Biology subjects

Tran, N.

Publications and source records attributed to Tran, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Mapping the regulatory wiring of endothelial cell differentiation reveals a critical role for Hippo mechanosignaling

At each step of development, stem cells encounter a branching decision to differentiate into one type of cell or another. This decision is executed through the action of competing gene programs that specify different cellular identities. Consequently, creating a comprehensive map of the gene programs that drive each branching step of human cell differentiation remains a long-sought goal of developmental and stem cell biology. Here, we introduce a framework combining genome-wide CRISPR screens, single-cell readouts, and gene program inference to systematically discover and characterize regulators of cell differentiation. This framework includes a method for CRISPR perturbations paired with single-cell RNA-seq called circular capture Perturb-seq (CC-Perturb-seq), which improves gRNA detection from split-pool combinatorial indexing protocols and enables perturbing many candidate regulators to map their effects on gene programs. We applied this framework to map how human pluripotent stem cells differentiate into arterial endothelial cells (ECs), and identified 174 regulators that promote or inhibit EC differentiation. By tracking gene programs across three stages of differentiation, we resolved when and how regulators divert cells toward alternative fates. This map revealed an unexpected requirement for the Hippo mechanosignaling pathway in EC specification. During lateral mesoderm differentiation, Hippo mechanosignaling was required to activate ETV2, the master transcriptional regulator of endothelial identity. Inhibiting Hippo blocked ETV2 even in the presence of VEGF and diverted progenitors to a mesenchymal fate in vitro. Likewise, Hippo signaling was required for maximal etv2 expression in developing zebrafish embryos. Conversely, pharmacologically activating the Hippo pathway increased the purity of both arterial and venous EC differentiation in vitro. Our framework thus identifies novel regulators of endothelial cell differentiation, improves stem-cell differentiation protocols via manipulation of mechanosignaling, and provides a generalizable platform for mapping the regulatory wiring of human development.

genomics↗

bioRxiv2026

Phylogenize2: robust phylogenetic methods link genes to phenotypes across host-associated and environmental microbiomes

In microbiome studies, associations between microbial functions and the environment are often confounded by phylogeny. While some methods explicitly account for this confounder, they require information about genome content, limiting their use in biomes where few genomes have been available. To make these methods more universally accessible, we have developed Phylogenize2, a redesigned phylogeny-aware tool for linking microbial gene families to abundance phenotypes. Phylogenize2 integrates large metagenome-assembled genome collections, including both biome-specific collections from MGnify and a broadly sampled general purpose database, GlobDB, to substantially expand species coverage, allowing its application in environments like the mouse gut and ocean. In addition, by default, Phylogenize2 uses a new robust phylogenetic testing framework that has been optimized for microbial abundance data, while also allowing the use of other comparative methods such as POMS. In an experimental mouse study, Phylogenize2 identifies that Muribaculaceae with higher abundance on a high-fat diet are enriched for proteins in the thioredoxin family, with likely roles in oxidative stress. When we apply Phylogenize2 to a polar ocean study, we find that a molybdenum-dependent PaoABC/YagTSR-like aldehyde oxidoreductase system differentiates mesopelagic from surface-dwelling Flavobacteriaceae, suggesting that aldehyde detoxification may be important for organisms that degrade marine snow. Together, these results show that Phylogenize2 expands phylogeny-aware microbiome analysis beyond the human gut and can provide insight into the genetic basis of microbiome-encoded traits in diverse environments. ImportanceMicrobiome studies often set out to identify which microbes are more or less abundant across environments, but these patterns can be difficult to interpret. Phylogenize2 is an open-source software package that allows researchers to ask whether individual microbial gene families are associated with the environment across independent branches of the microbial tree of life. By incorporating large collections of genomes from uncultivated microbes, as well as modern statistical methods designed for microbial abundance data, Phylogenize2 makes this approach practical for microbiomes beyond the human gut, including in model organisms like lab mice and free-living environments like the ocean. We also provide a pipeline that allows the use of new genome collections. In two case studies, we demonstrate that Phylogenize2 effectively prioritizes specific genes and pathways from metagenomic data, thereby leading researchers from changes in microbial abundance to more biologically interpretable explanations.

