Biology subjects

Smith, D. P.

Publications and source records attributed to Smith, D. P..

6 recordsLinked to original sources

bioRxiv2026

Hypoxia-activated prodrug and chemotherapy disrupt resistance-associated metabolism in osteosarcoma

Chemotherapy resistance remains a critical barrier in treating osteosarcoma. Hypoxia-activated prodrugs (HAPs) target oxygen-deprived tumor regions that evade conventional chemotherapy. Here, we applied integrated spatial multimodal mass spectrometry imaging of metabolites (DESI-MSI, MALDI-MSI), targeted proteomics (IMC), and metallomics (LA-ICP-MSI) to naive and newly developed doxorubicin-resistant osteosarcoma spheroids treated with a novel HAP tirapazamine analogue, TPZ-A-X, and doxorubicin. Combination treatment selectively downregulated GLUT1 and suppressed pro-survival pAkt in doxorubicin-resistant spheroids whilst inducing comparable DNA damage ({gamma}H2AX) across both phenotypes. Metabolomics imaging identified ferroptosis pathway suppression in doxorubicin resistance, which combination treatment reversed, whilst simultaneously depleting glycolytic fuels. Integrative protein-metabolite correlation analysis uncovered functional couplings between glucose transport and CoA-dependent metabolism and spatially revealed anabolic signaling at spheroid peripheries. Combination treatment induced endogenous copper, zinc and magnesium depletion, independent of ATP/ADP collapse reflecting an adaptive survival remodeling of the metalloproteome. HAP/chemotherapy combinations exploit metabolic vulnerabilities via coordinated disruption of ferroptosis suppression, glycolytic dependence, and survival pathways underlying apoptotic resistance. These findings demonstrate a framework for informing mechanistic reasoning and combination strategy design in chemotherapy-resistant tumors.

cancer biology↗

bioRxiv2024

Evolutionary genomics reveals variation in structure and genetic content implicated in virulence and lifestyle in the genus Gaeumannomyces

Gaeumannomyces tritici is responsible for take-all disease, one of the most important wheat root threats worldwide. High-quality annotated genome resources are sorely lacking for this pathogen, as well as for the closely related antagonist and potential wheat take-all biocontrol agent, G. hyphopodioides. As such, we know very little about the genetic basis of the interactions in this host-pathogen-antagonist system. Using PacBio HiFi sequencing technology we have generated nine near-complete assemblies, including two different virulence lineages for G. tritici and the first assemblies for G. hyphopodioides and G. avenae (oat take-all). Genomic signatures support the presence of two distinct virulence lineages in G. tritici (types A and B), with A strains potentially employing a mechanism to prevent gene copy-number expansions. The CAZyme repertoire was highly conserved across Gaeumannomyces, while candidate secreted effector proteins and biosynthetic gene clusters showed more variability and may distinguish pathogenic and non-pathogenic lineages. A transition from self-sterility (heterothallism) to self-fertility (homothallism) may also be a key innovation implicated in lifestyle. We did not find evidence for transposable element and effector gene compartmentalisation in the genus, however the presence of Starship giant transposable elements likely contributes to genomic plasticity in the genus. Our results depict Gaeumannomyces as an ideal system to explore interactions within the rhizosphere, the nuances of intraspecific virulence, interspecific antagonism, and fungal lifestyle evolution. The foundational genomic resources provided here will enable the development of diagnostics and surveillance of understudied but agriculturally important fungal pathogens.

evolutionary biology↗

bioRxiv2023

Exploring the family feud: a fungal endophyte induces local cell wall-mediated resistance in wheat roots against the closely related "take-all" pathogen

Take-all disease, caused by the ascomycete fungus Gaeumannomyces tritici, is one of the most important root diseases of wheat worldwide. The fungus invades the roots and destroys the vascular tissue, hindering the uptake of water and nutrients. Closely related non-pathogenic species in the Magnaporthaceae family, such as Gaeumannomyces hyphopodioides, occur naturally in arable and grassland soils and have previously been reported to reduce take-all disease in field studies. However, the mechanism of take-all protection has remained unknown. Here, we characterise the root infection biologies of G. tritici and G. hyphopodioides in wheat. We investigate the ultrastructure of previously described "subepidermal vesicles" (SEVs), produced in wheat roots by non-pathogenic G. hyphopodioides, but not by pathogenic G. tritici. We show that G. hyphopodioides SEVs share key characteristics of fungal resting structures; containing a greater number of putative lipid bodies and a significantly thickened cell wall compared to infection hyphae. We demonstrate that take-all control is achieved via local but not systemic host changes in response to prior G. hyphopodioides root colonisation. A time-course wheat RNA sequencing analysis revealed extensive transcriptional reprogramming in G. hyphopodioides colonised tissues, characterised by a striking downregulation of key cell-wall related genes, including cellulose synthase (CESA), and xyloglucan endotransglucosylase/hydrolase (XTH) genes. In the absence of take-all resistant wheat cultivars or non-virulent G. tritici strains, studying closely related non-pathogenic G. hyphopodioides provides a much-needed avenue to elucidate take-all resistance mechanisms in wheat.

