Biology subjects

Heslop, R.

Publications and source records attributed to Heslop, R..

4 recordsLinked to original sources

bioRxiv2023

FISHtoFigure: An easy-to-use tool for rapid, multi-target partitioning and analysis of sub-cellular mRNA transcripts in smFISH data

Single molecule fluorescence in situ hybridisation (smFISH) has become a valuable tool to investigate the mRNA expression of single cells. However, it requires a considerable amount of bioinformatic expertise to use currently available open-source analytical software packages to extract and analyse quantitative data about transcript expression. Here, we present FISHtoFigure, a new software tool developed specifically for the analysis of mRNA abundance and co-expression in QuPath-quantified, multi-labelled smFISH data. FISHtoFigure facilitates the automated spatial analysis of transcripts of interest, allowing users to analyse populations of cells positive for specific combinations of mRNA targets without the need for bioinformatics expertise. As a proof of concept and to demonstrate the capabilities of this new research tool, we have validated FISHtoFigure in multiple biological systems. We used FISHtoFigure to identify an upregulation of T-cells in the spleens of mice infected with influenza A virus, before analysing more complex data showing crosstalk between microglia and regulatory B-cells in the brains of mice infected with Trypanosoma brucei brucei. These analyses demonstrate the ease of analysing cell expression profiles using FISHtoFigure and the value of this new tool in the field of smFISH data analysis.

bioinformatics↗

bioRxiv2023

Spatially-resolved single cell transcriptomics reveal a critical role for γδ T cells in the control of skin inflammation and subcutaneous adipose wasting during chronic Trypanosoma brucei infection

African trypanosome parasites colonise the skin in a process important for parasite transmission. However, how the skin responses to trypanosome infection remain unresolved. Here, using a combination of spatial and single cell transcriptomics, coupled with in vivo genetic models, we investigated the local immune response of the skin in a murine model of infection. First, we detected a significant expansion of IL-17A-producing {gamma}{delta} T cells (primarily V{gamma}6+) in the infected murine skin compared to naive controls that occur mainly in the subcutaneous adipose tissue. Second, interstitial preadipocytes located in the subcutaneous adipose tissue upregulate several genes involved in inflammation and antigen presentation, including T cell activation and survival. In silico cell-cell communication suggests that adipocytes trigger {gamma}{delta} T cell activation locally via Cd40, Il6, Il10, and Tnfsf18 signalling, amongst others. Third, mice deficient in IL-17A-producing {gamma}{delta} T cells show extensive inflammation, increased frequency of skin-resident IFN{gamma}-producing CD8+ T cells and limited subcutaneous adipose tissue wasting compared to wild-type infected controls, independent of TH1 CD4+ T cells and parasite burden. Based on these observations, we proposed a model whereby adipocytes as well as V{gamma}6+ cells act concertedly in the subcutaneous adipose tissue to limit skin inflammation and tissue wasting. These studies shed light onto the mechanisms of {gamma}{delta} T cell-mediated immunity in the skin in the context of African trypanosome infection, as well as a potential role of immature and mature adipocytes as homeostatic regulators in the skin during chronic infection.

immunology↗

bioRxiv2022

Genome-wide libraries for protozoan pathogens drug target screening using yeast surface display

The lack of genetic tools to manipulate protozoan pathogens has limited the use of genome-wide approaches to identify drug or vaccine targets and understand these organisms biology. We have developed an efficient method to construct genome-wide libraries for yeast surface display (YSD) and developed a YSD fitness screen (YSD-FS) to identify drug targets. We show the robustness of our method by generating genome-wide libraries for Trypanosoma brucei, Trypanosoma cruzi, and Giardia lamblia parasites. Each library has a diversity of [~]105 to 106 clones, representing [~]6 to 30-fold of the parasites genome. Nanopore sequencing confirmed the libraries genome coverage with multiple clones for each parasite gene. Western blot and imaging analysis confirmed surface expression of the G. lamblia library proteins in yeast. Using the YSD-FS assay, we identified bonafide interactors of metronidazole, a drug used to treat protozoan and bacterial infections. We also found enrichment in nucleotide-binding domain sequences associated with yeast increased fitness to metronidazole, indicating that this drug might target multiple enzymes containing nucleotide-binding domains. The libraries are valuable biological resources for discovering drug or vaccine targets, ligand receptors, protein-protein interactions, and pathogen-host interactions. The library assembly approach can be applied to other organisms or expression systems, and the YSD-FS assay might help identify new drug targets in protozoan pathogens.

microbiology↗

bioRxiv2022

Integrative single cell and spatial transcriptomic analysis reveal reciprocal microglia - plasma cell crosstalk in the mouse brain during chronic Trypanosoma brucei infection

Human African trypanosomiasis, or sleeping sickness, is caused by the protozoan parasite Trypanosoma brucei and induces profound reactivity of glial cells and neuroinflammation when the parasites colonise the central nervous system. However, the transcriptional and functional responses of the brain to chronic T. brucei infection remain poorly understood. By integrating single cell and spatial transcriptomics of the mouse brain, we identified that glial responses triggered by infection are readily detected in the proximity to the circumventricular organs, including the lateral and 3rd ventricle. This coincides with the spatial localisation of both slender and stumpy forms of T. brucei. Furthermore, in silico predictions and functional validations led us to identify a previously unknown crosstalk between homeostatic Cx3cr1+ microglia and Cd138+ plasma cells mediated by IL-10 and B cell activating factor (BAFF) signalling. This study provides important insights and resources to improve understanding of the molecular and cellular responses in the brain during infection with African trypanosomes.

pathology↗