bioinformatics↗

bioRxiv2026

A robust, sensitive phylogenetic method enables gene-level metagenomic analyses

A key goal in the microbiome field is to move from taxonomic associations towards mechanistic hypotheses about microbial gene function. However, most methods for linking microbiome changes to specific genes are biased towards finding marker genes, with weak evidence for functional relevance. Phylogenetic regression can address this issue and has been previously applied to changes in microbial prevalence, but many environments (such as the gut in health vs. disease) are characterized more by changes in abundance, which presents unique statistical challenges. We show that when applied to real differential abundances from metagenomes, phylogenetic regression has an anti-conservative bias, indicating inflated false positives. We develop an alternative non-parametric method called "robust permutration," designed specifically for differential abundance data, and evaluate its performance against phylogenetic regression as well as several other phylogenetic comparative methods in realistic simulations of metagenomic data. These results show that robust permutration is the most powerful method that appropriately controls the false positive rate. We further apply robust permutration to a human case-control study of liver cirrhosis, revealing that Lachnospiraceae abundance in disease is linked to a previously uncharacterized iron- sulfur transcription factor encoded near homologs of the butyryl-CoA oxygen oxidoreductase system, a recently discovered system for oxygen detoxification. This illustrates how robust, sensitive phylogenetic methods can enable the generation of new molecular hypotheses directly from metagenomic case-control data. ImportancePreviously, we showed that phylogenetic regression can effectively detect genes associated with microbial presence or absence while correcting for evolutionary relationships. Unexpectedly, however, we here observe that this method can lead to high false positive rates when applied to microbial abundance data. In realistic simulations, other methods we test either have similar problems with false positives, or display very low power. We outline a new statistical test that better accounts for measurement uncertainty, outliers, and model violations, achieving more balanced sensitivity and accuracy than competing methods. Applying this test to a cirrhosis study reveals an uncharacterized transcription factor enriched in disease, with an apparent role in oxidative stress based on its sequence and gene neighborhood. This suggests a functional explanation for the observed taxonomic shifts, and demonstrates how improved phylogenetic methods could help inform future microbiome-targeted treatments.

bioinformatics↗

bioRxiv2026

Divergent Inclusion Body Structures and Stabilities Emerge from Native Monomer Properties

Protein aggregation is of broad importance in biotechnology and disease, yet the structural heterogeneity of cellular aggregates has confounded high-resolution structural analysis. Inclusion bodies (IBs) formed in Escherichia coli are an attractive, controllable system for unravelling the complexities of protein aggregation in a cellular context. Here, a multimodal analysis integrating residue-resolved quenched amide hydrogen-deuterium exchange (qHDX), proteolysis, FTIR, Congo red binding, and chemical denaturation is applied to IBs formed by proteins encompassing stable {beta}- and -globular folds, a partially structured protein fragment, and intrinsically disordered low complexity domains (LCDs). Remarkable conformational diversity is observed: IBs formed by well-folded proteins are extensively structured and include substantial local native-like features, whereas proteins with decreased access to stable native conformations form more heterogeneous and dynamic aggregates increasingly shaped by intrinsic sequence features. Strikingly, qHDX protection of TDP-43 LCD IBs strongly aligns with the core of cryo-EM structures of ex vivo pathological fibrils; however, peripheral regions that appear fully hydrogen-bonded in the cryo-EM structures exhibit little protection. The results reveal that individual protein IBs contain distinct mixtures of native-like, disordered, and amyloid-like conformers, informing the prediction and control of cellular aggregate structure and stability. Entry for the Table of Contents O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=192 SRC="FIGDIR/small/729379v2_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@1542626org.highwire.dtl.DTLVardef@194ad5forg.highwire.dtl.DTLVardef@26c13org.highwire.dtl.DTLVardef@1055573_HPS_FORMAT_FIGEXP M_FIG Inclusion body conformational heterogeneity. Left: aggregates retaining local native-like structure. Middle: assemblies populated by -helical intermediates coexisting with antiparallel -sheet oligomers. Right: initially disordered states undergo helix-helix interactions and progress towards -sheet-rich conformations, illustrating distinct routes of cellular aggregation. C_FIG

