Biology subjects

McCarthy, C.

Publications and source records attributed to McCarthy, C..

18 recordsLinked to original sources

bioRxiv2026

Golgi-localised Guanylate-binding protein 5 enhances glycolysis in macrophages

Guanylate-binding proteins (GBPs) are part of a family of large interferon gamma (IFN{psi})-inducible GTPases, with ascribed roles in infection control and induction of programmed cell death. While pathogen-specific functions of GBPs have been studied in detail, their broader regulation of frontline immune defences remain unexplored. Here, we analysed the global contribution of human GBP1-5 to cellular metabolism in IFN{psi}-stimulated macrophages. We found a robust role of GBP2 and GBP5 in macrophage glycolysis. Only GBP5, and not GBP2 deficiency impaired surface expression and cytokine production of classically IFN{psi}/LPS-activated macrophages. The GTPase activity of GBP5 was required for the regulation of glycolysis and cytokine production. We found that GBP5 deficiency impaired cellular glucose uptake and lactate production specifically. Isotopic tracing with [U-13C6]-Glucose confirmed a decrease in several glycolytic intermediates, including glucose 6-phosphate, pyruvate, and lactate, but stable levels of traced tricarboxylic acid cycle (TCA) intermediates. Elevated ribose-5-phosphate and glycerol levels suggest an altered cytosolic redox balance and enhanced breakdown of fatty acids. GBP5 localised predominantly to the cis-Golgi and in the absence of GBP5 we observed increased Golgi fragmentation, however the total Golgi size remained unchanged. Our results underscore the fundamental role of GBP5 in glycolytic fluxes and Golgi integrity in IFN{psi}-stimulated macrophages, highlighting its significance in immune function in general and immunometabolism specifically.

immunology↗

bioRxiv2025

Functional Activity of HIV-1 bNAbs Across Diverse Strains is Driven by Binding Site and Can be Enhanced Through Fc Engineering

Broadly neutralizing antibodies (bNAbs) are promising tools for HIV-1 treatment and prevention, due to their ability to mediate both Fab-dependent neutralization and Fc-dependent effector functions. While antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP) have been implicated in antiviral activity, the extent to which these functions vary across bNAb epitopes, viral strains, and Fc region remains unclear. Here, we systematically evaluated twenty bNAbs targeting five distinct Env epitopes against a diverse panel of nine HIV-1 strains. We found that epitope specificity and Env sequence both critically influenced bNAb effector functions. CD4 binding site (CD4bs)- and V3 glycan-targeting bNAbs mediated the broadest and most potent ADCC and ADCP, while V1/V2 apex-directed bNAbs preferentially induced ADCP. In contrast, MPER-targeting bNAbs triggered ADCC more selectively, and gp120/gp41 interface-targeting bNAbs showed limited activity. Irrespective of binding epitope, different strains exhibited a broad range of effector function sensitivities. To investigate the impact of Fc modifications on this variability, we subclass-switched and introduced previously identified Fc mutations known to change Fc{gamma} receptor affinity. Some of these mutations significantly boosted ADCC, while IgG3 subclass switching dramatically enhanced ADCP, even against highly resistant strains. Collectively, these results demonstrate that effector function is shaped by both antibody specificity and viral Env context and that rational Fc modification has the potential to improve antibody-based therapeutics against HIV. One Sentence SummaryThis study systematically evaluates the impact of bNAb epitope specificity, Env sequence, and Fc engineering on antibody-mediated effector functions.

immunology↗

bioRxiv2025

Epistasis between Na+/K+-ATPase Substitutions May Influence Salinity Tolerance in Steinernema Entomopathogenic Nematodes

