bioRxiv Science⌕ Search

Biology subjects

Graham, G.

Publications and source records attributed to Graham, G..

16 recordsLinked to original sources

Cell-type Plasticity Supports Behavioral Adaptations at the Water-to-Land Interface

Animals inhabiting aquatic or terrestrial habitats experience different constraints on their physiology and locomotion, and are exposed to fundamentally different sensory environments. Across evolutionary timescales, most species have adapted to live exclusively either in water or on land. Newts are among the vertebrates that defy this rule and split their adult lives between freshwater ponds and terrestrial habitats. In these amphibians, transitions across environments cause remarkable phenotypic plasticity in their body morphology. But whether and how the nervous system and behavior also adapt to these environmental changes remains poorly explored. Here, we establish the Iberian ribbed newt Pleurodeles waltl as a new model to study the neurobiology of environmental plasticity in a vertebrate. We first show that experimental transitions between aquatic and terrestrial laboratory settings recapitulate morphological changes observed in the wild. Furthermore, aquatic and terrestrial newts display plasticity in sensory and motor behaviors, including differences in walking gait and odor responsiveness. In the olfactory system, the transition from water to land involves a profound remodeling of the nasal epithelium, including reversible transcriptomic changes in secretory and support cells, and an increase of neurogenesis. Together, our findings reveal how plasticity of specific cell types in the nervous system supports behavioral adaptations across environments. More broadly, this work establishes newts as a model to study the functional constraints and convergent adaptations that may have shaped the evolution of vertebrate nervous systems in water and on land.

neuroscience↗

Ultraviolet exposure remodels skin to enhance arbovirus infection and mosquito biting behaviour

AbstractMosquito-borne viruses are inoculated into skin, yet how environmental exposures shape susceptibility remains unclear. We identify ultraviolet (UV) exposure as an unrecognised determinant of mosquito-borne virus infection. In mice, prior UV exposure increased Semliki Forest virus replication, viraemia and mortality, and also enhanced Zika virus infection. Early susceptibility was driven by recruited CCR2-dependent myeloid cells that were preferentially infected and amplified virus. This phase was transient: by one week, infection shifted toward proliferating fibroblasts within repairing skin, accompanied by a glycolytic tissue signature. In primary human dermal fibroblasts, viral replication was governed by metabolic state rather than proliferation alone, suggesting that repair-associated metabolic reprogramming underlies stromal permissiveness. Topical steroids partially alleviated UV-conditioned enhancement of virus susceptibility. UV also warmed skin and increased mosquito probing. Together, these findings establish UV exposure as a driver of conditioned states that determine arbovirus susceptibility, identifying sunlight as a modifiable determinant of vector-borne disease risk. In Brief / eTOC blurbMcCafferty-Brown et al. show that ultraviolet exposure conditions skin to enhance mosquito-borne virus infection. Susceptibility shifts from infected myeloid cells early after UV to proliferating fibroblasts with a glycolytic tissue signature during repair, while UV-exposed skin also increases Aedes aegypti probing.

microbiology↗

Chemokine receptor expression defines a trajectory from monocytes to mature macrophages.

CCR1, CCR2 and CCR5 direct recruitment of monocytes and macrophages in inflammation. However, the discrete role for each receptor in monocyte/macrophage biology remains poorly understood, with previous reports citing receptor redundancy. Using transcriptomic approaches to examine inflammatory chemokine receptor expression on lung interstitial macrophage populations, we demonstrate that interstitial macrophages can be divided into three distinct subsets, each of which express specific patterns of chemokine receptors, and that there are dynamic changes in chemokine receptor expression as macrophages differentiate from monocytes in the lung. Furthermore, macrophages expressing different combinations of chemokine receptors are transcriptionally distinct, suggesting non-redundant functions for CCR1, 2 and 5. Finally, we examined changes in macrophage chemokine receptor expression in vitro after treatment with varied TLR ligands, and show that CCR1 is specifically increased in response to bacterial but not viral ligands. Our data provide compelling evidence that macrophage chemokine receptor expression is not redundant, but specific and malleable in response to discrete inflammatory stimuli.

