Biology subjects

Pearson, J.

Publications and source records attributed to Pearson, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Neuropeptide Y4 receptor activation delays autoimmune diabetes by reprogramming β-cell stress and immune tolerance

Type 1 diabetes (T1D) involves immune-mediated destruction of pancreatic {beta}-cells, yet current disease-modifying therapies mainly target immunity without enhancing {beta}-cell resilience. We show selective neuropeptide Y4 receptor (Y4R) agonism protects {beta}-cells while reshaping islet immunity across T1D models. Multi-modal localisation using cell sorting, qPCR, RNAscope and fluorescent ligand competition demonstrated predominant Y4R expression and functional accessibility on mouse and human {beta}-cells. Selective Y4R agonism was non-toxic and did not impair islet network integrity, Ca{superscript 2} dynamics, glucose-stimulated insulin secretion or systemic glucose tolerance. Y4R activation conferred cytoprotection against inflammatory cytokines, streptozotocin, lipotoxicity and ER stress, reducing caspase-3/7 activation and {beta}-cell loss whilst sustaining insulin release and promoting proliferation in both mouse and human islets. Bulk RNA-seq revealed a coordinated {beta}-cell resilience programme characterised by reinforced identity and insulin processing, KEAP1-NFE2L2-driven antioxidative and proteostatic activation, and suppression of EIF2 signalling and associated biosynthetic and ER stress pathways. Concurrently, Y4R agonism dampened pathogenic chemokine and cytokine networks, including CXCL10, CCL3/4/7 and IL-6, while preserving IL-2 and Foxp3 signals, thereby limiting CD8 T cell, CD4 T cell and macrophage chemotaxis toward cytokine-stressed islets. Reduced immune-cell recruitment was conserved in a fully human immune-islet system, where Y4R activation significantly attenuated IL-2-activated human PBMC migration and invasion toward cytokine-stressed human islets. In a stringent NY8.3 CD8 T cell adoptive-transfer model, systemic Y4R agonism significantly delayed diabetes onset. These data position Y4R as a {beta}-cell-centric therapeutic target coupling intrinsic resilience with local immune modulation, offering a complementary approach for {beta}-cell preservation in T1D and islet replacement therapies. Graphical abstractThe selective Y4 receptor agonist K22 binds {beta}-cell-enriched NPY4R in mouse and human islets, activates a {beta}-cell resilience programme that preserves insulin secretion under inflammatory and metabolic stress, and simultaneously dampens islet chemokine output, thereby limiting innate and adaptive immune-cell recruitment and delaying autoimmune diabetes onset. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/736290v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@7efd48org.highwire.dtl.DTLVardef@1268860org.highwire.dtl.DTLVardef@c38a81org.highwire.dtl.DTLVardef@1ba3e6c_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Dynamic Compression Flows for Neuroscience Data

While neuroscience experiments have repeatedly demonstrated the involvement of large populations of neurons in even simple behaviors, these studies have just as often reported that the collective dynamics of neural activity are approximately low-dimensional. As a result, methods for identifying low-dimensional latent representations of time series data have become increasingly prominent in neuroscience. However, most existing methods either ignore temporal structure or model time evolution using latent dynamical systems approaches. In the first case, dynamics may be distorted or even scrambled in the latent space, while in the second, many possible latent dynamics may give rise to the same data. Here, we address these challenges using a novel flow-matching approach in which data are generated by a pair of flow fields, one governing time evolution, the other a mapping between data and a low-dimensional latent space. Importantly, the dimension-reducing flow is trained to minimize distortions of the temporal dynamics, learning an identifiable low-dimensional representation that preserves temporal relations in the original data. Additionally, we constrain our latent spaces to have low-dimensional support in a soft, parameterized manner, taking inspiration from ideas on nested dropout. Across both neural and behavioral data, we show that this dual flow approach produces both more interpretable dynamics and higher-quality reconstructions than competing models, including in noise-dominated data sets where conventional approaches fail.