Soil salinity varies widely across geographies both due to natural factors and human activities, including agriculture, road salt application, sea level rise, and desertification. Increases in soil salinity may affect organisms widely and particularly impact soil foodwebs. As parasites, entomopathogenic nematodes (EPNs) occupy crucial links in soil foodwebs and are important for agriculture as biological control agents of insect pests. Previous research found that the EPN Steinernema carpocapsae may exhibit higher salt tolerance than several of its congeners. We recently identified that S. carpocapsae uniquely evolved two amino acid substitutions in the first extracellular loop of the sodium pump (Na{square}/K{square}-ATPase). Here, we tested if these substitutions explain S. carpocapsaes reported lower sensitivity to salt. Our results confirm that S. carpocapsae exhibits higher salt tolerance and show it can more effectively locate and infect insect hosts than its congeners S. feltiae and S. hermaphroditum in highly saline environments. We then retraced the evolution of the two amino acid substitutions in S. carpocapsae by introducing them alone and in combination in Caenorhabditis elegans using CRISPR genome engineering. We found that C. elegans mutants with single substitutions showed improved salt tolerance. However, this improvement disappeared in the double mutant, whose sodium pump mimicked that of S. carpocapsae. This pattern of negative epistasis between the amino acid substitutions suggests they are not responsible for variation in salt tolerance between Steinernema species. Sodium pump evolution in S. carpocapsae might instead be driven by encounters with cardiac glycosides, which are released into soil by several clades of plants including milkweeds, sequestered by some of this EPNs herbivorous insect hosts, and known to target the first extracellular loop of the sodium pump. Our findings provide valuable insights into EPN adaptation to changes in environmental sodium levels and may have implications for their use in biological control.

ecology↗

bioRxiv2025

Amino Acid Substitutions in the Na+/K+-ATPase May Contribute to Salinity Tolerance in Insects

O_LIEnvironmental salinity levels vary naturally across terrestrial ecosystems but can be heightened locally by coastal proximity and desertification as well as human activities such as road salt application and agriculture. Since salt is essential for many physiological processes in insects, rising environmental sodium concentrations may drive behavioral changes, where insects select environments and food sources with suitable sodium levels, or evolutionary changes in constitutive or plastic physiological mechanisms to process salt, potentially altering ecological dynamics and species interactions. C_LIO_LINumerous hematophagous (blood feeding) insects such as the yellow-fever mosquito Aedes aeqypti are known to be able to breed in relatively saline environments. Among phytophagous (plant feeding) insects, grasshoppers can be important herbivores in arid and coastal salt-affected regions, whereas the monarch butterfly (Danaus plexippus) appears to perform relatively well on milkweed host plants growing in roadsides influenced by salt runoff. Several of these insects share a common trait: amino acid substitutions in the first extracellular loop of the Na+/K+-ATPase (NKA), a sodium pump crucial for maintaining ion balance. For the monarch these substitutions confer resistance to toxic cardenolides from milkweeds, but it is unclear whether NKA substitutions may influence salt tolerance. C_LIO_LIHere, we investigate whether the NKA substitutions found in these insects may contribute to salt tolerance using gene-edited Drosophila melanogaster mutant strains as models. We show that flies with substitution Q111L (found in Aedes mosquitoes) or a combination of Q111L and A119S (found in grasshoppers) exhibited greater salt tolerance, whereas flies carrying the combination of substitutions found in the monarch (Q111V, A119S, and N122H) did not. C_LIO_LIOur results suggest that the monarch may rely on alternate mechanisms for salt tolerance and that its NKA substitutions are important primarily for cardenolide resistance. However, substitution Q111L and the combination of Q111L and A119S may be relevant for salt tolerance in a variety of insects. Uncovering mechanisms of salt tolerance enhances our understanding of species distributions, ecological interactions, and evolutionary physiology in response to changing environmental salinity levels. C_LI

genetics↗

bioRxiv2024

A robustly rooted tree of eukaryotes reveals their excavate ancestry.

