Biology subjects

Brown, M.

Publications and source records attributed to Brown, M..

At least 19 recordsLinked to original sources

bioRxiv2026

BUDDY: An interactive web platform to accelerate the functional modeling of human missense variants using Saccharomyces cerevisiae orthologs

The advent of next-generation sequencing has transformed clinical genetics, accelerating the identification of human genetic variants. However, the labor-intensive process of functional validation of Variants of Uncertain Significance (VUS) remains a significant diagnostic barrier. While expressing humanized genes in Saccharomyces cerevisiae is a common approach for modeling missense variants with functional assays, using native yeast orthologs provides a more streamlined approach that preserves species-specific interactions within multisubunit complexes. However, taking this approach relies on a fragmented workflow that requires bioinformatic experience. To address this issue, we developed the Bioinformatic Utility for Diagnostic Discovery in Yeast (BUDDY), an integrated web platform designed to streamline variant analysis by connecting bioinformatic tools and databases including ClinVar. Features include amino acid alignments, a protein structure viewer that displays a superposition of yeast and human proteins, pathogenicity prediction data, CRISPR-Cas9 reagent design, and yeast phenotypes to provide potential functional assays. The platform also contains an artificial intelligence (AI)-assisted experimental design feature that evaluates the utility of modeling specific variant and gene combinations in yeast and can assist with phenotype selection. BUDDY significantly accelerated the bioinformatic preparation time needed for ortholog variant modeling by an experienced biologist. Additionally, without prior bioinformatics training, a first-year medical student used BUDDY to develop a self-directed project and proposed a study of five Lynch syndrome-associated VUS using a forward mutation rate assay. BUDDY is designed to accelerate the investigation of human variants in yeast and has a high potential utility for use in resource-constrained settings such as course-based undergraduate research experiences (CUREs).

bioinformatics↗

bioRxiv2026

Quantitative evidence for foraging preferences of shrill carder bumble bee (Bombus sylvarum) queens

Introduction Bumblebees are facing declines globally due to agricultural intensification and climate change. In the UK, the shrill-carder bumble bee, Bombus sylvarum, has dramatically declined and is now restricted to five isolated populations across England and Wales. A key life-cycle stage for bumblebees is the spring queen, who is responsible for colony establishment, but we lack quantitative data to inform conservation practice for this life stage. Aim/methods To quantify foraging preferences and floral resource dependency of spring queens in B. sylvarum. We determined the floral resources preferred by B. sylvarum queens across their activity period, along with the potential for inter-specific resource competition. Results At the start of the season, B. sylvarum queens foraged solely on Lamium album and Trifolium repens. Later they increased their foraging breadth but predominantly foraged on Vicia villosa and Rhinanthus minor. Plant-pollinator networks indicate the potential for competition with more common bumble bee species, with B. sylvarum queens exhibiting a broader foraging range than these potential competitors. Discussion As the season progresses, the foraging diversity of B. sylvarum queens increases. Later in the season, the lower species specificity index for B. sylvarum queens suggests that these queens are less specialised than their congeneric competitors. Implications for insect conservation: Our results show that early in the season B. sylvarum queens rely on two floral species. Managing sites to maintain and increase strong populations of these plant species will likely enhance queen success, which is crucial to enable colony establishment and population growth.

ecology↗

bioRxiv2026

A tumor-cell MHC-II program is associated with checkpoint-blockade outcomes across stages of bladder cancer

