Biology subjects

Collins, M.

Publications and source records attributed to Collins, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Scalable proteomics with multiDIA resolves proteoforms in neurodegenerative disease

Deep proteome characterization has traditionally required multidimensional chromatographic fractionation, long acquisition times and large sample amounts, thus limiting scalability. Here, we introduce multiDIA, which combines independent digestions with multiple proteases and data-independent acquisition (DIA) to increase sequence coverage without extensive chromatographic fractionation. By generating complementary and overlapping peptide representations of proteins, multiDIA identifies about 270,000 distinct peptides per sample, including 3,649 phosphosites. This is more than twice the coverage of unfractionated workflows and exceeds the coverage of multidimensional fractionation workflows that use 10-fold more material and time. We demonstrate the approach in Parkinson's disease (PD) brain samples, showing that multiDIA substantially expands sequence coverage while retaining the sensitivity, reproducibility, and scalability of DIA. This enabled the identification of disease-associated proteoform changes undetectable by single-protease DIA and the quantification of many disease-relevant post-translational modifications. MultiDIA thus enables deep, high-confidence proteome characterization from limited sample quantities without the throughput and sensitivity constraints of multidimensional fractionation.

systems biology↗

bioRxiv2026

Beyond Environmental Matching: Maternal Effects Depend on Offspring Environmental Complexity and Fitness Traits

The consequences of maternal effects for offspring fitness can depend on the environmental conditions offspring encounter and the fitness traits considered. We used a transgenerational experiment in Daphnia magna to test how maternal exposure to warming and elevated salinity influenced offspring survival, reproduction and body size across matching, mismatching and multiple-stressor environments. Maternal exposure to salinity enhanced offspring survival under matching salinity, and benefits extended to mismatching environments. In contrast, maternal exposure to warming provided no survival benefit under matching warming and reduced survival in mismatching environments, while accelerating reproduction across contexts. Multiple-stressor conditions revealed pronounced maternal effects, while contrasting responses across survival, reproduction and body size showed that benefits to one fitness trait did not extend to others. Our findings demonstrate that environmental matching alone is insufficient to predict maternal effects, whose consequences depend on offspring environmental complexity and the fitness trait considered.

ecology↗

bioRxiv2026

Repurposing clofarabine against enteric pathogens via metabolic starvation

Enteropathogenic and enterohaemorrhagic Escherichia coli (EPEC/EHEC) cause severe global diarrhoeal disease, exacerbated by rising antimicrobial resistance. Pathogenesis relies on "attaching and effacing" lesions, where bacteria generate actin pedestals to adhere, replicate, and destroy intestinal microvilli. To identify novel anti-virulence candidates targeting this process, we conducted a high-throughput phenotypic screen quantifying pedestal formation via high-content fluorescence microscopy. We identified the anticancer nucleotide analogue clofarabine as a potent inhibitor of EPEC growth and pathogenesis. Distinct from its oncology mechanism - inducing DNA chain termination and apoptosis - clofarabine competes with bacterial ATP-dependent processes to impede gene transcription, protein synthesis, and Type III Secretion System (T3SS) function. Remarkably, EPEC counteracts this inhibition by cleaving clofarabine, enabling restored protein synthesis and resumed growth. Furthermore, we report for the first time that clofarabine suppresses protein translation in human monocytes, suggesting an uncharacterised translational impact on mammalian cells. These findings reveal host and bacterial translation as interconnected vulnerabilities to purine antimetabolites, offering a novel strategy to disarm enteric pathogens while uncovering a bacterial enzymatic mechanism for neutralizing host-targeted therapeutics.

microbiology↗

bioRxiv2026

Localized SARS-CoV-2 Infection Triggers a Tissue-Wide Antiviral Response and Functional Impairment of Olfactory Sensory Neurons

