Biology subjects

Kumar, D.

Publications and source records attributed to Kumar, D..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

AI-Driven Generation of Cortisol-Binding Peptides for Non-Invasive Stress Detection

Cortisol is a primary biomarker of stress, released in sweat at concentrations that directly correlate with physiological stress levels. Detecting cortisol non-invasively offers significant potential for real-time stress monitoring and healthcare applications. Biosensors capable of binding cortisol can thus enable the development of novel diagnostic platforms for personalised health management. In our earlier work, a 38-mer peptide fragment derived from the protein 2V95 was identified as a functional binder to cortisol. In the present study, we applied generative artificial intelligence (AI) approaches to expand the sequence space and identify superior candidate peptides with improved binding affinity. By integrating sequence-based and structure-based AI models, we generated and screened a peptide library of nearly 10,000 sequences against cortisol, leading to the identification of high-affinity candidates for further evaluation.

bioengineering↗

bioRxiv2026

Short-chain PFAS exposure alters embryonic development and behavior in zebrafish

Per- and polyfluoroalkyl substances (PFAS) are manmade chemicals that are persistent in the environment and have been linked to various physiological and neurobehavioral outcomes, including anxiety disorders. Trifluoroacetic acid (TFA), a short chain PFAS and the most common PFAS degradation product, is increasingly detected in water, soil, and human blood, raising significant concerns about its developmental toxicity. However, the impact of early-life TFA exposure on neurodevelopment and behavior remain insufficiently characterized. In this study, we employed Zebrafish (Danio rerio) embryos as a New Approach Methodology (NAM), to evaluate the development, behavior, and protein expression changes in response to early-life TFA exposure. Embryos were exposed to environmentally relevant low and high concentrations of TFA beginning at one-cell stage. Early developmental physiology was assessed by measuring viability, tail twitch response, hatching rates, and chorion diameters during embryogenesis. Anxiety-like behaviors were evaluated at 5- and 6-days post-fertilization using validated behavioral assays such as the Light-Dark Test and Startle Response. Each test evaluates distinct anxiety-related behaviors by measuring locomotor activity, thigmotaxis (wall preference), and stimulus reactivity, with anxious zebrafish larvae showing increased movement in light and greater wall preference. Then to identify molecular pathways underlying observed developmental phenotypes with TFA exposure, proteomic analyses were performed on embryos at 24- and 48-hours post-fertilization. Our results indicate that TFA exposure altered developmental physiology, evidenced by reduced chorion diameters, and lead to increased anxiety-like behaviors with larvae exhibiting thigmotaxis. These phenotypic changes were accompanied by detectable alterations in the embryonic proteome. Collectively, our findings provide insight into how short-chain PFAS exposure during critical windows of development may contribute to neurobehavioral dysfunction, highlighting potential risks relevant to inform public health policies and environmental regulations.

developmental biology↗

bioRxiv2026

Unsupervised anomaly detection for tumor delineation in a preclinical model of glioblastoma using CEST MRI