Purpose: A minority of patients with bladder cancer derive lasting benefit from immunotherapy, and current biomarkers capture only part of the biology. We evaluated whether tumor-cell MHC class II defines an immune state associated with outcome across disease stages and after PD-1/PD-L1 blockade. Experimental Design: We localized differential MHC-II activity to malignant epithelial cells by single-nucleus and single-cell RNA sequencing and confirmed HLA-DR expression by immunohistochemistry in 122 specimens. Chromatin profiling and IFN-{gamma} stimulation of cell lines and primary tumors supported derivation of an 11-gene tumor-cell program. Associations were tested in 434 patients with non-muscle-invasive disease, 82 receiving neoadjuvant pembrolizumab, and 288 receiving atezolizumab for metastatic disease. Results: Tumor-cell MHC-II was present in approximately one third of bladder cancers, and malignant cells accounted for the differential signal between MHC-II-high and MHC-II-low tumors. The program was inducible by IFN-{gamma} through JAK/STAT signaling. Within luminal non-muscle-invasive disease, MHC-II-low status was associated with progression (HR 3.31, 95% CI 1.37 to 7.99). In PURE-01, the 11-gene program was associated with pathological complete response (52% versus 24%, p = 0.018) and recurrence-free survival (p = 0.0054), retaining an independent association in models including tumor mutational burden and PD-L1. In bladder-primary metastatic disease, program-high status was associated with overall survival in unadjusted analysis (HR 0.62, 95% CI 0.44 to 0.89); the association did not extend to upper tract tumors (interaction p = 0.0018). Conclusions: Tumor-cell MHC-II defines an inducible state associated with outcomes across bladder cancer stages and after checkpoint blockade, supporting prospective evaluation by RNA and immunohistochemistry.

cancer biology↗

bioRxiv2026

Voice and linguistic features support early attentional filtering of irrelevant stimuli

In cocktail party-type environments, listeners must segregate simultaneous acoustic sources and select one for processing. Behavioral studies have established that both low-level voice differences (e.g., pitch) and high-level linguistic differences (e.g., word content) aid these processes. Electroencephalography (EEG) studies have demonstrated that the brain filters voices based on low-level features early in sensory processing, but it is unclear whether linguistic differences also support early filtering. In this EEG study, listeners attended to a lateralized auditory stream of target syllables while ignoring distractor stimuli from the opposite hemifield. In contrast to previous auditory attention studies, target stimuli were always attended and statistically identical across conditions; instead, we manipulated the distractors. Specifically, we manipulated whether targets and distractors were spoken in the same voice or different voices, as well as whether they were composed of the same or different linguistic content. Critically, distractors were temporally offset from targets, enabling an investigation of whether acoustically matched, always attended target stimuli are differentially encoded as a function of surrounding context. Differences in either voice or linguistic features supported target recall: Recall was poor only when both streams were in the same voice and had similar linguistic content. However, voice and linguistic features had independent, additive effects on neural processing. Specifically, target dissimilarity in acoustics and linguistic content both contributed to more robust, larger-magnitude target-evoked EEG responses. Overall, results demonstrate that both linguistic dissimilarity and low-level acoustic dissimilarity improve early attentional filtering of distractors in multi-source acoustic scenes.

neuroscience↗

bioRxiv2026

The human RNA-DNA interactome is cell type-specific and dynamic

More than twenty years ago, the FANTOM consortium uncovered that mammalian genomes are pervasively transcribed, revealing multitudes of RNAs with unknown functions. A subset of these transcripts has since then been linked to transcriptional control and to chromatin organization via their ability to interact with DNA, suggesting that chromatin-associated RNAs could be key players in genome regulation. Although recent technological advances now enable the mapping of genome-wide RNA-DNA contacts, a lack of analyses integrating these methods with other genomic features and across multiple cellular contexts hinders our comprehensive understanding of the principles underlying RNA-DNA interactions and of their biological importance. As part of the FANTOM6 project, we thus generated RNA-DNA interaction maps in 16 different human cell types, then combined these contacts with multiple layers of other genomic data to investigate how patterns of interaction between RNA and DNA relate to chromatin organization and function. We show that the RNA-DNA interactome is highly dynamic yet reproducibly organized in cell-type specific networks, constituted of a great diversity of interactions that vary in function of their distance, the nature of their sources and the chromatin state of their targets. In particular, we detected numerous regulatory elements that exhibit marked changes in activity when differentially bound by transcripts, implying that thousands of RNA-DNA interactions can play a mechanistic role in gene expression. This regulatory function correlates with RNA-protein interactions and significantly associates with cell type-relevant and disorder-related traits. In addition to providing essential resources for future research in RNA-mediated chromatin regulation, cellular biology and human diseases, our study thus establishes the RNA-DNA interactome as a new genome regulatory layer that defines and maintains cellular identity and behavior.

