Biology subjects

Ahmed, H.

Publications and source records attributed to Ahmed, H..

At least 19 recordsLinked to original sources

bioRxiv2026

PFKFB3 inhibition restores β-cell responsiveness to acetylcholine in a 3xTg-AD pancreatic tissue-slice mode

The glycolytic regulator PFKFB3 supports dysfunctional {beta}-cell states, but its role in pancreatic Ca2+ signaling remains unclear. We examined responses to PFKFB3 inhibitors (AZ67, AZ26) in pancreatic tissue slices from aged 3xTg-AD mice, a model of Alzheimer's disease that develops impaired glucose tolerance and diabetes as comorbidity. Compared to wild-type controls, {beta}-cells showed weaker glucose-stimulated and acetylcholine-potentiated Ca2+ activity, accompanied by increased nuclear PFKFB3 positivity in insulin-defined islet-cell populations, used here as a PFKFB3-associated stress-state marker. During glucose and acetylcholine stimulation, AZ67 increased {beta}-cell Ca2+ event frequency while maintaining short events. In neighboring acinar cells, PFKFB3 inhibitor exposure was followed by renewed oscillations after acetylcholine-evoked activity had waned. {beta}-cell recruitment was preserved during adrenergic inhibition, and enhanced activity persisted after inhibitor withdrawal, although these recordings were exploratory and residual tissue drug exposure could not be excluded. An effect that survives both drug removal and adrenergic opposition identifies a Ca2+ signaling phenotype in 3xTg-AD {beta}-cells that is acutely inducible yet not transient, and establishes PFKFB3 as a regulator of muscarinic responsiveness in the stressed {beta}-cell.

physiology↗

bioRxiv2026

Cross-Sectional Physiological and Neuromuscular Profiling of Elite and Recreational University Badminton Athletes: Preliminary Benchmarks for Exercise-Based Injury Risk Stratification

Background and PurposeBadminton imposes considerable cardiovascular and musculoskeletal stress. Physiological profiling can identify modifiable injury risk factors and inform exercise-based prevention and rehabilitation. This study compared cardiovascular recovery, neuromuscular activation, and limb strength between elite and recreational male university badminton players to derive preliminary physiological benchmarks for injury risk stratification and exercise rehabilitation guidance. MethodsForty male athletes (20 elite: national/university representatives with [≥]5 years of competitive experience; 20 recreational: <3 years of experience) completed assessments of heart rate recovery (HRR), biceps brachii surface electromyography (sEMG; SENIAM protocol), handgrip strength (JAMAR dynamometry), and maximal bodyweight squat repetitions. Independent-sample t-tests with Cohens d ( = 0.05) and Pearson correlations were applied. ResultsElite players demonstrated significantly greater handgrip strength (49.00{+/-}6.12 vs. 39.00{+/-}5.45 kg, p = 0.001, d = 1.72) and lower-limb (LL) strength (60.35{+/-}11.29 vs. 41.75{+/-}6.72 repetitions, p < 0.001, d = 1.96). Normalized sEMG root mean square (RMS) was higher in elite athletes during flexion (11.56{+/-}4.16% vs. 7.26{+/-}5.15%, p = 0.004, d = 0.94) and extension (12.67{+/-}4.56% vs. 7.85{+/-}5.73%, p = 0.003, d = 0.94). HRR did not differ significantly between groups (p = 0.17, d = 0.43, observed power = 0.34). Elite players nonetheless showed a more favorable recovery distribution. sEMG -HRR correlations were weak and non-significant in both groups. ConclusionsElite badminton players exhibit a distinct physiological profile of greater strength and more efficient neuromuscular activation. These preliminary cross-sectional findings may support the design of exercise-based injury-prevention and rehabilitation in university badminton.

biophysics↗

bioRxiv2026

Structure-guided generative design of peptides targeting the FtsQBL divisome complex inhibit Escherichia coli cell division.