IntroductionGlioblastoma is characterized by heterogeneous tumor characteristics and infiltrative tumor boundaries, making accurate delineation difficult with extensive manual annotations. Chemical exchange saturation transfer (CEST) is a non-invasive MRI technique used for in vivo assessment of metabolic and macromolecular information through a Z-spectrum. CEST may provide insight into metabolic changes present in early-stage disease that are not visible in routine clinical imaging, thereby improving tumor delineation. In this work, we use an unsupervised anomaly detection (UAD) strategy to learn the distribution of features present in Z-spectra of healthy tissue and capture their deviations in pathology, foregoing the need for extensive labels. The approach leverages the metabolic information provided by CEST to improve the detection and delineation of glioblastoma and inform further treatment planning. MethodsA 1D convolutional autoencoder (CAE) was implemented to reconstruct Z-spectra from individual tissue voxels. The network was trained on Z-spectra acquired at 9.4T from healthy Sprague-Dawley rats and tested on data acquired from F98 glioma-bearing rats post Gd-administration. For baseline comparisons, Isolation Forest and Local Outlier Factor, which have shown success in anomaly detection, were implemented. For the CAE, our anomaly score was determined to be the mean squared reconstruction error. To facilitate clinical translation and evaluate the robustness of our model for under sampled Z-spectra, acceleration factors of 2x and 7x were performed with two sampling schemes: uniformly skipping frequency offsets and selecting offsets based on feature importance identified by Shapley value analysis and Integrated Gradients (IG). Binarization was performed by determining an optimal anomaly threshold, followed by comparison to ground truth tumor masks. Metrics related to model performance were assessed for baseline anomaly detectors on the fully sampled dataset and for the CAE on fully and under sampled datasets. ResultsThe best baseline anomaly detector was Isolation Forest, with an ROC-AUC of 0.967 and an F1-score of 0.584. Our method, the CAE, accurately reconstructed Z-spectral features, achieving Dice scores of up to 0.72 and outperforming the baseline model with an ROC-AUC of 0.968 and F1-score of 0.642. This model performance remained robust across sampling schemes and acceleration factors, with ROC-AUCs of [~]0.96 and similar Dice scores (up to 0.7). Feature importance analysis indicated that offsets in the range of {+/-}3.0 to 5.0ppm contributed most to the anomaly score. DiscussionThis study successfully demonstrated a UAD pipeline utilizing the Z-spectrum from CEST MRI for metabolically informed tumor delineation. The framework captures biochemical deviations that may precede or extend beyond morphologic abnormalities, enabling sensitive detection of tumor regions and intra-tumoral heterogeneity that previous methods may fail to capture. The offsets from the feature analysis indicated a strong contribution from the magnetization transfer (MT) pool to the spectral deviations captured by the model, with additional contributions from relayed nuclear Overhauser effect (rNOE) and amide proton transfer (APT). Model robustness with under sampling further highlights the pipelines potential in accelerated acquisitions, thus improving clinical practicality. While there is a need for validation on larger cohorts and clinical datasets, the current results demonstrate that this label-free, Z-spectral anomaly mapping can serve as an interpretable and scalable tool for monitoring tumor heterogeneity and progression, with potential applicability to other diffuse or metabolically subtle pathologies.

cancer biology↗

bioRxiv2026

Early exposure to PFAS disrupts neuro-muscular development in zebrafish embryos

Development is a tightly regulated process that establishes body axes and orchestrates the spatial organization of tissues and organs. Although developmental programs contain inherent redundancies, they remain highly sensitive to environmental cues. Among environmental contaminants, per- and polyfluoroalkyl substances (PFAS), chemicals that resist degradation and bioaccumulate in the body, are of particular concern. These "forever chemicals" are widespread in our household products, including non-stick and waterproof materials, and drinking water remains a major source of exposure. PFAS accumulate in specific tissues and have been associated with developmental delays, childhood leukemia, and other adverse health outcomes, yet the cellular and molecular mechanisms by which they disrupt early development remain largely unknown. To address this, we employ zebrafish embryos as a New Approach Methodology (NAM) to investigate how perfluorooctanoic acid (PFOA), a prevalent environmental PFAS, alters early embryogenesis. Embryos were exposed to physiologically relevant low and high doses of PFOA and analyzed at 24 hours post-fertilization (hpf), a key stage of organogenesis. We also included a parental exposure group, in which adults were treated with PFOA and their offspring were collected to assess whether the effects of exposure were transmitted to the next generation. Developmental processes are inherently plastic, and we wanted to understand the extent to which PFOA impacts normal cellular processes as well as the redundancy in the system (different developmental signaling pathways) which ensures that an embryo develops properly. Towards this, we performed single-nucleus RNA sequencing at 24 hpf, and it revealed that neuronal and muscle tissue clusters are particularly sensitive to PFOA exposure. These molecular perturbations correspond with anxiety-like behavioral phenotypes we observed in the exposed larvae, linking early developmental disruptions to organism-level outcomes. Overall, our findings provide mechanistic insight into the way in which PFAS exposure alters development, disrupting gene expression patterns and chromatin organization in developing tissues, revealing how early molecular perturbations can give rise to long-term behavioral consequences. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC="FIGDIR/small/700343v1_ufig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@1fec69aorg.highwire.dtl.DTLVardef@1a0b3beorg.highwire.dtl.DTLVardef@17883e2org.highwire.dtl.DTLVardef@11a7571_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2025

