show, for the first time, that propionate metabolism is dysregulated in patients with non-small cell lung cancer. MMA is elevated in lung tumors and in the serum of patients with metastatic NSCLC. Metabolism of cobalamin associated B (MMAB), a key regulatory gene of propionate metabolism, is downregulated in NSCLC and drug-tolerant persister cells, leading to MMA accumulation and EMT activation. We show that restoring expression of MMAB in NSCLC enhances targeted therapy and suppresses TGFB signaling. These findings reveal propionate metabolism dysregulation as a non-genetic mechanism of drug resistance and highlight propionate metabolism as a potential therapeutic target.

cancer biology↗

bioRxiv2025

Novel chromosome-length genome assemblies of three distinct subspecies of pine marten, sable, and yellow-throated marten (genus Martes, family Mustelidae)

The genus Martes consists of medium-sized carnivores within the family Mustelidae that are commonly known as martens, many of which exhibit extensive geographic variation and taxonomic uncertainty. Here, we report chromosome-length genome assemblies for three subspecies, each representing a different marten species: the Tobol sable (M. zibellina zibellina), the Ural pine marten (M. martes uralensis), and the Far East yellow-throated marten (M. flavigula aterrima). Using linked-read sequencing and Hi-C scaffolding, we generated assemblies with total lengths of 2.39-2.45 Gbp, N50 values of 137-145 Mbp, and high BUSCO scores (93.6-96.4%). We identified 19 chromosomal scaffolds for sable and pine marten, and 20 for yellow-throated marten, which agrees with the known karyotypes of these species (2n=38 and 2n=40, respectively). Annotation predicted ~20,000 protein-coding genes per genome, of which >90% were assigned functional names. Repeats encompass 36.9-40.4% of the assemblies, with a prevalence of LINEs and SINEs, and is conservative across the genus. Synteny analysis of our generated and available marten genome assemblies revealed assembly artifacts in previously published assemblies, which we confirmed through investigation of Hi-C contact maps. Among other rearrangements, we verified a sable-specific inversion on chromosome 11 using the published cytogenetic data. Our assemblies broaden the genomic resources available for Martes, extending coverage to geographically distant and taxonomically significant subspecies. Together, they provide a robust framework for assessing intraspecific genetic diversity, identifying signatures of hybridization, and refining the complex taxonomy of the genus. Beyond conservation and evolutionary applications, these references will facilitate comparative genomics across Mustelidae and other carnivorans.

genomics↗