genomics↗

bioRxiv2026

A cargo receptor entrapment complex is a therapeutic node for genetically and clinically distinct proteinopathies

Severe proteinopathies--such as retinitis pigmentosa, a form of inherited blindness--are driven by genetic mutations that overwhelm the quality control of the post-endoplasmic reticulum (post-ER) secretory pathway, causing toxic protein accumulation. Here, we identify a therapeutic node defined by a hetero-oligomeric cargo receptor complex consisting of TMED7, 2, 9, and 10. This "entrapment complex" anchors structurally and functionally diverse mutant clients within the early secretory pathway via TMED7 binding to the integral Golgi protein GRASP55. Disruption of the entrapment complex results in the clearance of accumulated protein cargoes. In vivo ablation of the entrapment node via inducible genetic deletion or via the small molecule BRD7635 reverses histopathological hallmarks and rescues functional deficits in clinically distinct proteinopathies of the kidney and the eye, including mitigating vision loss in a mouse model of retinitis pigmentosa.

cell biology↗

bioRxiv2026

Circadian misalignment underlies immune escape in breast cancer

Circadian regulation shapes tissue physiology, yet how it organizes cellular and molecular dynamics within the tumor microenvironment (TME) and influences tumor immunity remains unclear. Using temporal single-nucleus multiomic profiling of mouse breast tumors, we uncovered extensive circadian programs that are both cell-type-specific and shared across the TME, governing proliferation and immune responses. Notably, cancer epithelial cells exhibited global acrophase misalignment relative to immune populations. This intercellular desynchrony manifests as temporal decoupling between tumor proliferation and immune activation, discordant antigen presentation and T cell recognition with intrinsic activation-exhaustion overlap in T cells, and asynchronous PD-1/PD-L1 oscillations that sustain checkpoint-mediated suppression. Similar patterns were observed in human triple-negative breast cancer (TNBC). Together, these findings establish intercellular circadian misalignment as a mechanism of tumor immune evasion and position the circadian architecture of the tumor-immune ecosystem as a previously underappreciated determinant of tumor development and therapeutic response. HIGHLIGHTSO_LISingle-cell multiomics maps circadian regulation of tumor-immune programs. C_LIO_LICircadian regulation in cancer epithelial cells is misaligned with immune cell populations. C_LIO_LITumor-immune temporal misalignment undermines antitumor immunity. C_LIO_LICircadian misalignment in human TNBC suggests relevance for immunotherapy timing. C_LI

cancer biology↗

bioRxiv2026

Attomolar fecal cytokine profiling reveals gut immune dynamics and disease states

The gut modulates systemic health, influencing immune, neurological, and cardiovascular processes. While fecal sequencing of microbial nucleic acids provides a non-invasive view of microbial composition, sensitive measurement of host-derived signals in stool remains limited. Here we introduce DIGEST (Digital Immunoassay for Gut-Environment Single-molecule Targets), an ultrasensitive digital immunoassay that quantifies proteins in fecal extracts to attomolar levels. In mice, longitudinal profiling during a high-fat diet perturbation revealed coordinated host cytokine responses that occurred within 24 hours, with sustained elevation after diet withdrawal, enabling non-invasive tracking of within-subject immune dynamics. Application of DIGEST to quantify a panel of host inflammatory cytokines in patients with inflammatory bowel disease distinguished active ulcerative colitis from quiescent disease and non-IBD controls (AUC=0.98). In advanced melanoma patients receiving PD-1 blockade, pretreatment fecal IL-23 concentrations discriminated responders from non-responders with an AUC of 0.87. Together, these results establish DIGEST as a generalizable platform for sensitive, non-invasive quantification of host protein activity at the gut interface, with broad applications in basic science discovery, disease surveillance, and therapy response prediction.

