Biology subjects

Brown, A. S.

Publications and source records attributed to Brown, A. S..

13 recordsLinked to original sources

bioRxiv2026

Widespread Regulatory Turnover Across Human Segmental Duplications

Segmental duplications (SDs) are a pervasive feature of eukaryotic genomes, enabling genomic innovation via the duplication of genes and cis-regulatory elements. However, the regulatory mechanisms that govern these regions of the genome after duplication are not well understood. The repetitive nature of SDs pose problems for short-read assays such as ChIP-seq and DNase-seq as they create reads that map to more than one location along the genome. Moreover, the newest Telomere-to-Telomere (T2T) human genome assembly has revealed previously unknown segmental duplications. In this study, we used the Telomere-to-Telomere genome assembly along with the probabilistic allocation of multi-mapped reads by our software Allo to better understand the regulatory mechanisms governing segmental duplications in the human genome. Using 134 transcription factor ChIP-seq datasets in GM12878, we found that transcription factor binding sites within segmental duplications are rarely conserved across paralogous copies. Similarly, chromatin states defined via histone ChIP-seq datasets are also poorly conserved across segmentally duplicated regions. In contrast, paralogous genes within SDs exhibit highly correlated expression patterns. Hi-C analysis revealed that many SD paralogs have higher than expected spatial proximity, suggesting that three-dimensional genome organization may buffer transcriptional divergence following duplication despite the loss of cis-regulatory regions. Together, our results suggest that regulatory regions undergo rapid turnover following segmental duplication, but the regulatory impact may be buffered by spatial proximity within the nucleus. Tissue-specific genes and transcription factors showed greater divergence, highlighting the role of SDs in expanding specialized cellular functions.

bioinformatics↗

bioRxiv2026

IL-1 instructs para-bronchial cuff fibroblasts to organize lung antibody secreting cell niches during continued antigen exposure

Secondary lymphoid organs (SLO) are prototypic sites of antibody production, yet mucosal sites also generate and maintain mucosal antibodies during continued inflammation. Using a murine model of house dust mite-induced airway inflammation, we show that prolonged allergen exposure induces tertiary lymphoid organs (TLO) within para-bronchial adventitial cuffs. Within these regions, IL-1 signaling instructs fibroblasts to form niches that recruit, retain, and sustain lung antibody-secreting cells (ASCs) through chemokine induction. These mucosal ASCs share immunoglobulin repertoires with TLO-derived germinal center B cells. Thus, continued allergen exposure reshapes the lung microenvironment by converting para-bronchial fibroblasts into IL-1-dependent supportive niches for non-IgE antibody production, revealing a fibroblast-mediated mechanism for local immune regulation in chronic inflammation. One sentence summaryContinued allergen exposure drives lung TLO to generate ASCs that home to IL1-instructed para-bronchial cuffs.

immunology↗

bioRxiv2025

Chromatin state dynamics during the Plasmodium falciparum intraerythrocytic development cycle

The interdependence of chromatin states and transcription factor (TF) binding in eukaryotic genomes is critical for the proper regulation of gene expression. In this study, we explore the connection between TFs and chromatin states in the human malaria parasite, Plasmodium falciparum, throughout its 48-hour asexual intraerythrocytic developmental cycle (IDC). Most P. falciparum genes are expressed in a periodic manner during the IDC, accompanied by dynamic shifts in histone modifications and chromatin accessibility. Leveraging genome-wide profiles of chromatin accessibility, histone modifications, and Heterochromatin Protein 1 (HP1) occupancy, we characterize chromatin state dynamics during the IDC. Our results indicate that several chromatin states remain stable throughout the lifecycle, while others are dynamic and are linked to gene activation or repression. We further characterize chromatin state dynamics at the genome-wide DNA binding sites for a selection of Plasmodium TFs, allowing us to group TFs according to their chromatin preferences. By correlating changes in chromatin accessibility, histone modifications, and TF binding, we provide a global overview of the chromatin state dynamics that coordinate P. falciparum asexual blood stage development.

genomics↗

bioRxiv2025

Contrasted effects of human pressure on biodiversity in the UK: a multi-taxonomic assessment using airborne environmental DNA

Human activities have significantly modified habitats, resulting in a global biodiversity crisis. Here, we leveraged the first national-scale biodiversity survey based on airborne environmental DNA, comparing the effects of three human pressure indices increasing in complexity and scope across diverse vertebrates, insects, plants and fungi. While most taxa exhibited higher diversity in urban areas compared to rural ones, we uncovered more complex patterns using the landscape-pollution and human footprint indices, including dual diversity peaks at both high and moderate levels of human pressure. We also show an effect of human pressure on community composition even when local species richness remained stable: regardless of the human pressure index, anthropogenic sites were mostly characterized by synanthropic and invasive species. Overall, our results underscore the complex interactions among anthropogenic pressures, taxon diversity and community composition, demonstrating the value of multi-taxon analyses and multiple indices to better understand biodiversity patterns at large scales.

