Biology subjects

Johnson, E. M.

Publications and source records attributed to Johnson, E. M..

9 recordsLinked to original sources

bioRxiv2025

Antifungal susceptibility profile of clinically relevant species of the genus Sporothrix: establishment of Epidemiological Cutoff Values (ECVs) according to CLSI broth microdilution methodology

Sporotrichosis is a globally distributed subcutaneous mycosis caused mainly by Sporothrix brasiliensis, S. schenckii, and S. globosa. Cat-transmitted sporotrichosis, primarily caused by S. brasiliensis in South America and to a lesser extent by S. schenckii in Southeast Asia, is emerging as a significant public health concern, due its outbreak potential. Itraconazole is the first-choice drug for treatment of human and cats, but reduced susceptibility has been reported based on previously proposed epidemiological cut-off values (ECVs). To support resistance surveillance, we aimed to establish CLSI-endorsed ECVs for these clinically relevant Sporothrix species. A total of 3,588 minimum inhibitory concentration (MIC) values for seven antifungal agents (amphotericin B, itraconazole, posaconazole, voriconazole, isavuconazole, olorofim, and terbinafine) were obtained from 19 international laboratories. Four of seven antifungals met the CLSI M57 guidelines criteria to determine the ECV. Established ECVs for amphotericin B were found to be high with 8 {micro}g/mL for S. brasiliensis and S. globosa, and 4 {micro}g/mL for S. schenckii. Itraconazole ECVs were 4 {micro}g/mL for S. brasiliensis and S. schenckii. Posaconazole ECVs were 4 {micro}g/mL for all three species (tentative for S. globosa), while the terbinafine ECV for S. brasiliensis was 0.12 {micro}g/mL. Olorofim demonstrated good in vitro activity, particularly against S. brasiliensis. Overall, this study establishes validated ECVs for key antifungals against Sporothrix species and identifies a low prevalence of non-wild type (NWT) isolates, supporting ongoing antifungal resistance monitoring.

microbiology↗

bioRxiv2025

Integrated in silico and in vitro approaches identify SNX.2112 as a drug vulnerability in t(7;12) AML stem-like cells

The t(7;12) translocation is a chromosomal rearrangement characteristic of infant Acute Myeloid Leukemia (AML). It arises in utero and results in ectopic overexpression of homeobox gene MNX1. Using a 3-dimensional (3D) model of blood development, we recently showed that t(7;12)-AML originates at the endothelial-to-hematopoietic transition, explaining its characteristic gene expression signature. Herein, we employ that signature to interrogate the transcriptional profiles of hundreds of human cell lines against the GDSC database of drug sensitivities to identify candidate drugs against t(7;12)-AML. We employ a cell line in which we engineered t(7;12) and systematically test the candidate drugs by cell surface phenotype and clonogenic assays. Importantly, we identify HSP90 inhibitor SNX.2112 as a potential therapeutic agent against t(7;12)-AML. SNX.2112 selectively eliminates colony-initiating leukemia progenitors in vitro and decreases MNX1 expression, effects recapitulated by other HSP90 inhibitors. SNX.2112 acts at least partly through destabilisation of STAT5 signalling. Critically, SNX.2112-differential signatures uniquely map to progenitors with hemato-endothelial characteristics in t(7;12)-AML patient blasts, suggesting targeting of leukemia-initiating cells. Combinatorial treatment with chemotherapeutic agents indicates synergy, suggesting SNX.2112 potential as a targeted and cytotoxicity-sparing therapeutic approach. Overall, we successfully use an integrated computational and multi-model experimental approach to identify a drug vulnerability of t(7;12)-AML. Key pointsO_LIClassifier-based in silico drug screening identifies vulnerabilities of t(7;12)-infant leukemia C_LIO_LI2D and 3D models of t(7;12)-leukemia match HSP90 inhibition cellular and molecular responses to candidate leukemia stem cells in t(7;12) patient analysis. C_LI

cancer biology↗

bioRxiv2023

Strain and temperature dependent aggregation of Candida auris is attenuated by inhibition of surface amyloid proteins