Olfactory dysfunction is a hallmark of COVID-19, yet the mechanisms by which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes widespread sensory impairment remain incompletely understood. We compared the olfactory epithelial tropism of multiple SARS-CoV-2 variants in a mouse model and observed that Alpha and Beta variants exhibited the greatest infectivity for the olfactory epithelium (OE), whereas Omicron rarely infected this tissue despite comparable pulmonary viral titers. We further defined the effects of SARS-CoV-2 on olfactory sensory neurons (OSNs) using immunohistochemistry, single-cell RNA sequencing, spatial gene expression characterization, and functional odor stimulation. The localized infection of sustentacular cells triggered a tissue-wide interferon-stimulated antiviral response that extended beyond infected regions for Alpha and Beta but was largely absent following Omicron infection. Mature OSNs transiently adopted an interferon-responsive state before exhibiting persistent downregulation of odorant signal transduction, mitochondrial, and activity-dependent gene pathways. Consistent with these transcriptional changes, odor stimulation failed to elicit normal activity-dependent gene expression during SARS-CoV-2 infection, indicating impaired neuronal function without widespread neuronal loss. Progressive accumulation of macrophages further indicated sustained inflammatory remodeling of the OE. Together, these findings demonstrate that SARS-CoV-2 infection initiates tissue-wide antiviral signaling in the OE that persistently disrupts OSN function, providing a mechanistic framework for COVID-19-associated anosmia.

neuroscience↗

bioRxiv2026

WaterFlow: Prediction of Ordered Water Molecule Positions on Protein Structures

Ordered water molecules mediate many protein functions, including stability, ligand binding, and catalysis. Predicting their positions with sub-angstrom accuracy would support protein design, binding affinity prediction, and automated model building in X-ray crystallography and cryo-EM. However, water molecule prediction lags behind protein and other molecule structure predictions. Here, we introduce WaterFlow, a flow-matching-based generator model and confidence model for predicting the positions of ordered water molecules in protein structures. WaterFlow outperforms the existing state of the art at every precision level. We demonstrate that WaterFlow can accurately predict ground truth modeled water molecules, including those around protein-ligand interactions and on predicted structures. We also show that WaterFlow predictions fit well directly to experimental data, and therefore propose that it may be used for both prediction and modeling water molecules. This includes novel predictions that are often associated with positive electron difference density, meaning the model places water molecules at sites the original structure depositions omitted. We use this improved model to address the data constraint. By mapping the Pareto front of achievable accuracy of water molecule prediction, alongside analysis of different training data schemas, we quantified the trade-off between data quantity and data quality, demonstrating that the diversity of high-quality structures is limiting the possible results. Overall, WaterFlow predicts ordered water to serve as a solvent module for structure-based drug design and for water molecule placement during crystallographic refinement.

biophysics↗

bioRxiv2026

3,500 years of sheeppox virus evolution inferred from archaeological and codicological genomes

Sheeppox virus (SPPV) is a major livestock pathogen causing economic hardship through reduced production and death of vulnerable sheep, with written descriptions of sheeppox-like disease recorded since antiquity. We report 21 novel ancient SPPV genomes spanning the Eurasian steppe Bronze Age ([~]1,700 BCE) to the Early Modern period in Western Europe, including multiple genomes obtained from medieval parchment. We estimate that major capripoxvirus lineages diverged [~]11,500-3,700 years ago, overlapping known translocations and bio-cultural developments in sheep. Our dataset supports SPPV diverging first within the lineage leading to goatpox virus and lumpy skin disease virus, and that known gene inactivation events within SPPV and goatpox virus occur in our earliest SPPV genomes. These findings reveal that the food security of Eurasian communities have been threatened by sheeppox for over 3,700 years, and provide new insights to the genomic evolution and potential host adaptation of sheeppox virus. TeaserAncient viral genomes from manuscripts and teeth illuminate the evolutionary history of sheeppox virus.

genetics↗

bioRxiv2026

Cell-matrix mechanosensing and cellular metabolic demand are linked through SKT and mTORC2