systems biology↗

bioRxiv2026

Live triatomine bug, vector of Trypanosoma cruzi (Chagas disease), found engorged in Lisbon hotel room: A first for Portugal and for Europe

Triatomine bugs are blood feeding insects that transmit the parasite Trypanosoma cruzi, causative agent of Chagas disease. The bugs are found primarily in the Americas with a few species in Asia and Africa. Here we report the first case of a live triatomine bug in Europe, found in a Lisbon hotel room. In August, 2025, the hotel room occupants discovered a triatomine bug perched on the headboard of their bed. Upon capture, bright red blood emerged from the bug; the occupants suspected that it had bitten them during the night. The bug was identified morphologically as triatomine species Hospesneotomae protracta, which was confirmed molecularly. Hospesneotomae protracta is native to the southwestern United States where it is a competent T. cruzi vector. Trypanosoma cruzi was not detected in this specimen. Although this case likely represents an accidental importation, it illustrates the ease with which disease vectors can be unknowingly transported globally. Ergo it is crucial to document and share these findings to prevent introductions of non-native arthropods of medical importance.

ecology↗

bioRxiv2025

Setting priorities for the acquisition of primary plant occurrence data

AimEffective implementation of the Global Biodiversity Framework and Global Strategy for Plant Conservation depends on accurate species distribution data. Current vascular plant distribution data, while crucial for understanding terrestrial ecosystems, is often sparse and biased and requires significant expansion. This study developed a scalable approach to prioritize areas for plant occurrence data acquisition, adaptable to national priorities and providing a framework for botanical institutions to coordinate efforts and allocate resources. LocationGlobal. MethodsUsing a Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) analysis, we prioritized areas based on: (a) ecosystem service value; (b) floristic value threatened by climate or land-use change; and (c) uncertainty in species richness estimates, stratified by biome and region. Regional prioritization maps for Africa & Madagascar; East, South and Southeast Asia; Siberia and the Russian Far East; South America; and North & Central America were reviewed by botanical experts for validation. Scalability was assessed by comparing regional and global analyses. ResultsData-driven priority maps, divided into tree-dominated and grassland/deforested areas, largely received expert support. High similarity between global and regional maps demonstrated scalability. Main conclusionsOur approach provides a framework for supporting national implementation of the Global Biodiversity Framework. Variables and their weights can be tailored to national or local needs. The methods flexibility and adaptability extend to other taxonomic groups and objectives, such as protected area selection By prioritizing data acquisition, whether field-based or digital, this research promotes the efficient use of resources. A key advantage of this approach is its capacity to systematically translate expert opinion into explicit and quantitative criteria, which in turn facilitates clear communication with policymakers and funders.

plant biology↗

bioRxiv2025

Evaluation of combined root exudate and rhizosphere microbiota sampling approaches to elucidate plant-soil-microbe interaction

O_LIDeciphering the root exudate-driven interplay between plants and the rhizosphere microbiota is essential for understanding plant adaptation to the environment and future-proofing crop production. However, sampling root exudates and rhizosphere soil remains challenging due to the low throughput and destructive nature of the process. C_LIO_LIWe used the staple crop barley [Hordeum vulgare] as a model to benchmark different sampling approaches for simultaneous exudation and microbiota profiling of soil-grown plants. C_LIO_LIExudate profiles and total dissolved organic carbon exudation rates were consistent across different sampling approaches, whereas root biomass, root morphology measurements, and organic nitrogen exudation varied. C_LIO_LIHigh-throughput amplicon sequencing and quantitative PCR (qPCR) of phylogenetic markers and nitrogen cycle-selected genes revealed a protocol-specific footprint in the composition and abundance of rhizosphere bacterial and fungal microbiota. Yet, on average, 75% of microbes enriched in, and differentiating between, barley rhizosphere and unplanted soil controls were recovered across all the sampling approaches evaluated. C_LIO_LIOur results demonstrated that, under the tested conditions, different sampling approaches produced comparable microbiota and exudation patterns, enabling the integrated study of root exudation and microbial profiles from the same plant. The observed differences across sampling approaches must be considered according to the experimental scope. C_LI

plant biology↗

bioRxiv2025

Trophoblast stem cells and syncytiotrophoblasts lack inflammatory responses to LPS but retain robust interferon-mediated antiviral immunity