The eukaryote Tree of Life (eToL) depicts the relationships among all eukaryotic organisms; its root represents the last eukaryotic common ancestor (LECA) from which all extant complex lifeforms are descended. Locating this root is crucial for reconstructing the features of LECA, both as the endpoint of eukaryogenesis and the start-point for the evolution of the myriad complex traits underpinning the diversification of living eukaryotes. However, the position of the root remains contentious due to pervasive phylogenetic artefacts stemming from inadequate evolutionary models, poor taxon sampling, and limited phylogenetic signal. Here, we estimate the root of the eToL with unprecedented resolution based on a new, much larger, dataset of mitochondrial proteins which includes all known eukaryotic supergroups. Our comprehensive analyses with state-of-the-art phylogenetic models reveal that the eukaryotic root lies between two multi-supergroup assemblages: Opimoda+ and Diphoda+. Compellingly, this position is consistently supported across different models and robustness analyses. Notably, groups containing typical excavates are placed on both sides of the root, suggesting the complex features of the excavate cell architecture trace back to LECA. This study is the most comprehensive phylogenetic investigation of the eukaryote root to date, shedding light on the ancestral cells from which extant eukaryotes arose and providing a crucial framework for investigating the origin and evolution of canonical eukaryotic features.

evolutionary biology↗

bioRxiv2024

Iron deficiency in people with obesity drives defective natural killer cell mitochondrial fitness and function

Natural killer (NK) cells are a population of innate effector lymphocytes, involved in host-defences against viral infections and cancer. Upon activation, NK cells can produce a milieu of cytotoxic molecules and cytokines, which can directly target infected and transformed cells, but also amplify an immune response. Metabolic rewiring underpins NK cell effector functionality, providing the required signals, energy and biointermediates to support their immune responses. Obesity is associated with significant defects in the functionality of human NK cells, especially in the periphery. Dysregulated cellular metabolism has been demonstrated to be a major mechanistic driver of the reported defects. However, how obesity links to defective NK cell metabolism and functionality remains unclear. Iron deficiency is a common co-morbidity in people living with obesity (PWO). Recent studies have highlighted the importance for iron in host immunity, with murine models of iron deficiency resulting in defective cellular metabolism and function. We hypothesized that obesity-driven iron deficiency might underpin the reported defects in NK cells. Our data demonstrates that in response to cytokine stimulation, healthy human NK cells utilize iron to support their metabolic activity and cytokine responses. In a cohort of PWO, we demonstrate alterations in NK cell metabolism, mitochondrial fitness and cytokine production. Furthermore, upon stratification into PWO with normal iron status versus low iron status, we show the observed obesity-related defects in NK cell metabolism, mitochondrial fitness and cytokine production are concentrated in the PWO with low-iron status. Collectively, our data highlights the importance of iron for human NK cell responses and provides evidence that obesity-driven defects in NK cell metabolism and function are linked in part to altered iron availability.

immunology↗

bioRxiv2023

Chemotherapeutic regulation of the ROS/MondoA-dependent TXNIP/GDF15 axis; and derivation of a new organoid metric as a predictive biomarker

Chemotherapy, the standard of care treatment for cancer patients with advanced disease, has been increasingly recognised to activate host immune responses to produce durable outcomes. Here, in colorectal adenocarcinoma (CRC) we identify chemotherapy-induced Thioredoxin Interacting Protein (TXNIP), a MondoA-dependent tumor suppressor gene, as a negative regulator of Growth/Differentiation Factor 15 (GDF15). GDF15 is a negative prognostic factor in CRC and promotes the differentiation of regulatory T cells (Tregs), through CD48 ligation. Intriguingly, multiple models including patient-derived tumor organoids demonstrate that loss of TXNIP/GDF15 axis functionality is associated with advanced disease or chemotherapeutic resistance, with transcriptomic or proteomic GDF15/TXNIP ratios showing potential as a prognostic biomarker. These findings illustrate a potentially common pathway where chemotherapy-induced epithelial stress drives local immune remodelling for patient benefit, with disruption of this pathway seen in refractory or advanced cases.

