Biology subjects

Weaver, D.

Publications and source records attributed to Weaver, D..

10 recordsLinked to original sources

bioRxiv2026

Transcriptome-wide Differential Expression and Splicing in Inflammatory Bowel Disease Patients

The inflammatory bowel diseases (IBD), comprising mainly Crohn's disease (CD) and ulcerative colitis (UC), are characterized by chronic intestinal inflammation driven in part by complex genetic and gene regulatory mechanisms. Although transcriptomic studies have defined broad expression changes in IBD, the contribution of alternative splicing to disease-associated molecular variation remains less clear. We therefore integrated differential expression (DE) and differential splicing (DS) analyses in macroscopically uninvolved colonic mucosal biopsies from patients with either CD or UC along with non-IBD controls to define gene expression and intron-usage changes across disease subtypes. We identified 491 DS and 316 DE genes in CD vs. non-IBD, and 1,298 DS and 1,107 DE genes in UC vs. non-IBD. DS and DE genes were nearly mutually exclusive, with no overlapping genes in CD and 16 in UC. Consistent with this result, pathway analysis showed that differentially expressed and differentially spliced genes were associated with related but distinct biological programs. DE genes were involved in chromatin organization, transcriptional regulation, and metabolic pathways for glycans and drugs, whereas DS genes were enriched for splicing, cellular signaling, and lipid metabolism. We found substantial similarity in enriched pathways across CD and UC with some notable exceptions, including increased enrichment of DS and DE genes involved in extracellular vesicles and exosomes in CD and enrichment of DS genes in ER-to-Golgi trafficking and stress granules in UC. Direct comparisons of CD and UC patients additionally show differential splicing usage in genes involved in cell adhesion pathways. These findings identify alternative splicing as a major contributor to transcriptomic changes in IBD that is largely distinct from changes in expression level and provide a broader view of molecular contributors to IBD.

genomics↗

bioRxiv2026

Fatty Acid Oxidation Suppression Reprograms Fibroblasts in Fibrostenotic Crohns Disease

Fibrostenotic complications represent a major cause of morbidity in Crohns disease (CD), yet the cellular mechanisms that drive intestinal fibrosis independent of active inflammation remain poorly understood. Here, we identify impaired fatty acid oxidation (FAO) as a defining metabolic feature of fibroblasts in fibrostenotic CD. Untargeted lipidomics of non-inflamed colonic tissue from CD patients demonstrated enrichment of triacylglycerols and long-chain acylcarnitines, suggesting altered lipid utilization. Across three independent RNA-sequencing cohorts, including treatment-naive pediatric ileal biopsies, FAO genes (CPT1A, CPT2, SLC25A20) were selectively downregulated in patients with or destined to develop fibrostenotic disease. Single-cell RNA-sequencing localized these transcriptional alterations specifically to fibroblasts within strictured ileum. Primary fibroblasts derived from fibrostenotic CD exhibited increased neutral lipid accumulation, impaired mitochondrial fatty acid trafficking, and diminished responsiveness to PPAR{gamma}-mediated suppression of TGF{beta}-induced myofibroblast activation. Together, these findings demonstrate that FAO impairment is a conserved, fibroblast-specific metabolic program associated with intestinal fibrosis in CD and suggest that metabolic modulation of stromal cells represents a potential therapeutic strategy for fibrostenotic disease.

genomics↗

bioRxiv2025

Reference-guided Genome Assembly of Long Non-coding RNA Transcripts reveals Target Genes Associated With Crohn's Disease