immunology↗

Tumor intrinsic regulation of PD-L1 and of interferon Type I via an SLC25A1-driven mitochondrial pathway, influences the anti-tumor immune response

Immune checkpoint inhibitors (ICIs) have transformed cancer therapy, but variable patient responses highlight the need to better regulators of immune sensitivity. Here, we identify the mitochondrial citrate carrier SLC25A1 as a determinant of anti-PD-L1 antibody therapy responsiveness through a dual regulation of type I interferon (IFN-I) signaling and of PD-L1 expression. SLC25A1 promotes a mitochondrial-to-nuclear retrograde signaling via cytosolic accumulation of mitochondrial DNA, activation of the cGAS-STAT1 axis, and establishment of a virus mimicry state that triggers the IFN-I response. This activation is enriched in cancer stem cell populations, consistent with the role for SLC25A1 in tumor stemness and therapy resistance. Moreover, SLC25A1 also regulates PD-L1 protein levels through a newly identified fumarate-Keap1-PD-L1 axis, whereby fumarate inhibits Keap1, leading to PD-L1 up-regulation. In vivo, tumors expressing high levels of SLC25A1 exhibit an inflammatory environment and increased sensitivity to PD-L1 blockade, but accelerated growth in the absence of anti-PD-L1 treatment. These findings position SLC25A1 as a novel regulator of mitochondrial-driven IFN-I signaling and PD-L1 stability, and suggest that SLC25A1 exploits PD-L1 to evade immune surveillance, while at the same time creating an intrinsic tumor vulnerability to checkpoint blockade. Thus, SLC25A1 may serve both as a biomarker of response and as a target to enhance the efficacy of immunotherapy.

cancer biology↗

Eosinophils promote monocyte to macrophage differentiation and anti-bacterial immunity

Chemokine receptors control cell migration within the body. Here we reveal a novel interaction between eosinophils and monocytes in the bone marrow, indirectly controlled by the atypical chemokine receptor ACKR2. We demonstrate that ACKR2 maintains eosinophil levels within the bone marrow by scavenging CCL11. In the absence of ACKR2, elevated CCL11 leads to increased egress of eosinophils from the bone marrow into the bloodstream. As a result, eosinophil and monocyte interactions are reduced within the bone marrow niche, leading to changes in monocyte gene expression. Monocytes from ACKR2-/- mice are recruited to the tissues but are fundamentally altered in their ability to differentiate into macrophages, in the lung, peritoneal cavity and cavity wall. Bacterial elimination is impaired in ACKR2-/- mice during peritoneal infection. ACKR2 is therefore a key regulator of eosinophil-driven monocyte education in the bone marrow, required for full monocyte differentiation and macrophage function within the tissues.

immunology↗

CCR2-driven monocyte recruitment is protective against radiotherapy-induced intestinal toxicity

Radiotherapy (RT) is essential in treating abdominal and pelvic cancers but often damages the healthy tissues, particularly the intestines, leading to radiation-induced toxicities with limited treatment options. While the immune system is known to help regulate tissue damage, immune mechanisms involved in RT-induced intestinal toxicity are not fully understood. Following CT-guided localised intestinal irradiation, single-cell RNA sequencing (scRNA-seq) and flow cytometry revealed RT-induced chemokine-dependent recruitment of innate immune cells. Deletion of C-C chemokine receptor (Ccr)1, Ccr2, Ccr3 and Ccr5, blocked recruitment and worsened radiation induced toxicities, suggesting an important role for an innate immune cell population in limiting RT-mediated bowel damage. Furthermore, CCR2-deficient mice showed exacerbated weight loss and intestinal permeability, while the transfer of Ly6C+ monocytes alleviated symptoms. Mechanistically, IL-17 cytokine production by group 3 innate lymphoid cells (ILC3s), a critical factor in maintaining intestinal barrier integrity, was found to be reduced in irradiated CCR2-/-, however the transfer of Ly6C+ monocytes resulted in increased IL-17 levels. These findings demonstrate the critical importance of CCR2-mediated monocyte recruitment in mitigating RT-induced toxicities. One Sentence SummaryCCR2-mediated monocyte recruitment protects against RT-induced intestinal toxicity via IL-17, highlighting a therapeutic target.

