Biology subjects

Thompson, J.

Publications and source records attributed to Thompson, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Machine learning-guided design of human gut microbiome dynamics in response to dietary fibers

Dietary fibers are key modulators of human gut microbiome dynamics and functions, yet we lack the ability to predict community dynamics and functions in response to fibers. We integrate machine learning, Bayesian optimization, and high-throughput community construction to investigate how dietary fibers shape health-relevant functions of human gut microbial communities. To efficiently navigate the landscape of fiber-microbiome interactions, we implemented a design-test-learn cycle to identify fiber-species combinations that maximize a multi-objective function capturing beneficial community properties. Our model-guided approach revealed a highly butyrogenic and robust ecological motif characterized by the copresence of inulin, Bacteroides uniformis, and Anaerostipes caccae and a higher-order interaction with Prevotella copri. In germ-free mice, model-designed species-fiber combinations impacted colonization, community diversity and short-chain fatty acid profiles. In sum, our work establishes a novel framework for designing microbial communities with desired functions in response to key nutrients such as dietary fibers.

systems biology↗

bioRxiv2025

Elucidating the molecular landscape of centronuclear myopathies in mouse models: an integrative multi-omics and network analysis

Centronuclear myopathies (CNM) are rare inherited muscle disorders characterized by muscle atrophy, weakness, and altered muscle fiber structure, primarily due to mutations in genes like MTM1, DNM2, and BIN1. The pathomechanisms implicated in CNM are only partially understood, and no curative therapies are available for patients. This study exploits a unique multi-omics dataset and network-based analyses to elucidate the molecular pathways involved in CNM. First, we performed Weighted Gene Co-expression Network Analysis (WGCNA) to identify gene modules correlated with CNM phenotypes. We find that modules correlated to a positive muscular phenotype were enriched for genes involved in muscle contraction, RNA processes and oxidative phosphorylation, while modules associated with impaired muscle structure and function were enriched in immune response, innervation, vascularization processes, and fatty acid oxidation. Next, we integrated transcriptomic, proteomic, and metabolomic data from the Mtm1-/y mouse model with public knowledge bases using a multilayer network approach and explored the network using a random walk with restart approach. This study revealed novel metabolites that could be targeted through dietary supplementation as potential therapeutic strategies. Our findings demonstrate how multi-omics network analyses can reveal new aspects of CNM pathomechanisms and identify avenues for intervention.

bioinformatics↗

bioRxiv2024

Modelling co-development between somites and neural tube with human Trunk-like Structures (hTLS)

Human stem cell-based embryo models have opened new avenues of research in development by providing experimentally amenable in vitro systems. One of the features of embryo models is their multilineage differentiation, which allows the co-development of, and interactions between, tissues. Here, we utilise a human Trunk-like Structure (hTLS) model to explore trunk development. We show that hTLS have morphologically organised somites and a neural tube that form through self-organised, endogenous signalling including anteroposterior FGF, Wnt and Retinoic Acid (RA) gradients that modulate the fate of neuromesodermal progenitors. Comparison to an existing dataset from organogenesis-stage human embryos shows that hTLS cells approximate Carnegie Stage 13-14 (28-35 days post-fertilisation). The absence of a notochord leads to a dorsal identity, but exogenous exposure to smoothened agonist (promoting Sonic Hedgehog signalling) progressively ventralises both somites and neural tube in a dose-dependent manner. Furthermore, we identify endogenous signalling from the neural tube to the somites, which leads to medially localised ALDH1A2, and subsequent RA signalling from the somites to the neural tube, which leads to spontaneous neural progenitor patterning and PAX6 expression. Together, our data highlight the value of modularity in embryo models which we leverage to explore human trunk co-development. SummaryUsing a 3D, stem cell-based model of human embryonic trunk development, we examine the interactions across somitic and neural tissues to better understand the dynamics of human trunk co-development.