Crohns disease (CD) is highly heterogeneous in presentation and progression with no cure. Molecular phenotyping has been used to elucidate cellular and tissue-based alterations to characterize drivers and effects of disease. One currently understudied class of functional molecules is long non-coding RNAs (lncRNAs). Studying the full lncRNA landscape in IBD is challenging due in part to an incomplete lncRNA annotation and a lack of their functional characterization in tissues of interest. We used a genome-guided alignment strategy to assemble predicted lncRNA transcripts using short RNA-sequencing data from colon tissue of adult patient samples. When combining our predicted lncRNAs with previous lncRNA annotations, we determined 98 that were differentially expressed, recapitulating many from previous IBD studies while also uncovering new ones. We built gene co-expression networks to cluster lncRNAs with functionally characterized protein-coding genes. Clusters containing differential lncRNAs were correlated to disease status and associated with pathways related to the humoral immune response, metabolism, and tissue regeneration. We uncovered multiple differential lncRNAs whose expression significantly correlated with nearby differential protein-coding genes that have also been differentially expressed in other IBD datasets, such as PITX2. We focused on a predicted lncRNA that is antisense to the PITX2-adjacent lncRNA PANCR, which we called PANCR-AS1, and provide multiple lines of evidence that support PANCR-AS1 functioning as an enhancer of PITX2 expression. Overall, we determined lncRNAs that are potential contributors to CD pathogenesis. We developed a robust pipeline for identifying lncRNAs in diseased and non-diseased tissue that are absent from reference annotations. We also outlined a framework to pinpoint significant disease-associated lncRNAs with potential functional activity related to their nearby protein-coding genes.

genomics↗

bioRxiv2023

Tumor microenvironmental determinants of high-risk DCIS progression

ABSTRACT/SUMMARYDuctal carcinoma in situ (DCIS) constitutes an array of morphologically recognized intraductal neoplasms in the mammary ductal tree defined by an increased risk for subsequent invasive carcinomas at or near the site of biopsy detection. However, only 15-45% of untreated DCIS cases progress to invasive cancer, so understanding mechanisms that prevent progression is key to avoid overtreatment and provides a basis for alternative therapies and prevention. This study was designed to characterize the tumor microenvironment and molecular profile of high-risk DCIS that grew to a large size but remained as DCIS. All patients had DCIS lesions >5cm in size with at least one additional high-risk feature: young age (<45 years), high nuclear grade, hormone receptor negativity, HER2 positivity, the presence of comedonecrosis, or a palpable mass. The tumor immune microenvironment was characterized using multiplex immunofluorescence to identify immune cells and their spatial relationships within the ducts and stroma. Gene copy number analysis and whole exome DNA sequencing identified the mutational burden and driver mutations, and quantitative whole-transcriptome/gene expression analyses were performed. There was no association between the percent of the DCIS genome characterized by copy number variants (CNAs) and recurrence events (DCIS or invasive). Mutations, especially missense mutations, in the breast cancer driver genes PIK3CA and TP53 were common in this high-risk DCIS cohort (47% of evaluated lesions). Tumor infiltrating lymphocyte (TIL) density was higher in DCIS lesions with TP53 mutations (p=0.0079) compared to wildtype lesions, but not in lesions with PIK3CA mutations (p=0.44). Immune infiltrates were negatively associated with hormone receptor status and positively associated with HER2 expression. High levels of CD3+CD8-T cells were associated with good outcomes with respect to any subsequent recurrence (DCIS or invasive cancer), whereas high levels of CD3+Foxp3+ Treg cells were associated with poor outcomes. Spatial proximity analyses of immune cells and tumor cells demonstrated that close proximity of T cells with tumor cells was associated with good outcomes with respect to any recurrence as well as invasive recurrences. Interestingly, we found that myoepithelial continuity (distance between myoepithelial cells surrounding the involved ducts) was significantly lower in DCIS lesions compared to normal tissue (p=0.0002) or to atypical ductal hyperplasia (p=0.011). Gene set enrichment analysis identified several immune pathways associated with low myoepithelial continuity and a low myoepithelial continuity score was associated with better outcomes, suggesting that gaps in the myoepithelial layer may allow access/interactions between immune infiltrates and tumor cells. Our study demonstrates the immune microenvironment of DCIS, in particular the spatial proximity of tumor cells and T cells, and myoepithelial continuity are important determinants for progression of disease.

