Biology subjects

Mills, C.

Publications and source records attributed to Mills, C..

14 recordsLinked to original sources

bioRxiv2026

Dysregulation of epithelial differentiation architecture underlies field cancerization in head and neck cancer

Head and neck squamous cell carcinoma (HNSCC) has exceptionally high recurrence rates, exceeding 50%, contributing to mortality and morbidity. This recurrence rate is proposed to be due to field cancerization, a phenomenon where tumor-adjacent "field" tissue that appears histologically normal harbors molecular changes that prime it for subsequent tumor growth. Current models attribute field cancerization to shared driver mutations between tumors and adjacent at-risk tissue, but this assumption has never been directly tested. To comprehensively characterize this phenomenon, we profiled patient-matched tumor, normal-adjacent field (NAF), contralateral normal, and blood samples from HPV-negative HNSCC patients using whole genome sequencing, targeted driver gene sequencing, single-nucleus multiome profiling, spatial transcriptomics and functional proliferation assays. While histologically normal NAF tissues did harbor expanded mutant clones, these mutations rarely overlapped with paired tumors and were not shared across patients, suggesting molecular features beyond mutations are altered in NAF. Single-cell multiomics revealed that NAF epithelium loses its normal organizational hierarchy: basal stem cell markers persist in differentiated cells, while terminal differentiation programs fail to activate, with reconfiguration of both gene regulatory networks and cell-cell interactions. Proliferating cells appeared in tissue layers normally restricted to post-mitotic cells, a pattern typically seen only in overt dysplasia. Within this disrupted hierarchy, a distinct epithelial state arose in NAF that expressed both normal epithelial and tumor-associated markers, which we localized to the parabasal layers using immunofluorescence and spatial transcriptomics. Together, our findings demonstrate that field cancerization operates through epithelial hierarchy disorganization that disrupts differentiation, generates cells with tumor-like features, and may create a permissive environment for the expansion of cancer-associated mutations, all within tissue that appears histologically normal.

cancer biology↗

bioRxiv2026

End-of-outbreak determination under seasonal transmission

At the apparent end of an infectious disease outbreak, policymakers must decide when to relax interventions, balancing epidemiological safety and economic efficiency. Here, we extend a renewal equation framework for estimating the risk of additional cases to scenarios with seasonal transmission, such as Aedes-borne virus transmission in temperate settings. In simulations, we demonstrate that the time of year is key to when it is safe to relax interventions under seasonal transmission: measures can be relaxed sooner if the last observed case occurs towards the end of the transmission season. We apply our framework to the 2017 chikungunya outbreak in Italy, integrating incidence data with estimates of temperature suitability for transmission, and further extend our approach to account for case under-reporting. Our model incorporating an end-of-season decline in transmission indicates a lower risk of additional cases late in the outbreak than a model based on incidence alone: assuming 60% case reporting, the seasonal model reaches a 1% risk threshold 22 days after the last observed case, compared with 39 days for the incidence-only model. Incorporating seasonality in model-based assessments of transmission risks at the end of an outbreak can therefore support more timely and reliable decision making.

ecology↗

bioRxiv2026

Engineering the Self-assembly of Bacterial Microcompartment Shell Proteins via Charged Mutations

AbstractProtein self-assembly is a fundamental biological process of great importance for the design and synthesis of biomaterials. Developing the ability to precisely manipulate protein assembly would greatly expand both our understanding of the process and our biotechnological capabilities. Within bacteria, proteins that self-organize to form bacterial microcompartments (MCPs) offer an excellent model system for studying protein self-assembly and advancing biomaterial design capabilities. MCPs consist of irregular polyhedral shells that encase an enzyme core, functioning as enzymatic nanoreactors. In isolation, the abundant shell proteins of the 1,2-propanediol utilization (Pdu) MCP, PduA and PduJ, have a high propensity to self-assemble into tubular structures, analogous in form to carbon nanotubes. Here, we design and characterize tubular structures formed by hexameric PduA and PduJ proteins. We demonstrate that altering hexamer charge offers a systematic strategy for modulating the higherorder assembly of PduA and PduJ across multiple contexts by integrating molecular dynamics simulations with heterologous overexpression, cell-free, and in vivo Salmonella enterica serovar Typhimurium LT2 experiments. First, using molecular simulation, we find that tube chirality and radius play critical roles in determining structural stability and flexibility. Next, overexpression and cell-free experiments show that increasing the overall negative charge of assembling subunits consistently promotes self-assembly into tubular structures. We find that this holds true in the native MCP system, as these same mutations promote the formation of tubular MCP structures in S. enterica LT2. Our results collectively reveal that both electrostatic interactions and fields generated by charges on proteins can be leveraged to control protein-based nanostructures.