Multi-modal choroid plexus pathology in aging and Alzheimer's disease

Brain barriers, cerebrospinal fluid (CSF) dynamics, and peripheral factors are implicated as significant contributors to Alzheimers disease (AD). The choroid plexus (ChP) is a blood-brain interface that produces CSF and forms the blood-CSF barrier. However, how ChP pathology develops across the lifespan and contributes to AD has not been systematically characterized. Here, we report a multi-modal ChP atlas integrating single-nucleus transcriptomics from 49 individuals, AI-assisted quantitative histopathology across >500 postmortem samples age 16 to 105, spatial transcriptomics, and functional studies in 5xFAD mice. We identify fibrosis, calcification, and macrophage abnormalities as hallmarks of ChP aging, with AD pathology conferring additional effects, including expansion of a pro-inflammatory fibroblast-macrophage signaling niche. In 5xFAD mice, macrophage dysfunction is associated with impaired epithelial barrier maintenance and repair. Together, these data provide a foundational resource for understanding ChP dysfunction in aging and AD and propose the macrophage-fibroblast-epithelial barrier axis as a driver of ChP pathology.

neuroscience↗

bioRxiv2025

NLRP3 Inflammasome Exhibits Context-Dependent Roles in Glioblastoma-Astrocyte Crosstalk

Glioblastoma (GBM) is a highly aggressive brain tumor characterized by molecular and cellular heterogeneity and poor patient survival. NLRP3 inflammasome regulates inflammation and cell death with context-specific roles in cancer, but its functions in GBM tumour and astrocyte interactions remain unclear. In this study, we analyzed NLRP3 expression and function in GBM cell lines (LN-229 and LN18), astrocytes (SVG), patient-derived tissues, and organoids. Basal NLRP3 expression was higher in astrocytes than in GBM cells and increased after LPS stimulation, altering astrocyte morphology and NLRP3 subcellular localization. siRNA-mediated silencing of NLRP3 reduced GBM proliferation, migration, and viability in GBM cells, while enhancing proliferation and cytokine secretion in astrocytes, highlighting its context-dependent effects. NLRP3 deficiency exhibited reciprocal cytokine paracrine signaling, with GBM cells releasing elevated levels of IL-6 and TNF-, and astrocytes releasing elevated levels of IL-1{beta}. Glyburide treatment reduced NLRP3 expression and IL-1{beta} release in GBM cells but elevated NLRP3 and IL-1{beta} in astrocytes. Overall, these data reveal NLRP3s dual roles in GBM-astrocyte crosstalk, suggesting cell-type-selective inhibition for therapeutic exploration.

cancer biology↗

bioRxiv2025

HuBIE: The Human Blood Immunome Encyclopedia Of TCRs and BCRs in Bloodstream Infections and Cancer

T and B cells are central to adaptive immunity, where they identify and neutralize foreign antigens and cancer neo-antigens. Large-scale elucidation of T- and B-cell receptors (TCRs and BCRs) through immune-repertoire sequencing promises novel diagnostics, prognostic markers, and therapeutic strategies. However, progress is hampered by small cohort sizes, a lack of real-world patient diversity, and heterogeneous sample processing, impeding cross-study comparability. To overcome these limitations, here we introduce the Human Blood Immunome Encyclopedia (HuBIE), comprising immune-repertoire data from 2,614 samples collected from 1,941 participants. The cohort includes a range of bloodstream infections, several cancer types, and control participants, with many individuals providing longitudinal samples. We employed Roches immune receptor Primer Extension Target Enrichment (immunoPETE) platform to perform simultaneous targeted sequencing of T-cell receptor {beta} chains (TRB), T-cell receptor {delta} chains (TRD), and immunoglobulin heavy chains (IGH), thereby profiling TCRs and BCRs in all participants. We provide a comprehensive description of immune-repertoire diversity in cancer and bloodstream infections and examine variations across demographic variables such as age and race. We find significant differences in TRB and IGH composition across ethnic groups, and show that the fall in repertoire diversity with age follows distinct patterns for TRB, TRD, and IGH and is accompanied by age-related differences in VJ gene usage. Finally we demonstrate that greater immunological diversity is associated with improved survival but only for elderly participants. HuBIE thus constitutes a valuable resource for the immune-repertoire community, enabling large-scale mapping of the human immunome to accelerate development of diagnostics, prognostic biomarkers, and innovative therapeutic strategies.

immunology↗

bioRxiv2025

Bacteriophage-mediated reduction of uropathogenic E. coli from the urogenital epithelium