immunology↗

IL-27 maintains cytotoxic Ly6C+ gamma delta T cells that arise from immature precursors

In mice, {gamma}{delta} T cells that express the co-stimulatory molecule, CD27, are committed to the IFN{gamma}-producing lineage in the thymus, and in the periphery, these cells play a critical role in host defence and anti-tumor immunity. Unlike {beta} T cells that rely on MHC-presented peptides to drive their terminal differentiation, it is unclear whether MHC-unrestricted {gamma}{delta} T cells undergo further functional maturation after exiting the thymus. Here, we provide evidence of phenotypic and functional diversity within peripheral IFN{gamma}-producing {gamma}{delta} T cells. We found that immature CD27+Ly6C-- cells convert into mature CD27+Ly6C+ cells, and these mature cells control cancer progression while the immature cells cannot. The gene signatures of these two subsets were highly analogous to human immature and mature {gamma}{delta} T cells, indicative of conservation across species. We show that IL-27 supports the cytotoxic phenotype and function of mouse CD27+Ly6C+ cells and human V{delta}2+ cells, while IL-27 is dispensable for mouse CD27+Ly6C-- cells and human V{delta}1+ cells. These data reveal increased complexity within IFN{gamma}-producing {gamma}{delta} T cells, comprising of immature and terminally differentiated subsets, that offer new insights into unconventional T cell biology.

immunology↗

Disruption of maternal ACKR3 has profound effects on embryos and offspring.

ACKR3, scavenges and degrades the stem cell recruiting chemokine CXCL12 which is essential for proper embryonic, and in particular hematopoietic, development. Here we demonstrate strong expression of ACKR3 on trophoblasts. Using a pharmacological blocker we demonstrate that ACKR3 is essential for preventing movement of CXCL12 from the mother to the embryo with elevated plasma CXCL12 levels being detected in embryos from ACKR3-blocker treated mothers. Mice born to mothers treated with the blocker are lighter and shorter than those born to vehicle-treated mothers and, in addition, display profound anaemia associated with a markedly reduced bone marrow hematopoietic stem cell population. Importantly, whilst the hematopoietic abnormalities are corrected as mice age, our studies reveal a postnatal window during which offspring of ACKR3 blocker treated mice are unable to mount effective inflammatory responses to inflammatory/infectious stimuli. Overall, these data demonstrate that ACKR3 is essential for preventing CXCL12 transfer from mother to embryo and for ensuring properly regulated CXCL12 control over the development of the hematopoietic system.

developmental biology↗

Chemokine CXCL4 interactions with extracellular matrix proteoglycans mediate wide-spread non-receptor mediated immune cell recruitment

Leukocyte recruitment from the vasculature into tissues is a crucial component of the immune system, but is also key to inflammatory disease. Chemokines are central to this process but have yet to be therapeutically targeted during inflammation, due to a lack of mechanistic understanding. Specifically, CXCL4 (PF4) has no established receptor that explains its function. Here we use biophysical, in vitro and in vivo techniques to determine the mechanism underlying CXCL4 mediated leukocyte recruitment. We demonstrate that CXCL4 binds to glycosaminoglycan (GAG) sugars within the endothelial extracellular matrix resulting in increased vascular permeability and non-specific recruitment of a range of leukocytes. Furthermore, GAG sulphation confers selectivity onto chemokine localisation. These findings represent a new understanding of chemokine biology, providing novel mechanisms for future therapeutic targeting. One sentence summaryCXCL4 binds to extracellular matrix proteoglycans resulting in increased vascular permeability and recruitment of a wide range of different leukocytes via a non-canonical mechanism.

immunology↗

A scalable approach for continuous time Markov models with covariates

Existing methods for fitting continuous time Markov models (CTMM) in the presence of covariates suffer from scalability issues due to high computational cost of matrix exponentials calculated for each observation. In this paper we propose an optimization technique for CTMM which uses a stochastic gradient descent algorithm combined with differentiation of the matrix exponential using a Pade approximation which we show then makes fitting large scale data feasible. We compare two methods for computing standard errors, one using Pade expansion, and the other using power series expansion of the matrix exponential. Through simulations we find improved performance relative to existing CTMM methods, and we demonstrate the method on the large-scale multiple sclerosis NO.MS dataset.

