Biology subjects

Brown, K.

Publications and source records attributed to Brown, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Brain and kidney Extracellular Vesicle Morphology and Complementary Brain proteomics after Inflammatory Challenge

Shape, size variation, and protein composition describe different properties of tissue extracellular vesicle (EV) preparations. We compared brain and kidney EV shape and size using transmission electron microscopy (TEM). We also assessed repeated protein detection and reanalyzed a deposited brain proteomics cohort, with attribution to its original source. The study used intracerebroventricular lipopolysaccharide (LPS) and an intravenous miRNA-associated EV formulation. Each group contained three biological samples, as labelled in the source data. Source morphometry summaries included 385 brain and 101 kidney profiles. Kidney circularity was 0.9225, 0.8977, and 0.9288 in the control, LPS, and treatment groups, respectively. The corresponding values for diameter quartile dispersion, a measure of size variation, were 0.2603, 0.5334, and 0.6018. Thus, near-control outline shape coexisted with persistent size variation. None of the six primary morphology tests remained significant after Holm correction. Independent recalculation confirmed 1,527 eligible rat protein accessions across individual searches. The complete quantitative matrix contained 953 features. The main peptide filter combined unique and razor peptides. A stricter analysis retained 916 features. PTGFRN and LAMB2 remained the only significant treatment-versus-LPS findings. In the main analysis, PTGFRN increased 14.71-fold (q = 0.0365), and LAMB2 increased 6.23-fold (q = 0.00585). Their LPS levels were already close to control values. Exploratory normalization used the geometric mean of four measured EV-associated markers. The resulting treatment-versus-LPS increases were 16.43-fold and 6.96-fold, respectively. These ratios support selective changes in relative protein representation within the recovered mixture. They do not establish protein copies per EV. Analysis of the full protein profile and calibration of the complete selection process did not support an overall return to control. This study compares morphology and composition as separate outcomes. It identifies membrane and matrix associations as priorities for validation. Original TEM measurements were unavailable, sample matching remained unresolved, and kidney proteomics were absent. These limitations prevent causal conclusions and individual-sample comparisons between morphology and protein composition.

neuroscience↗

bioRxiv2026

Exploratory Proteomics of Brain Extracellular Vesicle Enriched Preparations After LPS Challenge and miRNA Associated Vesicle Administration

We used brain extracellular vesicle (EV) proteomics to identify protein responses to acute neuroinflammation and an EV-based microRNA intervention. Rats received vehicle, intracerebroventricular lipopolysaccharide (LPS), or LPS followed by an intravenous EV formulation containing anti-inflammatory microRNAs (miRNAs). Brains were collected 24 h after LPS or vehicle administration, and three independently processed animal-derived EV-enriched preparations per group were analyzed by label-free proteomics. Across all nine samples, 953 protein groups had complete normalized abundance measurements. Compared with vehicle controls, LPS exposure was associated with 227 exploratory protein changes, comprising 95 increases and 132 decreases at nominal P < 0.05 and an absolute log2 fold change >= log2(1.5). Increased proteins were enriched for translation-related annotations, whereas decreased proteins were enriched for plasma-membrane annotations. These LPS-associated changes did not remain significant after Benjamini-Hochberg correction at a false discovery rate (FDR) threshold of q < 0.05. Following treatment, 119 of the 227 candidates were closer to control abundance on the log2 scale; 23 candidates also showed nominal treatment-versus-LPS differences. Lamb2 and Ptgfrn were the two proteins that differed significantly between treated and LPS-only animals after FDR correction, identifying them as priorities for further validation. Nevertheless, 174 proteins differed significantly between treated animals and vehicle controls, and analysis across the measured proteins did not demonstrate an overall shift toward control values. Thus, the intervention was associated with specific protein responses, but treated animals retained substantial differences from controls. This study identifies candidate markers for investigating treatment responses in brain EV-enriched preparations and demonstrates the value of examining individual proteins alongside broader proteomic changes. Independent validation is needed to determine their functional relevance and distinguish miRNA-specific effects from contributions of the administered EV carrier.