Candida auris is a multi-drug resistant human fungal pathogen that has become a global threat to human health due to its drug resistant phenotype, persistence in the hospital environment and propensity for patient to patient spread. Isolates display variable aggregation that may affect the relative virulence of strains. Therefore, dissection of this phenotype has gained substantial interest in recent years. We studied eight clinical isolates from four different clades (I-IV); four of which had a strongly aggregating phenotype and four of which did not. Genome analysis identified polymorphisms associated with loss of cell surface proteins were enriched in weakly-aggregating strains. Additionally, we identified down-regulation of chitin synthase and chitinase genes involved in the synthesis and dissolution of the chitinous septum. Characterisation of the cells revealed no ultrastructural defects in cytokinesis or cell separation in aggregating isolates. Strongly and weakly aggregating strains did not differ in net surface charge or in cell surface hydrophobicity. The capacity for aggregation and for adhesion to polystyrene microspheres were also not correlated. However, aggregation and extracellular matrix formation were all increased at higher growth temperatures, and treatment with the amyloid protein inhibitor Thioflavin-T markedly attenuated aggregation. Genome analysis further indicated strain specific differences in the genome content of GPI-anchored proteins including those encoding genes with the potential to form amyloid proteins. Collectively our data suggests that aggregation is a complex strain and temperature dependent phenomenon that may be linked in part to the ability to form extracellular matrix and cell surface amyloids. HIGHLIGHTSThe amyloid inhibitor Thioflavin-T inhibited C. auris aggregation. Aggregating isolates do not exhibit any defects in cell separation. Genomic differences were identified between strongly aggregating and weakly-aggregating strains of C. auris. Aggregation did not correlate with surface charge or hydrophobicity of yeast cells.

microbiology↗

bioRxiv2023

Anticancer, anti-inflammatory, and immune modulatory activity of ferulic acid fructo-oligosaccharide conjugated microparticle

Background and purposeFerulic acid exhibit anticancer activity but almost most of the free ferulic acid taken orally are absorbed in the stomach and extensively metabolised by the liver and hence hardly any free ferulic acid reach the large intestine to exert its beneficial activity. Fructo-oligosaccharide (dietary fibre) are resistant to gastro-intestinal enzymes and are poorly absorbed by the stomach but bioavailable in the large intestine where they are digested by gut microbiota. Ferulic acid fructo-oligosaccharide conjugate was synthesized which could self-assemble in to disc shaped amorphous microparticles, it was found to be resistant to gastro-intestinal enzymes and digestion by gut microbiota. The synthesized microparticles could be used for targeted delivery to the colon and accessed for its ability to ameliorate colo-rectal cancer and inflammation. Experimental approachThe anti-cancer activity of the FA FOS microparticle (FA FOS I) was tested in human colon cancer cell lines HT29, LoVo and compared with the toxicity to normal human colon fibroblast CCD18-Co, relative to that of conventional chemotherapeutic colon cancer drug oxaliplatin. The apoptosis induction by FA FOS I was assessed by TUNNEL (Terminal deoxynucleotidyl transferase mediated dUTP Nick-end Labelling) and FACS. The ability of the FA FOS microparticle to induce cell cycle arrest was determined. The gene expression profiling of both apoptosis related genes and cell cycle arrest related genes were analysed by using RT-PCR analysis of an array of apoptosis related genes and cell cycle related genes. In-vivo pre-clinical anti-colorectal cancer studies of FA FOS I microparticle were carried out in AOM-DSS mediated colitis associated colon cancer mice model (AOM DSS CAC) to determine its anti-cancer efficacy in the physiological, immunological and innate host microbiota setting. Key resultsThe in-vitro studies in colon cancer and normal colon cells exhibited selective cytotoxicity and apoptosis induction in colon cancer cells. The microparticle arrested the cell cycle in the G0-G1 phase. There was a reduction in 60.83% of tumour lesions in FA FOS I treated group compared to control group. The H&E histochemistry of the colon tissue revealed that there was 48.27% reduction in the malignant cell or tumour cells in the colon tissue on treatment with FA FOS I. The FA FOS conjugate treatment enhanced the gut barrier function and tight junction with the intestinal barrier guarded by the mucosal lining. The immunohistochemistry (IHC) and the immunofluorescence of the mouse colon tissue revealed the suppression of inflammation and related inflammatory cytokines in the colon. The inhibition of cell proliferation, up-regulation of tumour suppressor protein and apoptosis of the malignant or tumour cells were detected and quantified by IHC and TUNEL staining. The evaluation of immune status of the AOM DSS CAC mouse treated with FA FOS I microparticle was determined using haematological analysis of the blood lymphocytes which revealed a 9% increase in WBC count and the multiplex immunofluorescence of the colon tissue revealed an increase in the infiltration of T-helper cells and cytotoxic T-cells into the tumour microenvironment followed by the cells of the innate immune system. There was a considerable decrease in the expression of tumour suppressing PD-L1 by the tumour cells on four weeks treatment with FA FOS I microparticle. Conclusion and implicationsAll these data implicate better efficacy of the FA FOS I microparticle delivery to colon and amelioration of colo-rectal cancer, inflammation, and positive immune modulation of tumour microenvironment against tumour proliferation.