neuroscience↗

bioRxiv2026

A synaptic locus of song learning

Learning by imitation is the foundation for verbal and musical expression, but its underlying neural basis remains obscure. A juvenile male zebra finch imitates the multisyllabic song of an adult tutor in a process that depends on a song-specialized cortico-basal ganglia circuit, affording a powerful system to identify the synaptic substrates of imitative motor learning. Plasticity at a particular set of cortico-basal ganglia synapses is hypothesized to drive rapid learning-related changes in song before these changes are subsequently consolidated in downstream circuits. Nevertheless, this hypothesis is untested and the synaptic locus where learning initially occurs is unknown. By combining a computational framework to quantify song learning with synapse-specific optogenetic and chemogenetic manipulations within and directly downstream of the cortico-basal ganglia circuit, we identified the specific cortico-basal ganglia synapses that drive the acquisition and expression of rapid vocal changes during juvenile song learning and characterized the hours-long timescale over which these changes consolidate. Furthermore, transiently augmenting postsynaptic activity in the basal ganglia briefly accelerates learning rates and persistently alters song, demonstrating a direct link between basal ganglia activity and rapid learning. These results localize the specific cortico-basal ganglia synapses that enable a juvenile songbird to learn to sing and reveal the circuit logic and behavioral timescales of this imitative learning paradigm.

neuroscience↗

bioRxiv2025

Closing the Loop on Phage-bacteria Coevolution

Bacteria and their viruses, bacteriophages (phages), continually coevolve in nature. In contrast, laboratory-based coevolution experiments usually last less than a month before becoming dormant or extinct as one species is outcompeted by the other. Consequently, there is a poor understanding of phage-bacteria coevolution and hence the long-term efficacy of bacteriophage therapies (an approach to tackling antimicrobial resistance). We propose a novel approach to coevolution experiments that would address this challenge: instead of open-loop resource-constrained cultures, we develop a closed-loop control approach to stabilise the typically unstable or oscillatory phage-bacteria population dynamics. Achieving this requires the control system to compensate for delays in phage incubation and respond to an evolving system, while only measuring bacterial density. To this end, we develop a model of phage-bacteria dynamics, prototype delay-compensating predictive control strategies, and demonstrate a measurement-aware state observer. Overall, this approach shows the ability to stabilise coevolution, avoiding the common outcomes of unstable dynamics or winner-takes-all competition.

evolutionary biology↗

bioRxiv2025

Motor Cortical Output Integrates Distorted Proprioceptive Feedback

Proprioceptive feedback from muscles is essential for continuous monitoring and precise control of limb movement, yet how such peripheral feedback is integrated into ongoing descending motor cortical dynamics remains largely unclear. Here we used precisely timed optogenetic stimulation of forelimb muscles to manipulate proprioceptive signals during a mouse reach-to-consume task. Mice were able to successfully reach and consume despite muscle stimulation-evoked forelimb deviations. Across the cortex, the caudal forelimb area (CFA) was preferentially activated by muscle-specific proprioceptive inputs and contributed to stabilizing perturbed forelimb movement. CFA extratelencephalic (ET) neurons encoded movement kinematics as well as proprioceptive feedback. At neuron population level, proprioceptive perturbations rapidly deflected CFA ET neural trajectories away from the task-relevant manifold yet exerted only limited effects on evolving task dynamics. These results reveal that descending cortical circuit implements activity subspace separation to encode and integrate distorted proprioceptive feedback while preserving task-relevant output.

neuroscience↗

bioRxiv2025

Correctness is its own reward: bootstrapping error signals in self-guided reinforcement learning

Reinforcement learning (RL) offers a compelling account of how agents learn complex behaviors by trial and error, yet RL is predicated on the existence of a reward function provided by the agents environment. By contrast, many skills are learned without external guidance, posing a challenge to RLs ability to account for self-directed learning. For instance, juvenile male zebra finches first memorize and then train themselves to reproduce the song of an adult male tutor through extensive practice. This process is believed to be guided by an internally computed assessment of performance quality, though the mechanism and development of this signal remain unknown. Here, we propose that, contrary to prevailing assumptions, tutor song memorization and performance assessment are subserved by the same neural circuit, one trained to predictively cancel tutor song. To test this hypothesis, we built models of a local forebrain circuit that uses contextual premotor signals to cancel tutor song auditory input via synaptic plasticity. After learning, excitatory projection neurons signaled mismatches between the tutor song and birds own performance, best matching experimental data when learning involved anti-Hebbian plasticity in recurrent interneurons. We also found that learning proceeds by both sharpening error sensitivity and minimizing responses to the tutor song. Finally, the error signals produced by this model can train a simple RL agent to replicate the spectrograms of adult bird songs. These results suggest that local learning via predictive cancellation suffices for bootstrapping error signals capable of guiding self-directed learning of natural behaviors. SignificanceMany species, including humans, learn new skills by trial and error. But in the absence of external rewards and punishments, individuals need a means of assessing the quality of their performance. Here, we model the process by which juvenile male zebra finches memorize the song of an adult tutor, showing how local changes in brain circuits responsible for hearing can give rise during this process to an internal error signal that later allows for self-guided learning.