biochemistry↗

bioRxiv2026

Fasting disrupts the InsP6 HDAC3 axis to drive ER stress-mediated clearance of DNA-damaged cells and enforce tissue quality control.

Fasting drives metabolic adaptation but also elicits acute cellular stress. How this stress shapes tissue integrity is unknown. Here, we show that in the intestine, fasting depletes growth factor signaling, which triggers cellular stress. This response functions as a tissue quality-control checkpoint that selectively eliminates pre-existing DNA-damaged cells while sparing healthy counterparts. A short-term fast diminishes TGF-{beta} signaling and elicits endoplasmic reticulum (ER) stress, driving DNA-damaged intestinal cells beyond an apoptotic threshold, thereby reducing the inflammatory burden. Mechanistically, loss of TGF-{beta} signaling triggers FBXO22-Cullin1-mediated degradation of the inositol kinase IPMK, leading to depletion of inositol hexaphosphate (InsP). InsP loss attenuates HDAC3 activity and initiates coordinated epigenetic and post-translational reprogramming, thereby increasing CDK5RAP3 abundance. Elevated CDK5RAP3 inhibits ribosomal RPL26 UFMylation, thereby amplifying ER stress and selectively licensing apoptosis in DNA-damaged cells. Collectively, fasting disrupts a TGF-{beta}-InsP6-HDAC3 axis to drive ER stress-dependent clearance of DNA-damaged cells, enforcing tissue quality control.

cell biology↗

bioRxiv2026

VesSynth: Tubes Are All You Need for Robust Cross-Scale Cross-Modal 3D Vessel Segmentation

The cerebral vasculature is central to brain function, with alterations linked to numerous cerebrovascular and neurological disorders. Yet, no single imaging modality can capture the entire cerebral vascular network in humans. Instead, an array of techniques are sensitized to different spatial scales, while trading off resolution for coverage. Magnetic Resonance Imaging (MRI) typically resolves only large pial vessels, while high-resolution microscopy allows micrometer-scale vessels to be mapped over limited spatial extents. These techniques must therefore be combined to obtain a complete mapping of the cerebral angioarchitecture, which underscores the need for automatic, cross-modal vessel segmentation. Here, we introduce VesSynth, a flexible vessel segmentation framework that achieves state-of-the-art accuracy across multiple modalities and spatial resolutions (MR, optical and X-ray imaging), despite being trained entirely on synthetic data. By enabling consistent vascular mapping across scales, this framework paves the way to comprehensive investigation of cerebrovascular organization and its role in health and disease.

bioengineering↗

bioRxiv2026

A comprehensive CRISPR screen of the Drosophila glutamate receptome reveals Ekar as a selective regulator of presynaptic homeostatic plasticity