ecology↗

bioRxiv2025

Dexamethasone-Induced p57-Mediated Quiescence Drives Chemotherapy Resistance in Sonic Hedgehog Medulloblastoma

Medulloblastoma (MB), the most common malignant pediatric brain tumor, remains difficult to cure upon relapse, with only 12.4% of patients surviving five years post-recurrence. While specific quiescent tumor cell populations are known to contribute to treatment-resistance, the molecular mechanisms that maintain quiescence remain poorly defined. Here, we identify the cell cycle inhibitor p57 as a regulator of quiescence and chemotherapy resistance in Sonic Hedgehog (SHH) MB. Nuclear p57 was enriched in Sox2+ and Nestin+ stem-like MB cells compared to proliferative Atoh1+ cells. Inducing p57 expression in SHH MB cells led to a six-fold increase in G0-phase cells and conferred resistance to the frontline chemotherapeutic vincristine. Clinically, dexamethasone is a glucocorticoid given to nearly all MB patients to manage cerebral edema and is administered with wide variability in timing and dosing. We show that dexamethasone significantly increased nuclear p57 levels and expanded the G0 population in both Ptch1+/- and Ptch1+/-;Trp53-/- SHH MB mouse models. Pre-treatment with dexamethasone reduced vincristine sensitivity in SHH MB cells. Together, our findings reveal a clinically relevant and previously unrecognized mechanism of treatment resistance, whereby dexamethasone, despite its benefits in managing edema, may inadvertently contribute to tumor persistence or recurrence by driving a quiescent, drug-resistant state. Addressing the lack of standardization in steroid use or targeting p57 may improve treatment response and reduce recurrence in patients diagnosed with SHH MB.

cancer biology↗

bioRxiv2025

First national survey of terrestrial biodiversity using airborne eDNA

Near real-time data across taxa are necessary for quantifying biodiversity at regional to continental scales and evaluating conservation measures. Yet, standardized methods and globally distributed infrastructure are still lacking. In this study, we conducted the first national survey of terrestrial biodiversity using a metabarcoding approach on airborne environmental DNA collected by a national ambient air quality monitoring network. Our goal was to perform a multi-taxonomic biodiversity assessment at a national scale, compare detections with those of another large-scale monitoring approach (citizen sciences) and estimate a tentative minimum eDNA transportation distance. We identified over 1,100 taxa, including vertebrates, invertebrates, protists, fungi and plants covering a wide range of life history traits and ecological niches. Citizen science and eDNA detections were complementary, with eDNA better mapping less charismatic and difficult to spot taxa, demonstrating its potential to align with global conservation goals. Airborne eDNA signals were relatively local, likely due to the deposition of the larger particles from the air over shorter distances and limited wind transportation at near ground level. Overall, our results show that molecular protocols integrated into existing air quality monitoring networks can provide standardized, biodiversity monitoring at relatively low field cost, with potential for broad scalability.

ecology↗

bioRxiv2024

Ezh2 Delays Activation of Differentiation Genes During Normal Cerebellar Granule Neuron Development and in Medulloblastoma

Medulloblastoma (MB) is the most common malignant brain tumour in children. The Sonic Hedgehog (SHH)-medulloblastoma subtype arises from the cerebellar granule neuron lineage. Terminally differentiated neurons are incapable of undergoing further cell division, so an effective treatment for this tumour could be to force neuronal differentiation. Differentiation therapy provides a potential alternative for patients with medulloblastoma who harbor mutations that impair cell death pathways (TP53), which is associated a with high mortality. To this end, our goal was to explore epigenetic regulation of cerebellar granule neuron differentiation in medulloblastoma cells. Key regulators were discovered using chromatin immunoprecipitation with high-throughput sequencing. DNA-bound protein and chromatin protein modifications were investigated across all genes. We discovered that Ezh2-mediated tri-methylation of the H3 histone (H3K27me3), occurred on more than half of the 787 genes whose transcription normally increases as granule neurons terminally differentiate. Conditional knockout of Ezh2 led to early initiation of differentiation in granule neuron precursors (GNPs), but only after cell cycle exit had occurred. Similarly, in MB cells, neuronal differentiation could be induced by preventing H3K27me3 modifications using an Ezh2 inhibitor (UNC1999), but only when UNC1999 was combined with forced cell cycle exit driven by a CDK4/6 inhibitor (Palbociclib). Ezh2 emerges as a powerful restraint upon post-mitotic differentiation during normal GNP development and combination of Ezh2 inhibition with cell cycle exit leads to MB cell differentiation.

