Biology subjects

Welch, G.

Publications and source records attributed to Welch, G..

6 recordsLinked to original sources

bioRxiv2026

R-pyocin-mediated selection reverses pan-drug resistance in Pseudomonas aeruginosa

The global escalation of antibiotic resistance is a critical threat necessitating the development of innovative strategies to provide new therapeutic options and restore the efficacy of conventional drugs. Pseudomonas aeruginosa exemplifies this challenge by utilizing a robust genomic resistome to persist in clinical settings. Here, we demonstrate that R-pyocins (phage-like bactericidal particles) can be leveraged not merely as conventional biocides, but as precise selective forces to drive an evolutionary "checkmate" strategy. We subjected the laboratory strains PAO1 and PAK and the clinical pan-drug-resistant (PDR) wound isolate MRSN 6220 to R-pyocin selective pressure. To evade R-pyocins targeting the host lipopolysaccharide (LPS) core, resistance consistently emerges through large-scale chromosomal deletions spanning 250-388 kbp. Crucially, these deletions encompass a conserved region harboring the galU gene (essential for LPS synthesis), the hmgA gene (yielding a pyomelanogenic brown phenotype), and the mexXYZ multidrug efflux operon. While the loss of galU confers broad cross-resistance to R-pyocins by likely truncating the LPS receptor, the concurrent excision of mexXY induces profound collateral sensitivity to aminoglycosides. Furthermore, these large deletions systematically eliminate critical virulence factors and biofilm clusters, including the hcnABC, exoY, phzABCDEFG, and cup operons. In Galleria mellonella and murine chronic wound models, the resulting brown mutants were rendered non-lethal and exhibited a significant 3-log reduction in bacterial load following gentamicin treatment. Ultimately, this work establishes a framework for utilizing R-pyocins as potent evolutionary steering agents to force the predictable reversion of multidrug resistance into an attenuated, biofilm-deficient, and clinically manageable state. Significance StatementPan-drug-resistant (PDR) pathogens demand novel strategies that both kill and restore antibiotic efficacy. Here, we describe an evolutionary checkmate for Pseudomonas aeruginosa, where selection for R-pyocin resistance drives large-scale ([~]300 kb) chromosomal remodeling. Although these deletions confer R-pyocin immunity via loss of the galU gene, they simultaneously collapse the pathogens virulence and defense. Crucially, the excision of the mexXY efflux operon resensitizes PDR strains to conventional aminoglycosides, while the collateral loss of critical virulence and biofilm clusters abrogates pathogenesis. By coupling resistance acquisition to substantial fitness costs, our work establishes a framework for using R-pyocins to force predictable evolutionary trade-offs, driving the reversion of multidrug resistance to an attenuated, biofilm-deficient, and clinically manageable state.

microbiology↗

bioRxiv2026

A field method to optimize dried blood spot sampling for mercury biomonitoring

O_LIHeavy metals are pervasive environmental contaminants that can impair the health of organisms globally. As the largest anthropogenic source of the potent neurotoxin mercury (Hg), gold mining has amplified these threats throughout the tropics. Consequently, there is a mounting need to monitor Hg contamination of the richest biological communities on Earth. Venous whole blood provides a reliable, nonlethal measurement of recent dietary and site-derived contamination, but collecting and cold-storing samples can be impractical in field conditions. C_LIO_LITo overcome these challenges, we developed and evaluated a method to assay Hg exposure in vascular organisms by measuring the volume of dried blood spots (DBS) in the field, which can be stored at ambient temperatures until analysis. We explored the methods precision and accuracy in estimating whole blood Hg concentrations by collecting paired whole blood and DBS aliquots from birds (n = 527 individuals, 140 species) along a trophic gradient (i.e., granivores to piscivores) in Belize and Peru. C_LIO_LIUsing a Bayesian linear mixed-effects model, we found a highly precise and unbiased relationship between DBS and whole blood total Hg concentrations that was centered at perfect unity (R2 = 0.99; {beta} = 1.00 {+/-} 0.03; 95% CrI: 0.95-1.05). Agreement between individual paired aliquots was more variable, in which approximately 12% of DBS containing at least 1 ng THg differed from whole blood by more than {+/-}20%. However, DBS accuracy increased at higher THg concentrations, suggesting that disagreement at low concentrations is an expected consequence of higher measurement error near the analytical limit of detection of our instruments. C_LIO_LICompared to whole-blood collection and analysis workflows, DBS offer substantial logistical advantages by eliminating cold-chain dependence and reducing transport burden, laboratory handling time, and overall operational costs. Consequently, volume-measured DBS provide a practical and highly reliable alternative for monitoring Hg contamination in both humans and wildlife, particularly for ecological and population-level applications in remote and resource-limited environments. C_LI

