Biology subjects

Jain, S.

Publications and source records attributed to Jain, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

α-Synuclein Triggers Intercellular Nanotubes Formation to Prevent Apoptosis in Astroglia by Promoting Stemness

Astrocytes play a significant role in neuroprotection by internalizing neurodegenerative aggregates and facilitating their degradation. Recent studies indicate that -Synuclein (-SYN) protofibrils promote the transfer of pathogenic aggregates and dysfunctional mitochondria between astroglia via tunneling nanotubes (TNTs), which enhances cell survival and resistance to apoptosis. However, the underlying mechanism of TNT-driven apoptosis resistance remains unclear. We find that -SYN protofibrils induce aberrant mitochondria with decreased membrane potential ({Psi}m) and promote dynamic actin remodeling by relocating phosphorylated focal adhesion kinase (pFAK) to the nucleus, which triggers TNT formation in human astrocytoma cell lines and primary murine astrocytes. The important novel finding of this study is that pFAK in the nucleus co-localizes with Nanog, a crucial transcription factor for preserving stemness, and the interaction between pFAK and Nanog is critical for promoting p53 degradation via Mdm2-mediated ubiquitination and upregulating autophagy, thereby supporting the survival of astroglia exposed to toxic -SYN protofibrils. ROCK inhibitor y-27632 also drives TNT-formation via pFAK translocation to the nucleus, colocalizes with Nanog, and enhances stemness-related gene expression. Inhibiting TNT with the actin depolymerizing agent cytochalasin-D prevents pFAK co-localization with Nanog in the nucleus and fails to protect cells from -SYN-induced apoptosis. Nanog knockdown does not degrade p53 and hinders cell rescue from apoptosis. Furthermore, these transient TNTs transfer mitochondria to adjacent cells, potentially helping maintain metabolic stability. This study reveals that the TNT formation pathway promotes pFAK-Nanog interaction in the nucleus, leading to p53 degradation, which protects astroglia against -SYN proteotoxicity and prevents apoptosis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/727344v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@18d8675org.highwire.dtl.DTLVardef@76a383org.highwire.dtl.DTLVardef@e92202org.highwire.dtl.DTLVardef@1b7ee4b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

DigitAb: Domain-Adaptive Cell Type Prediction Method from Light Microscopy Images

Light microscopy imaging with histological stains is central to disease diagnosis and research. It is enhanced with immunostaining to reveal cellular composition and complexity linked to clinical utility and biological mechanisms. Emerging multiplex imaging technologies like Phenocycler markedly increase the coverage to capture the cellular diversity but are costly, technically demanding, and inaccessible to most clinical laboratories. We developed DigitAb, a deep learning framework that classifies cell types directly from hematoxylin and eosin (H&E) stained slides, eliminating the need for specialized assays. Using Phenocycler imaging, we generated highlZlresolution ground truths for [~]3.5 million cells from 29 human kidney samples across four multi-institutional datasets to train a semantic segmentation model for 10 cell types, achieving a balanced accuracy of 0.78. By employing an integrated adversarial domain adaptation module, we tested DigitAb on unlabeled and untested biopsy samples from kidney transplant and diabetic samples. We were able to predict several cell types just from histology images, without using any special technology or immunostains, and demonstrate high concordance with clinical gold-standard Banff schema in kidney transplant rejection, and clinical characteristics of diabetic nephropathy. Our cloudlZlbased tool, DigitAb, provides scalable, accessible, labellZlfree cellular segmentation for research and clinical pathology.

pathology↗

bioRxiv2026

Influence of Physicochemical Parameters on the in vitro Stability of DNA Tetrahedral Nanostructures

Tetrahedral DNA nanostructures (TDNs) are promising nanocarriers due to their structural precision, biocompatibility, and efficient cellular uptake. However, their stability under physiological conditions remains a key challenge. In this study, TDNs were synthesized via a one-pot thermal annealing method and characterized using native PAGE, dynamic light scattering (DLS), and zeta potential analysis, confirming uniform size ([~]13 nm) and negative surface charge. Their stability was systematically evaluated across different biological media (DMEM complete, serum-free DMEM, and E3), temperatures (4 {degrees}C, 25 {degrees}C, and 37 {degrees}C), and pH conditions (4.0, 7.0, and 8.5) over 24 h. Results revealed rapid degradation in serum-containing medium, increased instability at higher temperatures, and reduced stability under acidic conditions, while serum-free, lower-temperature, and neutral to mildly basic environments enhanced structural integrity. These findings highlight the strong environmental dependence of TDN stability and provide insights for optimizing their design for biomedical applications.