Homeostatic mechanisms protect synapses from destabilizing challenges throughout an organisms lifespan, ensuring stable yet flexible neural network activity. To delineate the molecular basis of presynaptic homeostatic potentiation (PHP), we conducted a comprehensive, in vivo CRISPR/Cas9-based screen of all 16 glutamate receptor (GluR) genes encoded in the Drosophila genome. We first generated a complete expression atlas across larval and adult stages, identifying nine GluRs expressed in presynaptic motor neurons. We then generated null mutants for all 16 GluRs and screened them at the larval neuromuscular junction. While the loss of any single presynaptic GluR did not affect baseline synaptic growth or neurotransmission, our screen revealed a selective and critical requirement for the kainate receptor subunit ekar in the expression of chronic PHP. Further genetic analysis indicates that Ekar functions coordinately with the kainate receptor subunits KaiRID and Ukar within a shared pathway to promote this plasticity. Mechanistically, Ekar acts downstream of active zone remodeling to drive the homeostatic enhancement of presynaptic Ca2+ influx, which is the defining feature of chronic PHP. Together, this genome-wide analysis establishes a definitive functional atlas for the Drosophila glutamate receptome and highlights a specialized, essential role for Ekar in stabilizing long-term synaptic homeostasis.

neuroscience↗

bioRxiv2026

Structural Basis of Glycolytic Control in Trypanosoma cruzi: Insights from Enolase and PGI

Trypanosoma cruzi, the etiological agent of Chagas disease, depends on glycolysis for ATP production, rendering its glycolytic enzymes attractive targets for therapeutic development. Here, we report the high-resolution crystal structures of two essential glycolytic enzymes, glucose-6-phosphate isomerase (Tc PGI, 1.8 [A]) and enolase (Tc enolase, 2.4 [A]) and provide structural and computational analyses to support structure-based drug design. Tc PGI adopts a dimeric {beta} sandwich fold and features a parasite-specific 53-residue N-terminal extension and a unique C-terminal hook region which both distinguish it from its human ortholog. Tc enolase exhibits the conserved (/{beta}) 8 TIM barrel fold but harbors minor distinct structural deviations, including an extended 17 helix and a structured 1 region, which differentiate it from human isoforms. Both enzymes exhibited high thermal stability, consistent with adaptation to the parasites complex life cycle. Structure-based virtual screening using a scaffold with known multi-target potential identified distinct high-affinity inhibitors for each enzyme. Molecular dynamics simulations further confirmed stable enzyme-inhibitor interactions and favorable binding energetics. Collectively, these findings reveal structural signatures unique to T. cruzi glycolytic enzymes and lay the groundwork for the development of selective antiparasitic therapeutics.

biochemistry↗

bioRxiv2025

Matrix Stiffness Governs Fibroblast-Driven Immune Homeostasis in Gingival Tissues

Periodontal disease is associated with inflamed gingival tissues and degradation of the gingival extracellular matrix (ECM), yet the role of mechanical cues is poorly understood. Gingival ECM in periodontal disease showed a loss of fibrillar collagen compared to healthy samples. We hypothesized that ECM softening in periodontal disease contributes to inflammation due to dysregulated gingival fibroblasts (GFs). A mechanically tunable hydrogel model of the gingival ECM was developed to investigate the mechano-immune crosstalk. Stiff collagen-alginate hydrogels matched the rheological properties of gingival biopsies. Human donor GFs encapsulated in these stiff hydrogels showed significantly suppressed toll-like receptor inflammatory responses compared to soft. Stiffness-dependent inflammatory responses of GFs were directed by the non-canonical NF{kappa}B pathway and epigenetic nuclear organization. The direct impact of mechanical cues on immune responses was investigated with human donor cells ex vivo by co-culture of human GFs with myeloid cells and in human gingival explants. Myeloid progenitors co-cultured with GFs in stiff hydrogels differentiated into immunomodulatory dendritic cells. Ex vivo crosslinking of human gingival tissue increased stiffness and reduced inflammatory cytokines. Gingival mechano-immune regulation provides a new avenue for biomaterials-based treatments in periodontitis.

bioengineering↗

bioRxiv2025

Dynamics and interplay of gene expression and chromosome organization across a predatory lifecycle