developmental biology↗

bioRxiv2024

pnetr: An R package for the PnET family of forest ecosystem models

O_LIEcosystem models offer a rigorous way to formalize scientific theories and are critical to evaluating complex interactions among ecological and biogeochemical processes. In addition to simulation and prediction, ecosystem models are a valuable tool for testing hypotheses about mechanisms and empirical findings because they reveal critical internal processes that are difficult to observe directly. C_LIO_LIHowever, many ecosystem models are difficult to manage and apply by scientists who lack advanced computing skills due to complex model structures, lack of consistent documentation, and low-level programming implementation, which facilitates computing but reduces accessibility. C_LIO_LIHere, we present the pnetr R package, which is designed to provide an easy-to-manage ecosystem modeling framework and detailed documentation in both model structure and programming. The framework implements a family of widely used PnET (net photosynthesis, evapotranspiration) ecosystem models, which are relatively parsimonious but capture essential biogeochemical cycles of water, carbon, and nutrients. We chose the R programming language since it is familiar to many ecologists and has abundant statistical modeling resources. We showcase examples of model simulations and test the effects of phenology on carbon assimilation and wood production using data measured by the Environmental Measurement Station (EMS) eddy-covariance flux tower at Harvard Forest, MA. C_LIO_LIWe hope pnetr can facilitate further development of ecological theory and increase the accessibility of ecosystem modeling and ecological forecasting. C_LI

ecology↗

bioRxiv2024

Redox Signaling Mediates Differentiation of Adipose Progenitors in Response to Inflammatory Cytokines in the Adipose Tissue Secretome

Adipogenesis, the terminal differentiation of adipose progenitor cells (APCs), is critical in maintaining the functional integrity of adipose depots under obesogenic conditions. It is thought that a signal arising from the adipose microenvironment triggers APC differentiation; yet the identity and source of the signal remains unknown. This study sought to uncover the signal responsible for activating adipogenesis. Redox signaling was shown to influence adipogenesis in primary murine APCs treated with pharmacologic agents to manipulate the levels of reactive oxygen species (ROS). Increased generation of superoxide (O2-) and hydrogen peroxide (H2O2) via redox cyclers amplified both early and late APC differentiation, while ROS scavengers and antioxidants blunted differentiation. The impact of specifically targeting H2O2 with the antioxidant, catalase, or a catalase inhibitor, was restricted to lipid accumulation in late adipogenesis. Protein was concentrated from conditioned media of adipose tissue explants cultured ex vivo to capture signals within the adipose secretome. Differentiation was enhanced in APCs cultured in the presence of the adipose secretome, an effect that was diminished with scavenging of ROS and amplified when the secretome was collected from mice fed a high fat diet for 8 weeks. Proteomic analysis revealed that the adipose secretome from animals on a high fat diet was enriched in pathways related to immune cell-mediated inflammation, with interleukin 6 (IL-6) as a central regulator of differentially expressed proteins. A multiplex assay to measure cytokines confirmed higher IL-6 in the adipose secretome of high fat-fed animals. Exposure of APCs to IL-6 increased adipogenesis, while treatment of APCs with an IL-6 blocking antibodies diminished the adipogenic effect of the adipose secretome. Together, these findings substantiate a role for redox signaling in the regulation of adipogenesis and identify IL-6 as a novel activator of adipogenesis that may mediate APC differentiation via generation of ROS under obesogenic conditions.

systems biology↗

bioRxiv2024

Diet-induced hyperplastic expansion in subcutaneous adipose tissue and protection against adipose progenitor exhaustion in female mice are lost with ovariectomy.