biochemistry↗

bioRxiv2025

Evaluation of Bacterial Microcompartment Cofactor Recycling and Permeability with a Model Guided In Vitro Assay

Biomanufacturing is a promising strategy for sustainable chemical production. However, challenges such as cofactor competition and low pathway flux prevent competitive titers. Some bacteria address these challenges by encapsulating metabolic pathways in bacterial microcompartments (MCPs), many of which contain dedicated cofactor recycling enzymes. We sought to determine how pathway cofactor recycling and intermediate sequestration in MCPs benefit pathway performance using an in vitro assay and kinetic model of the 1,2-propanediol utilization (Pdu) system. Guided by model simulations, we performed experimental design to characterize permeability, a key and difficult-to-measure property of MCPs. Using our model and measurements of metabolite concentrations over time, we estimate MCP permeability values in the range of 10-5 cm/s. We also demonstrated that NAD+/NADH recycling in the Pdu MCP benefits increased pathway flux. This study integrates experiments and systems modeling to advance our understanding of why pathways are encapsulated and to inform bioengineering applications.

biochemistry↗

bioRxiv2024

Neurocognitive Mechanism of Radiologists Perceptual Errors: Results of Preliminary Studies

BackgroundThe most prevalent type of radiologist error is failing to detect abnormalities on images, the so-called "perceptual error." The prevalence of this type of false-negative (FN) error remains essentially unchanged since it was first described in 1949. PurposeThe purpose of this research is to identify a potential neurocognitive mechanism contributing to radiologists susceptibility to perceptual error, in order to inform intervention strategies to reduce such errors in practice. These experiments evaluated the relationship between brain network activation states and radiologists perceptual errors on two distinct visual tasks utilizing functional MRI (fMRI) and functional Near Infrared Spectroscopy (fNIRs). Materials and MethodsA prospective study consisting of three experiments was carried out on a small number of radiologist subjects. The first two experiments used fMRI, with participants performing two distinct types of visual tasks, respectively: the first was a task requiring subjects continuous attention and the second task required visual search. For the first of these experiments, simultaneous functional Near-Infrared Spectroscopic Imaging (fNIRs) was utilized along with fMRI. The second experiment was combined fMRI and eye-tracking. A third experiment using fNIRs alone was an observational study of subjects neurocognitive states during their usual practice. ResultsAn approximately threefold increased risk of FN perceptual errors (misses) was observed in the presence of a particular error-prone neurocognitive state (EPS) involving simultaneous co-activation of elements of the Default Mode Network (DMN) and Frontoparietal Network (FPN), which was detectable by both functional imaging modalities, with high concordance. EPS episodes appeared to be stochastic in occurrence, and occurred without operator awareness. We also found a high prevalence of the EPS in radiologists performing their normal interpretive tasks in their actual practice setting. ConclusionOur results suggest that dynamic interactions between brain networks leading to a particular error-prone state (EPS) may underlie a substantial fraction of radiologists perceptual errors. We demonstrate that this EPS can be detected unobtrusively in the clinical setting. These results suggest potential intervention strategies for perceptual error, the largest class of radiologist errors in practice. Key Results/HighlightsO_LIPeriodic episodes of a discrete neurocognitive state were observed in radiologists during specific visual tasks and in actual clinical settings. C_LIO_LIThere was an approximately threefold increased risk of perceptual error during this state. Most FN errors for the two visual tasks occurred during these brief episodes (p < 0.01). C_LIO_LIThere was also a highly significant anti-correlation of the prevalence of the error-prone neurocognitive state (EPS) with subject age (p < 0.001). C_LI ConflictsThe authors report no conflicts of interest or potential competing interests. Summary StatementWe report experimental results corelating perceptual errors by radiologists to episodic fluctuations in brain network activation, which appear to occur on a stochastic basis. These produce an error-prone neurocognitive state outside of operator awareness or control that is associated with an approximately threefold increase in the risk of perceptual error.

neuroscience↗

bioRxiv2024

Smad4 Loss in the Mouse Intestinal Epithelium Alleviates the Pathological Fibrotic Response to Injury in the Colon