The obligate predatory bacterium Bdellovibrio bacteriovorus alternates between a motile attack phase and a growth phase inside another bacterium, during which it undergoes multiple rounds of DNA replication followed by non-binary division and progeny release. How its chromosome is dynamically reorganized across these contrasting states remains unclear. Here, we used synchronized predatory infections combined with time-resolved RNA-seq, Hi-C, ChIP-seq, and quantitative microscopy to map transcriptional activity and chromosome architecture across seven key stages of the predatory lifecycle. We uncover a dramatic shift in nucleoid organization - from an ultra-compact, transcriptionally restricted state in attack-phase cells to a progressively decompacted, ori-centered conformation during intracellular replication. Notably, distinct transcriptional and chromosome folding states not only mark the canonical attack and growth phases, but also critical transitions such as prey invasion, replication onset, and predator division. Temporal gene expression profiles reflect the coordinated regulation of core cellular functions across the predatory cycle. Furthermore, spatial localization of RNA polymerase, ribosomes, DNA-binding proteins, and freely diffusing proteins highlight the tight, cell cycle-dependent coupling between nucleoid compaction, chromosome accessibility, and transcriptional activity. Altogether, our findings reveal the intricate dynamics and coordination of genome folding and gene expression in a complex bacterial cell cycle driven by prey-predator interactions.

microbiology↗

bioRxiv2025

Region-specific Brain Targets Drive Circuit Formation and Maturation of Human Retinal Ganglion Cells

Human vision relies on retinal ganglion cells (RGCs), and their connectivity with distinct brain regions enables higher order visual processing. RGCs vary considerably between species, and many model organisms display distinct RGC types and innervation patterns from those in humans. There is thus a need for robust models of human RGC circuit formation that preserves innervation specificity. Here, we developed an in vitro microfluidics eye-to-brain connectivity model using human pluripotent stem cell (hPSC)-derived RGCs to assess brain region-specific connectivity features. We found that cultured human RGCs segregate their dendrites and axons and display axonal features that align with those of their in vivo human RGC counterparts. To identify brain target surrogates, we conducted bioinformatic similarity assessments, which revealed high conservation and lower variability between human LGN and mouse counterparts relative to available thalamocortical organoids. We thus provided region-specific mouse visual targets to assess specificity and activity. We found that human RGC axons terminals differentially connected with distinct mouse retinorecipient brain regions and promoted region-specific neural activity. Increased synapse formation occurred between RGCs and lateral geniculate neurons relative to that with suprachiasmatic nucleus neurons, modeling retina brain connectivity differences. Both retinorecipient partners induced the formation of more synapses relative to non-retinorecipient brain target controls. These results suggest that human RGC innervation properties are preserved in culture systems and that human RGCs can differentially sense and respond to retinorecipient targets to control wiring outcomes. These systems may aid in the discovery of wiring factors for potential therapeutic applications. Significance StatementThis study presents a novel in vitro model to investigate human retinal ganglion cell (RGC) connectivity, using human pluripotent stem cell-derived RGCs and specific mouse brain targets. By modeling eye-to-brain connections in a microfluidics device, we reveal that cultured human RGCs can form selective, region-specific synapses with mouse-derived brain areas like the lateral geniculate nucleus and the suprachiasmatic nucleus. The findings demonstrate that human RGCs retain their innervation specificity presences in culture, mimicking in vivo human connectivity patterns. This model thus provides a powerful tool for understanding the factors controlling human-specific brain wiring, with potential applications in therapies for visual and neurological disorders.

neuroscience↗

bioRxiv2025

Fieldable isothermal nucleic acid test for rapid semi-quantitative visual readout of Enterococci in recreational waters