neuroscience↗

bioRxiv2026

Cell cycle dependent regulation of mRNA export in response to replication stress

Nuclear export of mRNA is extensively coupled to transcription and processing of mRNA. How mRNA export is mechanistically regulated remains poorly understood. Here, we uncover a physical checkpoint at nuclear speckles that regulates mRNA export during DNA replication in S-phase of the cell cycle. Unbiased screening approaches identify WEE1 and CHK1 as novel mRNA export regulators. mRNA export complexes are recruited to sites of replication stress in S-phase. WEE1 inhibition prematurely activates CDK1 and PLK1, leading to accumulation of R-loop associated mRNA in large nuclear speckles, with late markers of replication stress present around their periphery. This recruitment is dependent on CDK1 activity. Phosphorylation of ALYREF by CDK1 and PLK1 regulates nuclear speckle accumulation of mRNA following replication stress. mRNA export factors including ALYREF are subsequently mis-localised from these speckles, preventing nuclear export of R-loop associated mRNA. Thus, WEE1, CDK1 and PLK1 enforce a cell cycle regulated checkpoint at nuclear speckles that serves to protect the cell from major sources of genome instability by ensuring that R-loop associated mature mRNA is not exported to the cytoplasm.

molecular biology↗

bioRxiv2026

Spatial MALDI-MSI Reveals a Coordinated Vicious Cycle of Oxidative Membrane Damage and Ceramide-Driven Sphingolipid Dysregulation in the Chronically Neuroinflamed Brain

BackgroundChronic neuroinflammation is a major driver of cognitive decline, vascular cognitive impairment, and Alzheimers disease. However, the spatial lipidomic alterations underlying neuroinflammatory brain injury remain poorly defined. Oxidative stress and sphingolipid dysregulation have been implicated, but their regional distribution and interplay in the brain are not well characterized. MethodsWe performed positive-ion mode matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) on coronal brain sections from middle-aged spontaneously hypertensive rats (SHR), a model of chronic neuroinflammation, and normotensive Wistar-Kyoto (WKY) controls. Spatial distributions and relative abundances of multiple lipid classes, including phosphatidylcholines (PCs), sphingomyelins (SMs), hexosylceramides (HexCers), ceramides, phosphatidylserines (PSs), phosphatidylinositols (PIs), phosphatidylethanolamines (PEs), phosphatidic acids (PAs), and sulfatides, were mapped and compared between genotypes. Region-of-interest analysis was used to quantify changes across cortex, hippocampus, and white-matter tracts. ResultsSHR brains exhibited a coordinated lipidomic signature characterized by pronounced oxidative stress and membrane remodeling. Oxidized and short-chain PCs were markedly upregulated (up to 11.6-fold), while major structural diacyl PCs were broadly downregulated. Concurrently, sphingolipids were significantly altered, with robust upregulation of SM(d36:1) (7.5-fold) and multiple HexCer species (1.5-1.9-fold), accompanied by accumulation of ceramides. These changes were accompanied by heterogeneous redistribution of PS, PI, and PE species, particularly within the hippocampus. Sulfatide patterns in white-matter tracts were also altered, suggesting myelin remodeling. Region-of-interest analysis confirmed that the most pronounced lipid alterations were concentrated in the hippocampus and white-matter regions. ConclusionsChronic neuroinflammation induces a spatially organized, multi-class lipid remodeling response in the brain, driven by advanced oxidative membrane damage and a shift toward a pro-apoptotic sphingolipid profile. The convergence of these pathways creates a vicious cycle of membrane injury, mitochondrial dysfunction, and sustained neuroinflammation that is especially prominent in the hippocampus and white matter. These spatially resolved findings provide direct evidence that oxidative stress and sphingolipid dysregulation are central, interrelated mechanisms contributing to neurovascular injury and increased risk of cognitive impairment. The study highlights the power of MALDI-MSI to uncover region-specific lipid pathology and identifies potential lipid-based targets for therapeutic intervention in neuroinflammatory brain disease. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/738110v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@853af9org.highwire.dtl.DTLVardef@e2d079org.highwire.dtl.DTLVardef@e4e065org.highwire.dtl.DTLVardef@480d80_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Age-Dependent Spatiotemporal Remodeling of Brain Sphingolipids During LPS-Induced Neuroinflammation: MALDI-MSI Reveals Accelerated Sphingomyelin Depletion and Sulfatide Accumulation Linked to Mitochondrial Oxidative Stress