cancer biology↗

bioRxiv2024

Opposing roles of resident and infiltrating immune cells in the defence against Legionella longbeachae via IL-18R/IFN-γ/ROS axis

The immune response against Legionella longbeachae, a causative agent of the often-fatal Legionnaires pneumonia, is poorly understood. Here we investigated the specific roles of tissue-resident alveolar macrophages (AM) and infiltrating phagocytes during infection with this pathogen. AM were the predominant cell type that phagocytosed bacteria o day after infection. Three and five days after infection, AM numbers were greatly reduced while there was an influx of neutrophils and later monocyte-derived cells (MC) into lung tissue. AM carried greater numbers of viable L. longbeachae than neutrophils and MC, which correlated with a higher capacity of L. longbeachae to translocate bacterial effector proteins required for bacterial replication into the AM cytosol. Cell ablation experiments demonstrated that AM promoted infection whereas neutrophils and MC were required for efficient bacterial clearance. IL-18 was important for IFN-{gamma} production by IL-18R+ NK cells and T cells which, in turn, stimulated ROS-mediated bactericidal activity in neutrophils resulting in restriction of L. longbeachae infection. Ciliated epithelial cells also expressed IL-18R but did not play a role in IL-18-mediated L. longbeachae clearance. Our results have identified opposing innate functions of tissue-resident and infiltrating immune cells during L. longbeachae infection that may be manipulated to improve protective responses. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/578217v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@107c421org.highwire.dtl.DTLVardef@dd76f5org.highwire.dtl.DTLVardef@1acf746org.highwire.dtl.DTLVardef@9e2c17_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIAM serve as a replicative niche and promote L. longbeachae infection. C_LIO_LIInfiltrating neutrophils and MC kill L. longbeachae. C_LIO_LIIFN-{gamma} from IL-18R+ NK and T cells stimulates ROS and bacterial clearance. C_LI

immunology↗

bioRxiv2023

DNA sequence context and the chromatin landscape differentiate sequence-specific transcription factor binding in the human malaria parasite, Plasmodium falciparum

Development of the human malaria parasite, Plasmodium falciparum, is regulated by a limited number of sequence-specific transcription factors (TFs). However, the mechanisms by which these TFs recognize genome-wide binding sites is still largely unknown. To address TF specificity, we investigated the binding of two TF subsets that either bind CACACA or GTGCAC DNA sequence motifs and further characterized PfAP2-G and PfAP2-EXP which bind unique DNA motifs (GTAC and TGCATGCA). We interrogated the impact of DNA sequence and chromatin context on P. falciparum TF binding by integrating high-throughput in vitro and in vivo binding assays, DNA shape predictions, epigenetic post-translational modifications, and chromatin accessibility. We determined that DNA sequence context minimally impacts binding site selection for CACACA-binding TFs, while chromatin accessibility, epigenetic patterns, co-factor recruitment, and dimerization contribute to differential binding. In contrast, GTGCAC-binding TFs prefer different DNA sequence context in addition to chromatin dynamics. Finally, we find that TFs that preferentially bind divergent DNA motifs may bind overlapping genomic regions in vivo due to low-affinity binding to other sequence motifs. Our results demonstrate that TF binding site selection relies on a combination of DNA sequence and chromatin features, thereby contributing to the complexity of P. falciparum gene regulatory mechanisms. Key PointsO_LISequence and chromatin context determine differential DNA-binding specificity of P. falciparum TFs C_LIO_LITFs with paralogous DNA-binding domains in P. falciparum are not functionally redundant C_LIO_LITFs with differing sequence-specificity can co-occupy sites through low-affinity DNA interactions C_LI

genomics↗

bioRxiv2023

A metagenomic library cloning strategy that promotes high-level expression of captured genes to enable efficient functional screening

Functional screening of environmental DNA (eDNA) libraries is a potentially powerful approach to discover enzymatic "unknown unknowns", but is usually heavily biased toward the tiny subset of genes preferentially transcribed and translated by the screening strain. We have overcome this by preparing an eDNA library via partial digest with restriction enzyme Fatl (cuts CATG), causing a substantial proportion of ATG start codons to be precisely aligned with strong plasmid-encoded promoter and ribosome-binding sequences. Whereas we were unable to select nitroreductases from standard metagenome libraries, our Fatl strategy yielded 21 nitroreductases spanning eight different enzyme families, each conferring resistance to the nitro-antibiotic niclosamide and sensitivity to the nitro-prodrug metronidazole. We showed expression could be improved by co-expressing rare tRNAs and encoded proteins purified directly using an embedded Hisg-tag. In a transgenic zebrafish model of metronidazole-mediated targeted cell ablation, our lead MhqN-family nitroreductase proved [~]5- fold more effective than the canonical nitroreductase NfsB.