pharmacology and toxicology↗

bioRxiv2025

Genome-wide CRISPR screen reveals Wnt signaling defects regulate lipid accumulation in APOE4 oligodendrocytes

APOE4 is the largest genetic risk factor for late-onset Alzheimers disease, but the cellular mechanisms by which APOE variants influence risk of disease remain incompletely understood. We have previously found that APOE4 expression led to the intracellular accumulation of lipid droplets in oligodendrocytes, causing decreased myelination. However, the mechanisms by which APOE4 alters lipid metabolism are not fully understood. Here, we leveraged a genome-wide CRISPR screen and ATAC-sequencing in human induced pluripotent stem cell (iPSC)-derived oligodendrocytes to dissect APOE4s lipid-associated mechanisms of action. Using these approaches, we identified decreased Wnt signaling, and overactive GSK3b activity, as regulators of lipid droplet accumulation in oligodendrocytes. Genetic and pharmacological inhibition of GSK3b reduced lipid droplets in APOE4 oligodendrocytes, and increased myelination in three-dimensional iPSC-derived brain organoids. Finally, we show that pharmacological inhibition of GSK3b reduces lipid droplets and improves myelination in APOE4;PS19 Tau transgenic mice. Together, our results provide a framework for understanding the mediation of APOE4-related changes to oligodendrocyte lipid metabolism and myelination.

neuroscience↗

bioRxiv2023

A single-cell atlas of ABCA7 loss-of-function reveals lipid disruptions, mitochondrial dysfunction and DNA damage in neurons

Loss-of-function (LoF) variants in the lipid transporter ABCA7 significantly increase Alzheimers disease risk (odds ratio {approx} 2), yet the underlying pathogenic mechanisms and specific neural cell types affected remain unclear. To investigate this, we generated a single-nucleus RNA sequencing atlas of 36 human postmortem prefrontal cortex samples, including 12 carriers of ABCA7 LoF variants and 24 matched non-carriers. ABCA7 LoF variants were associated with transcriptional changes across all major neural cell types. Excitatory neurons, which expressed the highest levels of ABCA7, showed significant alterations in oxidative phosphorylation, lipid metabolism, DNA damage responses, and synaptic signaling pathways. ABCA7 LoF-associated transcriptional changes in neurons were similarly perturbed in carriers of the common AD missense variant ABCA7 p.Ala1527Gly (n = 240 controls, 135 carriers) predicted by molecular dynamic simulations to disrupt ABCA7 structure -, indicating that findings from our study may extend to large portions of the at-risk population. Human induced pluripotent stem cell (iPSC)-derived neurons carrying ABCA7 LoF variants closely recapitulated the transcriptional changes observed in human postmortem neurons. Biochemical experiments further demonstrated that ABCA7 LoF disrupts mitochondrial membrane potential via regulated uncoupling, increases oxidative stress, and alters phospholipid homeostasis in neurons, notably elevating saturated phosphatidylcholine levels. Supplementation with CDP-choline to enhance de novo phosphatidylcholine synthesis effectively reversed these transcriptional changes, restored mitochondrial uncoupling, and reduced oxidative stress. Additionally, CDP-choline normalized amyloid-{beta} secretion and alleviated neuronal hyperexcitability in ABCA7 LoF neurons. This study provides a detailed transcriptomic profile of ABCA7 LoF-induced changes and highlights phosphatidylcholine metabolism as a key driver in ABCA7-induced risk. Our findings suggest a promising therapeutic approach that may benefit a large proportion of individuals at increased risk for Alzheimers disease.