Aging is a major risk factor for exacerbated neuroinflammation and neurodegenerative diseases, yet the underlying lipid metabolic mechanisms remain incompletely understood. Here, we employed high-resolution matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) combined with quantitative peak-area analysis and conceptual kinetic modeling to investigate age-dependent sphingolipid remodeling in the rat brain following intracerebro-ventricular (ICV) LPS challenge. In old rats, MALDI-MSI revealed pronounced and progressive sphingolipid dysregulation compared with young animals. Quantitative analysis showed a dramatic [~]10-fold reduction in SM(d36:1) and [~]4-fold reduction in SM(d42:2), accompanied by significant accumulation of long-chain sulfatides (2.12-fold increase in C24:1-sulfatide and 1.45-fold increase in C24(OH)-sulfatide) at both 24 h and 72 h post-LPS. Spatial imaging demonstrated that these changes were markedly amplified in white matter regions and became more widespread and intense at 72 h. A simplified Michaelis-Menten kinetic model successfully recapitulated the experimental data, identifying increased nSMase2 activity (higher Vmax) as the primary driver of accelerated sphingomyelin hydrolysis and subsequent ceramide rerouting into sulfatide synthesis. This metabolic shift generates excess ceramide that promotes Drp1-mediated mitochondrial fission, elevates mitochondrial ROS production, and disrupts bioenergetics, establishing a feed-forward loop linking sphingolipid remodeling to mitochondrial oxidative stress and white matter vulnerability in the aged brain. These findings provide the first spatially and temporally resolved demonstration of age-dependent sphingolipid metabolic reprogramming during neuroinflammation. By integrating multimodal MALDI-MSI, quantitative lipidomics, and kinetic modeling, this study reveals a previously underappreciated nSMase2-ceramide-mitochondrial axis in neuroinflammaging. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/734865v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@be7a9eorg.highwire.dtl.DTLVardef@164499dorg.highwire.dtl.DTLVardef@11cea50org.highwire.dtl.DTLVardef@15b2ac2_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Self-antigen disrupts cDC1 mediated antitumor responses

Conventional dendritic cells navigate complex tissues and sample peripheral antigens, balancing immune suppression and activation to achieve tissue homeostasis. However, it remains unclear how an individual dendritic cells reconciles co-incident signals from immunological opposing antigens within the tissue or tumor microenvironment, where tolerogenic self-antigen and immunogenic tumor antigen or microbes coexist. Here, using complementary in vivo fluorescent reporter systems, high-resolution imaging and endosomal profiling, we simultaneously tracked uptake, intracellular processing and cross-presentation of cutaneous self, tumor and microbial antigens in murine skin tissue, tumors and draining lymph nodes. We find that a substantial fraction of dendritic cells acquire antigen from multiple sources and that localization within endosomal compartments is dictated by antigen source. Notably, type 1 conventional dendritic cells that co-process self and tumor antigen represent a significant proportion of tumor antigen-bearing dendritic cells in the tumor and tumor draining lymph node. These dual-antigen loaded dendritic cells display a diminished capacity to prime tumor-specific CD8+ T cells and a marked reduction in tumor derived peptide presented on surface MHCI, while cross-priming of self-antigen specific T cells is significantly increased. These changes occur despite equivalent or greater tumor antigen uptake relative to self-antigen and high expression of surface MHCI and costimulatory molecules. Together, these data support a model in which multiantigen processing within dendritic cells can bias peptide loading away from tumor-derived epitopes, thereby limiting tumor-specific cross-priming. Modulating the antigenic context of the tumor microenvironment or endosomal routing after antigen uptake may therefore represent a strategy to restore effective dendritic cell-mediated antitumor immunity.

immunology↗

bioRxiv2026

Ontological Analysis of Brain Proteostasis Highlights the Sex-Dependent Trajectory of ApoE Isoform-Specific Regulation