cancer biology↗

bioRxiv2023

Several independent adaptations of archaea to hypersaline environments

Several archaeal lineages thrive in high, saturating salt concentrations. These extremely halophilic archaea, including Halobacteria, Nanohaloarchaeota, Methanonatronarchaeia, and Haloplasmatales, must maintain osmotic equilibrium with their environment. For this, they use a salt-in strategy, which involves pumping molar concentrations of potassium into the cells, which, in turn, has led to extensive proteome-wide modifications to prevent protein aggregation. However, the evolutionary history underlying these adaptations remains poorly understood. In particular, the number of times that these dramatic proteome-sweeping changes occurred is unclear due to the conflicting phylogenetic positions found for several of these lineages. Here, we present a resolved phylogeny of extremely halophilic archaea obtained using improved taxon sampling and state-of-the-art phylogenetic approaches designed to cope with the strong compositional biases of their proteomes. We describe two new uncultured lineages, Afararchaeaceae and Asboarchaeaceae, which break the long branches at the base of Haloarchaea and Nanohaloarchaeota, respectively. Our extensive phylogenomic analyses show that at least four independent adaptations to extreme halophily occurred during archaeal evolution. Finally, gene-tree/species-tree reconciliation suggests that gene duplication and horizontal gene transfer played an important role in this process, for example, by spreading key genes (such as those encoding potassium transporters) across the various extremely halophilic lineages.

evolutionary biology↗

bioRxiv2023

A drug repurposing screen for whipworms informed by comparative genomics

Hundreds of millions of people worldwide are infected with the whipworm Trichuris trichiura. Novel treatments are urgently needed as current drugs, such as albendazole, have relatively low efficacy. We have investigated whether drugs approved for other human diseases could be repurposed as novel anti-whipworm drugs. In a previous comparative genomics analysis, we identified 409 drugs approved for human use that we predicted to target parasitic worm proteins. Here we tested these ex vivo by assessing motility of adult worms of Trichuris muris, the murine whipworm, an established model for human whipworm research. We identified 14 compounds with EC50 values of[≤] 50 M against T. muris ex vivo, and selected nine for testing in vivo. However, the best worm burden reduction seen in mice was just 19%. The high number of ex vivo hits against T. muris shows that we were successful at predicting parasite proteins that could be targeted by approved drugs. In contrast, the low efficacy of these compounds in mice suggest challenges due to their chemical properties (e.g. lipophilicity, polarity, molecular weight) and pharmacokinetics (e.g. absorption, distribution, metabolism, and excretion) that may (i) promote absorption by the host gastrointestinal tract, thereby reducing availability to the worms embedded in the large intestine, and/or (ii) restrict drug uptake by the worms. This indicates that identifying structural analogues that have reduced absorption by the host, and increased uptake by worms, may be necessary for successful drug repurposing against whipworms. Therefore, we recommend that prior to in vivo studies, future researchers first assess drug absorption by the host, for example, using human intestinal organoids or cell lines, and drug uptake by whipworms using intestinal organoids infected with T. muris.

pharmacology and toxicology↗

bioRxiv2022

IL-1β turnover by TRIP12 and AREL1 ubiquitin ligases and UBE2L3 limits inflammation