The discovery of antibiotics targeting Gram-negative bacteria remains limited in part by the difficulty of pharmacologically modulating protein-protein interactions essential for bacterial physiology. The divisome complex formed by FtsQ, FtsB and FtsL represents an attractive but challenging target, as its assembly relies on {beta}-strand-mediated interface interactions within the bacterial periplasm. Here, we combined interpretable interface mapping using InDeep with hotspot-constrained RFdiffusion design to generate peptides targeting the FtsB-binding site of Escherichia coli FtsQ. The designed peptides mimic the native {beta}-augmentation interaction and selectively engage the FtsQ interface both in bacterial cells and in vitro. X-ray crystallography of one of these peptides in complex with FtsQ reveals that it accurately adopts the native binding geometry while introducing additional stabilizing interactions within a hydrophobic pocket. Complementary NMR analyses further show that optimized peptides adopt pre-organized {beta}-hairpin conformations in solution consistent with the bound state. Several of these peptides disrupt bacterial cell division and inhibit growth in an E. coli strain exhibiting increased outer membrane permeability. Together, these results establish a structurally validated framework in which predictive interface analysis and generative design can be combined to target cooperative protein-protein interfaces in bacteria and provide a foundation for the development of divisome-targeting antibacterial strategies.

microbiology↗

bioRxiv2026

L-pentahomoserine correlates with therapy outcome in esophageal cancer and promotes metabolic adaptations that support cell survival under nutrient-deprived conditions

Esophageal adenocarcinoma (EAC) is the sixth-leading cause of cancer-related death. Although pyrimidine analogue-based neoadjuvant and adjuvant therapies are widely used, patient responses remain variable. Emerging evidence indicates that bacteria-derived metabolites influence tumor biology and therapy outcomes. To identify non-canonical plasma metabolites linked to cancer biology, we performed correlation analyses between untargeted metabolomics profiles and overall survival. This approach revealed a bacterial metabolite called L-pentahomoserine, or L-2-amino-5-hydroxypentanoic acid (L-2A5HPA), to be positively associated with overall survival. Notably, L-2A5HPA promoted cell survival under nutrient limitation by redirecting glucose metabolism towards aspartate and pyrimidine biosynthesis. In vitro, L-2A5HPA uptake varied among cell lines and was controlled by stereospecific transporters. Furthermore, metabolic profiling in mouse models of liver cancer showed different levels of L-2A5HPA and a strong correlation with pyrimidine intermediates, dihydroorotate and orotate. The link between L-2A5HPA, pyrimidine nucleotide metabolism, and cell survival provides mechanistic insight into its association with patient outcome. Our findings position L-2A5HPA as a metabolite with potential to become a prognostic biomarker for EAC and underscores its role in metabolic adaptation under nutrient-deprived conditions.

cancer biology↗

bioRxiv2025

Advancing Knock-In Approaches for Robust Genome Editing in Zebrafish

Precise genome editing remains a major challenge in functional genomics, particularly for generating knock-in (KI) alleles in model organisms. Here, we introduce the mini-golden system, a versatile Golden Gate-based subcloning platform that enables rapid assembly of donor constructs containing homology arms and a gene of interest. This system offers a library of middle entry vectors including diverse genes, enhancing the preparation of donor minicircles for KI applications. Using the mini-golden system, we efficiently generated a foxd3CreER KI zebrafish line, allowing conditional recombination in neural crest cells. To further improve genome editing precision, we developed a synthetic exon-based donor template strategy combined with fluorescence screening. Using this approach, we successfully engineered a targeted isoleucine-to-valine substitution (Ile-to-Val) in hbaa1.2, one of the two adult hemoglobin alpha genes in zebrafish. Importantly, despite the high sequence similarity between hbaa1.2 and its paralog hbaa1.1, our strategy specifically edited hbaa1.2, demonstrating the effectiveness of the synthetic exon approach. This method minimized undesired recombination and significantly improved the identification of lines carrying the edited genome. Together, we provide a robust toolkit for efficient and precise genome engineering in zebrafish, with broad applicability to other model systems.

developmental biology↗

bioRxiv2025

Integrated microdroplet workflow for high-throughput cell-free transcription in double emulsion picoreactors