Apolipoprotein E (ApoE) is the strongest genetic predictor of Alzheimers disease (AD) risk, with ApoE4 increasing and ApoE2 decreasing risk relative to ApoE3. Using a global LC-MS proteomic approach, we integrated protein abundance and kinetics in Human-APOE knock-in mice for young (3-month) and aged (18-month) cohorts to quantify the changes in steady-state proteostasis. By mapping 6,052 identified proteins and 3,986 associated turnover rates into ontological groups, we observed that vesicle trafficking and mitochondrial dysregulation occur as early as 3 months in ApoE4 mice accompanied by hyperactive metabolism that eventually reduces with age. In contrast, young and old ApoE2 mice retain similar signatures to ApoE3 mice in metabolic, mitochondrial, cellular regulation, and membrane trafficking ontologies. We found that females had more isoform-induced ontological changes relative to ApoE3, providing insight into sex-dependent vulnerabilities. Our global proteomic approach for ApoE proteostasis crucially unifies independent literature observations while providing turnover kinetics to uncover the underlying mechanism behind abundance changes. Data are available via ProteomeXchange with identifier PXD079261. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/735293v1_ufig2.gif" ALT="Figure 1000"> View larger version (45K): org.highwire.dtl.DTLVardef@28ebfforg.highwire.dtl.DTLVardef@9dc6f2org.highwire.dtl.DTLVardef@704577org.highwire.dtl.DTLVardef@e0b0e2_HPS_FORMAT_FIGEXP M_FIG C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/735293v1_ufig1.gif" ALT="Figure 1001"> View larger version (48K): org.highwire.dtl.DTLVardef@17d0474org.highwire.dtl.DTLVardef@af771borg.highwire.dtl.DTLVardef@1b49f67org.highwire.dtl.DTLVardef@14d3aa2_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Global Proteomics Investigation of SAMT-247 Targets: An Antiviral Thioester that Acetylates Zinc Finger Proteins

Covalent modification of target proteins is a well-established mechanism of action for small molecule inhibitors. Cysteine residues in particular have been exploited for their reactivity toward electrophilic molecules. SAMT-247 is a mercaptobenzamide thioester that covalently acetylates cysteines in the zinc-coordinating domains of the HIV nucleocapsid protein. This SAMT-247-promoted reaction leads to loss of zinc binding by the protein, with concomitant loss of protein structure and function. Although it has low cytotoxicity in animal models, recent studies have indicated that it affects other protein targets in uninfected cells, for example leading to increased immune cell functions. In this study, global proteomics approaches have been used to better understand other protein targets of SAMT-247. Minimal effects are observed when unstimulated THP-1 monocyte cells were treated with SAMT-247. In contrast, thermal proteome profiling identified 170 proteins with altered thermal stability when THP-1 cells were stimulated with phorbol 12-myristate 13-acetate/Ionomycin (PMA/Iono) before SAMT-247 treatment. Among the affected proteins, 81 contain a zinc-coordinating domain and/or have been shown to have a reactive cysteine residue. Among these, several play a role in cellular metabolism, and Seahorse assays demonstrated that SAMT-247 significantly increased the anti-metabolic and pro-glycolytic effect of PMA/Iono in THP-1 cells. Two of the most-affected proteins were ZC3H7A, a microRNA-binding protein with four zinc finger domains, and MGMT, a DNA damage repair protein with a reactive cysteine. Both proteins were modified by SAMT-247 when tested alone or in the presence of THP-1 cell lysate, indicating that they are bona fide targets of the inhibitor. The low activity of SAMT-247 in unstimulated THP-1 cells is consistent with its low cytotoxicity. The increased effects of SAMT-247 in stimulated immune cells suggests that this molecule could be developed to target diseases other than HIV.

cell biology↗

bioRxiv2026

Bone microarchitecture and material properties decline differently across midlife for male and female F344 x BN F1 rats