Enterococci are fecal indicator bacteria whose presence in water suggests the potential for gastrointestinal pathogens. Culture-based detection is slow and may require expensive apparatus and proprietary media. Molecular tests based on qPCR can be technically difficult and require complex devices. Loop-mediated isothermal amplification (LAMP) tests that need minimal instrumentation have been described but they only qualitatively indicate presence or absence of Enterococci, which is difficult to compare with quantitative contamination standards for assessing water quality. Here, we demonstrate semi-quantitative thresholded LAMP that uses internal competition with pre-defined false targets and an oligonucleotide strand displacement (OSD) probe to measure the degree of Enterococcus contamination in water. The assay needs only one hour of incubation at a single temperature following which a simple visual examination of endpoint OSD fluorescence allows order of magnitude scale estimation of Enterococcus amounts. Environmental water samples with low, medium, and high Enterococcus contamination could be readily distinguished by thresholded LAMP-OSD without interference from non-specific signals. LAMP-OSD performance correlated with the outcomes of both qPCR and plate cultures of the samples. The simplicity of implementing thresholded LAMP-OSD makes it well suited for point-of-need and low-cost water quality monitoring.

molecular biology↗

bioRxiv2025

Role of Long Chain Acyl-CoA Synthetases in MASH-driven Hepatocellular Carcinoma and Ferroptosis

Metabolic-associated steatohepatitis-driven hepatocellular carcinoma (MASH-HCC) incidence is rapidly rising worldwide. Lipid metabolic reprogramming is a hallmark of solid tumors to satisfy cancer high metabolic demand. However, it may confer sensitivity to ferroptosis, a cell death mode driven by iron-dependent lipid peroxidation. In this report, we describe the lipid metabolic landscape in MASH-HCC and characterize long chain acyl-CoA synthetases (ACSLs), a family of enzymes involved in synthesis of cellular lipids. Bulk RNA-sequencing, single-cell RNA-sequencing, spatial transcriptomics and immunohistochemistry analyses of human MASH-HCC were integrated to identify differentially expressed lipid metabolism genes. Ferroptosis in vitro was assessed in human HCC cell lines. A characterization of ACSLs was also conducted at the single-cell level in a diet-induced experimental murine model of MASH-HCC. Our analysis revealed that in human MASH-HCC, ACSLs exhibit a heterogeneous expression, with ACSL4 notably enriched in tumor tissues, contrasting with ACSL5 upregulation in non-cancerous MASH. We identified a unique lipid metabolic gene signature of MASH-HCC, which included genes associated with ferroptosis vulnerability. In vitro, ACSL4 upregulation was associated with increased ferroptosis sensitivity in human HCC cell lines. Lastly, single-cell RNA-sequencing revealed elevated ACSL4 expression in immune cells in a murine MASH-HCC model, suggesting a role of ACSL4 in shaping the tumor immune microenvironment. Overall, this report offers new insights into lipid metabolic landscape and ferroptosis sensitivity for novel MASH-HCC treatments. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/642692v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@2ab7f7org.highwire.dtl.DTLVardef@93d903org.highwire.dtl.DTLVardef@8c8891org.highwire.dtl.DTLVardef@5a235e_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2025

Structure of the Thomasclavelia ramosa immunoglobulin A protease reveals a modular and minimizable architecture distinct from other immunoglobulin A proteases

Immunoglobulin A proteases (IgAPs) are a diverse group of enzymes secreted from bacteria that inhabit human mucosal tissues. These enzymes have convergently evolved to cleave human immunoglobulin A as a means of modulating and evading host immunity. Only two of three known IgAP families have been biochemically characterized beyond their initial discovery. Here, we show using solution-scattering, steady-state kinetic, and crystallographic approaches that the protease from Thomasclavelia ramosa, representing the uncharacterized third family, has a truly modular and minimizable protein architecture. This analysis also revealed a unique metal-associated domain that likely functions as a molecular spacer and generated a working hypothesis detailing the structural mechanism behind the enzymes high substrate specificity. Our work provides the first in-depth biochemical account of this IgAP family, paving the way for advancing clinically relevant IgAP-related research and our understanding of IgAPs as a whole.