bioinformatics↗

Reproductive resilience but not root architecture underpin yield improvement in maize

Plants capture soil resources to produce the grains required to feed a growing population. Because plants capture water and nutrients through roots, it was proposed that changes in root systems architecture (RSA) underpin the three-fold increase in maize grain yield over the last century1,2,3,4. Within this framework, improvements in reproductive resilience due to selection are caused by increased water capture1. Here we show that both root architecture and yield have changed with decades of maize breeding, but not the water capture. Consistent with Darwinian agriculture5 theory, improved reproductive resilience6,7 enabled farmers increase the number of plants per unit land8,9,10, capture soil resources, and produced more dry matter and grain. Throughout the last century, selection operated to adapt roots to crowding, enabling reallocation of C from large root systems to the growing ear and the small roots of plants cultivated in high plant populations in modern agriculture.

plant biology↗

Chemokine receptors CCR1 and ACKR2 coordinate mammary gland development

Macrophages are key regulators of developmental processes, including those involved in mammary gland development. We previously demonstrated that the atypical chemokine receptor, ACKR2, contributes to control of ductal epithelial branching in the developing mammary gland by regulating macrophage dynamics. ACKR2 is a chemokine-scavenging receptor, which mediates its effects through collaboration with inflammatory chemokine receptors (iCCRs). Here we reveal that ACKR2, and the iCCR CCR1, reciprocally regulate branching morphogenesis in the mammary gland, whereby stromal ACKR2 modulates levels of the shared ligand CCL7 to control the movement of a key population of CCR1-expressing macrophages to the ductal epithelium. In addition estrogen, which is essential for ductal elongation during puberty, upregulates CCR1 expression on macrophages. The age at which girls develop breasts is decreasing, which raises the risk of diseases including breast cancer. This study presents a previously unknown mechanism controlling the rate of mammary gland development during puberty and highlights potential therapeutic targets. SummaryIn the mammary gland during puberty, availability of the chemokine CCL7 is controlled by a scavenging receptor ACKR2 and provides a key signal to macrophages which have the receptor CCR1. Together, this controls the timing of development.

immunology↗

A novel methodology for defining stromal expression of atypical chemokine receptors in vivo

Analysis of chemokine receptor, and atypical chemokine receptor, expression is frequently hampered by the lack of availability of high-quality antibodies and the species-specificity of those that are available. We have previously described methodology utilising Alexa-Fluor labelled chemokine ligands as versatile reagents to detect receptor expression. Previously this has been limited to haematopoietic cells and methodology for assessing expression of receptors on stromal cells has been lacking. Amongst chemokine receptors the ones most frequently expressed on stromal cells belong to the atypical chemokine receptor subfamily. These receptors do not signal in the classic sense in response to ligand but scavenge their ligands and degrade them and thus sculpt in vivo chemokine gradients. Here we demonstrate the ability to use either intratracheal, or intravenous, Alexa-Fluor labelled chemokine administration to detect stromal cell populations expressing the atypical chemokine receptor ACKR2. Using this methodology we demonstrate, for the first time, expression of ACKR2 on blood endothelial cells. This observation sets the lung aside from other tissues in which ACKR2 is exclusively expressed on lymphatic endothelial cells. In summary therefore we described a novel method for the in situ labelling of atypical chemokine receptor expressing cells appropriate for subsequent flow cytometric analysis. We propose that this methodology will work in a range of species and for a range of receptors and therefore will have significant versatility