Urinary tract infections (UTIs), primarily caused by uropathogenic Escherichia coli (UPEC), affect millions annually. UPEC gains access to the urinary tract through mucosal reservoirs including the vaginal tract. With rising antibiotic resistance and frequent recurrence, alternative non-antibiotic strategies like bacteriophage (phage) therapy are gaining attention. We explored the potential of a lytic phage, {Phi}HP3, as well as a phage cocktail to decolonize UPEC from the urogenital tract using in vitro and in vivo models. Phage significantly inhibited UPEC growth in both bacteriologic medium and simulated vaginal fluid. Pretreatment of human vaginal epithelial cells (VK2/E6E7) and bladder carcinoma cells (HTB-9) with phage reduced adhesion and invasion of UPEC compared with controls. Phage treatment was further able to reduce intracellular UPEC in VK2 cells. Notably, phage pretreatment did not impact phage resistant UPEC strains, indicating that phage lysis was the primary driver of phenotypes. Live confocal microscopy confirmed interaction of phage particles with UPEC and with both epithelial cell lines. In vivo, daily intravaginal {Phi}HP3 administration in humanized microbiota mice significantly reduced vaginal UPEC burden after 4 days. Treatment with a phage cocktail also reduced vaginal and cervical tissue burdens by day 7 post-treatment. UPEC dissemination was observed to uterine and kidney tissues, but burdens were not different between phage and mock-treated groups. In conclusion, we demonstrate that phage and phage cocktails can modestly reduce UPEC urogenital colonization, highlighting the potential of phage therapy as a viable treatment option for UTI prevention. IMPORTANCEUrinary tract infections (UTIs) are among the most common infections worldwide, with millions of cases each year. Due to frequent recurrence and increasing antibiotic resistance, UTIs are becoming more difficult to treat, and non-antibiotic prevention options remain limited. The bacteria responsible for UTIs, such as uropathogenic E. coli (UPEC), often colonize other body sites, such as the intestines or vagina, before causing infection. In this study, we investigated whether bacteriophage (phage), viruses that infect bacteria, could reduce UPEC colonization. We found that phage treatment decreased UPEC adherence to vaginal and bladder cell lines, but only modestly reduced UPEC vaginal colonization in a mouse model. These findings suggest that phages may offer a potential strategy for UTI prevention, though further research is needed to optimize their therapeutic use.

microbiology↗

bioRxiv2025

Multimodal MR Imaging for quantification of brain lipid in mice at 9.4T

BackgroundAdvanced MR imaging techniques like steady state Nuclear Overhauser enhancement (ssNOE), transient NOE (tNOE), and myelin water fraction (MWF) provide a non-invasive way to assess the biochemical and structural integrity of brain tissue. Their sensitivity to endogenous lipids and macromolecules allows for the early detection of neuropathological changes, making them valuable tools in studying brain health and disease progression. In this study, we systematically evaluate the repeatability and sensitivity of NOEMTR, tNOE, and MWF for quantifying lipid and myelin content in the brains of wild-type (WT) mice, correlating the results with immunohistochemistry (IHC). MethodsFive 6-month-old C57BL6/J mice were imaged using 3D-NOE, and four mice underwent imaging with 2D tNOE and MWF across four repeated sessions using a 9.4T Scanner. For ssNOE imaging, CEST-weighted images at 56 frequency offsets were acquired using B1rms of 1.0 T and 3s saturation duration. For tNOE, 52 offsets were acquired with a hyperbolic secant inversion pulse (bandwidth = 400Hz, duration = 44ms) and a mixing time of 200ms. For MWF, a multi-echo spin-echo (MESE) sequence was acquired with 40 evenly spaced echoes from 5.5ms to 200ms. For both ssNOE and tNOE, B0 correction was performed using WASSR. Repeatability was quantified using intra- and inter-subject coefficients of variation (COV%). Pearson correlation was performed to see the association between imaging matrices and IHC measures, Luxol fast blue (LFB) stained sections, and myelin basic protein (MBP). ResultsAll techniques demonstrated high repeatability across the whole brain (WB) and selected regions of interest (ROIs). Whole-brain intra-subject COV% for NOEMTR ranged from 1.92% to 3.40%, with corresponding inter-subject COVs of 1.50%. tNOE exhibited improved intra-subject repeatability with COVs ranging from 0.75% to 5.57%, but a reduced inter-subject COV of 2.97%. MWF imaging showed the highest stability overall, with an intra-subject COV ranging from 0.47% to 2.03% and an inter-subject COV of 0.75%. Visually, tNOE offers superior contrast in myelin-rich areas compared to NOEMTR and MWF imaging, showing greater sensitivity to myelinated regions. tNOE strongly correlates with histological markers: r = 0.83 with MBP staining and r = 0.72 with LFB staining (both p < 0.001). MWF and NOEMTR showed correlations with MBP (r = 0.63 and r = 0.57, respectively). ConclusionNOEMTR, tNOE, and MWF imaging are reliable and repeatable methods for quantifying macromolecules in the brain. Among these, tNOE emerges as the most sensitive for detecting myelin lipids as confirmed by histological validation. These findings highlight the translational potential of tNOE for studying demyelinating disorders and neurodegenerative diseases.