neuroscience↗

bioRxiv2025

Crosslinked CXCR4 Signals Decreased Motility and Increased Adhesion of T Cells

Pancreatic ductal adenocarcinoma (PDA) is a highly aggressive cancer known for its ability to evade immune surveillance, primarily through mechanisms that prevent T cell infiltration. While the coating of cancer cells with the chemokine, CXCL12, is required for the exclusion of T cells, the precise molecular mechanisms behind the failure of T cell migration into the tumor remain unclear. In this study, we identify a potential mechanism by demonstrating that crosslinking CXCR4 is associated with decreased motility of T cells secondary to their adhesion to fibronectin. Using human lymphoblastoid T cells and primary human T cells, we show that polymeric CXCL12-induced crosslinked CXCR4 triggers the non-G i-dependent pathway of tyrosine phosphorylation of FAK-related proline-rich tyrosine kinase 2 (PTK2B) in T cells. This response is necessary for the decreased motility and increased adhesion of T cells. We also find that the downstream cellular reactions of this pathway is secondary to CXCR4-crosslinking and require the integrin subunit, 4, and TNF stimulation of TNFRSF1B. These findings provide insights into the mechanisms mediating the exclusion of T cells from nests of PDA cells and further support therapeutic strategies aimed at blocking the interaction of CXCR4 on T cells with the CXCL12-coating of PDA cells.

immunology↗

bioRxiv2024

Characterization and Functional Assessment of Epicardial Secretome: Epicardium-Derived Extracellular Vesicles and Matrix

AimThe epicardium, an epithelial layer covering the heart, plays pivotal roles in embryonic heart development and responses to cardiac damage. Epicardial secreted molecular agents are known to be involved in the regulation of these phenomena, but how this regulation occurs is poorly understood. In this study, we have investigated extracellular vesicle (EV) and extracellular matrix (ECM) components of epicardial secretions using a continuous mouse embryonic epicardial-derived cell (EPIC) line. Methods and resultsEpicardial-derived EVs were isolated using differential ultracentrifugation from EPIC cultured at 1% (EVs-H1%), 5% (EVs-H5%), and 21% oxygen (EVs-N). EVs protein content was determined by tandem mass tag (TMT) proteomic analysis. The results showed that epicardial-derived EVs cargo is sensitive to the oxygen level of their parenteral cells, increasing their content on glycolytic proteins. Moreover, hypoxic-derived EVs were found to both increase EPIC proliferation and affect the metabolism of Primary Human Umbilical Vein Endothelial Cells (HUVECs). On the other hand, epicardial-derived extracellular matrix (EPIC-ECM) was characterized by subjecting decellularized EPIC to shotgun proteomics and comparing it to decellularized perinatal hearts and Matrigel(R). We found that EPIC-ECM composition closely resembles that of embryonic cardiac tissue. Although the structural and basement membrane-associated proteins of EPIC-ECM were similar to those found in Matrigel(R)(R), EPIC-ECM exhibited higher protein diversity and was a more potent inducer of HUVEC proliferation. ConclusionThis work represents the first comprehensive and systematic proteomic analysis of two important components of the epicardial-derived secretome. Our experiments reveal that the epicardium responds to hypoxia by secreting EVs capable of modifying the metabolic responses of surrounding cells. Furthermore, EPIC-ECM promotes endothelial cell proliferation. These findings demonstrate the significant signaling abilities of the epicardial secretome, consistent with reports of endothelial responses following cardiac ischemic damage.

developmental biology↗

bioRxiv2024

Female lineages and changing kinship patterns in Neolithic Catalhöyük

Arguments have long suggested that the advent of early farming in the Near East and Anatolia was linked to a Mother Goddess cult. However, evidence for a dominant female role in these societies has been scarce. We studied social organisation, mobility patterns and gendered practices in Neolithic Southwest Asia using 131 paleogenomes from Catalhoyuk East Mound (7100-5950 BCE), a major settlement in Central Anatolia with an uninterrupted occupation and an apparent egalitarian structure. In contrast to widespread genetic evidence for patrilocality in Neolithic Europe, the Catalhoyuk individuals revealed no indication of patrilocal mobility. Analysing genetic kin ties among individuals buried in the same house (co-burials) across 35 Catalhoyuk buildings, we identified close ties concentrated within buildings and among neighbours in Catalhoyuks Early period, akin to those in the preceding Pre-Pottery Neolithic in Southwest Asia. This pattern weakened over time: by the late 7th millennium BCE, subadults buried in the same building were rarely closely genetically related, despite sharing similar diets. Still, throughout the sites occupation, genetic connections within Catalhoyuk buildings were much more frequently connected via the maternal than the paternal line. We also identified differential funerary treatment of female subadults compared to those of males, with a higher frequency of grave goods associated with females. Our results reveal how kinship practices changed while key female roles persisted over one thousand years in a large Neolithic community in western Eurasia.