Integrin-based adhesion complexes mediate cell adhesion to the extracellular matrix and enable the cell to interpret and respond to both biochemical and mechanical cues. Such cues can affect a cells metabolic rate; however, how mechanical signals are converted into metabolic rate changes is not clear. We identified an uncharacterised protein; Sickle Tail Protein Homolog (KIAA1217), SKT to be enriched in cell-matrix adhesion complexes in stiff microenvironments. Low SKT expression correlates with an improved prognosis in pancreatic ductal adenocarcinoma (PDAC), suggesting an important role for SKT in extracellular matrix dependent tumour progression. Here, we show that SKT interacts with the mechanistic target of rapamycin complex 2 (mTORC2), a pivotal signalling complex in glucose metabolism, cell growth, and survival. SKT recruits mTORC2 to cell-matrix adhesions in a mechanoresponsive manner. SKT mediated mTORC2 signalling from adhesions is required for maintaining glycolytic flux and control of adhesion dynamics. Our findings show that SKT serves as a rheostat that controls metabolic adaptation of cells to their matrix microenvironment. Collectively, our research provides insights into the molecular mechanisms and interplay between cell adhesion and metabolic signalling in complex and stiff tumour microenvironments. The novel functions identified for SKT in cell-matrix adhesions, mTORC2 signalling and glycolysis unveils a signalling axis between the tumour microenvironment and cellular metabolism that are required for PDAC growth and invasion.

cell biology↗

bioRxiv2026

Human fallopian tube-on-a-chip for preclinical testing of non-hormonal contraceptives with living human sperm

The fallopian tube serves as a sperm reservoir, and it is the site where the oocytes become fertilized. Here, we describe development of an organ-on-a-chip microfluidic model of the fallopian tube (FT Chip) lined by primary human epithelial cells and stromal fibroblasts derived from the FT ampulla. Abundant tissue folds lined by hormone-responsive, epithelial cells resembling those seen in vivo formed on-chip, but not in epithelial organoids cultured in gel cultures. Comparative time-resolved analysis of human sperm versus oocyte-sized microparticles introduced into the epithelial channel in the presence of estradiol revealed that sperm movement was significantly reduced, while the oocyte-sized particles increased, relative to movements in acellular chips. When the non-hormonal contraceptive TDI-11861 was administered to the chip, dose-dependent inhibition of human sperm motility was detected. Thus, this FT Chip may offer a human preclinical tool to study FT physiology and assess the efficacy and mechanism of action of contraceptives.

cell biology↗

bioRxiv2025

Secondary nucleation of α-Synuclein drives Mitochondria dysfunctions and Lewy body formation in Parkinson's Disease

The seeding of -Synuclein (Syn) is a key driver of Lewy pathology propagation in Parkinsons disease (PD) and forms the basis for recent diagnostic advances. However, it remains unclear how the structural and biochemical features of Syn seeds dictate their propagation efficiency, capacity to induce Lewy body formation, and resulting cellular toxicity. Using genetic and idiopathic PD cell models, we map the pathogenic cascade beginning with the seed-driven conversion of endogenous Syn, followed by impaired degradation, mitochondrial dysfunction, and ultimately Lewy body formation. By coupling kinetic modelling of aggregation with functional readouts, we identify secondary nucleation as the predominant mechanism generating toxic Syn aggregation intermediates, identifying the critical process that links seeding to pathology. Extending this framework to PD brain, we quantitatively correlate seeding capacity with the spatiotemporal spread and severity of Lewy pathology, revealing a mechanistic connection between Syn aggregation dynamics and disease progression at molecular, cellular, and anatomical levels. By unifying molecular mechanism with clinicopathological progression, our work identifies catalytic Syn fibrillar seeds as tractable targets for both disease-modifying therapy and biomarker development in PD. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC="FIGDIR/small/676873v1_ufig1.gif" ALT="Figure 1"> View larger version (79K): org.highwire.dtl.DTLVardef@1eca299org.highwire.dtl.DTLVardef@a714d4org.highwire.dtl.DTLVardef@1486db5org.highwire.dtl.DTLVardef@1aa895_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISyn fibril-oligomer interplay drives mitochondrial abnormalities and Lewy pathology C_LIO_LIFibrillar Syn catalyse toxic aggregate formations via secondary nucleation C_LIO_LIPhosphorylated Syn evades lysosomal clearance and drives enhanced dysfunctions C_LIO_LISeeding capacity of Syn predicts Lewy pathology burden and disease progression C_LI