BackgroundThe protection of females against cardiometabolic disease is in part attributable to a tendency for fat accumulation in subcutaneous depots, which promote lipid homeostasis by serving as a metabolic sink. At menopause this protection is lost, and body fat distribution resembles the male-like pattern of visceral adiposity. Adipose progenitor cells (APCs) can be recruited to support adipose expansion in the setting of obesity. Sex differences in diet-induced APC responses may in part explain sexual dimorphism in risk for obesity-associated insulin resistance; however, the role of sex and estrogen in governing APC function remains unclear. MethodsFour groups of C57BL/6 mice were assessed: intact males vs. females, and sham vs. ovariectomized (ovx) with or without 17{beta}-estradiol (E2). Adipogenesis was stimulated by rosiglitazone (rosi), while obesity was induced by high fat/fructose diet (HHFD). Flow cytometry quantified the total number of APCs and identify committed preadipocytes by the loss of CD24 expression. Body composition was measured by NMR, while adipose function assessed by measuring circulating adipokines and free fatty acids and lipolysis in adipose explants. ResultsDespite greater accumulation of fat mass in response to rosi, females were protected against the depletion in subcutaneous APCs and preadipocytes that was observed in rosi-treated males. Similar to intact males, APC and preadipocytes in subcutaneous depots of ovx females were reduced after rosi treatment. The protection of obese females against the development of insulin resistance and adipose dysfunction was lost with ovx, and E2 re-supplementation rescued HFFD- induced APC exhaustion. Exposure to HFFD after discontinuation of rosi exacerbated glucose intolerance in males only. ConclusionsEstrogen-mediated hyperplastic expansion in subcutaneous depots permits renewal of the APC pool and preservation of adipose function. PLAIN ENGLISH SUMMARYDespite well-established sex differences in the risk for type 2 diabetes that vary across the lifespan, very little is known regarding sex-specific mechanisms in its pathophysiology. In the setting of obesity, stem cells resident in fat tissue can be recruited for the generation of new fat cells, an important mechanism that maintains metabolic health. It is thought that a reduced availability or dysfunction in fat-residing stem cells is an important pathophysiological event that triggers the onset of obesity-associated type 2 diabetes. Herein, we aimed to determine how sex and estrogen influence stem cell availability and function. Our data show that the ability of fat- residing stem cells to respond to an obesogenic environment is greater in females in an estrogen- dependent manner. Estrogen-dependent stem cell responses to an obesogenic environment may contribute to the protection of females against obesity-induced type 2 diabetes and loss of this protection after menopause. HIGHLIGHTSSexual dimorphism in activation of adipogenesis by rosiglitazone is mediated by estrogen. Exhaustion of the APC pool occurs in subcutaneous depots of male mice, while estrogen mediates protection of females against APC exhaustion. Preservation of subcutaneous adipose expansion capacity due to renewal of the progenitor pool may contribute to protection of females against obesity-associated insulin resistance.

physiology↗

bioRxiv2024

Attenuation of Atherosclerosis with PAR4 Deficiency: Differential Platelet Outcomes in apoE-/- vs. Ldlr-/- Mice

ObjectiveCardiovascular disease (CVD) is a significant burden globally and, despite current therapeutics, remains the leading cause of death. Platelet inhibitors are of interest in CVD treatment to reduce thrombus formation post-plaque rupture as well their contribution to inflammation throughout the progression of atherosclerosis. Protease activated receptor 4 (PAR4) is a receptor highly expressed by platelets, strongly activated by thrombin, and plays a vital role in platelet activation and aggregation. However, the role of PAR4 Approach and ResultsMice on a low-density lipoprotein receptor-deficient (Ldlr-/-) background were bred with Par4 deficient (Par4-/-) mice to create Ldlr-/-/Par4+/+ and Ldlr-/-/Par4-/- cousin lines. Mice were fed high fat (42%) and cholesterol (0.2%) Western diet for 12 weeks for all studies. Bone marrow transplant (BMT) studies were conducted by irradiating Ldlr-/-/Par4+/+ and Ldlr-/- /Par4-/- mice with 550 rads (2x, 4 hours apart) and then repopulated with Par4+/+ or Par4-/- bone marrow. To determine if the effects of thrombin were mediated solely by PAR4, the thrombin inhibitor dabigatran was added to the Western diet. Ldlr-/-/Par4-/- given dabigatran did not further decrease their atherosclerotic burden. Differences between apolipoprotein E deficient (apoE-/-) and Ldlr-/- platelets were assessed for changes in reactivity. We observed higher PAR4 abundance in arteries with atherosclerosis in human and mice versus healthy controls. PAR4 deficiency attenuated atherosclerosis in the aortic sinus and root versus proficient controls. BMT studies demonstrated this effect was due to hematopoietic cells, most likely platelets. PAR4 appeared to be acting independent of PAR1, as there werer no changes with addition of dabigatran to PAR4 deficient mice. apoE-/- platelets are hyperreactive compared to Ldlr-/- platelets. ConclusionsHematopoietic-derived PAR4, most likely platelets, plays a vital role in the development and progression of atherosclerosis. Specific targeting of PAR4 may be a potential therapeutic target for CVD. HighlightsO_LIDeficiency of protease-activated receptor 4 attenuates the development of diet-induced atherosclerosis in a Ldlr-/- mouse model. C_LIO_LIPAR4 deficiency in hematopoietic cells is atheroprotective. C_LIO_LIPAR4 deficiency accounts for the majority of thrombin-induced atherosclerosis in a Ldlr-/- mouse model. C_LIO_LIThe examination of platelet-specific proteins and platelet activation should be carefully considered before using the apoE-/- or Ldlr-/- mouse models of atherosclerosis. C_LI