genomics↗

bioRxiv2023

Adherent reformed islets: a long-term primary cell-based platform for exploring mouse and human islet biology.

Pancreatic islets are 3-dimensional micro-organs that maintain {beta}-cell functionality via cell-cell and cell-matrix communication. Isolated primary islets are the gold standard for in vitro models. However, native islets present experimental challenges for long-term mechanistic studies owing to their short culture life (approximately 1 week). We developed a novel long-term protocol to study the function of primary islets. The protocol employed reformed islets following dispersion and a fine-tuned culture environment. Reformed islets are highly similar to their primary counterparts across various physiological characteristics. Long-term culture of reformed islets enables high-resolution imaging, repeated functional assessment, and the study of cell-cell communication. Unlike other platforms such as stem cell-derived organoids, reformed islets retain their resident immune populations, making them ideal for studying both resident and infiltrating immune cells and their interactions with hormone-producing islet cells. Qualitative and quantitative analyses revealed that the composition and cytoarchitecture of the reformed islets mimicked those found in primary islets, including the presence of macrophages and CD4+ and CD8+ T cells, which are the key resident immune cell types. Reformed islets secrete insulin and are glucose-responsive, and their {beta}-cells can be stimulated to proliferate using GLP-1 receptor agonism. Furthermore, a comparison of the transcriptomic landscape of isolated human islets and reformed islets generated from the same donor demonstrated a high degree of similarity. Our reformed islets provide an ideal platform to study diabetes pathology. We recapitulated both the T1DM and T2DM disease milieu and validated our model for studying islet immune trafficking and invasion using activated macrophages and T cells. Our data illustrates that reformed islets are an anatomical and functional alternative to native human and mouse islets. Moreover, reformed islets have an advantage over mouse and human {beta}-cell lines, including MIN6 and EndoC-{beta}H1cells, that lack the signalling input of non-{beta}-endocrine cells and immune cell crosstalk. In this study, we showed that reformed islets are a durable paradigm (cell-based model) for islet-based exploration and a means of target discovery/validation for diabetes research. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/568245v2_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1201151org.highwire.dtl.DTLVardef@510ea8org.highwire.dtl.DTLVardef@19937c1org.highwire.dtl.DTLVardef@1b85a6_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2023

Global Sensitivity Analysis of the Onset of Nasal Passage Infection by SARS-CoV-2 With Respect to Heterogeneity in Host Physiology and Host Cell-Virus Kinetic Interactions

Throughout the COVID-19 pandemic, positive nasal swab tests have revealed dramatic population heterogeneity in viral titers spanning 6 orders-of-magnitude. Our goal here is to probe potential drivers of infection outcome sensitivity arising from (i) physiological heterogeneity between hosts and (ii) host-variant heterogeneity in the detailed kinetics of cell infection and viral replication. Toward this goal, we apply global sensitivity methods (Partial Rank Correlation Coefficient analysis and Latin Hypercube Sampling) to a physiologically faithful, stochastic, spatial model of inhaled SARS-CoV-2 exposure and infection in the human respiratory tract. We focus on the nasal passage as the primary origin of respiratory infection and site of clinical testing, and we simulate the spatial and dynamic progression of shed viral load and infected cells in the immediate 48 hours post infection. We impose immune evasion, i.e., suppressed immune protection, based on the preponderance of clinical evidence that nasal infections occur rapidly post exposure, largely independent of immune status. Global sensitivity methods provide the de-correlated outcome sensitivities to each source of within-host heterogeneity, including the dynamic progression of sensitivities at 12, 24, 36, and 48 hours post infection. The results reveal a dynamic rank-ordering of the drivers of outcome sensitivity in early infection, providing insights into the dramatic population-scale outcome diversity during the COVID-19 pandemic. While we focus on SARS-CoV-2, the model and methods are applicable to any inhaled virus in the immediate 48 hours post infection.