neuroscience↗

bioRxiv2025

Reducing Foetal Bovine Serum Culture Conditions does not affect GPCR Signalling

Animal use in research extends beyond the use of animal models to study physiology and disease. Many aspects of in vitro research use reagents derived from animals, most prolifically the use of foetal bovine serum (FBS) in growth media for cellular models. With the aim to reduce animal use, we investigated the effect of reduced FBS culture conditions on cell growth, as well as different stages of G protein-coupled receptor (GPCR) signalling, a wide area of research which might therefore impact many groups. We identified little differences on cell growth or GPCR signalling when reducing culture FBS percentage from 10% to 5%, using assays ranging from receptor activation to downstream transcription factors stimulation. In addition to diminishing animal use, the reduction of FBS use will also have economic and environmental benefits, which we hope will be of benefit to the wider research community.

pharmacology and toxicology↗

bioRxiv2024

An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research

Archaeological dental calculus can provide detailed insights into the ancient human oral microbiome. We offer a multi-period, multi-site, ancient shotgun metagenomic dataset consisting of 174 samples obtained primarily from archaeological dental calculus derived from various skeletal collections in the United Kingdom. This article describes all the materials used including the skeletons historical period and burial location, biological sex, and age determination, data accessibility, and additional details associated with environmental and laboratory controls. In addition, this article describes the laboratory and bioinformatic methods associated with the dataset development and discusses the technical validity of the data following quality assessments, damage evaluations, and decontamination procedures. Our approach to collecting, making accessible, and evaluating bioarchaeological metadata in advance of metagenomic analysis aims to further enable the exploration of archaeological science topics such as diet, disease, and antimicrobial resistance (AMR).

microbiology↗

bioRxiv2024

Rapid degradation of Histone Deacetylase 1 (HDAC1) reveals essential roles in both gene repression and active transcription

Histone Deacetylase 1 (HDAC1) removes acetyl groups from lysine residues on the core histones, a critical step in the regulation of chromatin accessibility. Despite histone deacetylation being an apparently repressive activity, suppression of HDACs causes both up- and down-regulation of gene expression. Here we exploited the degradation tag (dTAG) system to rapidly degrade HDAC1 in embryonic stem cells (ESCs) lacking its paralog, HDAC2. Unlike HDAC inhibitors that lack isoform specificity, the dTAG system allowed specific degradation and removal of HDAC1 in <1 hour (100x faster than genetic knockouts). This rapid degradation caused increased histone acetylation in as little as 2 hours, with H2BK5 and H2BK11 being the most sensitive. The majority of differentially expressed genes following 2 hours of HDAC1 degradation were upregulated (275 genes up vs 15 down) with increased proportions of downregulated genes observed at 6 (1,153 up vs 443 down) and 24 hours (1,146 up vs 967 down) respectively. Upregulated genes showed increased H2BK5ac and H3K27ac around their transcriptional start site (TSS). In contrast, decreased acetylation of super-enhancers (SEs) was linked to the most strongly downregulated genes. These findings suggest a paradoxical role for HDAC1 in the maintenance of histone acetylation levels at critical enhancer regions required for the pluripotency-associated gene network.

molecular biology↗

bioRxiv2024

Mechanical control of the splicing factor PTBP1 regulates extracellular matrix stiffness-induced cell proliferation and mechanomemory

Cells sense and respond to mechanical cues from their environment. Mechanical cues are important for many biological processes, including embryonic development, ageing, cellular homeostasis, and diseases. Cells translate mechanical cues into cellular biochemical signals that govern cellular behaviour, like cell proliferation or migration, via a process called mechanotransduction. However, this process and the proteins involved remain incompletely understood. Here, we present an unbiased and large-scale approach to identify proteins involved in mechanotransduction. The screen revealed that the splicing factor PTBP1 is a novel mechanotransducer. We show that the nuclear localisation of PTBP1 depends on extracellular matrix stiffness, cell density, and the actomyosin-based contractility of the cell. Furthermore, we demonstrate that PTBP1 promotes the mechanosensitive splicing of the adapter protein Numb and that alternative splicing of Numb is crucial for matrix stiffness-induced cell proliferation and mechanomemory. Our results support the idea that changes in alternative splicing are an integral part of mechanotransduction and provide a mechanism by which matrix stiffness regulates cell proliferation and the formation of a mechanomemory in cells.