pathology↗

bioRxiv2024

Temperature drives seagrass recovery across the Western North Atlantic

Climate-driven shifts in herbivores, temperature and nutrient runoff threaten coastal ecosystem resilience. However, our understanding of ecological resilience, particularly for foundation species, remains limited due to a rarity of field experiments that are conducted across appropriate spatial and temporal scales and that investigate multiple stressors. This study aimed to evaluate the resilience of a widespread tropical marine plant (turtlegrass) to disturbances across its geographic range and how this is impacted by environmental gradients in (a)biotic factors. We assessed the resilience (i.e. recovery) of turtlegrass to a simulated disturbance (complete above- and belowground biomass removal) over a year. Contrary to temperate studies, higher temperature generally enhanced seagrass recovery. While nutrients and light availability had minimal impact, combined high levels of nutrients and herbivore grazing (meso and megaherbivore) reduced aboveground recovery. Our results suggest that the resilience of some tropical species, especially in cooler subtropical waters, may initially increase with warming.

ecology↗

bioRxiv2024

Human gut microbiota interactions shape the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile

Clostridioides difficile can transiently or persistently colonize the human gut, posing a risk factor for infections. This colonization is influenced by complex molecular and ecological interactions with human gut microbiota. By investigating C. difficile dynamics in human gut communities over hundreds of generations, we show patterns of stable coexistence, instability, or competitive exclusion. Lowering carbohydrate concentration shifted a community containing C. difficile and the prevalent human gut symbiont Phocaeicola vulgatus from competitive exclusion to coexistence, facilitated by increased cross-feeding. In this environment, C. difficile adapted via single-point mutations in key metabolic genes, altering its metabolic niche from proline to glucose utilization. These metabolic changes substantially impacted inter-species interactions and reduced disease severity in the mammalian gut. In sum, human gut microbiota interactions are crucial in shaping the long-term growth dynamics and evolutionary adaptations of C. difficile, offering key insights for developing anti-C. difficile strategies.

systems biology↗

bioRxiv2024

Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes

The human gut pathogen Clostridioides difficile displays extreme genetic variability and confronts a changeable nutrient landscape in the gut. We mapped gut microbiota inter-species interactions impacting the growth and toxin production of diverse C. difficile strains in different nutrient environments. Although negative interactions impacting C. difficile are prevalent in environments promoting resource competition, they are sparse in an environment containing C. difficile-preferred carbohydrates. C. difficile strains display differences in interactions with Clostridium scindens and the ability to compete for proline. C. difficile toxin production displays substantial community-context dependent variation and does not trend with growth-mediated inter-species interactions. C. difficile shows substantial differences in transcriptional profiles in the presence of the closely related species C. hiranonis or C. scindens. In co-culture with C. hiranonis, C. difficile exhibits massive alterations in metabolism and other cellular processes, consistent with their high metabolic overlap. Further, Clostridium hiranonis inhibits the growth and toxin production of diverse C. difficile strains across different nutrient environments and ameliorates the disease severity of a C. difficile challenge in a murine model. In sum, strain-level variability and nutrient environments are major variables shaping gut microbiota interactions with C. difficile.

systems biology↗

bioRxiv2024

Multi-Omics after O-GlcNAc Alteration Identifies Cellular Processes Working Synergistically to Promote Aneuploidy