Precise characterization of regulatory sequence performance is fundamental to synthetic biology and next-generation gene therapies, driving the need for scalable and quantitative screening of genetic libraries. While droplet-based microfluidics offers the ultra-high throughput required to scale these assays, it often depends on complex, custom fluorescence-activated droplet sorting platforms. To address this limitation, we introduce an integrated microfluidic workflow that enables cell-free transcription in water-in-oil-in-water double emulsion picoreactors compatible with commercial flow cytometers. The core innovation is an integrated device that combines emulsion reinjection, electric-field-mediated step-injection of in vitro transcription (IVT) reagents, and downstream double emulsification, thereby reducing manual handling and preserving droplet integrity across multistep workflows. We validate the system by coupling isothermal rolling circle amplification (RCA) of DNA templates with on-chip IVT and Mango III aptamer-based fluorescence readout, demonstrating robust detection, binning, and sorting of transcription-active droplets. This workflow provides an accessible and modular platform for quantitative, high-throughput functional screening of regulatory sequences without the need for specialized optical sorting instrumentation.

synthetic biology↗

bioRxiv2025

Quantifying the role of pre-existing tissue resident cellular immunity in limiting respiratory virus transmission

Viral transmission from infected donors to uninfected recipients is the key event underlying the spread of viral pathogens at the level of a host population. Successful viral transmission from a donor to a recipient depends on several factors including the infectiousness of the donor. Donor infectiousness in turn can depend on the viral kinetics and viral load of the donor, donor behavior and symptoms, and donor immunity. Here, we use a mouse model of murine respirovirus (otherwise known as Sendai virus SeV) infection to quantitatively explore donor determinants of respiratory virus transmission. The experimental transmission studies we analyze are specifically designed to address the effect that pre-existing donor immunity may have on transmission potential by studying SeV transmission from both immunized and control (placebo-immunized) donors to naive recipients. We specifically focus on the impact of tissue resident memory (TRM) CD8 T cells on donor transmission potential by considering immunization strategies that primarily generate CD8 T cell immunity. Through quantitative analyses of these experiments, we find that pre-existing CD8 TRMs act to reduce donor transmission potential. This reduction can be in part explained by a reduction in total infection load in immunized donors. However, even once differences in infection load between immunized and control donors are accounted for, immunized donors still have reduced infectiousness relative to control donors. We explore possible reasons for this unexpected pattern using a mathematical model that integrates within-host viral dynamics and between-host transmission occurrences. Analysis of model simulations, along with observations from knock-out experiments, suggests that interferon gamma (IFN-{gamma}) may be partly responsible for the observed differences in infectiousness between control and pre-immune donors. Future experimental transmission studies should consider measuring IFN-{gamma} levels when interpreting transmission outcomes in the context of host immunity.

immunology↗

bioRxiv2025

Synaptic Dysfunction and Compensation After NMDA Receptor Ablation in the Mouse Medial Prefrontal Cortex

N-methyl-D-aspartate receptors (NMDARs) in the prefrontal cortex (PFC) are critical regulators of neuronal excitability, synaptic plasticity, and cognitive function. NMDAR disruptions, including pharmacological blockade and anti-NMDAR encephalitis, can mimic symptoms of schizophrenia. These observations support the glutamate hypothesis of schizophrenia, which posits that symptoms arise from abnormal corticolimbic glutamatergic signaling. Further evidence for this theory includes abnormal expression of NMDARs and decreased dendritic spine density in the PFC of individuals with schizophrenia, as well as altered spine density and synaptic transmission caused by genetic manipulation of NMDARs. However, it is unknown how progressive loss of NMDAR function in the PFC during adolescence - a developmental time period associated with significant synaptic pruning and symptom onset in schizophrenia - affects excitatory synaptic structure and function. In this study, we used in vivo genome editing to ablate expression of the Grin1 gene, which encodes the obligate GluN1 subunit of NMDARs, in medial PFC neurons of female and male adolescent mice. We assessed synaptic density and function in layer V pyramidal neurons at multiple time points using whole-cell patch-clamp electrophysiology, integrated with confocal imaging of dendritic spine architecture in recorded neurons. NMDAR ablation caused an early decrease in basilar dendritic spine density, followed by a rebound in spine density and corresponding increase in AMPAR-mediated synaptic transmission, suggesting that synaptic compensation maintains an allostatic set point. Our findings demonstrate that NMDAR ablation initially disrupts local PFC networks, followed by recovery via compensatory processes that could be impaired in disease states.