plant biology↗

bioRxiv2023

Phage-bacteria dynamics during the first years of life revealed by trans-kingdom marker gene analysis

Humans are colonized with commensal bacteria soon after birth, and, while this colonization is affected by lifestyle and other factors, bacterial colonization proceeds through well-studied phases. However, less is known about phage communities in early human development due to small study sizes, inability to leverage large databases, and lack of appropriate bioinformatics tools. In this study, whole genome shotgun sequencing data from the TEDDY study, composed of 12,262 longitudinal samples from 887 children in 4 countries, is reanalyzed to assess phage and bacterial dynamics simultaneously. Reads from these samples were mapped to marker genes from both bacteria and a new database of tens of thousands of phage taxa from human microbiomes. We uncover that each child is colonized by hundreds of different phages during the early years, and phages are more transitory than bacteria. Participants samples continually harbor new phage species over time whereas the diversification of bacterial species begins to saturate. Phage data improves the ability for machine learning models to discriminate samples by country. Finally, while phage populations were individual-specific, striking patterns arose from the larger dataset, showing clear trends of ecological succession amongst phages, which correlated well with putative host bacteria. Improved understanding of phage-bacterial relationships may reveal new means by which to shape and modulate the microbiome and its constituents to improve health and reduce disease, particularly in vulnerable populations where antibiotic use and/or other more drastic measures may not be advised.

microbiology↗

bioRxiv2021

A point mutation in the kinase domain of CRK10 leads to xylem vessel collapse and activates defence responses

Cysteine-rich receptor-like kinases (CRKs) are a large family of plasma membrane-bound receptors ubiquitous in higher plants. They are transcriptionally regulated by a wide variety of environmental cues and stresses, however their precise biological roles remain largely unknown. Here we report a novel mutant isolated for the CYSTEINE-RICH RECEPTOR-LIKE KINASE 10 (CRK10) of Arabidopsis thaliana which harbours the substitution of alanine 397 by a threonine in the C-helix of its kinase domain and which we registered as crk10-A397T in the community database. In situ phosphorylation assays with the His-tagged wild type (WT) and crk10-A397T versions of the CRK10 kinase domain revealed that both alleles are active kinases capable of auto-phosphorylation with the newly introduced threonine acting as an additional phosphorylation site in crk10-A397T. Phenotypically the mutant is a dwarf and the analysis of thin cross sections with light and transmission electron microscopy revealed that collapsed xylem vessels in roots and hypocotyls are very likely the cause for this reduction in stature. Transcriptomic analysis of WT and mutant hypocotyls revealed that predominantly biotic and abiotic stress-responsive genes are constitutively up-regulated in the mutant. Root-infection assays with the vascular pathogen Fusarium oxysporum demonstrated that the crk10-A397T mutant has enhanced resistance to this pathogen compared to WT plants. Taken together our results suggest that crk10-A397T is a gain-of-function allele of CRK10 and open up new avenues for the investigation of this elusive receptor-like kinase family.

plant biology↗

bioRxiv2018

The Division of Amyloid Fibrils

The division of amyloid protein fibrils is required for the propagation of the amyloid state, and is an important contributor to their stability, pathogenicity and normal function. Here, we combine kinetic nano-scale imaging experiments with analysis of a mathematical model to resolve and compare the division stability of amyloid fibrils. Our theoretical results show that the division of any type of filament is uniquely described by a set of three characteristic properties, resulting in convergence to self-similar length distributions distinct to each fibril type and conditions applied. By applying these results to profile the dynamical stability towards breakage for four different amyloid types, we reveal particular differences in the division properties of disease-related amyloid formed from alpha-synuclein compared with non-disease associated model amyloid, the former showing lowered intrinsic stability towards breakage and increased likelihood of shedding smaller particles. Our results enable the comparison of protein filaments intrinsic dynamic stabilities, which are key to unravelling their toxic and infectious potentials.

biophysics↗