Pharmacologic or genetic manipulation of O-GlcNAcylation, an intracellular, single sugar post-translational modification, are difficult to interpret due to the pleotropic nature of O-GlcNAc and the vast signaling pathways it regulates. To address this issue, we employed either OGT (O-GlcNAc transferase), OGA (O-GlcNAcase) liver knockouts, or pharmacological inhibition of OGA coupled with multi-Omics analysis and bioinformatics. We identified numerous genes, proteins, phospho-proteins, or metabolites that were either inversely or equivalently changed between conditions. Moreover, we identified pathways in OGT knockout samples associated with increased aneuploidy. To test and validate these pathways, we induced liver growth in OGT knockouts by partial hepatectomy. OGT knockout livers showed a robust aneuploidy phenotype with disruptions in mitosis, nutrient sensing, protein metabolism/amino acid metabolism, stress response, and HIPPO signaling demonstrating how OGT is essential in controlling aneuploidy pathways. Moreover, these data show how a multi-Omics platform can discern how OGT can synergistically fine-tune multiple cellular pathways.

cell biology↗

bioRxiv2024

Highly conserved brain vascular receptor ALPL mediates transport of engineered viral vectors across the blood-brain barrier

Delivery of systemically administered therapeutics to the central nervous system (CNS) is restricted by the blood-brain barrier (BBB). Bioengineered Adeno-Associated Virus (AAV) capsids have been shown to penetrate the BBB with great efficacy in mouse and non-human primate models, but their translational potential is often limited by species selectivity and undefined mechanisms of action. Here, we apply our RNA-guided TRACER AAV capsid evolution platform to generate VCAP-102, an AAV9 variant with markedly increased brain tropism following intravenous delivery in both rodents and primates. VCAP-102 demonstrates a similar CNS tropism in cynomolgus macaque, african green monkey, marmoset and mouse, showing 20- to 400-fold increased transgene expression across multiple brain regions relative to AAV9. We demonstrate that the enhanced CNS tropism of VCAP-102 results from direct interaction with alkaline phosphatase (ALPL), a highly conserved membrane-associated protein expressed on the brain vasculature. VCAP-102 interacts with human, primate and murine ALPL isoforms, and ectopic expression of ALPL is sufficient to initiate receptor-mediated transcytosis of VCAP-102 in an in vitro transwell model. Our work identifies VCAP-102 as a cross-species CNS gene delivery vector with a strong potential for clinical translation and establishes ALPL as a brain delivery shuttle capable of efficient BBB transport to maximize CNS delivery of biotherapeutics.

neuroscience↗

bioRxiv2024

A resource to enable chemical biology and drug discovery of WDR Proteins

Protein class-focused drug discovery has a long and successful history in pharmaceutical research, yet most members of druggable protein families remain unliganded, often for practical reasons. Here we combined experiment and computation to enable discovery of ligands for WD40 repeat (WDR) proteins, one of the largest human protein families. This resource includes expression clones, purification protocols, and a comprehensive assessment of the druggability for hundreds of WDR proteins. We solved 21 high resolution crystal structures, and have made available a suite of biophysical, biochemical, and cellular assays to facilitate the discovery and characterization of small molecule ligands. To this end, we use the resource in a hit-finding pilot involving DNA-encoded library (DEL) selection followed by machine learning (ML). This led to the discovery of first-in-class, drug-like ligands for 9 of 20 targets. This result demonstrates the broad ligandability of WDRs. This extensive resource of reagents and knowledge will enable further discovery of chemical tools and potential therapeutics for this important class of proteins.