cell biology↗

bioRxiv2023

BRG1/BRM inhibitor targets AML stem cells and exerts superior preclinical efficacy combined with BET or Menin inhibitor

BRG1 (SMARCA4) and BRM (SMARCA2) are the core ATPases of chromatin remodeling BAF (BRG1/BRM-associated factor) complexes, which enable transcription factors/co-factors to modulate gene-expressions, mediating growth, differentiation-arrest and survival of AML cells. In AML with MLL1r (MLL1 rearrangement) or mutant (mt) NPM1, although monotherapy with Menin inhibitor (MI) induces clinical remissions, most patients either fail to respond or relapse. FHD-286 is a selective BRG1/BRM inhibitor, undergoing clinical development in AML. Here, FHD-286 induced differentiation and lethality in AML cells with MLL1r or mtNPM1, reducing chromatin accessibility and repressing c-Myc, PU.1 and CDK4/6. Whereas FHD-286 monotherapy reduced AML burden, leukemia-initiating potential and improved survival, FHD-286 combinations with MI, BET inhibitor, decitabine or venetoclax was significantly more effective in reducing AML burden and improved survival, without significant toxicity, in xenograft models of AML with MLL1r or mtNPM1. These findings highlight promising FHD-286-based combinations for therapy of AML with MLL1r or mtNPM1. Statement of SignificanceInhibition of BRG1/BRM ATPases by FHD-286 reduced chromatin accessibility, repressed c-Myc, PU.1 and CDK4/6, inducing differentiation, leukemia-initiating potential and lethality in AML stem-progenitor cells. FHD-286-based combinations with Menin or BET inhibitor or decitabine reduced AML burden and improved survival in xenograft models of AML with MLL rearrangement or mutant NPM1.

cancer biology↗

bioRxiv2023

The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions

Bacterial RNP bodies (BR-bodies) are non-membrane-bound structures that facilitate mRNA decay by concentrating mRNA substrates with RNase E and the associated RNA degradosome machinery. However, the full complement of proteins enriched in BR-bodies has not been defined. Here we define the protein components of BR-bodies through enrichment of the bodies followed by mass spectrometry-based proteomic analysis. We found 111 BR-body enriched proteins, including several RNA binding proteins, many of which are also recruited directly to in vitro reconstituted RNase E droplets, showing BR-bodies are more complex than previously assumed. While most BR-body enriched proteins that were tested cannot phase separate, we identified five that undergo RNA-dependent phase separation in vitro, showing other RNP condensates interface with BR-bodies. RNA degradosome protein clients are recruited more strongly to RNase E droplets than droplets of other RNP condensates, implying that client specificity is largely achieved through direct protein-protein interactions. We observe that some RNP condensates assemble with preferred directionally, suggesting that RNA may be trafficked through RNP condensates in an ordered manner to facilitate mRNA processing/decay, and that some BR-body associated proteins have the capacity to dissolve the condensate. Finally, we find that RNA dramatically stimulates the rate of RNase E phase separation in vitro, explaining the dissolution of BR-bodies after cellular mRNA depletion observed previously. Altogether, these results suggest that a complex network of protein-protein and protein-RNA interactions controls BR-body phase separation and RNA processing. HighlightsO_LIBR-body proteomics identified 111 proteins enriched in BR-bodies. C_LIO_LIBR-bodies associate with an interconnected network of RNP condensates. C_LIO_LIBR-body condensation is modulated by its interaction network. C_LIO_LIRNA is required for rapid BR-body condensation. C_LI Graphical AbstractSummary of the BR-body protein interactome. Lines between two protein circles represent a direct interaction.

microbiology↗

bioRxiv2022

A human DCC variant causing mirror movement disorder reveals an essential role for the Wave regulatory complex in Netrin/DCC signaling