neuroscience↗

bioRxiv2025

Multi-site phosphorylation of BCL2L13 in a TBK1- and AMPK-dependent manner reveals new modes of mitophagy regulation

Mitophagy is a selective autophagic process that eliminates damaged mitochondria via lysosomal degradation, playing a crucial role in maintaining cellular metabolic balance. Mitophagy can occur through two pathways: ubiquitin-dependent and ubiquitin-independent. Recently, we and others have shown that, upon mitochondrial stress, AMP-activated protein kinase (AMPK) contributes to Parkin-mediated, ubiquitin-dependent mitophagy. The ubiquitin-independent pathway involves multiple outer mitochondrial membrane (OMM) "mitophagy receptors" that contain LC3-interacting region (LIR) motifs, including BNIP3, NIX/ BNIP3L, FUNDC1, and BCL2L13. LIR motifs bind Atg8/LC3 family proteins, facilitating the recruitment of the autophagosome membrane to target damaged mitochondria for degradation. The kinase Unc-51 Like autophagy activating kinase 1 (ULK1) phosphorylates the serine preceding the LIR motif in BNIP3, NIX, and FUNDC1, enhancing their binding to LC3 and promoting mitophagy. However, while BCL2L13 has been identified as a ULK1 binding partner, its regulation by phosphorylation remains unclear. We utilized mass spectrometry (MS) to map phosphorylation sites in BCL2L13 following mitochondrial stress and developed phospho-specific antibodies against two sites, Ser261 and Ser275, which were induced after exposure to the mitochondrial uncoupler, CCCP. Endogenous BCL2L13 Ser261 and Ser275 were both phosphorylated in an AMPK-dependent manner in cells and tissues. As neither site matches the established AMPK substrate consensus motif, we sought to identify which kinases directly mediate their phosphorylation downstream of AMPK. Surprisingly, genetic studies revealed that ULK1 is not regulating either site, but instead, TBK1 is controlling Ser275. This work reveals that BCL2L13 is unique amongst mitophagy receptors in being activated by mitochondrial stress and innate immune stimuli in an AMPK- and TBK1-dependent manner.

cell biology↗

bioRxiv2024

Blood metabolomic profiling reveals new targets in the management of psychological symptoms associated with alcohol use disorder

Alcohol use disorder (AUD) is a global health problem with limited therapeutic options. The biochemical mechanisms that lead to this disorder are not yet fully understood, and in this respect, metabolomics represents a promising approach to decipher metabolic events related to AUD. The plasma metabolome contains a plethora of bioactive molecules that reflects the functional changes in host metabolism but also the impact of the gut microbiome and nutritional habits. In this study, we investigated the impact of severe AUD (sAUD), and of a three-week period of alcohol abstinence, on the blood metabolome (non-targeted LC-MS metabolomics analysis) in 96 sAUD patients hospitalized for alcohol withdrawal. We found that the plasma levels of different lipids ((lyso)phosphatidylcholines, long-chain fatty acids), short-chain fatty acids (i.e. 3-hydroxyvaleric acid) and bile acids were altered in sAUD patients. In addition, several microbial metabolites, including indole-3-propionic acid, p-cresol sulfate, hippuric acid, pyrocatechol sulfate, and metabolites belonging to xanthine class (paraxanthine, theobromine and theophylline) were sensitive to alcohol exposure and alcohol withdrawal. 3-Hydroxyvaleric acid, caffeine metabolites (theobromine, paraxanthine and theophylline) and microbial metabolites (hippuric acid and pyrocatechol sulfate) were correlated with anxiety, depression and alcohol craving. Metabolomics analysis in post-mortem samples of frontal cortex and cerebrospinal fluid of those consuming a high level of alcohol revealed that those metabolites can be found also in brain tissue. Our data allow to for the identification of neuroactive metabolites, from interactions between food components and microbiota, which may represent new targets in the management of neuropsychiatric diseases such as sAUD.

neuroscience↗

bioRxiv2024

The integration of tandem gene repeats via a bacterial type-II toxin-antitoxin-mediated gene amplification (ToxAmp) system and stability visualisation in Saccharomyces cerevisiae