biochemistry↗

bioRxiv2018

MTSS1/Src family kinase Dysregulation Underlies Multiple Inherited Ataxias

The genetically heterogeneous Spinocerebellar ataxias (SCAs) are caused by Purkinje neuron dysfunction and degeneration, but their underlying pathological mechanisms remain elusive. The Src family of non-receptor tyrosine kinases (SFK) are essential for nervous system homeostasis and are increasingly implicated in degenerative disease. Here we reveal that the SFK suppressor Missing-in-Metastasis (MTSS1) is a novel ataxia locus that links multiple SCAs. MTSS1 loss results in increased SFK activity, reduced Purkinje neuron arborization, and low basal firing rates, followed by cell death. Surprisingly, mouse models for SCA1, SCA2, and SCA5 show elevated SFK activity, with SCA1 and SCA2 displaying dramatically reduced MTSS1 protein levels through reduced gene expression and protein translation, respectively. Treatment of each SCA model with a clinically-approved Src inhibitor corrects Purkinje basal firing, and delays ataxia progression in MTSS1 mutants. Our results identify a common SCA therapeutic target and demonstrate a key role for MTSS1/SFK in Purkinje neuron survival and ataxia progression.\n\nSignificance StatementThe Src family of non-receptor tyrosine kinases (SFK) are essential for nervous system function, and may contribute to neurodegeneration. Spinocerebellar ataxias (SCAs) are neurodegenerative diseases where Purkinje neurons fire irregularly and degenerate leading to motor problems. We show that the SFK suppressor Missing-in-Metastasis (MTSS1) is a novel ataxia gene that links multiple SCAs. MTSS1 loss results in increased SFK activity, degenerating Purkinje neurons with low basal firing rates, and cell death. Surprisingly, mouse models for three different SCAs show elevated SFK activity, with SCA1 and SCA2 models displaying dramatically reduced MTSS1 protein levels. Treatment of each SCA model with SFK inhibitor corrects Purkinje basal firing, and delays ataxia progression in MTSS1 mutants. Our results identify a common link among disparate neurodegenerative diseases.

neuroscience↗

bioRxiv2017

Epigenome-Based Drug Repositioning in Acute Myeloid Leukemia

BackgroundRepositioning approved drugs for the treatment of new indications is a promising avenue to reduce the burden of drug development. Most currently available computational methods based on molecular evidence can only utilize gene expression for repositioning despite a growing interest in the epigenome in human disease. We recently described a novel repositioning method, ksRepo, that enables investigators to move beyond microarray-based gene expression and utilize a variety of other sources of molecular evidence, such as DNA methylation differences.\n\nMethodsWe downloaded differential DNA methylation data from two publicly available acute myeloid leukemia (AML) datasets, a cancer with known, extensive epigenomic perturbations. We consolidated CpGs-level to non-directional gene-level differential methylation using Browns correction to Fishers method. We then used ksRepo, which ignores directionality in disease- and gene-drug associations, to mine the resulting prioritized gene lists and and the Comparative Toxicogenomics Database (CTD) for predicted repositioning candidates.\n\nResultsWe successfully recovered four compounds that were significant (FDR < 0.05) in two AML datasets: cytarabine, alitretinoin, panobinostat, and progesterone. Cytarabine is the most commonly used frontline therapy for AML and alitretinoin, panobinostat, and progesterone have all been investigated for the treatment of AML.\n\nConclusions. Combining a method for consolidating CpG methylation to the gene level with ksRepo provides a pipeline for deriving drug repositioning hypotheses from differential DNA methylation. We claim that our platform can be extended to other diseases with epigenetic perturbations and to other epigenomic modalities, such as ChIP-seq.

bioinformatics↗

bioRxiv2017

Leveraging population-based clinical quantitative phenotyping for drug repositioning

Computational drug repositioning methods can scalably nominate approved drugs for new diseases, with reduced risk of unforeseen side effects. The majority of methods eschew individual-level phenotypes despite the promise of biomarker-driven repositioning. In this study, we propose a framework for discovering serendipitous interactions between drugs and routine clinical phenotypes in cross-sectional observational studies. Key to our strategy is the use of a healthy and non-diabetic population derived from the National Health and Nutrition Examination Survey, mitigating risk for confounding by indication. We combine complementary diagnostic phenotypes (fasting glucose and glucose response) and associate them with prescription drug usage. We then sought confirmation of phenotype-drug associations in un-identifiable member claims data from Aetna using a retrospective self-controlled case analysis approach. We identify bupropion hydrochloride as a plausible antidiabetic agent, suggesting that surveying otherwise healthy individuals cross-sectional studies can discover new drug repositioning hypotheses that have applicability to longitudinal clinical practice.

bioinformatics↗