The cytokine interleukin-1{beta} (IL-1{beta}) has pivotal roles in antimicrobial immunity, but also incites inflammatory pathology. Bioactive IL-1{beta} is released following proteolytic maturation of the pro-IL-1{beta} precursor by caspase-1 inflammasomes. UBE2L3/UBCH7, a conserved ubiquitin conjugating enzyme, promotes pro-IL-1{beta} ubiquitylation and proteasomal disposal. However, UBE2L3 actions in vivo and ubiquitin ligases involved in this process are unknown. Here we report that deletion of Ube2l3 in mice markedly reduces pro-IL-1{beta} turnover in macrophages, leading to excessive mature IL-1{beta} production, neutrophilic inflammation and disease symptoms following inflammasome activation. A family-wide siRNA screen identified two ubiquitin ligases, TRIP12 and AREL1, which we show add K27-, K29- and K33- poly-ubiquitin chains on lysine residues in the pro domain and destabilise pro-IL-1{beta}. Mutation of ubiquitylation sites increased pro-IL-1{beta} stability, but did not affect proteolysis by caspase-1. The extent of mature IL-1{beta} production is therefore determined by precursor abundance, and UBE2L3, TRIP12 and AREL1 limit inflammation by shrinking the cellular pool of pro-IL-1{beta}. Our study has uncovered fundamental processes governing IL-1{beta} homeostasis and provided molecular insights that could be exploited to mitigate its adverse actions in disease.

immunology↗

bioRxiv2021

Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lung cancer

Although cancer immunotherapy with PD-(L)1 blockade is now routine treatment for patients with lung cancer, remarkably little is known about acquired resistance. We examined 1,201 patients with NSCLC treated with PD-(L)1 blockade to clinically characterize acquired resistance, finding it to be common (occurring in more than 60% of initial responders), with persistent but diminishing risk over time, and with distinct metastatic and survival patterns compared to primary resistance. To examine the molecular phenotype and potential mechanisms of acquired resistance, we performed whole transcriptome and exome tumor profiling in a subset of NSCLC patients (n=29) with acquired resistance. Systematic immunogenomic analysis revealed that tumors with acquired resistance generally had enriched signals of inflammation (including IFN{gamma} signaling and inferred CD8+ T cells) and could be separated into IFN{gamma} upregulated and stable subsets. IFN{gamma} upregulated tumors had putative routes of resistance with signatures of dysfunctional interferon signaling and mutations in antigen presentation genes. Transcriptomic profiling of cancer cells from a murine model of acquired resistance to PD-(L)1 blockade also showed evidence of dysfunctional interferon signaling and acquired insensitivity to in vitro interferon gamma treatment. In summary, we characterized clinical and molecular features of acquired resistance to PD-(L)1 blockade in NSCLC and found evidence of ongoing but dysfunctional IFN response. The persistently inflamed, rather than excluded or deserted, tumor microenvironment of acquired resistance informs therapeutic strategies to effectively reprogram and reverse acquired resistance.

cancer biology↗

bioRxiv2021

Daily rhythms in the transcriptomes of the human parasite Schistosoma mansoni

BackgroundThe consequences of the earths daily rotation have led to 24-hour biological rhythms in most organisms. Even parasites have daily rhythms, which, when in synchrony with host rhythms, optimize their fitness. Understanding these rhythms may enable development of novel control strategies that take advantage of rhythmic vulnerabilities. Recent work on blood-dwelling protozoan parasites has revealed daily rhythms in gene expression, physiology, drug sensitivity and the presence of an intrinsic circadian clock. However, similar studies on metazoan parasites are lacking. The aims of this study were to investigate if a metazoan parasite has daily molecular oscillations, whether they give us insight into how these longer-lived organisms can survive host daily cycles over a life-span of many years and to determine whether canonical metazoan circadian clock genes are present and rhythmic. We addressed these questions using the human blood fluke Schistosoma mansoni, that lives in the vasculature for decades and causes the serious neglected tropical disease schistosomiasis. ResultsUsing round-the-clock transcriptomics of male and female adult worms we discovered that [~]2% of its genes followed a daily pattern of expression. Rhythmic processes included a night-time stress response and a day-time metabolic rush hour. Transcriptional profiles in the female reproductive system were mirrored by daily patterns in egg laying (eggs are the main drivers of the host pathology). Genes cycling with the highest amplitudes include drug targets and a vaccine candidate. These 24hr rhythms may be driven by host rhythms and/or generated by a circadian clock. However, core clock genes are missing and orthologues of secondary clock genes show no 24hr rhythmicity in transcript abundance. ConclusionsThe daily rhythms identified here reveal temporally compartmentalised internal processes and host interactions over the daily cycle, including processes relevant to within-host survival and between-host transmission. Our findings suggest that if these daily rhythms are generated by an intrinsic circadian clock then the oscillatory mechanism must be distinct from that in other Metazoa. Most importantly, knowing which gene transcripts oscillate at this temporal scale is relevant to functional genomic studies that will lead to the development and delivery of therapeutics against schistosomiasis.

