Biology subjects

Sue, A.

Publications and source records attributed to Sue, A..

6 recordsLinked to original sources

bioRxiv2026

Hydrogen sulfide dynamically upregulates copper uptake and localization

The reactivity of copper, an essential micronutrient that undergoes facile cycling between Cu1+ and Cu2+ redox states, is carefully controlled within the confines of protein binding sites, and by sequestration in storage vesicles, or harnessed to kill pathogens by active pumping of Cu1+ into phagosomes. We have discovered that hydrogen sulfide, a signaling metabolite generated in copious quantities at the host-microbiome interface, upregulates Cu accumulation in diffusely dispersed puncta across the cell, as visualized by X-ray fluorescence microscopy. The Cu is predominantly in the Cu2+ state with oxygen/nitrogen ligands. Cu import occurs via the non- canonical ZNT1 transporter, while export, following sulfide withdrawal, is ATP7A-dependent. Cu accumulates at the apices of colon crypts in a mouse model of elevated sulfide exposure due to SQOR deficiency in the intestinal epithelium, establishing in vivo relevance. Our study reveals that sulfide is a dynamic regulator of the Cu pool, stimulating Cu2+ influx into highly concentrated puncta.

cell biology↗

bioRxiv2026

Functional screening of ZIP8 naturally occurring variants identifies pathogenic mutations and trafficking defects

The rapid expansion of human genomic data has revealed a large number of naturally occurring variants, creating a major challenge for functional annotation. The human metal transporter SLC39A8 (ZIP8) is a clinically important, promiscuous divalent metal transporter, yet most of its documented variants remain uncharacterized. Here, we developed a workflow to functionally evaluate ZIP8 variants by integrating laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOF-MS) with scaled-up cell-based transport assays. Using this method, we systematically analyzed 33 naturally occurring missense variants located in the extracellular domain (ECD) of ZIP8. The assay enables direct quantification of intracellular metal accumulation with substantially improved throughput ([~]150 samples per hour). Functional screening identified 14 potential pathogenic variants with significantly reduced transport activity. Comparison with computational predictions revealed a moderate correlation between activity and AlphaMissense pathogenicity scores (R2 = 0.423), while an error rate of [~]20% underscores the need for experimental validation. Flow cytometry analysis showed that most loss-of-function variants exhibit impaired trafficking of the protein to the cell surface possibly due to mutation-caused protein misfolding or instability. Structural mapping of activity-compromised variants, together with functional assessment of the ZIP8-ECD, highlights the importance of this domain in ZIP8 expression and intracellular trafficking. Together, this work establishes a scalable approach for functional screening of metal transporter variants and provides new insights into the structure-function relationships of ZIP8.

biochemistry↗

bioRxiv2026

On-slide Preparation of Caenorhabditis elegans Towards Quantitative, High-Resolution LA-ICP-TOF Mass Spectrometry Imaging

Metal homeostasis is a complex process wherein essential metals serving structural, catalytic and regulatory roles are acquired, trafficked, and exported once they are present in excess. Understanding changes in metal content and localization in heterogenous tissue types is critical to understanding fundamental physiology as well as a growing number of disease states. Laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOF-MS) imaging is a powerful technique for untargeted quantitation and mapping of metals in biological systems. While the nematode Caenorhabditis elegans (C. elegans) is a well-established model organism for fundamental biological research and metal-based diseases, there have been few reports of mass spectrometry-based imaging of C. elegans, mostly due to challenges preparing samples that maintain the native distribution of the elements. In this study, we developed an embedding, quantitation and imaging workflow that preserves C. elegans using 3D-printed uniform layer media application tools (ULMATs). Multiple embedding media were evaluated, and petrolatum, commercially known as Vaseline, stood out for its performance in preserving C. elegans for imaging applications. Worms were subjected to microscopy and LA-ICP-TOF-MS imaging where we achieved a 2-m spatial resolution by over-sampling laser shots during ablation. Quantitative elemental maps were obtained using a series of gelatin standards that were sectioned at a 40-m thickness to closely mimic the average tissue ablation depth of a Day 1 gravid adult C. elegans. Our results establish a new workflow for comprehensive elemental profiling of C. elegans using LA-ICP-TOF-MS, which holds high potential for future spatial metal biology research with C. elegans. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/698490v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@7c66c5org.highwire.dtl.DTLVardef@13f4934org.highwire.dtl.DTLVardef@1df3215org.highwire.dtl.DTLVardef@512fd2_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

An All-In-One Software Solution for Automated Processing of LA-ICP-TOF-MS datasets