bioengineering↗

bioRxiv2026

Hamelia patens-Derived Red-Emitting Carbon Quantum Dots: Surface-State Luminescence, Antioxidant Potency, and In Vitro Bioimaging

Red-emitting carbon quantum dots (HP-CQDs) were synthesised for the first time from aqueous leaf extracts of Hamelia patens through single-step, reagent-free microwave-assisted carbonisation (750 W). The resulting nanoparticles displayed a narrow hydrodynamic size distribution centred at 3.9 nm, consistent with atomic force microscopy measurements showing a maximum height of 2.81 nm. Under 400 nm excitation, the CQDs exhibited a characteristic red emission maximum at 675 nm, representing a rare example of long-wavelength-emitting green CQDs derived from plant biomass. UV-Vis absorption bands at 224 and 256 nm were assigned to {pi}-{pi}* transitions of aromatic carbon domains and n-{pi}* transitions associated with carbonyl-containing surface groups, respectively. X-ray photoelectron spectroscopy (XPS) indicated a carbon-rich composition (C: 67.24%, O: 31.25%, N: 1.52%) with prominent C-O (42.67%) and C-C/C=C (42.64%) contributions. ATR-FTIR further confirmed the retention of hydroxyl, ether, and aliphatic functionalities following carbonisation. The excitation-wavelength-independent emission peak position implicates discrete surface molecular states rather than a heterogeneous distribution of emitters. HP-CQDs exhibit potent DPPH radical scavenging activity (ICOO = 141.8 {micro}g mLO{superscript 1}), comparable to ascorbic acid (ICOO = 114.8 {micro}g mLO{superscript 1}), and maintain >95% cell viability in both HeLa and RPE-1 cells up to 250 {micro}g mLO{superscript 1}. Confocal microscopy demonstrates concentration-dependent cytoplasmic accumulation and selective perinuclear localization at 300 {micro}g mLO{superscript 1}. In vivo biodistribution in zebrafish larvae confirms systemic uptake with statistically significant fluorescence enhancement at 500 {micro}g mLO{superscript 1} (p < 0.01), establishing HP-CQDs as biocompatible red-fluorescent probes with dual imaging-antioxidant functionality. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=148 SRC="FIGDIR/small/724069v2_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@17be668org.highwire.dtl.DTLVardef@153d874org.highwire.dtl.DTLVardef@1a7e6edorg.highwire.dtl.DTLVardef@29f13a_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Targeting COL4A1-Related Small Vessel Disease: Repurposed Pharmacotherapies for Genetic Vasculopathies

COL4A1-related disorders cause early-onset stroke, intracerebral haemorrhage, visual impairment and kidney disease, often affecting children and young adults, yet no disease-modifying therapies exist. These disorders arise from pathogenic COL4A1 variants that disrupt type IV collagen and impair small-vessel integrity, leading to cerebral small-vessel disease and endothelial dysfunction. We performed a mechanism-guided screen in human brain endothelial cells using a CRISPR-engineered COL4A1 p.G755R line and patient-specific COL4A1 p.G773R iPSC-derived endothelial cells. Simvastatin, L-carnosine, and XPD-101 restored impaired endothelial proliferation, migration, and other markers of endothelial function, including transendothelial electrical resistance (TEER). In a Col4a1Svc/+ mouse model, simvastatin increased pre-weaning survival, improved functional behaviour and reduced cerebral microhaemorrhage burden. These findings identify mechanism-informed candidates that rescue COL4A1-mutant endothelial dysfunction in vitro, with simvastatin demonstrating in vivo efficacy, supporting prioritisation for further preclinical development.

molecular biology↗

bioRxiv2026

Aneuploidy sensitizes cells to SREBP-pathway inhibition in squamous cell carcinoma