Mucosal healing is associated with better clinical outcomes in patients with inflammatory bowel diseases (IBDs). Unresolved injury and inflammation, on the other hand, increases pathological fibrosis and the predisposition to cancer. Loss of Smad4, a tumor suppressor, is known to increase colitis-associated cancer in mouse models of chronic IBD. Since common biological processes are involved in both injury repair and tumor growth, we sought to investigate the effect of Smad4 loss on the response to epithelial injury. To this end, Smad4 was knocked out specifically in the intestinal epithelium and transcriptomic and morphological changes compared between wild type mice and Smad4 knock out mice after DSS-induced injury. We find that Smad4 loss alleviates pathological fibrosis and enhances mucosal repair. The transcriptomic changes specific to epithelium indicate molecular changes that affect epithelial extracellular matrix (ECM) and promote enhanced mucosal repair. These findings suggest that the biological processes that promote wound healing alleviate the pathological fibrotic response to DSS. Therefore, these mucosal repair processes could be exploited to develop therapies that promote normal wound healing and prevent fibrosis. NEW AND NOTEWORTHYWe show that transcriptomic changes due to Smad4 loss in the colonic epithelium alleviates the pathological fibrotic response to DSS in an IBD mouse model of acute inflammation. Most notably, we find that collagen deposition in the epithelial ECM, as opposed to that in the lamina propria, correlates with epithelial changes that enhance wound healing. This is the first report on a mouse model providing alleviated fibrotic response in a DSS-IBD mouse model in vivo.

cell biology↗

bioRxiv2022

Systematic Engineering of Virus-Like Particles to Identify Self-Assembly Rules for Shifting Particle Size

Virus-like particles (VLPs) are promising scaffolds for biomaterials as well as diagnostic and therapeutic applications. However, there are some key challenges to be solved, such as the ability to engineer alternate sizes for varied use cases. To this end, we created a library of MS2 VLP variants at two key residues in the coat protein which have been implicated as important to controlling VLP size and geometry. By adapting a method for systematic mutagenesis coupled with size-based selections and high-throughput sequencing as a readout, we developed a quantitative assessment of two residues in MS2 coat protein that govern the size shift in MS2 VLPs. We then applied the strategy to the equivalent residues in Q{beta} VLPs, an MS2 homolog, and demonstrate that the analogous pair of residues are also able to impact VLP size and shape. These results underscore the power of fitness landscapes in identifying critical features for assembly.

bioengineering↗

bioRxiv2022

A cross-sectional study of the commercial plant-based landscape across the US, UK and Canada.

As plant-based foods comprise an ever-increasing proportion of the diet, understanding the nutritional composition of these products is critical. In this study we assess the nutritional content of all commercial plant-based products across multiple sectors (supermarkets, fast food & sit down restaurants, food delivery companies and manufacturers) in the US, UK and Canada. We identified 3488 unique products. Across all sectors, 45% of main meals had >15g protein, 60% had <10%kcal from saturated fat; 29% had >10g fibre per meal; 86% had <1000mg sodium. At restaurants, meat-based main meals were significantly higher in protein and sodium compared to vegetarian and vegan meals. The meat-based options were also significantly higher in saturated fat than the vegan but not vegetarian options. We conclude that plant-based items tend to be lower in saturated fat and sodium than their meat-based counterparts but improvements are needed to optimise their nutritional composition.

scientific communication and education↗

bioRxiv2021

A LINCS microenvironment perturbation resource for integrative assessment of ligand-mediated molecular and phenotypic responses

The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods (synapse.org/LINCS_MCF10A). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes.

systems biology↗

bioRxiv2020

Proteomic profiling of breast cancer cell lines and models

We performed quantitative proteomics on 61 human-derived breast cancer cell lines to a depth of ~13,000 proteins. The resulting high-throughput datasets were assessed for quality and reproducibility. We used the datasets to identify and characterize the subtypes of breast cancer and showed that they conform to known transcriptional subtypes, revealing that molecular subtypes are preserved even in under-sampled protein feature sets. All datasets are freely available as public resources on the LINCS portal. We anticipate that these datasets, either in isolation or in combination with complimentary measurements such as genomics, transcriptomics and phosphoproteomics, can be mined for the purpose of predicting drug response, informing cell line specific context in models of signalling pathways, and identifying markers of sensitivity or resistance to therapeutics.