neuroscience↗

bioRxiv2025

Clodronate liposomes untangle the role of hemocytes in Apis mellifera response to temperature variation and microbial infection

IntroductionThe cellular immune response, mediated by hemocytes, is a fundamental component of honey bee (Apis mellifera) health. However, the specific contribution of hemocyte subtypes to resilience against combined stressors remains poorly characterized. This study investigated the effect of temperature and bacterial challenge on hemocyte abundance. We employed clodronate liposomes (CLD) for the first time in honey bees as a novel tool for the selective depletion of hemocytes to investigate this gap. MethodsFive-day-old (nurses) and fifteen-day-old (foragers) honey bees were treated with CLD, control liposomes, PBS, or left untreated, then exposed at either 32{degrees}C or 22{degrees}C and challenged with the gram-negative bacterium, Escherichia coli, or the gram-positive bacterium, Staphylococcus aureus. Survival, hemolymph volume, total hemocyte counts, and differential hemocyte counts were monitored over seven days from the start of exposure. ResultsThe CLD application demonstrated significant reductions in granulocyte and prohemocyte populations, indicating the highest vulnerability. A temperature drop to 22{degrees}C buffered the negative impact on survival of CLD-induced immunosuppression. While bacterial challenges universally reduced hemocyte counts, we found an age-dependent difference where nurses maintained significantly higher baseline total hemocyte counts than foragers. Furthermore, temperature did not affect overall total hemocyte counts in 5-day-old nurse bees, but in 15-day-old foragers, it significantly modulated the hemocyte response to bacterial infection. ConclusionOur findings show that hemocyte function is non-uniform, with specific subtypes being essential for overall resilience. The results highlight a previously underappreciated role for temperature as a key modulator of immune capacity, particularly in immunocompromised bees. The age-related differences in hemocyte abundance suggest a life-history trade-off that may prompt the increased vulnerability of honey bees as they age. This work establishes CLD as a powerful tool for insect immunology and sets a precedent for using precise immune manipulation to study host-pathogen-environment interactions.

zoology↗

bioRxiv2025

Acute bee paralysis virus regulation of microRNA expression dynamics in the insect host (Apis mellifera) cell line, AmE-711

BackgroundHoney bees (Apis mellifera) are essential pollinators that support global food production and economic stability. Their health and survival are threatened by diminishing floral resources, pesticide exposure, parasitic mites, and microbial and viral diseases. Among these stressors, viral infections are particularly challenging, often exacerbated by the parasitic mite, Varroa destructor, a competent vector of multiple honey bee viruses. Understanding the mechanisms underlying honey bee-virus interactions is critical for mitigating the negative impact of infections on colony health. One understudied aspect is the role of microRNAs (miRNAs) in viral pathogenesis and antiviral defense. miRNAs are short, non-coding RNAs produced by both hosts and pathogens that act as post-transcriptional regulators of gene expression and can influence host-pathogen dynamics during infection. In this study, we used a honey bee-derived cell line to test the hypothesis that viral infection perturbs honey bee- and viral-encoded miRNA expression. MethodsSmall RNA libraries from honey bee AmE-711 cells subjected to one of four treatments: media change only (uninfected), heat-killed Acute bee paralysis virus (ABPV), the viral mimic Poly(I:C), or infectious ABPV, were prepared using an Illumina Truseq kit. Sequencing data were analyzed using miRDeep2 and sRNAtoolbox to identify differentially expressed (DE) miRNAs, which were subsequently validated by RT-qPCR assay. ResultsSequencing yielded > 3.6 x 108 raw reads that were assigned to 12 small RNA libraries, from which, 481 unique miRNAs were identified. Moreover, 15 miRNAs were DE in ABPV-infected cells compared to uninfected cells: miR-2b-5p, miR-33-5p, miR-133-3p, miR-6001-3p, miR-996-3p, miR-965-3p, miR-125-5p, miR-13b-3p, miR-79-3p, miR-971-3p, miR-277-3p, miR-92c-5p, miR-6065-3p, miR-965-5p, and miR-3786-5p. We highlight some of the DE miRNAs identified in ABPV-infected cells that show regulatory effects in other systems in response to infection. ConclusionThis study identified miRNAs differentially expressed in ABPV-infected cells, suggesting roles in either antiviral defense or in promoting viral pathogenesis through suppression of host immune responses. These results provide a foundation for functional studies using honey bee cell lines to clarify the cellular mechanisms governing honey bee-virus interactions.