neuroscience↗

bioRxiv2022

Lipid Accumulation Induced by APOE4 Impairs Microglial Surveillance of Neuronal-Network Activity

Apolipoprotein E4 (APOE4) is the greatest known genetic risk factor for developing late- onset Alzheimers disease and its expression in microglia is associated with pro- inflammatory states. How the interaction of APOE4 microglia with neurons differs from microglia expressing the disease-neutral allele APOE3 is currently unknown. Here, we employ CRISPR-edited induced pluripotent stem cells (iPSCs) to dissect the impact of APOE4 in neuron-microglia communication. Our results reveal that APOE4 induces a distinct metabolic program in microglia that is marked by the accumulation of intracellular neutral lipid stores through impaired lipid catabolism. Importantly, this altered lipid-accumulated state shifts microglia away from homeostatic surveillance and renders APOE4 microglia weakly responsive to neuronal activity. By examining the transcriptional signatures of APOE3 versus APOE4 microglia before and after exposure to neuronal conditioned media, we further established that neuronal soluble cues differentially induce a lipogenic program in APOE4 microglia that exacerbates pro- inflammatory signals. Pharmacological blockade of lipogenesis in APOE4 microglia is sufficient to diminish intracellular lipid accumulation and restore microglial homeostasis. Remarkably, unlike APOE3 microglia that support neuronal network activity, co-culture of APOE4 microglia with neurons disrupts the coordinated activity of neuronal ensembles. We identified that through decreased uptake of extracellular fatty acids and lipoproteins, APOE4 microglia disrupts the net flux of lipids which results in decreased neuronal activity via the potentiation of the lipid-gated K+ channel, GIRK3. These findings suggest that neurological diseases that exhibit abnormal neuronal network-level disturbances may in part be triggered by impairment in lipid homeostasis in non-neuronal cells, underscoring a novel therapeutic route to restore circuit function in the diseased brain. O_FIG O_LINKSMALLFIG WIDTH=166 HEIGHT=200 SRC="FIGDIR/small/484146v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@4d4a9corg.highwire.dtl.DTLVardef@5d888corg.highwire.dtl.DTLVardef@afa191org.highwire.dtl.DTLVardef@984340_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2020

Cell type-specific histone acetylation profiling of Alzheimer's Disease subjects and integration with genetics

We profile genome-wide histone 3 lysine 27 acetylation (H3K27ac) of 3 major brain cell types from hippocampus and dorsolateral prefrontal cortex (dlPFC) of subjects with and without Alzheimers Disease (AD). We confirm that single nucleotide polymorphisms (SNPs) associated with late onset AD (LOAD) prefer to reside in the microglial histone acetylome, which varies most strongly with age. We observe acetylation differences associated with AD pathology at 3,598 peaks, predominantly in an oligodendrocyte-enriched population. Strikingly, these differences occur at the promoters of known early onset AD (EOAD) risk genes (APP, PSEN1, PSEN2, BACE1), late onset AD (LOAD) risk genes (BIN1, PICALM, CLU, ADAM10, ADAMTS4, SORL1 and FERMT2), and putative enhancers annotated to other genes associated with AD pathology (MAPT). More broadly, acetylation differences in the oligodendrocyte-enriched population occur near genes in pathways for central nervous system myelination and oxidative phosphorylation. In most cases, these promoter acetylation differences are associated with differences in transcription in oligodendrocytes. Overall, we reveal deregulation of known and novel pathways in AD and highlight genomic regions as therapeutic targets in oligodendrocytes of hippocampus and dlPFC.

genetics↗