The axon guidance cue, Netrin-1, signals through its receptor DCC to attract commissural axons to the midline. Pathogenic variants in DCC frequently lead to congenital mirror movements (CMM), but how these variants impact DCC function is largely unknown. Screening of DCC in individuals with CMM recently revealed a novel variant located in a conserved motif in the cytoplasmic tail of DCC that is predicted to bind to a central actin nucleation promoting factor, the WAVE regulatory complex (WRC). Here, we use biochemical and axon guidance assays to show that this CMM-associated DCC variant is pathogenic by disrupting the interaction between DCC and the WRC. This DCC-WRC interaction is evolutionarily conserved and is required for Netrin-1 mediated commissural axon outgrowth and guidance. Together, we identify the WRC as a pivotal component of Netrin-1/DCC signaling and further provide a molecular mechanism explaining how genetic variants in DCC may lead to CMM.

neuroscience↗

bioRxiv2022

The EGFR/ErbB inhibitor neratinib modifies the neutrophil phosphoproteome and promotes apoptosis and clearance by airway macrophages

Dysregulated neutrophilic inflammation can be highly destructive in chronic inflammatory diseases due to prolonged neutrophil lifespan and continual release of histotoxic mediators in inflamed tissues. Therapeutic induction of neutrophil apoptosis, an immunologically silent form of cell death, may be beneficial in these diseases, provided that the apoptotic neutrophils are efficiently cleared from the tissue. Our previous research identified ErbB inhibitors as able to induce neutrophil apoptosis and reduce neutrophilic inflammation both in vitro and in vivo (Rahman et al., 2019). Here we extend that work using a clinical ErbB inhibitor, neratinib, which has the potential to be repurposed in inflammatory diseases. We show that neratinib reduces neutrophilic migration to an inflammatory site in zebrafish larvae. Neratinib upregulates efferocytosis and reduces the number of persisting neutrophil corpses in mouse models of acute, but not chronic, lung injury, suggesting the drug may have therapeutic benefits in acute inflammatory settings. Phosphoproteomics analysis of human neutrophils shows that neratinib modifies the phosphorylation of proteins regulating apoptosis, migration and efferocytosis. This work identifies a potential mechanism for neratinib in treating acute lung inflammation by upregulating the clearance of dead neutrophils and, through examination of the neutrophil phosphoproteome, provides important insights into the mechanisms by which this may be occurring.

immunology↗

bioRxiv2022

HDAC6 inhibitor ACY-1083 shows lung epithelial protective features in COPD

Airway epithelial damage is a common feature in respiratory diseases such as COPD and has been suggested to drive inflammation and progression of disease. These features manifest as remodeling and destruction of lung epithelial characteristics including loss of small airways which contributes to chronic airway inflammation. Histone deacetylase 6 (HDAC6) has been shown to play a role in epithelial function and dysregulation, such as in cilia disassembly, epithelial to mesenchymal transition (EMT) and oxidative stress responses, and has been implicated in several diseases. We thus used ACY-1083, an inhibitor with high selectivity for HDAC6, and characterized its effects on epithelial function including epithelial disruption, cytokine production, remodeling, mucociliary clearance and cell characteristics. Primary lung epithelial air-liquid interface cultures from COPD patients were used and the impacts of TNF, TGF-{beta}, cigarette smoke and bacterial challenges on epithelial function in the presence and absence of ACY-1083 were tested. Each challenge increased the permeability of the epithelial barrier whilst ACY-1083 blocked this effect and even decreased permeability in the absence of challenge. TNF was also shown to increase production of cytokines and mucins, with ACY-1083 reducing the effect. We observed that COPD-relevant stimulations created damage to the epithelium as seen on immunohistochemistry sections and that treatment with ACY-1083 maintained an intact cell layer and preserved mucociliary function. Interestingly, there was no direct effect on ciliary beat frequency or tight junction proteins indicating other mechanisms for the protected epithelium. In summary, ACY-1083 shows protection of the respiratory epithelium during COPD-relevant challenges which indicates a future potential to restore epithelial structure and function to halt disease progression in clinical practice.

cell biology↗