zoology↗

bioRxiv2025

LFA-1 Interaction with GBP-130 on Plasmodium falciparum-infected Red Blood Cells mediates NK Cell Activation and Parasite Control

Natural Killer (NK) cells contribute to early immunity against Plasmodium falciparum by recognizing and eliminating infected red blood cells (iRBCs), a process mediated in part by the integrin LFA-1. However, the cognate parasite ligand for LFA-1 has remained unknown. Here, we identify Glycophorin Binding Protein-130 (PfGBP-130) as a surface-expressed ligand on iRBCs that binds the I-domain of LFA-1 (LFA-1 I). Using an LFA-1 I-Fc fusion protein, we demonstrate stage-specific binding to iRBCs, and LC-MS/MS analysis of immunopreciptates of I-Fc bound to iRBC revealed PfGBP-130 as a high-confidence interactor. Recombinant PfGBP-130 binds NK and THP-1 cells in an LFA-1-dependent manner. Co-culture assays show that PfGBP-130 promotes NK cell activation, degranulation, and facilitates contact-dependent killing of iRBCs. Neutralizing antibodies against PfGBP-130 significantly impair these responses. Our findings establish PfGBP-130 as the LFA-1 ligand on iRBCs, providing new insight into NK cell-mediated immunity in malaria and identifying a potential target for host-directed interventions.

immunology↗

bioRxiv2025

An effective primary and memory CD8+ T cell response is directed towards an H-2Kb restricted HSV1-gB-SSIEFARL epitope in the experimentally infected zebrafish

We sought to identify and characterize HSV1 specific CD8+ T cells in the experimentally infected zebrafish (zf), a model organism that offers real time tracking of cellular dynamics. We generated a fluorescently labelled class I MHC tetramer of zebrafish using an H-2Kb restricted peptide of gB protein of HSV1 (Uda-HSV1-gB-SSIEFARL-tetramer) for analysing the differentiation of virus-specific CD8+ T cell response. We show that the Uda-SSIEFARL-tetramer+CD8+ T cells rapidly expand in the lymphoid organs and are efficiently recruited to non-lymphoid tissues of HSV1 infected zebrafishes. The expanded cells upregulate effector cytokines; IFN-{gamma}, IL-2, TNF- and cytolyze SSIEFARL-peptide pulsed targets. Uda-SSIEFARL-tetramer+CD8+ T cells efficiently migrate to the infected tissues as demonstrated by fluorescent microscopy and in vivo imaging. The Uda-SSIEFARL-tetramer+ memory cells are recalled in the response following a secondary infection of zebrafish with HSV1. We, therefore, make a rather intriguing observation that zebrafishes infected with HSV1 generate an efficient CTL response against H-2Kb restricted HSV1-gB-SSIEFARL epitope despite their evolutionary divergence from mice [~]445 million years ago. We also argue that zebrafish could serve as a better accessible model organism for studying in vivo dynamics of virus-specific CD8+ T cells.

immunology↗

bioRxiv2025

Nutritional Triggers of PCOS and NAFLD: A Comparative Analysis of Diets in Female C57BL/6J Mice

ObjectiveObesity is a key factor in the development of Polycystic Ovary Syndrome (PCOS) and Non- alcoholic fatty liver disease (NAFLD). Its relationship with reproductive health and metabolic disorders remains an area of interest. Here we aimed to study the effects of two different obesogenic diets in female C57BL/6J mice on their metabolic and reproductive function. MethodsFemale C57BL/6J mice were fed high-fat high-sugar (HFHS) (45% fat and 10% sugar) diet and High fat diet (60% fat) for 21 weeks to investigate the effects on metabolic health and reproductive health. Mice were assessed for body weight, abdominal circumference, glucose tolerance (OGTT) and estrous cyclicity. At the end of the study biochemical analysis was done on isolated serum and, histological assessment of organs including liver and ovarian tissue was done to score for cystic follicle development and steatosis respectively. ResultsMice on the HFHS diet did not gain weight but developed dyslipidaemia, abnormal liver enzyme levels and severe hepatic steatosis. They did not show impaired glucose tolerance and did not develop any PCOS-like ovarian morphology indicating hepatic metabolic disturbances without significant impact on reproductive health. In contrast, mice on the 60% high-fat diet (HFD) showed marginal increase in body weight and developed altered estrous cyclicity and PCOS-like ovarian morphology. They also exhibited impaired glucose tolerance and insulin resistance, confirming a metabolic disturbance associated with PCOS. These mice did not develop significant liver fibrosis, suggesting a more specific impact on the ovaries and glucose metabolism. Our findings suggest that diet composition plays a crucial role in determining the specific metabolic and reproductive outcomes in obesity-related disorders in females.