systems biology↗

bioRxiv2020

Mouse models for V103I and I251L gain of function variants of the human MC4R display reduced adiposity and are not protected from a hypercaloric diet

ObjectiveThe melanocortin 4 receptor (MC4R) is a G protein-coupled receptor that plays major roles in the central control of energy balance. Loss-of-function mutations of MC4R constitute the most common monogenic cause of early-onset extreme obesity in humans, whereas gain-of-function mutations appear to be protective. In particular, two relatively frequent alleles carrying the non-synonymous coding mutations V103I or I251L have been associated with lower risks of obesity and type-2 diabetes. Although V103I and I251L MC4Rs showed more efficient signaling in transfected cells, their specific effects in live animals remain unexplored. Here, we investigated whether the introduction of V103I and I251L mutations into the mouse MC4R leads to a lean phenotype and provides protection against an obesogenic diet. MethodsUsing CRISPR/Cas9, we generated two novel strains of mice carrying single nucleotide mutations into the mouse Mc4r which are identical to those present in V103I and I251L MCR4 human alleles, and studied their phenotypic outcomes in mice fed with normal chow or a high- fat diet. In particular, we measured body weight progression, food intake and adiposity. In addition, we analyzed glucose homeostasis through glucose and insulin tolerance tests. ResultsWe found that homozygous V103I females displayed shorter longitudinal length and decreased abdominal white fat, whereas homozygous I251L females were also shorter and leaner due to decreased weight in all white fat pads examined. Homozygous Mc4rV103I/V103I and Mc4rI251L/I251L mice of both sexes showed improved glucose homeostasis when challenged in a glucose tolerance test, whereas Mc4rI251L/I251L females showed improved responses to insulin. Despite being leaner and metabolically more efficient, V103I and I251L mutants fed with a hypercaloric diet increased their fasting glucose levels and adiposity similar to their wild-type littermates. ConclusionsAltogether, our results demonstrate that mice carrying V103I and I251L MC4R mutations displayed gain-of-function phenotypes that were more evident in females. However, hypermorphic MC4R mutants were as susceptible as their control littermates to the obesogenic and diabetogenic effects elicited by a long-term hypercaloric diet, highlighting the importance of healthy feeding habits even under favorable genetic conditions. HighlightsO_LIIdentical single nucleotide substitutions to gain-of-function mutations of the human MC4R were introduced into the genome of inbred mice using CRISPR/Cas9 technology. C_LIO_LIHomozygous female carriers of V103I Mc4r alleles are shorter and display reduced adiposity, together with improved glucose homeostasis in both sexes. C_LIO_LIHomozygous females carrying the I251L mutation in the mouse MC4R also display shorter longitudinal length, decreased weight in all abdominal white fat pads and improved glucose clearance and insulin response. C_LIO_LIGain-of-function mutations V103I and I251L of MC4R do not protect against the diabetogenic and adipogenic effects of a high-fat diet. C_LI

genetics↗

bioRxiv2020

Defining the early stages of intestinal colonisation by whipworms

Whipworms are large metazoan parasites that inhabit distinct multi-intracellular epithelial burrows described as syncytial tunnels, in the large intestine of their hosts. How first-stage larvae invade host epithelia and establish infection remains unclear. Here, we investigate early infection events both using Trichuris muris infections of mice and murine caecaloids, the first in-vitro system for whipworm infection. We show that larvae degrade the mucus layers to access epithelial cells. In early syncytial tunnels, larvae are completely intracellular but woven through multiple live enterocytes and goblet cells. We also use single cell RNA sequencing for the first time to describe the mouse caecum. From infected caeca, the transcriptome data reveal the progression of infection results in cell damage and an expansion of enterocytes with a type-I interferon (IFN) signature, characterised by the expression of Isg15, instigating the host immune response to the whipworm and tissue repair. Our results unravel intestinal epithelium invasion by whipworms and reveal new specific interactions between the host and the parasite that allow the whipworm to establish its multi-intracellular niche.