cancer biology↗

bioRxiv2023

Robust and scalable single-molecule protein sequencing with fluorosequencing

The need to accurately survey proteins and their modifications with ever higher sensitivities, particularly in clinical settings with limited samples, is spurring development of new single molecule proteomics technologies. Fluorosequencing is one such highly parallelized single molecule peptide sequencing platform, based on determining the sequence positions of select amino acid types within peptides to enable their identification and quantification from a reference database. Here, we describe substantial improvements to fluorosequencing, including identifying fluorophores compatible with the sequencing chemistry, mitigating dye-dye interactions through the use of extended polyproline linkers, and developing an end-to-end workflow for sample preparation and sequencing. We demonstrate by fluorosequencing peptides in mixtures and identifying a target neoantigen from a database of decoy MHC peptides, highlighting the potential of the technology for high sensitivity clinical applications.

molecular biology↗

bioRxiv2023

Mycobiome analyses of critically ill COVID-19 patients suggests antifungal prophylaxis may be protective against A. fumigatus-associated mortality

RationaleCOVID-19-associated pulmonary aspergillosis (CAPA) is a life-threatening complication in patients with severe COVID-19. Previously, acute respiratory distress syndrome in patients with COVID-19 has been associated with lung fungal dysbiosis, evidenced by reduced microbial diversity and Candida colonisation. Increased fungal burden in the lungs of critically ill COVID-19 patients is linked to prolonged mechanical ventilation and increased mortality. However, specific mycobiome signatures associated with severe COVID-19 in the context of survival and antifungal drug prophylaxis have not yet been determined and such knowledge could have an important impact on treatment. ObjectivesTo understand the composition of the respiratory mycobiome in critically ill COVID-19 patients with and without CAPA and the impact of antifungal use in patient outcome. MethodsWe performed a multi-national study of 39 COVID-19 patients in intensive care units (ICU) with and without CAPA. Respiratory mycobiome was profiled using ITS1 sequencing and Aspergillus fumigatus burden was further validated using qPCR. Fungal communities were investigated using alpha diversity, beta diversity, taxa predominance and taxa abundances. ResultsRespiratory mycobiomes of COVID-19 patients were dominated by Candida and Aspergillus. There was no significant association with corticosteroid use or CAPA diagnosis and respiratory fungal communities. Increased A. fumigatus burden was associated with mortality and, the use of azoles at ICU admission was linked with an absence of A. fumigatus. ConclusionsOur findings suggest that mould-active antifungal treatment at ICU admission may be linked with reduced A. fumigatus-associated mortality in severe COVID-19. However, further studies are warranted on this topic.

microbiology↗

bioRxiv2022

gtexture: Haralick texture analysis for graphs and its application to biological networks

ObjectiveThe calculation of texture features, such as those derived by Haralick et al., has been traditionally limited to 2D-imaging data. We present the novel derivation of an extension to these texture features that can be applied to graphs and networks and set out to illustrate the potential of these metrics for use in cancer informatics. ApproachWe extend the pixel-based calculation of texture and generate analogous novel metrics for graphs and networks. The graph structures in question must have ordered or continuous node weights/attributes. To demonstrate the utility of these metrics in cancer biology, we demonstrate these metrics can distinguish different fitness landscapes, gene co-expression and regulatory networks, and protein interaction networks with both simulated and publicly available experimental gene expression data. Main ResultsWe demonstrate that texture features are informative of graph structure and analyse their sensitivity to discretization parameters and node label noise. We demonstrate that graph texture varies across multiple network types including fitness landscapes and large protein interaction networks with experimental expression data. We show the ability of these texture metrics, calculated on specific protein interaction subnetworks, to classify cell line expression by lineage, generating classifiers with 82% and 89% accuracy. SignificanceGraph texture features are a novel second order graph metric that can distinguish cancer types and topologies of evolutionary landscapes. It appears that no similar metrics currently exist and thus we open up the potential derivation of more metrics for the classification and analysis of network-structured data. This may be particularly useful in the complex setting of cancer, where large graph and network structures underlie the omics data generated. Network-based data underlies drug discovery, drug response prediction and single-cell dynamics and thus these metrics provide an additional tool in tackling these problems in cancer.