Tandem gene repeats naturally occur as important genomic features and determine many traits in living organisms, like human diseases and microbial productivities of target bioproducts. Here, we develop a bacterial type-II toxin-antitoxin-mediated method to manipulate genomic integration of tandem gene repeats in Saccharomyces cerevisiae and further visualise the evolutionary trajectories of gene repeats. We designed a tri-vector system to introduce toxin-antitoxin-driven gene amplification (ToxAmp) modules, and accidentally re-visited the high-level capacity of multi-fragment co-transformation in S. cerevisiae. This system delivered the multi-copy gene integration in the form of tandem gene repeats spontaneously and independently from toxin-antitoxin-mediated selection. Inducing the toxin (RelE) expressing via a copper (II)-inducible CUP1 promoter successfully drove the in-situ gene amplification of the antitoxin (RelB) module, resulting in [~]40 copies of a green fluorescence reporter (GFP) gene per copy of genome. The copy-number changes, increasing and decreasing, and stable maintenance were visualised using the GFP and blue chromoprotein AeBlue as reporters. Copy-number increasing happened spontaneously not depending on a selection pressure and was quickly enriched through toxin-antitoxin-mediated selection. In summary, the bacterial toxin-antitoxin systems provide a flexible mechanism to manipulate gene copy number in eukaryotic cells and can be exploited for synthetic biology and metabolic engineering applications. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/578080v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@75d1f3org.highwire.dtl.DTLVardef@12aafeforg.highwire.dtl.DTLVardef@184a1a5org.highwire.dtl.DTLVardef@90586a_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2023

Prodomain-driven enzyme dimerization, a potent pH-dependent autoinhibition mechanism to control Plasmodium Sub1 subtilisin-like activity prior to prime merozoite egress

Malaria symptoms are associated with the asexual multiplication of Plasmodium falciparum within human red blood cells (RBC) and fever peaks coincide with the egress of daughter merozoites following the rupture of the parasitophorous vacuole (PV) and the RBC membranes (RBC). Over the last two decades it has emerged that the release of competent merozoites is tightly regulated by a complex cascade of events, including the unusual multi- step activation mechanism of the pivotal subtilisin-like protease 1 (Sub1) that takes place in three different cellular compartments and remains poorly understood. Following an initial auto- maturation in the Endoplasmic Reticulum (ER) between its pro- and catalytic domains, the Sub1 prodomain (PD) undergo further cleavages by the parasite aspartic protease plasmepsin X (PmX) within acidic secretory organelles that ultimately lead to full Sub1 activation upon discharge into the parasitophorous vacuole (PV). Here we report the crystal structure of full- length P. falciparum Sub1 (PfS1FL) and demonstrate, through structural, biochemical and biophysical studies, that the atypical Plasmodium-specific Sub1 PD directly triggers the assembly of inactive enzyme homodimers at acidic pH, whereas Sub1 is primarily monomeric at neutral pH. Our results shed new light into the finely tuned Sub1 spatiotemporal activation during secretion, particularly the different compartmentalization of PmX processing and full Sub1 activation, and uncover a robust mechanism of pH-dependent subtilisin autoinhibition involved in the tight regulation of P. falciparum merozoites egress from host infected cells. SignificanceMalaria fever spikes are due to the rupture of infected erythrocytes, allowing the egress of Plasmodium sp. merozoites and further parasite propagation. This fleeting tightly regulated event involves a cascade of enzymes, culminating with the complex activation of the subtilisin- like protease 1, Sub1. Differently than other subtilisins, Sub1 activation strictly depends upon the processing by a parasite aspartic protease within acidic merozoite secretory organelles. However, Sub1 biological activity is requested in the pH neutral parasitophorous vacuole, to prime effectors involved in the rupture of the vacuole and erythrocytic membranes. Here we show that the unusual, parasite specific Sub1 prodomain is directly responsible for its acidic- dependent dimerization and autoinhibition, required for protein secretion, before its full activation at neutral pH in a monomeric form. pH-dependent Sub1 dimerization defines a novel, essential regulatory element involved in the finely tuned spatiotemporal activation of the egress of competent Plasmodium merozoites.

microbiology↗

bioRxiv2023

OCT5k: A dataset of multi-disease and multi-graded annotations for retinal layers