immunology↗

bioRxiv2019

Differentiation of Human Colon Tissue In Culture: Effects of calcium on trans-epithelial electrical resistance and tissue cohesive properties

Background and aimsHuman colonoid cultures maintained under low-calcium (0.25 mM) conditions undergo differentiation spontaneously and, concomitantly, express a high level of tight junction proteins, but not desmosomal proteins. When calcium is included to a final concentration of 1.5 - 3.0 mM (provided either as a single agent or as a combination of calcium and minerals), there is little change in tight junction proteins but a strong up-regulation of desmosomal proteins and an increase in desmosome formation. The aim of this study was to assess functional consequences of the differences in calcium-mediated barrier protein expression.\n\nMethodsHuman colonoid-derived epithelial monolayers were interrogated in transwell culture under low- or high-calcium conditions. Ion permeability and monolayer integrity were assessed by measuring trans-epithelial electrical resistance (TEER) across the confluent monolayer. Colonoid cohesiveness was assessed in parallel.\n\nResultsTEER values were high in the low-calcium environment and increased only modestly in response to calcium. In contrast, colonoid cohesiveness increased substantially with calcium supplementation. In both assays, the response to Aquamin was greater than the response to calcium alone. However, differences between interventions were small and only compared to the 0.25 mM calcium were they statistically significant. Consistent with these findings, occludin expression (a measure of tight junctions) was high at 0.25 mM calcium and did not increase with supplementation. Cadherin-17 and desmoglein-2 were weakly-expressed under low calcium conditions but increased with intervention.\n\nConclusionsThese findings indicate that low ambient calcium levels are sufficient to support formation of a permeability barrier in the colonic epithelium. Higher calcium levels are necessary to promote tissue cohesion and enhance barrier function. These findings may help explain how an adequate daily intake of calcium contributes to colonic health by improving barrier function, even though there is little change in colonic histological features over a wide range of calcium intake levels.

physiology↗

bioRxiv2019

Evaluation of DNA extraction methods on individual helminth egg and larval stages for whole genome sequencing

Whole genome sequencing is being rapidly applied to the study of helminth genomes, including de novo genome assembly, population genetics, and diagnostic applications. Although late-stage juvenile and adult parasites typically produce sufficient DNA for molecular analyses, these parasitic stages are almost always inaccessible in the live host; immature life stages found in the environment for which samples can be collected non-invasively offer a potential alternative, however, these samples are typically yield very low quantities of DNA, can be environmentally resistant, and are susceptible to contamination, often from bacterial or host DNA. Here, we have tested five low-input DNA extraction protocols together with a low-input sequencing library protocol to assess the feasibility of whole genome sequencing of individual immature helminth samples. These approaches do not use whole genome amplification, a common but costly approach to increase the yield of low input samples. We first tested individual parasites from two species spotted onto FTA cards - egg and L1 stages of Haemonchus contortus and miracidia of Schistosoma mansoni - before further testing on an additional six species - Ancylostoma caninum, Ascaridia dissimilis, Dirofilaria immitis, Dracunculus medinensis, Strongyloides stercoralis, and Trichuris muris - with an optimal protocol. Whole genome sequencing followed by analyses to determine the proportion of on- and off-target mapping revealed successful sample preparations for six of the eight species tested with variation between species, and within species but between life stages, described. These results demonstrate the feasibility of whole genome sequencing of individual parasites, and highlight a new avenue towards generating sensitive, specific, and information-rich data for the diagnosis and surveillance of helminths.