bioinformatics↗

bioRxiv2022

The wild life of ticks: using passive surveillance to determine the distribution and wildlife host range of ticks and the exotic Haemaphysalis longicornis, 2010-2021

BackgroundWe conducted a large-scale, passive regional survey of ticks associated with wildlife of the eastern U.S. Our primary goals were to better assess the current geographic distribution of exotic H. longicornis and to identify potential wild mammalian and avian host species. However, this large-scale survey also provided valuable information regarding the distribution and host associations for many other important tick species that utilize wildlife as hosts. MethodsTicks were opportunistically collected by cooperating state and federal wildlife agencies. All ticks were placed in the supplied vials and host information was recorded, including host species, age, sex, examination date, location (at least county and state), and estimated tick burden were recorded. All ticks were identified to species using morphology, suspect H. longicornis were confirmed through molecular techniques. ResultsIn total, 1,940 hosts were examined from across 369 counties from 23 states in the eastern U.S. From these submissions, 20,626 ticks were collected and identified belonging to 11 different species. Our passive surveillance efforts detected exotic H. longicornis from nine host species from eight states. Notably, some of the earliest detections of H. longicornis in the U.S. were collected from wildlife through this passive surveillance network. In addition, numerous new county reports were generated for Amblyomma americanum, A. maculatum, Dermacentor albipictus, D. variabilis, and Ixodes scapularis. ConclusionsThis study provided data on ticks collected from animals from 23 different states in the eastern U.S. between 2010 - 2021 with the primary goal of better characterizing the distribution and host-associations of the exotic tick H. longicornis; however new distribution data on tick species of veterinary or medical importance was also obtained. Collectively, our passive surveillance has detected numerous new county reports for H. longicornis as well as I. scapularis. Our study utilizing passive wildlife surveillance for ticks across the eastern U.S. is an effective method for surveying a diversity of wildlife host species allowing us to better collect widespread data on current tick distributions relevant to human and animal health.

ecology↗

bioRxiv2019

Dynamic evolution in the key honey bee pathogen Deformed wing virus

The impacts of invertebrate RNA virus population dynamics on virulence and infection outcomes are poorly understood. Deformed wing virus (DWV), the main viral pathogen of honey bees, negatively impacts bee health which can lead to colony death. Despite previous reports on the reduction of DWV diversity following the arrival of the parasitic mite Varroa destructor, the key DWV vector, we found high genetic diversity of DWV in infested United States (US) honey bee colonies. Phylogenetic analysis showed that the divergent US DWV genotypes are of monophyletic origin, which were likely generated as a result of diversification after a genetic bottleneck. To investigate the population dynamics of this divergent DWV, we designed a series of novel infectious cDNA clones corresponding to co-existing DWV genotypes, thereby devising a reverse genetic system for an invertebrate RNA virus quasispecies. Equal replication rates were observed for all clone-derived DWV variants in single infections. Surprisingly, individual clones replicated to the same high levels as their mixtures and even the parental highly diverse natural DWV population, suggesting that complementation between genotypes was not required to replicate to high levels. Mixed clone-derived infections showed a lack of strong competitive exclusion, suggesting that the DWV genotypes were adapted to co-exist. Mutational and recombination events were observed across clone progeny providing new insights into the forces that drive and constrain virus diversification. Accordingly, herein we propose a new model of Varroa-induced DWV dynamics whereby an initial selective sweep is followed by virus diversification fueled by negative frequency-dependent selection for new genotypes. This selection likely reflects the ability of rare lineages to evade host defenses, specifically antiviral RNA interference (RNAi). In support of this, we show that RNAi induced against one DWV strain is less effective against an alternate strain from the same population.\n\nAuthor SummaryVirulence of Deformed wing virus (DWV), a major pathogen of honey bees, showed a sharp and significant increase following the introduction of its vector, the mite Varroa destructor. Varroa vectoring resulted in genetic changes of DWV, including reduction of DWV diversity to nearly clonal levels in the UK and Hawaii. Contrary to the previous reports, we discovered that virulent DWV populations circulating across the Varroa-infested United States included many divergent genotypes generated following a strong bottleneck event. We designed a series of the full-length infectious cDNA clones that captured the diversity of a typical virulent DWV population from a declining Varroa-infested colony, effectively establishing first reverse genetic system for an invertebrate RNA virus quasispecies, in order to investigate interactions between the virus genotypes. We demonstrated that individual co-existing DWV genotypes and diverse natural DWV populations replicated equally well indicating that complementation between isolates was not required to enable DWV replication to high levels. Also, no obvious competitive exclusion was detected between genotypes in mixed infections suggesting DWV genotypes are adapted to co-exist to maintain overall population diversity. We suggest that introduction of Varroa resulted in an initial selective sweep of DWV diversity which was followed by DWV diversification driven by selection for new genotypes capable of evading host defenses, specifically antiviral RNA interference.