cancer biology↗

bioRxiv2023

Synthesis of water-soluble and gastrointestinal transit-resistant FA-FOS conjugate for targeted delivery to the colon: pharmacokinetics, pharmacodynamics, efficacy

Ferulic acid is known to be a water-insoluble compound present in many fruits and vegetables and is known to possess antioxidant, anti-cancer, and anti-inflammatory properties. They are quickly absorbed in the stomach and metabolized in the liver. Their colonic exposure is found to be low due to their quick absorption and metabolism in the upper gastrointestinal tract, and due to this reason, only a small fraction of FA found in a bound form is associated with the insoluble and soluble fiber of the food matrix reaching the colon. Here we describe the synthesis and characterization of ferulic acid (FA) bound to fructo oligosaccharide (FOS) rendering the resultant FA-FOS conjugate water soluble, resistant to gastrointestinal digestion and absorption, along with the capability to deliver a therapeutically meaningful dose of FA to the large intestine. Free FA is released from FA-FOS conjugate by the digestive action of gut microflora, and the pharmacokinetic profile and pharmacodynamics are evaluated in a rat model. The efficacy of FA-FOS conjugate in the delivery of FA to the large intestine and its accumulation in tumours were evaluated in colitis induced colon cancer model and their efficacy through plasma bioavailability is determined in xenograft mice model carrying tumour from human colon cancer cells. The accumulation of FA derived from FA-FOS conjugate in the tumour was demonstrated by the MALDI imaging technique. The major metabolites of FA-FOS conjugate in plasma were determined through a data-dependent MS/MS experiment of precursor ion scan, utilizing triple quad (QTRAP) equipped LC-MS.

pharmacology and toxicology↗

bioRxiv2022

Landscape-scale exposure to multiazole-resistant Aspergillus fumigatus bioaerosols

We demonstrate country-wide exposures to aerosolized spores of a human fungal pathogen, Aspergillus fumigatus, that has acquired resistance to first line azole clinical antifungal drugs. Assisted by a network of citizen scientists across the United Kingdom, we show that 1 in 20 viable aerosolized spores of this mold are resistant to the agricultural fungicide tebuconazole and 1 in 140 spores are resistant to the four most used azoles for treating clinical aspergillosis infections. Season and proximity to industrial composters were associated with growth of A. fumigatus from air samples, but not with the presence of azole resistance, and hotspots were not stable between sampling periods suggesting a high degree of atmospheric mixing. Genomic analysis shows no distinction between those resistant genotypes found in the environment and in patients, indicating that ~40% (58/150 sequenced genomes) of azole-resistant A. fumigatus infections are acquired from environmental exposures. Due to the ubiquity of this measured exposure, it is crucial that we determine source(s) of azole-resistant A. fumigatus, who is at greatest risk of exposure and how to mitigate these exposures, in order to minimize treatment failure in patients with aspergillosis. One sentence summaryUK-wide citizen science surveillance finds a ubiquitous exposure to aerosolized spores of a human fungal pathogen that have evolved in the environment cross-resistance to essential clinical antifungal drugs

microbiology↗

bioRxiv2021

Tracing patterns of evolution and acquisition of drug resistant Aspergillus fumigatus infection from the environment using population genomics