biochemistry↗

bioRxiv2023

Hurricanes Pose Substantial Risk to New England Forest Carbon Stocks

Nature-based climate solutions are championed as a primary tool to mitigate climate change, especially in forested regions capable of storing and sequestering vast amounts of carbon. New England is one of the most heavily forested regions in the United States (>75% forested by land area), and forest carbon is a significant component of regional climate mitigation strategies. Large infrequent disturbances, such as hurricanes, are a major source of uncertainty and risk for policies that rely on forest carbon for climate mitigation, especially as climate change is projected to alter the intensity and geographic extent of hurricanes. To date, most research into disturbance impacts on forest carbon stocks has focused on fire. Here we show that a single hurricane in the region can down between 121-250 MMTCO2e or 4.6-9.4% of the total aboveground forest carbon, much greater than the carbon sequestered annually by New Englands forests (16 MMTCO2e yr-1). However, the emissions from the storms are not instantaneous; it takes approximately 19 years for the downed carbon to become a net emission, and 100 years for 90% of the downed carbon to be emitted. Using hurricane reconstructions across a range of historical and projected wind speeds, we find that an 8% and 16% increase in hurricane wind speeds leads to a 10.7 and 24.8 fold increase in the extent of high-severity damaged areas (widespread tree mortality). Increased wind speed also leads to unprecedented geographical shifts in damage; both inland and northward into heavily forested regions traditionally unaffected by hurricanes. Given that a single hurricane can emit the equivalent of 10+ years of carbon sequestered by forests in New England, the status of these forests as a durable carbon sink is uncertain. Understanding the risks to forest carbon stocks from large infrequent disturbances is necessary for decision-makers relying on forests as a nature-based climate solution.

ecology↗

bioRxiv2023

An osmolarity dependent mechanism partially ameliorates retinal cysts and rescues cone function in a mouse model of X-linked Retinoschisis.

IntroductionX-linked retinoschisis (XLRS) is a vitreoretinal dystrophy caused by RS1 gene mutations which disrupt retinoschisin protein function. A vital protein for maintaining retinal architecture, the absence of functional retinoschisin leads to the development of intraretinal cysts. The preliminary goal of this study was to investigate a low dose gene therapy in Rs1 knockout (Rs1-KO) mice; however, our experiments revealed an unexpected therapeutic effect of a hypertonic buffer, which led to further exploration of this effect. Methods10 Rs1-KO mice were subretinally injected with an AAV2/4 vector containing the RS1 gene driven by an Ef1 promoter. 16 Rs1-KO mice were subretinally injected with a hypertonic buffer (180 mM NaCl 0.001% F68/PBS (pH 7.4)) or an isotonic buffer (155.2 mM NaCl 0.001% F68/PBS, pH 7.0) as a sham control. Endpoints included electroretinogram (ERG), optical coherence tomography (OCT), and a visually guided swim assay (VGSA). An immunohistochemistry assay was used to quantify cone density in buffer injected and treatment-naive eyes. ResultsUnexpectedly, hypertonic buffer-injected eyes had significantly reduced cyst severity at 1 month post-injection (MPI) (p=<0.0001), significantly higher amplitudes in cone-dominant ERGs persisting to 5 months post-injection (5 Hz flicker; p=0.0018; 3.0 Flash; p=0.0060) and demonstrated improved navigational vision in the light compared to untreated Rs1-KO eyes (p<0.0001). To investigate the role of tonicity on this effect, an isotonic buffer-injected cohort was created (155.2 mM NaCl 0.001% F68/PBS, pH 7.0) (n=6). Surprisingly, hypertonic buffer-injected eyes exhibited a greater reduction in cyst severity and demonstrated improved cone-dominant ERG metrics over isotonic buffer-injected eyes. Using an immunohistochemistry assay, we demonstrated greater cone density in hypertonic buffer-injected eyes than untreated controls (p=0.0147), suggesting a possible cone preservation mechanism. Moreover, our findings reveal a negative correlation between the peak severity of cysts and long-term cone-dominant ERG metrics, implying that effectively managing cysts could yield enduring benefits for cone function. Discussion/ConclusionThis study presents evidence that cyst resolution can be triggered through an osmosis-dependent pathway, and cyst resolution can have long term effects on cone signaling and survival, offering potential insights for the development of novel treatments for patients with XLRS.

genetics↗

bioRxiv2023

KRASG12D-mediated PanIN progression in mice is affected by gene driving cre recombinase expression