immunology↗

bioRxiv2023

Norovirus NS3 protein induces apoptosis through translation repression and dysregulation of BCL-2 pro-survival proteins

Norovirus infection is characterised by a rapid onset of disease and the development of debilitating symptoms including projectile vomiting and diffuse diarrhoea. Vaccines and antivirals are sorely lacking and developments in these areas are hampered by the lack of an adequate cell culture system to investigate human norovirus replication and pathogenesis. Herein, we describe how the model norovirus, Mouse norovirus (MNV), produces a viral protein, NS3, with the functional capacity to attenuate host protein translation which invokes the activation cell death via apoptosis. We show that this function of NS3 is conserved between human and mouse viruses and map the protein domain attributable to this function. Our study highlights a critical viral protein that mediates crucial activities during replication, potentially identifying NS3 as a worthy target for antiviral drug development.

microbiology↗

bioRxiv2023

The Neurochemical Mechanisms Underlying the Enhancing Effects of Rewards and Punishments on Motor Performance

Monetary rewards and punishments enhance motor performance and are associated with corticospinal excitability (CSE) increases within the motor cortex (M1) during movement preparation. However, such CSE changes have unclear origins; they could stem from increased glutamatergic (GLUTergic) facilitation and/or decreased type A gamma-aminobutyric acid (GABAA)-mediated inhibition within M1. To investigate this, paired-pulse transcranial magnetic stimulation was used to assess GLUTergic facilitation and GABAA inhibition within M1 whilst participants prepared to execute 4-element finger-press sequences. Behaviourally, rewards and punishments enhanced both reaction and movement times. Neurochemically, regardless of rewards or punishments, a digit-specific increase in GLUTergic facilitation and digit-unspecific decrease in GABAA inhibition occurred during preparation as movement onset approached. In parallel, both rewards and punishments non-specifically increased GLUTergic facilitation, but only rewards non-specifically decreased GABAA inhibition during preparation. This suggests that, to enhance performance, rewards both increase GLUTergic facilitation and decrease GABAA inhibition whilst punishments selectively increase GLUTergic facilitation. A control experiment revealed that such changes were not observed post-movement as participants processed reward and punishment feedback, indicating they were selective to movement preparation. Collectively, these results map the neurochemical changes in M1 by which incentives enhance motor performance.

neuroscience↗

bioRxiv2022

Huntingtin expression influences spontaneous seizure disorder susceptibility in FVN/B mice

Huntington disease (HD) is an adult-onset neurodegenerative disorder that is caused by a trinucleotide CAG repeat expansion in the HTT gene that codes for the protein huntingtin (HTT or Htt in mice). HTT is a multi-functional, ubiquitously expressed protein that is essential for embryonic survival, normal neurodevelopment, and adult brain function. The ability of wild-type HTT to protect neurons against various forms of death raises the possibility that loss of normal HTT function may worsen disease progression in HD. Huntingtin-lowering therapeutics are being evaluated in clinical trials for HD, but concerns have been raised that decreasing wild-type HTT levels may have adverse effects. Here we show that Htt levels modulate the occurrence of an idiopathic seizure disorder that spontaneously occurs in FVB/N mice. These abnormal FVB/N mice demonstrate various cardinal features of mouse models of epilepsy including spontaneous seizures, astrocytosis, neuronal hypertrophy, upregulation of brain-derived neurotrophic factor (BDNF), and sudden seizure-related death. Interestingly, decreasing wild-type Htt levels increased the frequency of this disorder, while over-expression of HTT completely prevented it. Examination of the mechanism underlying huntingtins ability to modulate the frequency of this seizure disorder indicated that over-expression of full length HTT can promote neuronal survival following seizures. Overall, our results demonstrate a protective role for huntingtin in this form of epilepsy and provide a plausible explanation for the observation of seizures in the juvenile form of HD, Lopes-Maciel-Rodan syndrome, and Wolf-Hirschhorn syndrome. Adverse effects caused by altering huntingtin levels has ramifications related to Huntingtin-lowering therapies in development to treat HD.

neuroscience↗

bioRxiv2022

Generalising uncertainty improves accuracy and safety of deep learning analytics applied to oncology