Infections caused by opportunistic fungal pathogens are increasingly resistant to first-line azole antifungal drugs. However, despite its clinical importance, little is known about the extent to which susceptible patients acquire infection from drug resistant genotypes in the environment. Here, we present a population genomic analysis of the mould Aspergillus fumigatus from across the United Kingdom and Republic of Ireland. First, we show occurrences where azole resistant isolates of near identical genotypes were obtained from both environmental and clinical sources, indicating with high confidence the infection of patients with resistant isolates transmitted from the environment. Second, we find that the fungus is structured into two clades ( A and B) with little interclade recombination and the majority of environmental azole resistance genetically clustered inside Clade A. Genome-scans show the impact of selective sweeps across multiple regions of the genome. These signatures of positive selection are seen in regions containing canonical genes encoding fungicide resistance in the ergosterol biosynthetic pathway, whilst other regions under selection have no defined function. Phenotyping identified genes in these regions that could act as modifiers of resistance showing the utility of reverse genetic approaches to dissect the complex genomic architecture of fungal drug resistance. Understanding the environmental drivers and genetic basis of evolving fungal drug resistance needs urgent attention, especially in light of increasing numbers of patients with severe viral respiratory tract infections who are susceptible to opportunistic fungal superinfections.

genomics↗

bioRxiv2020

A Statistical Approach to Dimensionality Reduction Reveals Scale and Structure in scRNA-seq Data

While single-cell "omics" based measurements hold the promise of unparalleled biological insight they remain a challenge to analyze owing to their high-dimensional nature. As a result, Dimensionality Reduction (DR) algorithms are necessary for data visualization and for downstream quantitative analysis. The lack of a principled methodology for separating signal from noise in DR algorithmic outputs has limited the confident application of these methods in unsupervised analyses of single-cell data, greatly hampering researchers ability to make data-driven discoveries. In this work we present an approach to quality assessment, EMBEDR, that works in conjunction with any DR algorithm to distinguish signal from noise in dimensionally-reduced representations of high-dimensional data. We apply EMBEDR to t-SNE- and UMAP-generated representations of published scRNA-seq data, revealing where lower-dimensional representations of the data are faithful renditions of biological signal in the data, and where they are more consistent with noise. EMBEDR produces easily interpreted p-values for each cell in a data set, facilitating the comparison of different DR methods and allowing optimization of their global hyperparameters. Most compellingly, EMBEDR allows for the analysis of single-cell data at a single-cell resolution, allowing DR methods to be used in a cell-wise optimal manner. Applying this technique to real data results in a biologically interpretable view of the data with no user supervision. We demonstrate the utility of EMBEDR in the context of several data sets and DR algorithms, illustrating its robustness and flexibility as well as its potential for making rigorous, quantitative analyses of single-cell omics data. EMBEDR is available as a Python package for immediate use.

bioinformatics↗

bioRxiv2019

Functional clusters of neurons in layer 6 of macaque V1

AbstracLayer 6 appears to perform a very important role in the function of macaque primary visual cortex, V1, but not enough is understood about the functional characteristics of neurons in the layer 6 population. It is unclear to what extent the population is homogeneous with respect to their visual properties or if one can identify distinct sub-populations. Here we performed a cluster analysis based on measurements of the responses of single neurons in layer 6 of primary visual cortex to achromatic grating stimuli that varied in orientation, direction of motion, spatial and temporal frequency, and contrast. The visual stimuli were presented in a stimulus window that was also varied in size. Using the responses to parametric variation in these stimulus variables we extracted a number of tuning response measures and used them in the cluster analysis. Six main clusters emerged along with some smaller clusters. Additionally we asked whether parameter distributions from each of the clusters were statistically different. There were clear separations of parameters between some of the clusters, particularly for f1/f0 ratio, direction selectivity, and temporal frequency bandwidth but other dimensions also showed differences between clusters. Our data suggest that in layer 6, across the spatial extent of a single cortical hypercolumn, there are multiple parallel circuits that provide information about different aspects of the visual stimulus.

neuroscience↗