microbiology↗

bioRxiv2018

A genomic island of Streptomyces coelicolor harbors the self-contained regulon of an ECF sigma factor

Streptomycetes constitute the largest genus of actinobacteria, living predominantly in soil and decaying vegetation. The bacteria are widely known for their filamentous morphologies and their capacity to synthesize antibiotics and other biologically active molecules. More than a decade ago, we and others identified 22 genomic islands that Streptomyces coelicolor M145 possesses and other Streptomyces strains lack. One of these genomic islands, Genomic Island (GI) 6, encodes an extracytoplasmic function (ECF) sigma factor that we were characterizing in separate work. Here we report that artificial induction of the ECF sigma factor, which is encoded by SCO3450, causes the transcription of approximately one-fourth of GI 6, or ~26 mostly contiguous genes, to increase. More than half of the regulon encodes putative enzymes involved in small molecule metabolism. A putative haloacid dehalogenase is present. Genes encoding two putative anti-sigma factors flank SCO3450, the three genes residing within the regulon. Our data suggest that the ECF sigma factor and its regulon are a self-contained transcriptional unit that can be transferred by horizontal gene transfer. To our knowledge, only one other example has been identified of an ECF sigma factor and its contiguous regulon appearing to be transferrable by horizontal gene transfer [18,19]. Because the regulon appears not to be induced by the 44 growth conditions recently examined by Byung-Kwan Cho and colleagues [20], if it confers fitness to S. coelicolor, the regulon likely does so in as-yet unknown situations. Those situations might range from scavenging to detoxification to even communication within microbial communities.\n\nIMPORTANCEStreptomyces bacteria grow as hyphae that colonize soil and differentiate into spores when nutrients become scarce. In their terrestrial habitats, the bacteria encounter diverse conditions. Presumably so that the bacteria can cope with those conditions, the chromosomes of streptomycetes are highly dynamic, varying greatly in structure not only between species but also between closely related strains of a single species. The bacteria also have large numbers of extracytoplasmic function (ECF) sigma factors, which undoubtedly help the microorganisms respond to the plethora of challenges coming from the environment. This work illustrates these two threads of Streptomyces biology dovetailing: Genetic adaptability through horizontal gene transfer seems to have enabled Streptomyces coelicolor to acquire a self-contained transcriptional unit that consists of an ECF sigma factor and its regulon. The suggested facile movement of the regulon between microbial hosts indicates the value of the metabolism of small molecules possibly mediated by the regulon.

microbiology↗