Biology subjects

Watson, L.

Publications and source records attributed to Watson, L..

6 recordsLinked to original sources

bioRxiv2021

Species richness determines C. difficile invasion outcome in synthetic human gut communities

Understanding the principles of colonization resistance of the gut microbiome to the pathogen Clostridioides difficile will enable the design of next generation defined bacterial therapeutics. We investigate the ecological principles of community resistance to C. difficile invasion using a diverse synthetic human gut microbiome. Our results show that species richness is a key determinant of C. difficile growth across a wide range of ecological contexts. Using a dynamic computational model, we demonstrate that C. difficile receives the largest number and magnitude of incoming negative interactions. We identify molecular mechanisms of inhibition including acidification of the environment and competition over glucose. We demonstrate that C. difficiles close relative Clostridium hiranonis strongly inhibits C. difficile via a pH-independent mechanism. While increasing the initial density of C. difficile can increase its abundance in the assembled community, the community context determines the maximum achievable C. difficile abundance. Our work suggests that the C. difficile inhibitory potential of defined bacterial therapeutics can be optimized by designing communities that feature a combination of mechanisms including species richness, environment acidification, and resource competition.

systems biology↗

bioRxiv2020

Bone marrow stromal cell transplantation ameliorates cytopenia caused by depletion FAP-α expressing cells.

The marrow microenvironment is a complex and heterogeneous mixture of hematopoietic and stromal progenitors necessary for haematopoiesis. Whilst the hematopoietic progenitors are well described, the stromal cellular composition is not fully elucidated due to the low cells numbers, localisation-distribution-accessibility, and the lack of specific biomarkers. Cellular taxonomy studies have recently identified new populations of stromal subsets with distinct gene signature and regulatory properties of hematopoietic regeneration. Fibroblast activation protein- (FAP), a stromal cell type first identified in cancer is also rarely found in normal tissues but might play an essential role in tissue homeostasis. Using FAPDM2 transgenic mouse in which FAP-expressing cells can be ablated with Diphtheria Toxin (DTX) FAP+ cells were depleted in healthy mice. Whilst FAP+ cells constituted 5% of all marrow cells; its ablation caused a rapid loss of PDGFR-, Leptin-R, gp38 and SDC2 stromal cells populations, endothelial cells and vascular disruption. These resulted in anaemia, thrombocytopenia and neutropenia in peripheral blood (PB) and extreme hypo-cellularity in marrow with abnormalities within the hematopoietic progenitors. In an effort to reverse the phenotypes caused by FAP+ cell loss, a single intravenous injection of syngeneic bone marrow-derived stromal cells was administered. In a short-term evaluation, anaemia, thrombocytopenia and neutropenia ameliorated in PB and the numbers of marrow hematopoietic progenitors increased. Our data suggest FAP-expressing cells are a non-redundant component of the marrow microenvironment, necessary for marrow homeostasis and haematopoiesis. These data also provided evidence that stromal cell ablation can be rescued by stromal cell therapy. Significance StatementFAP-expressing cells depletion led to collateral damage in PB and marrow, including haematological defects that can be ameliorated by adoptive transfer of low-dose, ex-vivo expanded FAP-expressing marrow stromal cells. We suggest that stromal cell loss is a feature of severe immune-mediated inflammatory diseases - such as Graft versus Host Disease and sepsis - and that FAPDM2 model represents a novel tool to explore the native function of the recently identified stromal cell sub-populations.

cell biology↗

bioRxiv2020

Single-cell RNA-seq analysis of human iPSC-derived motor neurons resolves early and predictive ALS signatures

Induced pluripotent stem cell (iPSC) derived neural cultures from amyotrophic lateral sclerosis (ALS) patients can reflect disease phenotypes targetable by treatments. However, widely used differentiation protocols produce mixtures of progenitors, neurons, glia, and other cells at various developmental stages and rostrocaudal neural tube segments. Here we present a methodology using single-cell RNA sequencing analysis to distinguish cell type expression in C9orf72 ALS, sporadic ALS, control, and genome-edited cultures across multiple subjects, experiments, and commercial platforms. Combinations of HOX and developmental gene expression with global clustering classified rostrocaudal, progenitor, and mantle zone fates. This demonstrated that iPSC-differentiated cells recapitulate fetal hindbrain and spinal cord development and resolved early, reproducible, and motor neuron-specific signatures of familial and sporadic ALS. This includes downregulated ELAVL3 expression, which persists into disease endstages. Single-cell analysis thus yielded predictive ALS markers in other human and mouse models which were otherwise undiscovered through bulk omics assays.