Squamous cell carcinomas (SCCs) in the lung, head and neck, cervix, and esophagus are characterized by widespread chromosome-arm aneuploidies, most frequently recurrent 3q-gain. However, how these alterations influence cancer development and therapeutic vulnerabilities remains unclear. To identify aneuploidy-driven therapeutic targets, we performed genome-wide CRISPR interference (CRISPRi) and drug-repurposing screens in isogenic immortalized lung epithelial cells harboring chromosome 3-disomy or 3q-gain. Both screens converged on a mevalonate pathway dependency specific to 3q-gain cells, which exhibited heightened sensitivity to sterol regulatory element-binding protein (SREBP) disruption. Rescue experiments demonstrated that these vulnerabilities were on target and that pathway inhibition preferentially causes apoptosis in 3q-gain cells. Transcriptomic and lipidomic profiling revealed 3q-gain-associated alterations in SREBP activation, cholesterol and fatty-acid biosynthesis, and lipid composition. Perturbing SREBP signaling impaired viability in SCC cell lines and suppressed tumor growth in xenografts with 3q-gain. These findings identify an aneuploidy-driven, targetable vulnerability in SCC. SignificanceHere, we demonstrate that SCC-recurrent 3q-gain is a selective vulnerability to SREBP-pathway inhibition. We identify an aneuploidy-driven therapeutic liability in squamous tumors for lipid-targeted precision therapies, providing a framework for targeted treatment in SCC.

cancer biology↗

bioRxiv2026

Characterization of genetically effective cells and EMS mutagenesis on the novel winter oil seed Pennycress (Thlaspi arvense)

Pennycress (Thlaspi arvense L.) is an intermediate winter oilseed crop that has only recently been domesticated for agronomic use. Improving agronomic traits requires sources of genetic variation, and mutagenesis is frequently used to help overcome the limitations of natural populations. We investigate the impact of Ethyl methanesulfonate (EMS) on genetically effective cells (GECs) to characterize the intra-individual genetic variation of EMS mutagenesis in pennycress. We identified that pennycress contains at least 4 GECs which, when treated with EMS, create unique mutations across different branches within the same individual plant. We then propagated the M2 plants for whole genome sequencing, providing extensive characterization of the EMS mutation profile and developing a gene index as a resource for future reverse genetic screenings. Article SummaryPennycress is an emerging winter oil seed crop in the American Midwest. Domestication efforts have advanced rapidly through a combination of genetic techniques. One of the most successful methods has been the use of a mutant gene index, a large collection of pennycress seed where new genetic variation has been created through Ethyl methanesulfonate (EMS). EMS mutations are not uniform however, and a single treated seed can have wide genetic variation within the resulting plant. We investigate the role of genetically effective cells on EMS variation, and present the full EMS population as a resource for further pennycress domestication efforts.

genomics↗

bioRxiv2026

Designed Minibinders Rewire Receptor Signaling to Enable Functional Human Myogenic Reprogramming

Sarcopenia, loss of muscle mass is a considerable health burden that demands immediate societal attention. Direct myogenic somatic cell reprogramming, a potential muscle regeneration method is constrained by an inability to control the signaling logic that governs cell fate. Here, we show that this barrier can be overcome using AI-designed receptor modulators. Screening de novo minibinders, we identify a synthetic protein cocktail, C6-DPC, that drives efficient human fibroblast-to-muscle transdifferentiation with robust structural and metabolic maturation. C6-DPC reprograms extracellular signaling by activating pro-myogenic FGFR1/2c pathways while suppressing anti-myogenic inputs through ALK1 and TGFBR2; targeted depletion of ALK1 is sufficient to lower the reprogramming barrier. Inflammatory signaling via gp130 emerges as a dominant checkpoint, and its inhibition further enhances conversion. Engineered tissues generate high twitch and tetanic forces in both wild-type and dystrophin-deficient human cells. These findings demonstrate that programmable synthetic ligands can rewrite receptor-level signaling to direct cell fate and enable functional tissue regeneration.

biochemistry↗

bioRxiv2026

Paternal folate deficiency reveals meiosis as a metabolic sensing window in the male germline