cancer biology↗

bioRxiv2020

Inhibition of Wnt signalling by Notch via two distinct mechanisms

Notch and Wnt are two essential signalling pathways that help to shape animals during development and to sustain adult tissue homeostasis. Although, they are often active at the same time within a tissue, they typically have opposing effects on cell fate decisions. In fact, crosstalk between the two pathways is important in generating the great diversity of cell types that we find in metazoans. However, several different mechanisms have been proposed that allow Notch to limit Wnt signalling, driving a Notch-ON/Wnt-OFF state. Here we explore these different mechanisms in vertebrate cells and demonstrate two distinct mechanisms by which Notch itself, can limit the transcriptional activity of {beta}-catenin. At the membrane, independently of DSL ligands, Notch1 can antagonise {beta}-catenin activity through an endocytosis mediated mechanism that is dependent upon its interaction with Deltex and sequesters {beta}-catenin into the membrane fraction. Within the nucleus, the intracellular domain of Notch1 can also limit {beta}-catenin induced transcription through the formation of a complex that requires its interaction with RBPj{kappa}. We believe these mechanisms contribute to the robustness of cell-fate decisions by sharpening the distinction between opposing Notch/Wnt responses.

cell biology↗

bioRxiv2019

Combined inhibition of mTOR and PIKKs exploits replicative and checkpoint vulnerabilities to induce death of PI3K-activated triple-negative breast cancer cells

SUMMARY SUMMARY HIGHLIGHTS INTRODUCTION RESULTS DISCUSSION FUNDING AUTHOR CONTRIBUTIONS STAR METHODS Cell lines METHOD DETAILS Western blotting Evaluation of drug sensitivity Immunofluorescence microscopy Primary antibodies and dilutions Single-stranded DNA ssDNA and... Live cell microscopy Extraction of polar metabolites Metabolomics profiling by... Isobolograms and analysis of... Cell cycle model and... QUANTIFICATION AND STATISTICAL... Viable cell counts ...

cancer biology↗

bioRxiv2017

Heterogeneity Within the Frontoparietal Control Network and its Relationship to the Default and Dorsal Attention Networks

The frontoparietal control network (FPCN) plays a central role in executive control. It has been predominantly viewed as a unitary domain general system. Here, we examined patterns of FPCN functional connectivity (FC) across multiple conditions of varying cognitive demands, in order to test for FPCN heterogeneity. We identified two distinct subsystems within the FPCN based on hierarchical clustering and machine learning classification analyses of within-FPCN FC patterns. These two FPCN subsystems exhibited distinct patterns of FC the default network (DN) and the dorsal attentional network (DAN). This 2-fold FPCN differentiation was observed across four independent data sets, across 9 different conditions (rest and 8 tasks), as well as in meta-analytic co-activation patterns. The extent of FPCN differentiation varied across conditions, suggesting flexible adaptation to task demands. These findings reveal a flexible and heterogeneous FPCN organization that may in part emerge from separable DN and DAN processing streams.

neuroscience↗

bioRxiv2017

Bird interactions with drones, from individuals to large colonies

Drones are rapidly becoming a key part of the toolkit for a range of scientific disciplines, as well as a range of management and commercial applications. This presents a number of challenges in context of how drone use might impact nearby wildlife. Interactions between birds and drones naturally come to mind, since they share the airspace. This paper details initial findings on the interactions between drones and birds for a range of waterbird, passerine and raptor species, across of a range of scientific applications and natural environments. The primary aims of this paper are to provide guidance for those planning or undertaking drone monitoring exercises, as well as provide direction for future research into safe and effective monitoring with drones. Our study sites we all located within Australia and spanned a range of arid, semi-arid, dunefield, floodplain, wetland, woodland, forest, coastal heath and urban environments. We particularly focus on behavioral changes towards drones during breeding season, interactions with raptors, and effects on nesting birds in large colonies - three areas yet to be explored in published literature. In over 70 hours of flight, there were no incidents with birds. Although some aggressive behavior was encountered from solitary breeding birds. Several large breeding bird colonies were surveyed, and included in our observations is monitoring and counting of nests in a colony of over 200,000 Straw-necked Ibis, the largest drone-based bird monitoring exercise to date. In addition to providing observations of interactions with specific bird species, we recommend procedures for flight planning, safe flying and avoidance. This paper also provides a basis for a number of critical and emerging areas of research into bird-drone interactions, most notably, territorial breeding birds, safety around large raptors, and the effect of drones on the behaviour of birds in large breeding colonies.

ecology↗