neuroscience↗

bioRxiv2020

Positively selected modifications in the pore of TbAQP2 allow pentamidine to enter Trypanosoma brucei

Mutations in the Trypanosoma brucei aquaporin AQP2 are associated with resistance to pentamidine and melarsoprol. We show that TbAQP2 but not TbAQP3 was positively selected for increased pore size from a common ancestor aquaporin. We demonstrate that TbAQP2s unique architecture permits pentamidine permeation through its central pore and show how specific mutations in highly conserved motifs affect drug permeation. Introduction of key TbAQP2 amino acids into TbAQP3 renders the latter permeable to pentamidine. Molecular dynamics demonstrates that permeation by dicationic pentamidine is energetically favourable in TbAQP2, driven by the membrane potential, although aquaporins are normally strictly impermeable for ionic species. We also identify the structural determinants that make pentamidine a permeant but exclude most other diamidine drugs. Our results have wide-ranging implications for optimising antitrypanosomal drugs and averting cross-resistance. Moreover, these new insights in aquaporin permeation may allow the pharmacological exploitation of other members of this ubiquitous gene family.

biochemistry↗

bioRxiv2019

Loss of acid sphingomyelinase ameliorates disease progression in a vertebrate model of Glucocerebrosidase deficiency

The additive effect of genetic risk variants on overall disease risk is a plausible but frequently unproven hypothesis. To test this hypothesis, we assessed the biological effect of combined glucocerebrosidase (GCase) and acid sphingomyelinase (ASM) deficiency. Variants in both glucocerebrosidase1 (GBA1) and sphingomyelinase (SMPD1) are genetic risk factors for Parkinsons disease. Unexpectedly, ASM deficiency resulted in normalized behaviour and prolonged survival in gba1-/-;smpd1-/- double-mutant zebrafish compared to gba1-/-. RNAseq-based pathway analysis confirmed a profound rescue of neuronal function and intracellular homeostasis. We identified complete reciprocal rescue of mitochondrial respiratory chain function and abolished lipid membrane oxidation in gba1-/-;smpd1-/- compared to gba1-/- or smpd1-/- as the underlying rescue mechanism. Complementing in vitro experiments demonstrated an unexpected reduction of -synuclein levels in human cell lines with combined GCase and ASM deficiency. Our study highlights the importance of functional validation for any putative interactions between genetic risk factors and their overall effect on disease-relevant mechanisms rather than readily assuming an additive effect. SummaryThe additive effect of genetic risk variants on disease risk is a popular but typically unproven hypothesis. We investigated this hypothesis mechanistically for Parkinsons disease risk factors and provide evidence of an unexpected rescue effect on neuronal function and survival.

genetics↗

bioRxiv2018

Magnetic resonance spectroscopy analysis of intramyocellular lipid composition in lipodystrophic patients and athletes

ContextParadoxically, intramyocellular lipid (IMCL) accumulation has been linked to both insulin-resistant and to insulin-sensitive (athletes) states. The composition of this lipid store is unknown in these states.\n\nDesign and MethodsWe used a recently validated and potentially widely applicable 1H magnetic resonance spectroscopy method to compare the compositional saturation index (CH2:CH3 ratio) and concentration independent of composition (CH3) of intramyocellular lipid in the soleus and tibialis anterior muscles of 16 female insulin-resistant lipodystrophic patients with that of age- and gender-matched athletes (n=14) and healthy controls (n = 41).\n\nMain OutcomeIMCL compositional saturation index (CH2:CH3 ratio).\n\nResultsThe IMCL CH2:CH3 ratio was significantly higher in both muscles of the lipodystrophic patients compared with age- and gender-matched controls but not compared to athletes. IMCL CH2:CH3 was dependent on IMCL concentration in the controls and after adjusting the composition index for quantity (CH2:CH3adj) was able to distinguish patients from athletes. With groups pooled, this CH2:CH3adj marker had the strongest relation to insulin resistance (HOMA-IR) compared to other measures of lipid concentration and composition, especially in the soleus muscle. Contrary to the athletes paradox, IMCL in athletes was similar in tibialis anterior (p>0.05) and significantly lower in the soleus (p < 0.004) compared to both controls and patients.\n\nConclusionsThe IMCL saturation index adjusted for quantity, which likely reflects accumulation of saturated IMCL, is more closely associated with insulin resistance than concentration alone.

biochemistry↗