The thickness and appearance of retinal layers are essential markers for diagnosing and studying eye diseases. Despite the increasing availability of imaging devices to scan and store large amounts of data, analyzing retinal images and generating trial endpoints has remained a manual, error-prone, and time-consuming task. In particular, the lack of large amounts of high-quality labels for different diseases hinders the development of automated algorithms. Therefore, we have compiled 5016 pixel-wise manual labels for 1672 optical coherence tomography (OCT) scans featuring two different diseases as well as healthy subjects to help democratize the process of developing novel automatic techniques. We also collected 4698 bounding box annotations for a subset of 566 scans across 9 classes of disease biomarker. Due to variations in retinal morphology, intensity range, and changes in contrast and brightness, designing segmentation and detection methods that can generalize to different disease types is challenging. While machine learning-based methods can overcome these challenges, high-quality expert annotations are necessary for training. Publicly available annotated image datasets typically contain few images and/or only cover a single type of disease, and most are only annotated by a single grader. To address this gap, we present a comprehensive multi-grader and multi-disease dataset fortraining machine learning-based algorithms. The proposed dataset covers three subsets of scans (Age-related Macular Degeneration, Diabetic Macular Edema, and healthy) and annotations for two types of tasks (semantic segmentation and object detection).

bioengineering↗

bioRxiv2023

Structural characterization of a novel luciferase-like-monooxygenase from Pseudomonas meliae an in silico approach

BackgroundLuciferase is a well-known oxidative enzyme that produces bioluminescence. The Pseudomonas meliae is a plant pathogen that causes wood rot on nectarine and peach and possesses a luciferase-like monooxygenase. After activation, it produces bioluminescence, and the pathogens bioluminescence is a visual indicator of diseased plants. MethodsThe present study aims to model and characterize the luciferase-like monooxygenase protein in P. meliae for its similarity to well-established luciferase. In this study, the luciferase-like monooxygenase from P. meliae infects chinaberry plants has been modeled first and then studied by comparing it with existing known luciferase. Also, the similarities between uncharacterized luciferase from P. meliae and template from Geobacillus thermodenitrificans were analyzed to find the novelty of P. meliae. ResultsThe results suggest that the absence of bioluminescence in P. meliae could be due to the evolutionary mutation in positions 138 and 311. The active site remains identical except for two amino acids; P. meliae Tyr138 instead of His138 and Leu311 instead of His311. Therefore, the P. meliae will have a potential future application, and mutation of the residues 138 and 311 can be restored luciferase light-emitting ability. ConclusionsThis study will help further improve, activate, and repurpose the luciferase from P. meliae as a reporter for gene expression.

bioinformatics↗

bioRxiv2023

Deep Active Learning for Robust Biomedical Segmentation

Deep learning for medical applications faces many unique challenges. A major challenge is the large amount of labelled data for training, while working in a relatively data scarce environment. Active learning can be used to overcome the vast data need challenge. A second challenged faced is poor performance outside of a experimental setting, contrary to the high requirement for safety and robustness. In this paper, we present a novel framework for estimating uncertainty metrics and incorporating a similarity measure to improve active learning strategies. To showcase effectiveness, a medical image segmentation task was used as an exemplar. In addition to faster learning, robustness was also addressed through adversarial perturbations. Using epistemic uncertainty and our framework, we can cut number of annotations needed by 39% and by 54% using epistemic uncertainty and a similarity metric.

bioengineering↗

bioRxiv2022

O-GlcNAc transferase modulates formation of clathrin-coated pits

Clathrin-mediated endocytosis (CME) controls the internalization and function of a wide range of cell surface proteins. CME occurs by the assembly of clathrin and many other proteins on the inner leaflet of the plasma membrane into clathrin-coated pits (CCPs). These structures recruit specific membrane protein cargo destined for internalization and trigger the generation of membrane curvature that precedes eventual scission of CCPs from the plasma membrane to yield intracellular vesicles. The diversity of cell surface protein cargo thus controlled by CME indicates that CCP formation is regulated to allow cellular adaptation under different contexts. Of interest is how cues derived from cellular metabolism may regulate CME, given the reciprocal role of CME in controlling cellular metabolism. The modification of proteins with O-linked {beta}-N-acetylglucosamine (O-GlcNAc) is sensitive to nutrient availability and may allow cellular adaptation to different metabolic conditions. We examined how the modification of proteins with O-GlcNAc may control CCP formation and thus CME. We used perturbation of key enzymes responsible for protein O-GlcNAc modification, as well as specific mutants of the endocytic regulator AAK1 predicted to be impaired for O-GlcNAc modification. We identify that CCP initiation and the assembly of clathrin and other proteins within CCPs is controlled by O-GlcNAc protein modification. This reveals a new dimension of regulation of CME and highlights the important reciprocal regulation of cellular metabolism and endocytosis.