Trust and transparency are critical for deploying deep learning (DL) models into the clinic. DL application poses generalisation obstacles since training/development datasets often have different data distributions to clinical/production datasets that can lead to incorrect predictions with underestimated uncertainty. To investigate this pitfall, we benchmarked one pointwise and three approximate Bayesian DL models used to predict cancer of unknown primary with three independent RNA-seq datasets covering 10,968 samples across 57 primary cancer types. Our results highlight simple and scalable Bayesian DL significantly improves the generalisation of uncertainty estimation (e.g., p-value = 0.0013 for calibration). Moreover, we demonstrate Bayesian DL substantially improves accuracy under data distributional shifts when utilising uncertainty thresholding by designing a prototypical metric that evaluates the expected (accuracy) loss when deploying models from development to production, which we call the Area between Development and Production curve (ADP). In summary, Bayesian DL is a hopeful avenue of research for generalising uncertainty, which improves performance, transparency, and therefore safety of DL models for deployment in real-world.

bioinformatics↗

bioRxiv2022

Gene expression profiling reveals B cells are highly educated by the pancreatic environment during autoimmune diabetes

B cells play an important role in driving the development of type 1 diabetes, however, it remains unclear how they contribute to local beta-cell destruction during disease progression. Using gene expression profiling of B cell subsets in the pancreas and pancreatic lymph nodes, we reveal that B cells are highly modified by the inflamed pancreatic tissue and can be distinguished by their transcriptional profile from those in the lymph node. We identified both a discrete and a core shared gene expression profile in islet CD19+CD138- and CD19+CD138+ B cell subsets, the latter known to have enriched autoreactivity during diabetes development. Upon localisation to pancreatic islets, CD138+ B cells overexpressed genes associated with adhesion molecules and growth factors compared to CD138- B cells. Their shared signature displayed gene expression changes related to the differentiation of antibody-secreting cells and gene regulatory networks associated with interferon signalling pathways, pro-inflammatory cytokines and toll-like receptor activation. Finally, abundant TLR7 expression was detected in islet B cells, and was enhanced specifically in CD138+ B cells. Our study, therefore, provides a detailed transcriptional analysis of islet B cells identifying specific gene signatures and interaction networks that point towards a functional role for B cells in driving autoimmune diabetes.

immunology↗

bioRxiv2022

Bacterial lipopolysaccharide modulates immune response in the colorectal tumor microenvironment

Immune responses can have opposing effects in colorectal cancer (CRC), the balance of which may determine whether a cancer regresses, progresses, or potentially metastasizes. These effects are evident in CRC consensus molecular subtypes (CMS) where both CMS1 and CMS4 contain immune infiltrates yet have opposing prognoses. The microbiome has previously been associated with CRC and immune response in CRC but has largely been ignored in the CRC subtype discussion. Using CMS subtyping, we aimed to determine the contributions of the microbiome to the pleiotropic effects evident in immune-infiltrated subtypes. We integrated host gene-expression and meta-transcriptomic data to determine the link between immune characteristics and microbiome contributions in these subtypes and identified lipopolysaccharide (LPS) binding as a potential functional mechanism. We identified candidate bacteria with LPS properties that could affect immune response, focusing on Fusobacterium periodonticum and Bacteroides fragilis in CMS1, and Porphyromonas asaccharolytica in CMS4. Treatment of peripheral blood mononuclear cells (PBMCs) with LPS isolated from these bacteria showed that F. periodonticum stimulates cytokine production in PBMCs while both B. fragilis and P. asaccharolytica had an inhibitory effect. Furthermore, LPS from the latter two species can inhibit the immunogenic properties of F. periodonticum LPS when co-incubated with PBMCs. We propose that different microbes in the CRC tumor microenvironment can alter the local immune activity, with important implications for prognosis and treatment response.

cancer biology↗

bioRxiv2022

Modeling predicts mechanisms altered by mutations of the SARS-CoV-2 delta and omicron variants

We apply our mechanistic, within-host, pre-immunity, respiratory tract infection model for unvaccinated, previously uninfected, and immune-compromised individuals. Starting from published cell infection and viral replication data for the SARS-CoV-2 alpha variant, we explore variability in outcomes of viral load and cell infection due to three plausible mechanisms altered by SARS-CoV-2 mutations of delta and omicron. We seek a mechanistic explanation of clinical test results: delta nasal infections express [~]3 orders-of-magnitude higher viral load than alpha, while omicron infections express an additional 1 to 2 orders-of-magnitude rise over delta. Model simulations reveal shortening of the eclipse phase (the time between cellular uptake of the virus and onset of infectious viral replication and shedding) alone can generate 3-5 orders-of-magnitude higher viral load within 2 days post initial infection. Higher viral replication rates by an infected cell can generate at most one order-of-magnitude rise in viral load, whereas higher cell infectability has minimal impact and lowers the viral load.

immunology↗