While bone mineral density (BMD) remains the clinical standard for assessing age-related fracture risk, accumulating evidence indicates that bone quality, including matrix properties and microarchitecture, contributes to fracture susceptibility in ways not captured by BMD alone. As matrix-targeted therapeutics emerge, preclinical models that exhibit translationally relevant bone quality changes are needed. Here, we evaluated the Fischer 344 x Brown Norway (F344xBN) F1 rat, a strain characterized by hybrid vigor and non-pathological aging, as a model for studying matrix-related mechanisms of skeletal aging. Femurs from male and female rats aged 7, 15, and 22 months were analyzed to quantify age- and sex-dependent changes in bone microarchitecture, fracture resistance, and matrix properties. Microcomputed tomography analyses revealed sexually dimorphic aging trajectories. From 7 to 22 months, females exhibited moderate declines in trabecular microarchitecture and no change in cortical porosity, whereas males showed pronounced trabecular deterioration and increased cortical porosity. Whole-bone flexural testing demonstrated age-related declines in material properties that were not attributable to changes in geometry, while females maintained geometry-scaled bone strength. Both sexes exhibited reduced bone toughness with age. Raman spectroscopy identified matrix-level alterations in males by 15 months, whereas systemic markers of bone turnover remained unchanged across age or sex. Together, these findings indicate that males exhibit combined tissue-scale and whole-bone deterioration by midlife, while females exhibit declining fracture resistance preceding substantial cortical bone loss or overt matrix deterioration. These results support the F344xBN F1 rat as a translational model for investigating matrix-driven skeletal aging. Lay summaryF344 x BN F1 hybrid rats provide a healthy, matrix-driven skeletal aging model. This strain exhibits distinct aging trajectories dependent on sex. Strength and toughness decrease in both sexes by midlife. Fracture resistance declines in females prior to substantial bone loss.

physiology↗

bioRxiv2026

YAP disrupts bile acid homeostasis to drive cancer-associated cachexia

Cancer-associated cachexia is a severe metabolic syndrome marked by dramatic loss of adipose and muscle mass. Although preclinical models have advanced our understanding of cachexia, there are still no approved therapies due to the limited insights into the mechanisms underlying tissue wasting. Here, we utilise a YAP-driven model of liver cancer in zebrafish, which rapidly develops cachexia, to uncover an evolutionarily conserved role for bile acid disruption in the onset of cachexia. Spatial transcriptomic analysis revealed that YAP induces a bi-lineage cholangiocarcinoma phenotype, which was associated with bile acid dysregulation. Mechanistically, we establish that both bile acid synthesis (via CYP7A1) and signalling through the bile acid receptor TGR5 are essential for cachexia induction. Notably, we find that the promotion of bile acid excretion with odevixibat ameliorates cachexia. Together, our findings reveal an evolutionarily conserved mechanism by which YAP promotes cachexia and suggest a potential therapeutic strategy to treat the syndrome.

cancer biology↗

bioRxiv2026

Expression of Retroviruses in Guinea Pig Lymphomas.

Retroviruses commonly cause neoplasia in many species but have not been described in guinea pigs. While historical evidence exists for the presence of an active retrovirus in domestic guinea pigs (Cavia porcella), there has been no description of the sequence of these viruses or their role in disease in guinea pigs. This paper uses genome mining of the published domestic and wild (Cavia aperea) guinea pig genomes for retroviral sequences to identify the gamma and beta-retroviral complement of the Cavia genome, describing eight groups of viruses with evidence of recombination between virus groups. The most intact group, gamma-like retroviruses related to HERV-T (integration estimates of 855,000 to 3.8 million years ago), has five near full length loci that are likely capable of active infection. RNA-Scope In-situ Hybridisation of archived formalin-fixed, paraffin embedded (FFPE) guinea pig lymphoma sections with a probe for one of these loci demonstrated viral RNA expression in lymphoma tissue, strengthening the case for a role of these viruses in the high incidence of leukaemia and lymphoma in this species.

microbiology↗

bioRxiv2026

Quantifying growth and lodging in Tef (Eragrostis tef) with Uncrewed Aerial Systems (UAS)

Lodging is a major contributor to decreased yield in tef, a staple cereal crop in Ethiopia. Semidwarf varieties have been developed with a goal to increase yield through reduced lodging, but studying lodging susceptibility currently requires a labor-intensive, imprecise, manual scoring method. Here we present workflows for analyzing tef stand height from UAS sensors across time to both predict lodging later in the season with early height and to measure the severity of lodging after a storm event. We compare 3D point clouds generated by photogrammetry from RGB images with those generated from LiDAR to estimate height, demonstrating that they produce similar results, despite differences in cost. Stand height and lodging can both be accurately measured with low-cost UAS, reducing the need for manual measurements and increasing precision and temporal resolution in plant breeding programs. Significance StatementExtreme weather or heavy grain can cause plant stems to bend, a process called lodging. Lodging significantly reduces crop yields globally, particularly in grain crops such as tef (Eragrostis tef). Semidwarf crops have previously been reported to be lodging-resistant, increasing crop yields. Here, we used uncrewed aerial systems (UAS) to measure plant growth, height, and lodging in gene edited semidwarf tef lines, and compared the results to ground-truth data. Using a UAS equipped with a red-green-blue (RGB) camera or LiDAR sensor, we measured plant height and lodging, and found that early-season height measurements could predict future lodging potential. The tools used were contributed to the open-source software PlantCV-Geospatial for community use. This work contributes to a broader understanding of genetic resistance to lodging, providing valuable insights for tef crop improvement and reduces the need for labor-intensive manual measurements.