LA-ICP-TOF-MS provides rapid, high resolution elemental analysis of biological and non-biological samples. However, accurate real-time data analysis frequently requires the user to account for several instrumental and experimental variables that can change during data acquisition. AutoSpect is a novel software tool designed to automate the processing and fitting of LA-ICP-TOF-MS data, addressing key challenges such as time-dependent spectral drift, instrument sensitivity drift calibration inaccuracies, and peak deconvolution, enabling researchers to rapidly and accurately process complex datasets. The tool is optimized to be robustly applicable across scientific fields (e.g., geochemistry, biology, and materials science), providing a streamlined solution for end users seeking to maximize the potential of LA-ICP-TOF-MS for high-resolution elemental mapping and isotopic analysis. Significance to JAASAnalysis of fast transient signals using laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOF-MS) has become mainstream for elemental mapping. Advancements in LA-ICP-TOF-MS technology continue to accelerate the collective understanding of the role inorganic chemistry plays in dynamic processes. To ensure accurate quantitative results, the vast amount of complex spectral data generated requires elegant solutions to perform a variety of functions including data partitioning, peak fitting, drift correction, mass-to-charge calibration, peak profiling, and spectral fitting. AutoSpect is an all-in-one software solution that provides high level automation with a user-friendly graphical interface to perform complex data analyses for ICP-TOF-MS datasets.

scientific communication and education↗

bioRxiv2025

Autoimmune regulator deficiency causes sterile epididymitis and impacts male fertility through disruption of inorganic physiology

Autoimmune regulator (AIRE), a transcription factor expressed by medullary thymic epithelial cells, is required for shaping the self-antigen tolerant T cell receptor repertoire. Humans with mutations in AIRE suffer from Autoimmune Polyglandular Syndrome Type 1 (APS-1). Among many symptoms, men with APS-1 commonly experience testicular insufficiency and infertility, but the mechanisms causing infertility are unknown. Using an Aire-deficient mouse model, we demonstrate that male subfertility is caused by sterile epididymitis characterized by immune cell infiltration and extensive fibrosis. In addition, we reveal that the presence of autoreactive immune cells and inflammation in epididymides of Aire-deficient mice are required for iron (Fe) deposition in the interstitium, which is brought on by macrophages. We further demonstrate that male subfertility is associated with a decrease in metals zinc (Zn), copper (Cu), and selenium (Se) which serve as cofactors in several antioxidant enzymes. We also show increase in DNA damage of epididymal sperm of Aire-/- animals as a key contributing factor to subfertility. The absence of Aire results in autoimmune attack of the epididymis leading to fibrosis, Fe deposition, and Cu, Zn and Se imbalance, ultimately resulting in sperm DNA damage and subfertility. These results highlight the requirement of Aire to promote immune tolerance throughout the epididymis, disruption of which causes an imbalance of inorganic elements with resulting consequence on male fertility. Key pointsBreakdown of epididymal self-tolerance promotes disruption of inorganic elements. Autoimmunity causes interstitial fibrosis resulting in sperm DNA damage and subfertility. Elevated interstitial iron and macrophages contribute to fibrosis.

pathology↗

bioRxiv2022

Modeling multiphage-bacteria kinetics to predict phage therapy potency and longevity

Pseudomonas aeruginosa is a frequent cause of life-threatening opportunistic infections in the critically ill and immunocompromised. Its treatment is challenging due to the increasing prevalence of resistance to most conventional antibiotics. Although numerous alternative therapies are currently under investigation, bacteriophage (phage) cocktail therapy appears poised for long-term success. Here, we investigate potency and longevity of individual Pseudomonas phages in cocktail to determine viral co-factors that promote optimal treatment efficacy. We combined in vitro and in silico models to predict sixty-eight treatment permutations with three phages that adsorb symmetrically and asymmetrically when administered singly, double simultaneously, or double sequentially. We showed that simultaneously administering two asymmetrically binding phages with high cell lysis efficiencies improved cocktail potency. Use of a higher-potency cocktail, along with a reduction in the net probability of independent gene mutations was associated with prolonged bacterial suppression. Nevertheless, in vitro we almost always observed evolution of multiphage resistance. Simulations also predict that when combining phages with polar potencies, susceptible host cells are monopolized by the more efficiently replicating phage. Thus, further perpetuating the growth demise of the weaker phage in cocktail. Our mathematical model was used to explore and predict changes in phage and bacterial populations that were difficult to measure experimentally. This framework has many inferential and exploratory uses for clinical investigation such as identifying the most sensitive parameters for phage selection and exploring different treatment regimens. Collectively, our findings attempt to dissect the mechanisms of phage cocktails combating P. aeruginosa infections and highlight the viral co-factors necessary for treatment efficacy.

microbiology↗