Folate-dependent one-carbon metabolism supplies methyl donors required for chromatin modification, yet how metabolic conditions shape epigenome establishment in the male germline remains poorly understood. Here, using a folate-deficient mouse model, we identify meiotic prophase I as a metabolically sensitive window in the male germline. By integrating in vivo germline analysis with bulk and single-cell transcriptomic and epigenomic profiling, we show that folate deficiency disturbs transcriptional programs in pachytene spermatocytes and preferentially perturbs CpG island (CGI)-associated promoters, which are characterized by bivalent H3K4me3 and H3K27me3 during meiosis. Consistent with this selective vulnerability, active chromatin marks, including H3K4me3 and H3K27ac, are markedly reduced at CGI-associated promoters under folate-deficient conditions. Notably, loci that later exhibit altered H3K4me3 enrichment in mature sperm show earlier chromatin perturbations during meiosis, suggesting that these sperm epigenomic alterations may originate during meiotic development. Together, these findings establish a mechanistic link between paternal folate deficiency and dynamic epigenomic remodeling of CGI-associated chromatin in the male germline.

developmental biology↗

bioRxiv2026

Brain2VLM: Hierarchical Alignment Between Cortical Representations and Vision-Language Latent Spaces

This work introduces Brain2VLM, a framework for analyzing how cortical representations align with latent spaces of pretrained diffusion-based vision-language models for brain-to-image reconstruction. While recent approaches achieve strong performance by mapping functional Magnetic Resonance Imaging (fMRI) signals to model latents, the structure of this mapping remains poorly understood. We hypothesize that brain-to-latent alignment is hierarchical, with early visual cortex exhibiting approximately linear correspondence to structural diffusion latents, and higher-order visual areas requiring nonlinear mappings to align with semantic embedding spaces. To test this, we decode diffusion latents and CLIP embeddings from fMRI signals across four subjects from the Natural Scenes Dataset (NSD) using both linear ridge regression and a nonlinear residual MLP. Our results reveal that nonlinear decoding provides only marginal improvements for diffusion latents ({Delta} {approx} 0.05 - 0.06 in correlation), but yields substantial gains for semantic embeddings ({Delta} {approx} 0.47), significantly improving distributional alignment (MMD: 0.042 vs 0.358). However, increased decoder expressivity can introduce shifts in latent distributions, highlighting a trade-off between prediction accuracy and generative compatibility. Despite using a simple reconstruction pipeline, Brain2VLM consistently improves semantic reconstruction quality across all four subjects while maintaining competitive pixel-level fidelity (PixCorr 0.36, CLIP 85%), suggesting that improvements in brain-to-latent alignment play an important role in reconstruction quality alongside generative modeling. These findings are consistent with a hierarchical pattern of alignment between cortical representations and model latent spaces, highlighting the brain-to-latent interface as an important component of brain decoding systems. Our code can be found at https://github.com/adarsh-crafts/Brain2VLM

neuroscience↗

bioRxiv2026

Retracing and rewriting the evolutionary trajectories of mammalian developmental enhancers

Cis-regulatory elements (CREs) such as enhancers play a central role in orchestrating mammalian development, yet how they have gained, lost, maintained or changed function over the course of mammalian evolution remains poorly understood. To address this gap, we densely mapped the functional evolution of five mouse developmental enhancers by testing orthologous sequences from 480 extant and ancestrally reconstructed mammalian genomes (Zoonomia1, Cactus2) with massively parallel reporter assays (MPRAs). This phylogenetic dissection revealed diverse modes of evolution, from lineage-restricted activity to deep functional conservation despite extensive sequence divergence. To pinpoint causal changes, we developed a model-driven reconstitution strategy that uses deep learning-based predictions of chromatin accessibility to re-introduce a succession of mutations into ancestral orthologs; this revealed critical transcription factor binding site (TFBS) changes and pervasive context-dependent epistasis, including instances where mutational effects were strongly contingent on the order of their introduction. When we extended this strategy to tune the activity of extant orthologs, we found that ablation of enhancer function required as few as one to seven mutations, whereas enhancement was constrained by element-specific activity ceilings--a striking asymmetry in the predictability of model-guided enhancer editing. Together, these results shed light on how the plasticity of mammalian enhancers intersects with their evolution, and advance a framework for reprogramming the activity of endogenous CREs at nucleotide resolution.

molecular biology↗

bioRxiv2026

RUNX1 aberrations in blast-phase CML induce the RBP SPATS2L which promotes growth, survival and stress granule assembly