Early pregnancy requires a tightly regulated pro-inflammatory environment shared between the primitive placenta and decidua. While immune balance supports successful implantation and placental invasion, disruptions in immune signaling during this period can impair implantation and lead to embryo loss. In this study, we investigated the molecular mechanisms underlying immune imbalance during implantation using a trophoblast stem cell (TSC) model. TSCs were cultured in either stem cell or syncytiotrophoblast (STB) differentiation medium and treated with either lipopolysaccharides (LPS) or interferon beta (IFNB). RT-qPCR and Western blotting revealed that LPS failed to induce a pro-inflammatory cytokine response in TSCs or STBs. In contrast, IFNB triggered a strong antiviral response in both TSCs and STBs. RNA-sequencing of IFNB-treated TSC and STB 3D spheroids revealed subtle differences between the TSCs and STB responses to interferons. Both TSC and STB IFNB-treated spheroids mount an interferon-mediated antiviral response; however, STB spheroid genes associated with the type I interferon response, viral RNA/DNA sensing, and antigen processing were upregulated. We also compared the interferon response between the CT27 (female) and CT29 (male) TSCs and STBs. While STBs showed minimal differences, the CT29 TSCs exhibited a markedly stronger interferon response than the CT27 TSCs. Collectively, these findings suggest that the primitive placenta is selectively responsive to interferon signaling rather than direct pathogen-associated stimuli. This implies that maternal immune activation, rather than microbial invasion, likely drives that placental immune response and embryo success at this stage. Understanding these dynamics underscores the importance of the maternal immune balance in early pregnancy success.

developmental biology↗

bioRxiv2025

Inhibition of cell-mediated immunity in type 1 diabetes by beta cell-targeted PD-1 agonists in pancreas tissue slices

Tissue-targeted immunotherapies for type 1 diabetes (T1D) hold potential to protect pancreatic beta cells while minimizing systemic immunosuppression. We used a bispecific agonist called Immune Modulating Monoclonal-TCR Against Autoimmune Disease (ImmTAAI), consisting of a T cell receptor (TCR) targeting domain fused with a PD-1 agonist to specifically bind beta cells and suppress autoreactive T cells. We used live pancreas slices to demonstrate targeting of ImmTAAI molecules to pre-proinsulin peptide-HLA-A2 complexes on human beta cells. ImmTAAI protected beta cells from T cell killing by increasing T cell motility and inhibiting cytokine secretion. ImmTAAI treatment also increased the motility of islet-infiltrating T cells in slices from a donor with recent-onset T1D and preserved insulin secretion in slices co-cultured with T cell avatars transduced with diabetogenic TCRs. These data demonstrate that ImmTAAI molecules have the potential to limit T cell activity locally, making this an attractive platform to elicit targeted immunoregulation in T1D. One Sentence SummaryWe demonstrate inhibition of cellular immunity in human type 1 diabetes using a beta cell-targeting, affinity-enhanced TCR fused to a PD-1 agonist.

bioengineering↗

bioRxiv2025

Complex HPV-human DNA structures revealed by large-scale DNA analyses in an HPV-cancer derived cell line