The fundamental biology of pancreatic ductal adenocarcinoma has been greatly impacted by the characterization of genetically modified mouse models that allow temporal and spatial activation of oncogenic KRAS (KRASG12D). The most commonly used model involves targeted insertion of a cre recombinase into the Ptf1a gene. However, this approach disrupts the Ptf1a gene, resulting in haploinsufficiency that likely affects sensitivity to oncogenic KRAS (KRASG12D). The goal of this study was to determine if Ptf1a haploinsufficiency affected the acinar cell response to KRASG12D before and after induction of pancreatic injury. We performed morphological and molecular analysis of three mouse lines that express a tamoxifen-inducible cre recombinase to activate KRASG12D in acinar cells of the pancreas. The cre-recombinase was targeted to the acinar-specific transcription factor genes, Ptf1a and Mist1/Bhlha15, or expressed within a BAC-derived Elastase transgene. Up to two months after tamoxifen induction of KRASG12D, morphological changes were negligible. However, induction of pancreatic injury by cerulein resulted in stark differences in tissue morphology between lines within seven days, which were maintained for at least five weeks after injury. Ptf1acreERT pancreata showed widespread PanIN lesions and fibrosis, while the Mist1creERT and Ela-creERT models showed reduced amounts of pre-neoplastic lesions. RNA-seq analysis prior to inducing injury suggested Ptf1acreERT and Mist1creERT lines have unique profiles of gene expression that predict a differential response to injury. Multiplex analysis of pancreatic tissue confirmed different inflammatory responses between the lines. These findings suggest understanding the mechanisms underlying the differential response to KRASG12D will help in further defining the intrinsic KRAS-driven mechanisms of neoplasia initiation.

cancer biology↗

bioRxiv2023

The adaptive immune response to Trichuris in wild versus laboratory mice: An established model system in context

Laboratory model organisms have provided a window into how the immune system functions. An increasing body of evidence, however, suggests that the immune responses of naive laboratory animals may differ substantially to those of their wild counterparts. Past exposure, environmental challenges and physiological condition may all impact on immune responsiveness. Chronic infections of soil-transmitted helminths impose significant health burdens on humans, livestock and wildlife, with limited treatment success. In laboratory mice, Th1 versus Th2 immune polarisation is the major determinant of helminth infection outcome. Here we compared antigen-specific immune responses to the soil-transmitted whipworm Trichuris muris between controlled laboratory and wild free-ranging populations of house mice (Mus musculus domesticus). Wild mice harbouring chronic, low-level infections produced lower levels of cytokines in response to Trichuris antigen than laboratory-housed C57BL/6 mice. Wild mouse effector/memory CD4+ T cell phenotype reflected the antigen-specific cytokine response across the Th1/Th2 spectrum. Increasing worm burden was associated with body condition loss. However, local Trichuris-specific Th1/Th2 balance was positively associated with worm burden only in older wild mice. Thus, although the fundamental relationships between the CD4+ T helper cell response and resistance to T. muris infection are similar in both laboratory and wild M.m.domesticus, there are quantitative differences and age-specific effects that are analogous to human immune responses. These context-dependent immune responses demonstrate the fundamental importance of understanding the differences between model and natural systems for translating mechanistic models to real world immune function.

immunology↗

bioRxiv2023

Exploring the interactome of PML nuclear subdomains during fatty acid stress using APEX2-mediated proximity labeling

When exposed to excess fatty acids, specific cell types produce nuclear lipid droplets (nLDs) that associate with promyelocytic leukemia (PML) protein to form Lipid Associated PML Structures (LAPS) that are enriched in lipid biosynthetic enzymes but deficient in canonical proteins associated with PML nuclear bodies (PML NBs). To identify the PML interactome during lipid stress, we employed proximity-dependent biotin identification (BioID) in U2OS cells expressing PMLI and PMLII fused to the ascorbate peroxidase APEX2 and cultured in the absence or presence of oleate to enhance lipid droplet formation. The resulting interactome included proteins enriched under oleate-treated conditions, such mitogen activated protein kinase-activated protein kinase 2 (MK2), ESCRT proteins and the COPII vesicle transport proteins Sec23B, Sec24A and USO1. COPII proteins co-localized with both PML-NBs and LAPS but were selectively enriched in PML-NBs following oleate treatment. The nuclear localization of USO1 was uniquely dependent on PML expression. Thus, the APEX2-PML proximity interactome implicates PML domains in the nuclear function of a non-canonical network of COPII vesicle trafficking proteins. SUMMARY STATEMENTThis is the first study to utilize APEX2 proximity labelling to identify the protein interactome of PML nuclear substructures and how interactions are modified under conditions of fatty acid-induced stress.

cell biology↗