The RUNX1 transcription factor is a critical regulator of hematopoiesis and frequently mutated in myeloid malignancies. In the myeloproliferative neoplasm, chronic myeloid leukemia (CML), secondary somatic RUNX1 mutations and RUNX1::MECOM/EVI1, are associated with tyrosine kinase inhibitor (TKI) resistance and progression to the blast-phase (BP-CML). Research has predominantly focussed on transcriptional dysregulation mediated by RUNX1 mutations in myeloid malignancies, whilst post-transcriptional dysregulation remains comparatively unexplored. To address this, we used orthogonal organic phase separation (OOPS), to characterise the RNA-binding proteome of RUNX1 deficient BP-CML cells. RUNX1 depleted BP-CML cells exhibited significant alterations to RBP abundance involved in stress response pathways and translation/ribosome-biogenesis (RiBi). Furthermore, RUNX1 depletion or expression of RUNX1::EVI1 in BP-CML cells induced expression and RNA binding activity of SPATS2L, a component of stress granules (SG); membraneless cytoplasmic condensates protecting mRNAs from degradation, promoting survival under stress. Whilst RUNX1 depletion increased SG-assembly, SPATS2L depletion reduced SG-assembly in BP-CML cells and inhibited the growth and survival of multiple BP-CML cell lines. The translation inhibitor homoharringtonine (HHT), used historically in TKI-resistant CML, ablated SG-assembly in BP-CML cells with RUNX1 depletion, and, primary BP-CML cells with LOF/hypomorphic RUNX1 mutations (characterised by defective DNA-binding/CBF{beta}-interaction) were preferentially sensitised to HHT. Finally, suppressing SPATS2L expression induced by RUNX1 depletion, increased the HHT-sensitivity of RUNX1 depleted BP-CML cells, suggesting SPATS2L contributes to therapeutic resistance in CML with RUNX1 mutations. This study suggests that SPATS2L and SG induction could be critical to RUNX1-mutant leukemias, and, provides preliminary evidence for a mutationally-targeted approach in CML with RUNX1 aberrations.

cancer biology↗

bioRxiv2026

NetTracer3D Enables User-Friendly Analysis of Diverse Microscopic and Medical 3D Datasets

Recent advances in high-resolution imaging and spatial transcriptomics have enabled reconstruction of complex 3D tissue maps, providing unprecedented insights into cellular connectivity, organization, and tissue architecture. However, standardization challenges hinder integration, sharing, and analysis of these datasets across research communities. We developed NetTracer3D to simplify three-dimensional image analysis across diverse datasets. NetTracer3D is an integrated tool for defining, processing, and sharing 3D tissue maps with standardized data formats and interactive exploration capabilities. It provides three broadly applicable network analysis modalities: Connectivity networks for analyzing functional tissue units or cells connected via secondary structures such as nerves or vasculature; Branch Adjacency and Branchpoint networks for converting branched anatomical structures into analyzable representations; and Proximity networks for grouping structures by spatial relationships to identify cellular organization patterns. We demonstrate several use cases applying NetTracer3D to analyze multidimensional data from CODEX and label free Raman spectroscopy, multiscalar data encompassing subcellular and anatomical scales and a range of modalities. NetTracer3D was able to characterize neural relationships between functional tissue units in human and mouse kidneys and mouse bronchi. Branchpoint networks were used to identify vascular defects in human brain angiogram and define the innervation structure of a lymph node. Finally, we demonstrate how proximity networks characterize the tumor microenvironment in 3D light sheet cancer images and auto-detect cellular neighborhoods in multiplexed 2D CODEX datasets. Beyond network creation, NetTracer3D enables analysis, spatial statistics, and visual analytics tailored for volumetric tissue data. By establishing interoperable formats and analysis workflows, this work provides accessible and reproducible analytical tools for 3D spatial biology, enabling new discoveries of relationships between structure and physiology.

genomics↗

bioRxiv2026

Bacteriophage utilize pseudolysogeny to target non-replicating bacteria and CRISPR-resistant phages eliminate recalcitrant implant infections