plant biology↗

bioRxiv2026

Smartphone image capture system and image analysis pipelines enable accurate and efficient phenotyping of spaced plant mapping populations

Plain Language SummaryThe lack of low-cost, user-friendly and expedient methods for plant phenotyping challenges researchers ability to efficiently collect accurate phenotypic data in large field experiments. Here, we demonstrate the use of a novel, smartphone-based image capture system and two user-friendly image analysis pipelines (utilizing PlantCV or Biodock AI) to increase the throughput of plant phenotyping in two large, spaced plant populations. We showed that the image capture system collected images of adequate quality for downstream analysis using either the PlantCV or Biodock AI pipeline. Both image analysis pipelines produced phenotype values in line with those obtained using manual image annotation. Together, these results provide researchers with a low-cost, user-friendly image-based phenotyping method that can be widely applied to increase phenotyping throughout in field experiments.

plant biology↗

bioRxiv2026

Comprehensive hallmark gene sequence, genomic and structural analysis of Picornavirales viruses clarifies new and existing taxa

The order Picornavirales is a group of highly diverse RNA viruses that includes many pathogens of significance to human and veterinary health, agriculture and the wider environment. However, the wide range of viruses assigned to the order, together with their genomic variability, and the recent description of numerous "picorna-like" viruses derived from metagenomic analyses of environmental samples, challenges the existing taxonomic classification of members of the order and the criteria for their classification. Here, we combine the existing gold standard, hallmark RNA-dependent RNA-polymerase (RdRp) gene sequence-based analysis with helicase sequence-based phylogeny, RdRp structural prediction through the use of ColabFold and Fold Tree, and analysis of coding complete genomes using GRAViTy-V2, to genetically classify 525 Picornavirales genomes and recently described "picorna-like" viruses. All analyses were conducted with a bespoke, fully automated pipeline for retrieval of genomes, domain classification and extraction, phylogenetic analysis, and output conditioning, which is available as open-source software. Our results reveal broad support for existing families as well as for six novel families, and 32 new genera. In instances where inconsistencies were found between classification methods, we demonstrate how examination of the pipelines output may be used to reconcile differences with respect to the genomic features quantified by the analysis. Automated multimodal taxonomic analysis may save significant resources over manual methods and better define demarcation criteria for families and genera.

microbiology↗

bioRxiv2025

Identifying High-Dimensional Genomic Factors Modulating Biological Networks Across Multi-Omics Data

Biological traits such as genes, metabolites, and microbial taxa interact within complex networks, yet how genomic factors shape these interactions remains poorly understood. Here, we introduce GFBioNet, a computationally efficient method for identifying factors that modulate direct associations between biological traits within network models. Our two-stage strategy first estimates a baseline network using Gaussian graphical models and then tests whether genomic factors modulate specific network edges (trait-trait relationships), enabling scalable analysis of high-dimensional multi-omics data while explicitly controlling the false discovery rate (FDR). Simulations demonstrate reliable FDR control and high statistical power across a broad range of settings. Applied to multiple datasets, GFBioNet reveals host genetic variants influencing oral microbiome relationships, gut microbial taxa modulating metabolite networks in colorectal cancer, and somatic mutations and copy-number alterations reshaping gene expression networks in lung adenocarcinoma. By expanding network analysis to evaluate modifiers of trait-trait relationships, GFBioNet offers a versatile tool for uncovering the genomic architecture of biological networks across multi-omics studies.

genomics↗

bioRxiv2025

Integrative multi-omic analysis identifies key transcription factors and target proteins in renal cell carcinoma and its subtypes