physiology↗

bioRxiv2025

GPR17 modulates oligodendrocyte precursor cell maturation during development but has limited impact on myelin regeneration following demyelinating insults

Pharmacological enhancement of myelin regeneration is broadly recognized as the next frontier in therapeutic approaches for demyelinating diseases of the CNS such as multiple sclerosis. However, although several molecular targets for remyelination have been tested preclinically and in clinical trials, an efficacious and safe myelin repair treatment is yet to be developed. One promising molecular target to enhance myelin repair is the G protein-coupled receptor (GPCR) GPR17, which has been proposed to play a central role in the transition from early oligodendrocyte progenitor cells (OPC) into pre-myelinating oligodendrocytes. These findings are largely supported by studies using transgenic mice where GPR17 deletion results in developmental hypermyelination. Additionally, pharmacological modulation of GPR17 activity has been reported to enhance oligodendrocyte precursor cell (OPC) maturation and myelination. In our studies aimed to characterize and pharmacologically validate GPR17 as a viable target for drug development, we established by means of transcriptional profiling of GPR17 knockout versus wild type OPCs, that absence of this GPCR results in a gene signature revealing minor changes in myelin protein gene expression. Furthermore, blocking GPR17 receptor activity in OPC cultures using selective and potent antagonists or inverse agonists, results in limited enhancement of maturation and myelination in vitro. Importantly, remyelination in both the cuprizone and lysolecithin-induced demyelination models was not enhanced in the absence of GPR17. Our data demonstrate that GPR17 plays a minor role in OPC differentiation during development, and pharmacological modulation of its activity has a marginal effect on oligodendrocyte precursor maturation and myelin regeneration after injury.

neuroscience↗

bioRxiv2025

SARS-CoV-2 infection disrupts syncytial and endothelial integrity and alters PLGF levels in the placenta

IntroductionSARS-CoV-2 infection during pregnancy has been associated with an increased risk for several pregnancy-related disorders, particularly preeclampsia (PE). However, there are limited studies determining the impact of SARS-CoV-2 on placental physiology and function. MethodsPlacental samples were acquired from two large prospective cohorts: STOP-COVID19 and REBRACO studies. Placental villous tissues (VTs) were collected from pregnant women who tested positive for SARS-CoV-2 without PE during pregnancy. Immunohistochemistry and immunofluorescence were used to assess pathological features known to be altered in PE, including 1) syncytial knot formation; 2) alterations in renin-angiotensin system components; 3) and endothelial integrity. Maternal serum was collected to examine AT1 autoantibodies levels using an immunoassay. ResultsSARS-CoV-2 viral proteins spike, nucleocapsid, and ORF3a were observed in the syncytiotrophoblast layer and stroma of placental VT. SARS-CoV-2-infected placentas exhibited increased numbers of syncytial knots, which were positive for Flt-1 and SARS-CoV-2 viral proteins. In addition, the presence of placental infarctions and excessive fibrin deposits was also observed in infected placentas. Infection was associated with decreased placental expression of PlGF and an increase in the placental Flt-1/PlGF expression ratio, mostly driven by PlGF. No significant changes in maternal serum AT1AA levels were observed. Finally, SARS-CoV-2-infected placentas exhibited a significant decrease in vimentin expression. DiscussionSARS-CoV-2 infection negatively impacts placental integrity in the form of increased syncytial knots, dysregulated RAS components, and endothelial damage. Since all these features are similarly disrupted in PE, this could be a mechanism through which SARS-CoV-2 infection during pregnancy increases the risk of a PE-like syndrome.

microbiology↗

bioRxiv2025

Super-silencers are crucial for development and carcinogenesis in B cells.