A key driver of bacterial infection treatment failure and relapse is the persistence of non-replicating bacterial subpopulations that emerge under stressors like nutrient starvation and immune pressure. These dormant cells evade antibiotics, fuelling recurrence and resistance. Bacteriophage therapy is a promising alternative, but its efficacy against non-replicating bacteria is poorly understood. Improving our understanding of bacteria-phage interactions under non-replicating conditions could greatly enhance phage therapeutic outcomes in clinics. By utilising various bacterial (Mycobacterium smegmatis, Mycobacterium tuberculosis, and Pseudomonas aeruginosa) and phage species, this study quantitatively demonstrates that lytic phages can infect non-replicating bacteria (under nutrient starvation, acidic pH or antibiotic pressure), persisting in a state of pseudolysogeny and resuming lysis upon bacterial regrowth. We find that the pseudolysogeny window is phage- and host-dependent, with degradation of extrachromosomal phage DNA leading to loss of pseudolysogeny. We find that Pseudomonas CRISPR defence plays a crucial role in phage DNA degradation even under non-replicating conditions, underscoring the need for its consideration in phage therapy design. We also demonstrated the in vivo relevance of pseudolysogeny and CRISPR-resistant bacteriophages in eliminating implant-associated and antibiotic-persistent Pseudomonas infections in mice. These findings highlight the need to consider phage-host dynamics and bacterial defences when designing phage-based strategies to target non-replicating bacteria and persistent infections.

microbiology↗

bioRxiv2026

Determination of GLP-1 Secretion Potential of Dead and Live Akkermansia muciniphila Using Human L-cells

Background/ObjectivesGlucagon-Like Peptide-1 (GLP-1) is a key incretin hormone that regulates glucose homeostasis and energy metabolism. Impaired GLP-1 signaling contributes to the development of obesity, metabolic syndrome, and type 2 diabetes. Emerging evidence indicates that gut microbiota-derived components can influence GLP-1 secretion, highlighting the therapeutic potential of microbial modulators. Akkermansia muciniphila, a next-generation probiotic associated with improved metabolic health, remains underexplored for its capacity to stimulate GLP-1 release. This study aimed to investigate the GLP-1- stimulatory effects of live and pasteurized (dead) A. muciniphila strains in human enteroendocrine cells. MethodsHuman enteroendocrine L-cells (NCI-H716) were treated with varying doses of live and dead A. muciniphila from Vidya Herbss proprietary VHAKM strain and a commercially available marketed strain (dead form). Following incubation, GLP-1 levels were quantified from culture supernatants using enzyme-linked immunosorbent assay (ELISA). Comparative analyses assessed differences in GLP-1 secretion between strains and treatment forms. ResultsBoth live and pasteurized VHAKM strains significantly increased GLP-1 secretion compared to untreated controls. The live VHAKM strain exhibited higher GLP-1 stimulatory activity than its pasteurized counterpart and the marketed strain. The results suggest a strain-specific and viability-dependent modulation of GLP-1 secretion in human L-cells. ConclusionsThis study demonstrates that A. muciniphila VHAKM enhances GLP-1 secretion in a strain- and form-dependent manner, with live cells showing superior efficacy. These findings provide foundational insights for developing microbiome-targeted interventions to boost endogenous GLP-1 levels and improve metabolic health outcomes.

microbiology↗

bioRxiv2026

Gene Expansion and Regulatory Rewiring Shape Sex-Biased Evolution of the Mouse Submandibular Gland Secretome

Background Mammalian saliva plays essential roles in digestion, immunity, and host-microbiome interactions, yet its protein composition varies widely across species and sexes. This diversity makes saliva a powerful model to study evolution of gene expression. Here, we compared mouse and human salivary glands at the genomic, transcriptomic, and proteomic levels to understand how saliva composition evolves. Results We found that evolution of gene expression in mouse salivary glands is driven by rapid gene turnover and sexual dimorphism. In the submandibular and sublingual glands, 68% and 73% of expression from genes encoding secreted proteins derives from lineage-specific genes that lack one-to-one human orthologs. This contrasts the prevailing view that gene expression is largely conserved across tissues and highlights saliva as an unusually dynamic system of molecular evolution. Mouse submandibular gland shows striking sexual dimorphism, with 1537 tissue specific sex-biased genes, 3.8 times higher than in the liver (p<0.001), a classic model of sex-biased expression. We also identified sex-specific expression of glycosylation genes associated with differential Muc19 sialylation. These results suggest that sexual dimorphism in mouse saliva arises from both transcriptional differences in secreted proteins and sex-specific post-translational modifications. Further, differentially expressed genes in submandibular gland cluster in genomic regions shaped by recent gene duplication, such as the kallikrein gene cluster, a mouse-specific expansion that accounts for ~16.4% of male-biased submandibular gland expression. Our analyses suggest that this bias arises through regulatory changes that are expanded by gene duplication, including the spread of a testosterone-associated regulatory motif and the expansion of a shared chromatin domain that promotes coordinated gene regulation. Conclusions Together, our results reveal that lineage-specific genes disproportionately shape the mouse salivary transcriptome and that gene duplication and regulatory rewiring contribute to the rapid evolution of sex-biased expression in the submandibular gland. We describe a novel mechanism through which lineage-specific gene duplication and regulatory rewiring drive rapid, sex-specific evolution of the mammalian saliva. Our findings support saliva as an evolutionarily dynamic system and are consistent with developmental systems drift, whereby similar phenotypes across species may be maintained despite substantial divergence in their underlying gene-regulatory programs.