genomics↗

bioRxiv2018

Exclusive dependence of IL-10Rα signalling on intestinal microbiota homeostasis and control of whipworm infection

The whipworm Trichuris trichiura is a soil-transmitted helminth that dwells in the epithelium of the caecum and proximal colon of their hosts causing the human disease, trichuriasis. Trichuriasis is characterized by colitis attributed to the inflammatory response elicited by the parasite while tunnelling through intestinal epithelial cells (IECs).\n\nThe IL-10 family of receptors, comprising combinations of subunits IL-10R, IL-10R{beta}, IL-22R and IL-28R, modulates intestinal inflammatory responses. Here we carefully dissected the role of these subunits in the resistance of mice to infection with T. muris, a mouse model of the human whipworm T. trichiura. Our findings demonstrate that whilst IL-22R and IL-28R are dispensable in the host response to whipworms, IL-10 signalling through IL-10R and IL-10R{beta} is essential to control caecal pathology, worm expulsion and survival during T. muris infections. We show that deficiency of IL-10, IL-10R and IL-10R{beta} results in dysbiosis of the caecal microbiota characterised by expanded populations of opportunistic bacteria of the families Enterococcaceae and Enterobacteriaceae. Moreover, breakdown of the epithelial barrier after whipworm infection in IL-10, IL-10R and IL-10R{beta}-deficient mice, allows the translocation of these opportunistic pathogens or their excretory products to the liver causing organ failure and lethal disease. Importantly, bone marrow chimera experiments indicate that signalling through IL-10R and IL-10R{beta} in haematopoietic cells, but not IECs, is crucial to control worm expulsion and immunopathology. These findings are supported by worm expulsion upon infection of conditional mutant mice for the IL-10R on IECs. Our findings emphasize the pivotal role of systemic IL-10R signalling on immune cells in promoting microbiota homeostasis and maintaining the intestinal epithelial barrier, thus preventing immunopathology during whipworms infections.\n\nAuthor summaryThe human gut is home to millions of bacteria, collectively called the microbiota, and also to parasites that include whipworms. The interactions between gut cells, the microbiota and whipworms define conditions for balanced parasitism. Cells lining the gut host whipworms but also interact with gut immune cells to deploy measures that control or expel whipworms whilst maintaining a barrier to prevent microbial translocation. Whipworms affect the composition of the microbiota, which in turn impacts the condition of the gut lining and the way in which immune cells are activated. In order to avoid tissue damage and disease, these interactions are tightly regulated. Here we show that signalling through a member of the IL-10 receptor family, IL-10R, in gut immune cells is critical for regulating of these interactions. Lack of this receptor on gut immune cells results in persistence of whipworms in the gut accompanied by an uncontrolled inflammation that destroys the gut lining. This tissue damage is accompanied by the overgrowth of members of the microbiota that act as opportunistic pathogens. Furthermore, the destruction of the gut barrier allows these bacteria to reach the liver where they cause organ failure and fatal disease.

immunology↗

bioRxiv2017

Endogenous synthesis of pyrethrins by cannabis

Pyrethrins are a class of natural terpenoid pesticides produced by Tanacetum cinerariifolium, commonly known as chrysanthemum. Here we present evidence that cannabis may be able to produce pyrethrins endogenously. Flower from a cannabis plant grown in a closed hydroponic environment contained 2.48 parts per million pyrethrin I by weight. A comparison of the genetics of T. cinerariifolium and Cannabis demonstrates Cannabis homologues of the genes that contribute to pyrethrins production in T. cinerariifolium. This provides a plausible pathway for the biosynthesis of pyrethrins in cannabis. Although preliminary, these data indicate a potentially significant confounding variable in both cannabis research and regulations on allowable pyrethrins residues in cannabis products.

plant biology↗