Biology subjects

Humphreys, D.

Publications and source records attributed to Humphreys, D..

5 recordsLinked to original sources

bioRxiv2026

Repurposing clofarabine against enteric pathogens via metabolic starvation

Enteropathogenic and enterohaemorrhagic Escherichia coli (EPEC/EHEC) cause severe global diarrhoeal disease, exacerbated by rising antimicrobial resistance. Pathogenesis relies on "attaching and effacing" lesions, where bacteria generate actin pedestals to adhere, replicate, and destroy intestinal microvilli. To identify novel anti-virulence candidates targeting this process, we conducted a high-throughput phenotypic screen quantifying pedestal formation via high-content fluorescence microscopy. We identified the anticancer nucleotide analogue clofarabine as a potent inhibitor of EPEC growth and pathogenesis. Distinct from its oncology mechanism - inducing DNA chain termination and apoptosis - clofarabine competes with bacterial ATP-dependent processes to impede gene transcription, protein synthesis, and Type III Secretion System (T3SS) function. Remarkably, EPEC counteracts this inhibition by cleaving clofarabine, enabling restored protein synthesis and resumed growth. Furthermore, we report for the first time that clofarabine suppresses protein translation in human monocytes, suggesting an uncharacterised translational impact on mammalian cells. These findings reveal host and bacterial translation as interconnected vulnerabilities to purine antimetabolites, offering a novel strategy to disarm enteric pathogens while uncovering a bacterial enzymatic mechanism for neutralizing host-targeted therapeutics.

microbiology↗

bioRxiv2025

Typhoid toxin of Salmonella enterica induces ISG15 response mediating host cell survival and bacterial dissemination

The typhoid toxin is a secreted virulence factor of typhoidal serovars of the bacterial pathogen Salmonella enterica implicated in typhoid fever and chronic infections. The toxin causes a DNA damage response in human cells, characterised by cell-cycle arrest and cellular distension, resulting in cellular senescence and increased bacterial burden. To better understand host responses to typhoid toxin, we performed a transcriptomic analysis of intoxicated host cells and found that the toxin induced expression of genes relating to the type-I interferon response, including the ubiquitin-like protein ISG15. ISG15 was upregulated in a STING-dependent manner, reduced bacterial burden, and was found to be critical to host cell survival in response to the typhoid toxin and purified interferon. This highlights ISG15 as an important component of the host cell defence to the typhoid toxin.

microbiology↗

bioRxiv2024

Typhoid toxin of Salmonella Typhi elicits host antimicrobial response during acute typhoid fever

Salmonella Typhi secretes typhoid toxin that activates cellular DNA damage responses (DDR) during acute typhoid fever. Human infection challenge studies revealed that the toxin suppresses bacteraemia via unknown mechanisms. Using quantitative proteomic analysis on the plasma of bacteraemic participants, we demonstrate that wild-type toxigenic Salmonella induced secretion of lysozyme (LYZ) and apolipoprotein C3 (APOC3). Recombinant typhoid toxin or infection with toxigenic Salmonella recapitulate LYZ and APOC3 secretion in cultured cells, which involved ATM/ATR-dependent DDRs and confirmed observations in typhoid fever. LYZ alone inhibited secretion of virulence effector proteins SipB and SopE. LYZ caused loss of Salmonella morphology characterised by spheroplast formation. Spheroplast formation was mediated by LYZ and enhanced by lactoferrin, which was identified by proteomics in participants with typhoid fever. Our findings may indicate that toxin-induced DDRs elicit antimicrobial responses, which suppress Salmonella bacteraemia during typhoid fever.

microbiology↗

bioRxiv2022

Typhoid toxin hijacks Wnt5a to potentiate TGFβ-mediated senescence and Salmonella infection

Damage to our genome causes acute senescence in mammalian cells, which undergo growth arrest and release a secretome that elicits cell cycle arrest in bystander cells through the senescence-associated secretory phenotype (SASP). Thus, acute senescence is a powerful tumour suppressor. Salmonella enterica hijacks senescence through its typhoid toxin, which usurps unidentified factors in the stress secretome of senescent cells to mediate intracellular infections. Here, transcriptomics of toxin-induced senescent cells (txSCs) and proteomics of their secretome identified secreted ligands that activate the TGF{beta} pathway through SMAD transcription factors. The ligand Wnt5a established a self-amplifying positive feedback loop driving TGF{beta} signalling, which enforced autocrine senescence in txSCs and paracrine senescence in naive bystander cells by activation of DDRs. Wnt5a and GDF15 increased host cell susceptibility to infection. The study reveals how an innate defence against cancer is co-opted by a bacterial pathogen to cause widespread damage and mediate infections.

cell biology↗

bioRxiv2019

Sierra: Discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

High-throughput single-cell RNA-seq (scRNA-seq) is a powerful tool for studying gene expression in single cells. Most current scRNA-seq bioinformatics tools focus on analysing overall expression levels, largely ignoring alternative mRNA isoform expression. We present a computational pipeline, Sierra, that readily detects differential transcript usage from data generated by commonly used polyA-captured scRNA-seq technology. We validate Sierra by comparing cardiac scRNA-seq cell-types to bulk RNA-seq of matched populations, finding significant overlap in differential transcripts. Sierra detects differential transcript usage across human peripheral blood mononuclear cells and the Tabula Muris, and 3UTR shortening in cardiac fibroblasts. Sierra is available at https://github.com/VCCRI/Sierra.

bioinformatics↗