The strength of the repressive histone H3 lysine 27 trimethylation modification signal varies drastically at individual silencers. Focusing on cases of an unusually strong repressive signal in regions that we refer to as super-silencers, we demonstrate that the regions that become B-cell super-silencers are originally associated with gene upregulation during development, and their target genes are highly expressed in stem cells, especially during early developmental stages. About 13% of B-cell super-silencers transmute to super-enhancers in B-cell lymphoma and 22% of these conversions recur across more than half of patients. Notably, genes associated with these conversions, like BCL6 and BACH2, are downregulated more swiftly than others when subjected to JQ1, a super-enhancer-disrupting bromodomain and extra-terminal domain inhibitor utilized in cancer chemotherapy. Furthermore, super-silencers are characterized by an over-representation of B-cell-cancer-associated mutations, both somatic and germline, and B-cell-cancer translocation breakpoints. This surpasses the prevalence found in other regulatory elements, such as CTCF binding sites, underlining the crucial role of super-silencers in forming and stabilizing regulatory topologies in standard B cells. For example, over 80% of cases involving the B-cell-lymphoma translocation t(3;14)(q27;q32) fuse super-silencers in the BCL6 locus with enhancer-rich domains. Finally, we demonstrate that the repressive mechanisms of super-silencers are partially governed by the CpG content in their sequences. While CpG-rich super-silencers often prevent promoters from interacting with enhancers, CpG-depleted super-silencers typically suppress the chromatin looping of nearby enhancers. In summary, our findings accentuate the critical role super-silencers play in the normal function of B-cells, suggesting that sequence mutations and activity modifications in these elements could be primary factors in B-cell carcinogenesis.

genomics↗

bioRxiv2025

Magnetic Resonance Imaging for Improved Brain Tumor Detection

Precise demarcation of brain tumor boundaries is critical for optimizing treatment strategies and improving patient outcomes. In vivo characterization of tumor using PET/CT and MRI is clinical standard. PET/CT highlights the metabolic aspects of the tumor, while MRI provides information on functional, metabolic and structural changes. Even with technological advancements in both PET/CT and MRI, a method that can precisely delineate infiltrative tumor boundaries from normal-appearing brain regions (NABR) in vivo is still lacking. To address this limitation, we explored a relatively new MR imaging method, the Nuclear Overhauser Effect Magnetization Transfer Ratio (NOEMTR), in conjunction with a gadolinium-based contrast agent (Gd-DOTA), to precisely delineate the tumor boundaries in a rat model of infiltrative gliosarcoma. NOEMTR imaging was performed in the rat model (n=5) before and after Gd-DOTA administration. The post-Gd-DOTA NOEMTR map was subtracted from the pre-Gd-DOTA map and compared with contrast-enhanced T1-weighted images and immuno-histological findings. The resulting NOEMTR difference map clearly highlighted both the tumor core and infiltrative boundaries, which was not discernible on the post-contrast T1-weighted images. The extended tumor boundaries observed on the NOEMTR difference map corroborated with the IHC image, which confirmed the presence of infiltrative tumor cells and macrophages in these regions. Guided by the NOEMTR difference map, regions of interest (ROI) were drawn to quantify NOEMTR signal changes in the tumor core, tumor boundaries, and NABR post-Gd-DOTA. Tumor core showed a significant [~]43% reduction in NOEMTR signal (plJ=lJ0.003), while the tumor periphery exhibited a moderate reduction of [~]10%, (plJ=lJ0.045). No appreciable change in was observed in the NABR (plJ=lJ0.371). In contrast, the post contrast T1-weighted signal changes in tumor core, tumor periphery and NABR were, 33.32% (p = 0.092), 3.8% (p = 0.478), and 8.7% (p = 0.464) respectively. These findings suggest that NOEMTR imaging provides enhanced tumor contrast, particularly at the infiltrative tumor margins, where conventional contrast enhanced T1-weighted MRI may underestimate tumor extent. Histological validation confirmed the presence of infiltrative tumor cells and macrophages in the tumor periphery, as highlighted by the NOEMTR difference map. Overall, NOEMTR imaging, in combination with Gd-DOTA administration, demonstrates superior delineation of brain tumor boundaries compared to conventional MRI. As NOEMTR imaging is a fast acquisition scan (under 10 minutes) and performed on standard 3 Tesla, it can be easily integrated into clinical protocols. By improving visualization of tumor infiltration and distinguishing tumor regions from NABR, NOEMTR imaging holds promise for advancing neuro-oncological diagnostics and treatment planning.

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