immunology↗

Functional arrays of human pluripotent stem cell-derived cardiac microtissues

To accelerate the cardiac drug discovery pipeline, we set out to develop a platform that would be amenable to standard multiwell-plate manipulations and be capable of quantifying tissue-level functions such as contractile force. We report a 96-well-based array of 3D human pluripotent stem cell (hPSC)-derived cardiac microtissues - termed Cardiac MicroRings (CaMiRi) - in custom printed multiwell plates capable of contractile force measurement. Within each well, two elastomeric microcantilevers are situated above a ramp. The wells are seeded with cell-laden collagen which, in response to the slope of the ramp, self-organizes around tip-gated microcantilevers to form contracting CaMiRi. The contractile force exerted by the CaMiRi is measured and calculated using the deflection of the cantilevers. Platform responses were robust and comparable across wells and we used it to determine an optimal tissue formulation. We validated contractile force response of CaMiRi using selected cardiotropic compounds with known effects. Additionally, we developed automated protocols for CaMiRi seeding, image acquisition, and analysis to enable measurement of contractile force with increased throughput. The unique tissue fabrication properties of the platform, and the consequent effects on tissue function, were demonstrated upon adding hPSC-derived epicardial cells to the system. This platform represents an open-source contractile force screening system useful for drug screening and tissue engineering applications.

bioengineering↗

Single molecule real time (SMRT) full length RNA-sequencing reveals novel and distinct mRNA isoforms in human bone marrow cell subpopulations

Hematopoietic cells are continuously replenished from progenitor cells that reside in the bone marrow. To evaluate molecular changes during this process, we analyzed the transcriptomes of freshly harvested human bone marrow progenitor (lineage-negative) and differentiated (lineage-positive) cells by single molecule, real time (SMRT) full length RNA sequencing. This analysis revealed a [~]5-fold higher number of transcript isoforms than previously detected and showed a distinct composition of individual transcript isoforms characteristic for bone marrow subpopulations. A detailed analysis of mRNA isoforms transcribed from the ANXA1 and EEF1A1 loci confirmed their distinct composition. The expression of proteins predicted from the transcriptome analysis was validated by mass spectrometry and validated previously unknown protein isoforms predicted e.g. for EEF1A1. These protein isoforms distinguished the lineage negative cell population from the lineage positive cell population. Finally, transcript isoforms expressed from paralogous gene loci (e.g. CFD, GATA2, HLA-A, B & C) also distinguished cell subpopulations but were only detectable by full length RNA sequencing. Thus, qualitatively distinct transcript isoforms from individual genomic loci separate bone marrow cell subpopulations indicating complex transcriptional regulation and protein isoform generation during hematopoiesis.

molecular biology↗

Discovery of the role of a SLOG superfamily biological conflict systems associated protein IodA (YpsA) in oxidative stress protection and cell division inhibition in Gram-positive bacteria

Bacteria adapt to different environments by regulating cell division and several conditions that modulate cell division have been documented. Understanding how bacteria transduce environmental signals to control cell division is critical to comprehend the global network of cell division regulation. In this article we describe a role for Bacillus subtilis YpsA, an uncharacterized protein of the SLOG superfamily of nucleotide and ligand-binding proteins, in cell division. We observed that YpsA provides protection against oxidative stress as cells lacking ypsA show increased susceptibility to hydrogen peroxide treatment. We found that increased expression of ypsA leads to cell division inhibition due to defective assembly of FtsZ, the tubulin-like essential protein that marks the sites of cell division. We showed that cell division inhibition by YpsA is linked to glucose availability. We generated YpsA mutants that are no longer able to inhibit cell division. Finally, we show that the role of YpsA is possibly conserved in Firmicutes, as overproduction of YpsA in Staphylococcus aureus also impairs cell division. Therefore, we propose ypsA to be renamed as iodA for inhibitor of division.\n\nIMPORTANCEAlthough key players of cell division in bacteria have been largely characterized, the factors that regulate these division proteins are still being discovered and evidence for the presence of yet-to-be discovered factors has been accumulating. How bacteria sense the availability of nutrients and how that information is used to regulate cell division positively or negatively is less well-understood even though some examples exist in the literature. We discovered that a protein of hitherto unknown function belonging to the SLOG superfamily of nucleotide/ligand-binding proteins, YpsA, influences cell division in Bacillus subtilis by integrating metabolic status such as the availability of glucose. We showed that YpsA is important for oxidative stress response in B. subtilis. Furthermore, we provide evidence that cell division inhibition function of YpsA is also conserved in another Firmicute Staphylococcus aureus. This first report on the role of YpsA (IodA) brings us a step closer in understanding the complete tool set that bacteria have at their disposal to regulate cell division precisely to adapt to varying environmental conditions.

microbiology↗