cell biology↗

bioRxiv2022

Identification of plasma proteins associated with oesophageal cancer chemotherapeutic treatment outcomes using SWATH-MS

Oesophageal adenocarcinoma (OAC) is an aggressive cancer with a five-year survival of <15%. Current chemotherapeutic strategies only benefit a minority (20-30%) of patients and there are no methods available to differentiate between responders and non-responders. We performed quantitative proteomics using Sequential Window Acquisition of all THeoretical fragment-ion spectra-Mass Spectrometry (SWATH-MS) on albumin/IgG-depleted and non-depleted plasma samples from 23 patients with locally advanced OAC prior to treatment. Individuals were grouped based on tumour regression (TRG) score (TRG1/2/3 vs TRG4/5) after chemotherapy, and differentially abundant proteins were compared. Protein depletion of highly abundant proteins led to the identification of around twice as many proteins. SWATH-MS revealed significant quantitative differences in the abundance of several proteins between the two groups. These included complement c1q subunit proteins, C1QA, C1QB and C1QC, which were of higher abundance in the low TRG group. Of those that were found to be of higher abundance in the high TRG group, GSTP1 was found to exhibit the lowest p-value and highest classification accuracy and Cohens kappa value. Concentrations of these proteins were further examined using ELISA-based assays. This study provides quantitative information relating to differences in the plasma proteome that underpin response to chemotherapeutic treatment in oesophageal cancers.

cancer biology↗

bioRxiv2021

Rest/Stress Myocardial Perfusion Imaging by Positron Emission Tomography with 18F-Flurpiridaz: A Feasibility Study in Mice

BackgroundMyocardial perfusion imaging by positron emission tomography (PET-MPI) is the current gold standard for quantification of myocardial blood flow. 18F-flurpiridaz was recently introduced as a valid alternative to currently used PET-MPI probes. Nonetheless, optimum scan duration and time interval for image analysis are currently unknown. Further, it is unclear whether rest/stress PET-MPI with 18F-flurpiridaz is feasible in mice. MethodsRest/stress PET-MPI was performed with 18F-flurpiridaz (0.6-3.0 MBq) in 29 mice aged 7-8 months. Regadenoson (0.1 g/g) was used for induction of vasodilator stress. Kinetic modeling was performed using a metabolite-corrected arterial input function. Image-derived myocardial 18F-flurpiridaz uptake was assessed for different time intervals by placing a volume of interest in the left ventricular myocardium. ResultsTracer kinetics were best described by a two-tissue compartment model. K1 ranged from 6.7-20.0 mL/cm3/min, while myocardial volumes of distribution (VT) were between 34.6 and 83.6 mL/cm3. Of note, myocardial 18F-flurpiridaz uptake (%ID/g) was significantly correlated with K1 at rest and following pharmacological stress testing for all time intervals assessed. However, while Spearmans coefficients (rs) ranged between 0.478 and 0.672, R2 values were generally low. In contrast, an excellent correlation of myocardial 18F-flurpiridaz uptake with VT was obtained, particularly when employing the averaged myocardial uptake from 20-40 min post tracer injection (R2 [≥]0.98). Notably, K1 and VT were similarly sensitive to pharmacological stress induction. Further, mean stress-to-rest ratios of K1, VT, and %ID/g 18F-flurpiridaz were virtually identical, suggesting that %ID/g 18F-flurpiridaz can be used to estimate CFR in mice. ConclusionOur findings suggest that a simplified assessment of relative myocardial perfusion and coronary flow reserve (CFR), based on image-derived tracer uptake, is feasible with 18F-flurpiridaz in mice, enabling high-throughput mechanistic CFR studies in rodents.

physiology↗