To characterize key transcription factors (TFs) whose differential DNA binding can be altered by genetic variants associated with risk for renal cell carcinoma (RCC), we conducted a series of mixed model-based analyses integrating 449 TF ChIP-seq profiles across 9 kidney-related cell lines and summary statistics from a multi-ancestry genome-wide association study of RCC. We identified 96 unique TFs for which presence of SNPs in a neighborhood of TF ChIP-seq peaks are significantly associated (p-value <1x10-4) with their effect on RCC, including EPAS1, ARNT, PAX8 and PBRM1, previously implicated in RCC pathogenesis. Most TFs overlapped active promoters/enhancers in RCC tumors but remained significant after adjusting for tumor chromatin accessibility. Further, we found the co-occupancy of 220 pairs of RCC-related TFs to be associated with RCC risk (FDR<5%) beyond effects of individual TFs, highlighting synergistic regulation between pairs of TFs. To further investigate distal (trans) regulation of TF-binding disruption at RCC associated loci on the proteome, we used a set-based regression to aggregate the trans-effects of multiple loci overlapping with TF binding sites. Across 2,732 proteins profiled in UKB-PPP, identified 169 trans-associated (p-value<1.6x10-7) proteins, nominating specific targets for each TF. For example, we identified TLR3 and ZP3 to be associated with EPAS1, ARNT, and PBRM1, indicating these proteins are likely affected by RCC-related variants disrupting binding sites of the corresponding TFs. These results characterize the landscape of RCC-related TFs and implicate TF-mediated proteomic mechanisms in RCC pathogenesis, nominating testable targets for laboratory studies.

genetics↗

bioRxiv2025

Contextual control of CD8+ T cell priming by dendritic cell subsets in tumor and inflammatory microenvironments

Conventional dendritic cells orchestrate adaptive immunity by trafficking peripheral antigens to draining lymph nodes and presenting peptide-MHC complexes to prime naive T cells. Migratory and lymph node resident conventional dendritic cell subsets occupy distinct anatomical niches and have been shown to shape T cell activation in a variety of immunologic contexts including infection, vaccination and cancer. How peripheral tissue context and dendritic cell subset specific transcriptional programs collaborate to determine CD8+ T cell priming remains incompletely defined. Using fluorescent antigen, we tracked antigen distribution, dendritic cell transcriptional programming, and functional cross-presentation across tumor, inflammatory, and steady state tissue contexts. We find that skin tumor antigen is more widely distributed amongst draining lymph node conventional dendritic cells than skin antigen derived from either steady state or inflamed skin tissue. Comparing across dendritic cell subsets, migratory type 1 dendritic cells display higher expression of MHCI antigen presentation machinery and genes associated with cross-presentation compared with lymph node resident type 1 dendritic cells in tumor and inflamed tissue contexts. Similarly, they exhibited superior per-cell cross-presentation and stronger induction of naive CD8+ T cell responses. We find that both antigen access in the lymph node and context-specific cross-presentation efficiency together predict the magnitude and quality of CD8+ T cell priming. These results identify migratory dendritic cells, particularly type 1, as central mediators of antitumor CD8+ T cell responses and support therapeutic strategies that augment the efficiency of resident dendritic cell cross-presentation.

immunology↗

bioRxiv2025

The ecology and adaptive function of clownfish color patterns

Anti-predator coloration strategies vary widely from conspicuous to cryptic, and everything between. Coloration serves multiple functions, and determining the selective pressures that drive this diversity is a long-standing mystery. Clownfishes display enormous inter- and intra-specific variation in coloration without the influence of sexual selection, providing an excellent system in which to explore these drivers in closely related and sympatric species. Across clownfishes, three color-pattern phenotypes have evolved convergently with host anemone use, implying adaptive functions linked to the hosts physical and chemical properties. Here we conducted a comprehensive study to infer the ultimate functions of clownfish color patterns. By integrating multiple levels of biological organization, including behavior, visual ecology, dietary niche, and microbiome, our data overwhelmingly indicate that specialist and generalist clownfish color patterns have different underlying ecologies and adaptive functions. Specialist clownfishes background match their anemones, remain near hosts, and have specialized diets and microbiomes. Generalists are highly contrasting with their anemones, remain far from hosts, and have variable diets and microbiomes. Taken together, specialist color patterns align with functional expectations of camouflage while generalists align with aposematic or disruptive coloration. Our study provides novel insights into how ecological conditions shape the evolution of multiple anti-predator coloration strategies.

ecology↗