Most human papillomavirus (HPV)-associated cancers harbor viral DNA integrated into the human genome as extrachromosomal circles, intrachromosomal segments, or both. Distinguishing intrachromosomal from identical-sequence extrachromosomal DNA (ecDNA) by sequencing alone is challenging, and the architecture of large-scale HPV-human DNA structures remains incompletely understood. To address this, we applied complementary genomic tools, spanning single-nucleotide to megabase resolution, to the HPV16-positive oropharyngeal cancer-cell line UM-SCC-47. These revealed that an initial integration event formed a 23 kb extrachromosomal heterocatemer circle comprising 7.5 kb of HPV16 DNA and 16 kb of the human TP63 gene. Subsequent genomic rearrangements generated heterocatemer tandem arrays extending to 0.6 megabases, plus additional large-scale rearrangements involving the HPV-TP63 structures, as revealed by long-read DNA sequencing and optical genome mapping. Fluorescent in situ Hybridization (FISH) showed that the heterocatemers were intrachromosomally localized at chromosome 3 at the TP63 locus in 100% of the cells. Long-read RNA sequencing further showed that these intrachromosomal templates produced spliced, polyadenylated transcripts. A subset of cells also harbored HPV16 ecDNA derived from the intrachromosomal HPV-TP63 DNAs. These findings define previously unrecognized higher-order architecture of integrated HPV DNA and highlight the power of FISH for distinguishing intrachromosomal from extrachromosomal DNA structures. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/680684v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@f3d584org.highwire.dtl.DTLVardef@470811org.highwire.dtl.DTLVardef@162c88corg.highwire.dtl.DTLVardef@5c80dd_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

AURKB-driven dissolution of CIZ1-RNA assemblies from the inactive X chromosome in mitosis

Cip1-interacting zinc-finger protein 1 (CIZ1) interacts with Xist lncRNA to form large RNA-protein assemblies at the inactive X-chromosome (Xi) in female mammalian nuclei, plus smaller assemblies in both sexes. CIZ1 assemblies influence underlying chromatin, and their disruption alters the expression of autosomal and X-linked gene clusters. Here, we explore the regulated dissolution of CIZ1-Xi assemblies during mitosis and show that, like Xist, CIZ1 is released in prometaphase under the regulation of Aurora Kinase B (AURKB). The part of human/mouse CIZ1 comprising 179/181 C-terminal amino-acids encodes a matrin-3 domain that facilitates dimerization to form a compact folded core with disordered C-terminal extensions. Mass spectrometry revealed 56 high-confidence interacting partners of the C-terminal fragment, predominantly chromatin, nuclear matrix and RNA-binding proteins. Phosphomimetic mutation of three conserved AURKB sites in the C-terminal extensions released CIZ1 from its nuclear anchor points, but did not affect its interaction with chromatin or nuclear matrix proteins. In contrast, the same mutations, or deletion of the C-terminal extensions, abolished interaction with RNAs including Xist. Together, the data suggest CIZ1 is a regulatable component of the protein-RNA assemblies that preserve epigenetic stability across the nucleus, and that AURKB drives their dissolution in mitosis via dissociation of CIZ1 from RNA. BulletsThe data show regulated dissolution of RNA-protein assemblies involved in protection of epigenetic state. RNA spatially constrains CIZ1 assemblies via multivalent interactions at sub-nuclear sites. CIZ1 dimerizes to present dual extensions whose phosphorylation by AURKB dissolves RNA interaction in mitosis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=181 SRC="FIGDIR/small/676856v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@107bec2org.highwire.dtl.DTLVardef@17cbb4aorg.highwire.dtl.DTLVardef@1ec0144org.highwire.dtl.DTLVardef@1474995_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

A Toolkit for In Vivo Mapping and Modulating Neurotransmission at Single-Cell Resolution

Understanding the organization and regulation of neurotransmission at the level of individual neurons and synapses requires tools that can track and manipulate transmitter-specific vesicles in vivo. Here, we present SynaptoTagMe, a suite of genetic tools in Caenorhabditis elegans to fluorescently label and conditionally ablate the vesicular transporters for glutamate, GABA, acetylcholine, and monoamines. Using a structure-guided approach informed by protein topology and evolutionary conservation, we engineered endogenously tagged versions for each transporter that maintain their physiological function while allowing for cell-specific, bright, and stable visualization. We also developed conditional knockout strains that enable targeted disruption of neurotransmitter synthesis or packaging in single neurons. We applied this toolkit to map co-expression of vesicular transporters across the C. elegans nervous system, revealing that over 10% of neurons exhibit co-transmission. Using the ADF sensory neuron as a case study, we demonstrate that serotonin and acetylcholine are trafficked in partially distinct vesicle pools. Our approach provides a powerful platform for mapping, monitoring, and manipulating neurotransmitter identity and use in vivo. The molecular strategies described here are likely applicable across species, offering a generalizable approach to dissect synaptic communication in vivo.