evolutionary biology↗

bioRxiv2026

VascFlexMap: Microvascular Ultrasound Imaging at Low Frame Rates Using Sparse Data and a Transformer-Decoder Network

ObjectiveSuper-resolution ultrasound (SR-US) reveals microvascular structures with exquisite resolution, but clinical translation remains limited by the need for ultrafast frame rates, massive data volumes, and long reconstruction times. This work proposes a deep learning framework that reconstructs microvascular maps from low-frame-rate enhanced ultrasound sequences, bypassing explicit microbubble localization and tracking. MethodsA transformer-decoder network with learned linear projections was designed to model spatiotemporal dependencies across sparse contrast-enhanced ultrasound sequences and reconstruct vessel probability maps, refined via a post-processing enhancement stage. Single-head self-attention captures temporal correlations under challenging conditions including overlapping microbubbles and low signal-to-noise ratios. Binary cross-entropy loss guided training to preserve vascular topology across synthetic and in vivo datasets. In vivo rat brain bolus data from the PALA challenge was used to evaluate this approach under up to 500 - fold data reduction (341 frames at 2 FPS vs. 170400 frames at 1000 FPS in standard ULM). ResultsDespite aggressive undersampling, the proposed pipeline recovered coherent microvascular architecture where conventional ULM pipelines applied to the same sparse data failed to produce continuous vascular networks. Major branches and higher-order microvessels remained visible with apparent vessel widths broadened by approximately three-fold relative to reference SR-US. End-to-end reconstruction completed in 28-133 seconds on an NVIDIA H100 GPU depending on the number of frames employed. ConclusionThe reported approach preserved vascular topology with fast reconstruction and low data overhead, albeit at lower resolution. The substantial reduction in frames and computation time highlights the translational potential of this SR-US-inspired microvascular imaging approach.

bioengineering↗

bioRxiv2026

In Vivo Selection of anti-glioblastoma DNA aptamer-drug conjugates in an orthotopic patient-derived xenograft model

Glioblastoma (GBM) is an aggressive, high-grade glioma with a near-universally fatal prognosis. Therapeutic failure is often attributed to the highly selective blood brain barrier (BBB), the diffuse infiltrative nature of the tumor, and the marked intratumoral heterogeneity of GBM. Although antibody drug conjugates ADCs have shown promise for high grade gliomas such as GBM, efficacy is limited by ADC size. Aptamers--short, synthetic, single-stranded DNA or RNA molecules--can be [~]6-fold lower in molecular weight than IgG antibodies and have the potential to cross the intact BBB. Unlike other nucleic acid-based therapies, aptamer function arises from three-dimensional shape rather than genetic coding. Here we aim to replace the targeting component of the ADC paradigm with a DNA aptamer, thus creating an aptamer-drug conjugate (ApDC). We employed in vivo SELEX using an orthotopic patient-derived xenograft (PDX) GBM mouse model and a vast ([~]100 trillion 80-mer sequences) ApDC library. We report the results from this first in vivo ApDC selection of its kind. We characterize target tissue binding ex vivo, cell association, biodistribution, and pharmacokinetics from this selection. This study exemplifies an unbiased approach to a problem that rational design has yet to overcome, offering a new direction for GBM therapeutic development.

cancer biology↗