neuroscience↗

bioRxiv2025

EZH2-TTP-mTORC1 Axis Drives Phenotypic Plasticity and Therapeutic Vulnerability in Lethal Prostate Cancer

Phenotypic plasticity is a recognized mechanism of therapeutic resistance in prostate cancer (PCa), however current knowledge of driver mechanisms and therapeutic interventions are limited. Using genetically engineered mouse models (GEMMs) devoid of Pten and Rb1, we previously demonstrated the chromatin reprogramming factor enhancer of zeste homolog 2 (EZH2) as an important regulator of alternative transcription programs promoting phenotypic plasticity. Here, using a multi-omics approach we demonstrate that EZH2 regulates multilineage cell states dependent on the RNA binding protein Tristetraprolin (TTP) that mediates RNA stability and activation of translation. Combined chemical inhibition of EZH2 and PI3K/mTORC1 resulted in superior anti-tumor activity in murine and human phenotypic plastic models and was most significant when this combination was used with castration or enzalutamide. Together, these data indicate phenotypic plasticity dependence on coordination between EZH2, TTP and mTORC1 signaling that represent novel therapeutic dependencies for this lethal PCa phenotype. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/669104v1_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@5ef713org.highwire.dtl.DTLVardef@af402forg.highwire.dtl.DTLVardef@19eedcforg.highwire.dtl.DTLVardef@10ee421_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementEZH2 plays a key role in driving cell state transitions in neuroendocrine prostate cancer (NEPC), guiding cancer cells towards a more aggressive, therapy-resistant cell type. This transformation creates a specific vulnerability, as NEPC cells become highly reliant on both EZH2 and PI3K/mTORC1-translation signaling. Targeting this dependency, we demonstrate that combining EZH2 with PI3K/mTORC1 inhibition provides effective suppression of NEPC cell growth, offering a promising therapeutic strategy for treating this challenging and aggressive prostate cancer subtype.

cancer biology↗

bioRxiv2025

snATAC-Express infers Gene Expression from Prioritized Chromatin Accessibility Peaks using Machine Learning

BackgroundSingle cell multi-omic investigation opens-up new opportunities to understand mechanisms of gene regulation. Existing methods for inferring transcript abundance from chromatin accessibility fail to prioritize the most relevant peaks and tend to assume positive associations between ATAC peaks and RNA counts. We hypothesize that gene regulation can be modeled as a function of combined positive and negative interactions among peaks and that causal regulatory variants are enriched in the vicinity of the most critical peaks. ResultsA machine learning pipeline leveraging single nuclear multiomic transcriptome and chromatin accessibility data is developed to model gene expression as a function of ATAC peak intensity. Multiome data was available for 18 immune cell types from 29 donors, 19 with Crohns disease. The pipeline aggregates results from three machine learning approaches (random forest regression, XGBoost, and Light GBM) as well as linear regression to identify which ATAC peaks contribute to explaining variation among donors and cell types in pseudobulk gene expression. The coefficient of determination with cross-validation was used to identify robust models which typically explain between 5% and 40% of transcript abundance, utilizing on average 47% of the ATAC peaks, representing a significant gain in predictive accuracy. The most important peaks are enriched in GWAS variants for inflammatory bowel disease and the autoimmune disease systemic lupus erythematosus, but not for rheumatoid arthritis. ConclusionAtlanta Plots visualize the proportion of ATAC peaks contributing to a predictive model of gene expression as well as the proportion of variance explained by the model. Software implementing our pipeline, "snATAC-Express", is freely available on GitHub.

bioinformatics↗