biochemistry↗

bioRxiv2024

Reengineering mRNA lipid nanoparticles for systemic delivery to pancreas

Lipid nanoparticles (LNPs) hold transformative potential for nucleic acid delivery, with applications ranging from clinical use, particularly in COVID-19 vaccines, to gene therapy and cancer immunotherapy. Traditional LNPs are composed of four components: ionizable lipids, cholesterol, helper lipids, and PEGylated lipids. However, a significant hurdle remains the need for more efficient and selective systemic delivery vehicles, as most targets are challenging to reach and primarily accumulate in the liver following intravenous administration, largely due to Apolipoprotein E (ApoE) mediated uptake in the blood. Recent studies have shown that introducing cationic or anionic lipids as a fifth component in the LNPs has resulted in lung- and spleen-specific mRNA expression. In this study, we report that incorporating endogenous ligands, such as vitamins, as a fifth component can enhance the extrahepatic localization of LNPs. Vitamins are highly biocompatible, possess excellent targeting potential, influence immune response, improve cellular uptake, and increase the stability of mRNA LNPs. We developed a library of 100 LNPs containing luciferase mRNA by partially replacing ionizable lipids with this fifth component and evaluated their efficacy both in vitro and in vivo. From comprehensive batch analysis screening, we identified two formulations with cholecalciferol (vitamin D3) as a fifth component that demonstrated selective systemic delivery to the pancreas (> 99%) with high efficacy. Among these, C-CholF3 emerged as the top formulation, exhibiting robust and sustained protein expression in the pancreas for up to 3 days in a dose-dependent manner with minimal toxicity that makes it suitable for repeated administration. Furthermore, C-CholF3 also demonstrated pancreas-specific gene editing in the Ai14 transgenic mouse model, showing high expression of TdTomato. This underscores its translational potential for protein replacement and CRISPR/Cas9-mediated gene editing in currently incurable pancreatic diseases.

bioengineering↗

bioRxiv2024

Inositol Hexaphosphate (InsP6) Activates the HDAC1/3 Epigenetic Axis toMaintain Intestinal Barrier Function

While HDAC inhibition shows promise in cancer treatment, pan-HDAC inhibitors cause gastrointestinal issues in 48% of patients. Understanding HDAC activation mechanisms is crucial to treat diverse diseases beyond cancer. Our study reveals the essential role of inositol polyphosphate multikinase (IPMK) and inositol hexakisphosphate (InsP6 or phytic acid), enriched in vegan diets, in activating the HDAC3 epigenetic axis and maintaining intestinal barrier integrity. IPMK binds to HDAC3, driving InsP6 synthesis, which selectively activates HDAC3 at 10nM concentration by recruiting the DAD domain of its corepressor protein. IPMK deletion diminishes HDAC3 activation, leading to histone hyperacetylation and MMP gene transcription, compromising intestinal barrier integrity. InsP6 treatment is sufficient to rescue these effects. In inflammatory bowel disease, diminished IPMK levels exacerbated intestinal permeability, while oral InsP6 treatment mitigated gut permeability by restoring the HDAC3 epigenetic axis, indicating the clinical implications of the IPMK-HDAC3 epigenetic axis and therapeutic potential of phytic acid.

cell biology↗

bioRxiv2024

Enhanced Suppression of Stenotrophomonas maltophilia by a Three-Phage Cocktail: Genomic Insights and Kinetic Profiling

In our era of rising antibiotic resistance, Stenotrophomonas maltophilia (STM) is an understudied, gram-negative, aerobic bacterium widespread in the environment and increasingly causing opportunistic infections. Treating STM infections remains difficult, leading to an increase in disease severity and higher hospitalization rates in people with Cystic Fibrosis (pwCF), cancer, and other immunocompromised health conditions. The lack of effective antibiotics has led to renewed interest in phage therapy; however, there is a need for well-characterized phages. In response to an oncology patient with a respiratory infection, we collected 18 phages from Southern California wastewater influent that exhibit different plaque morphology against STM host strain B28B, cultivated from a blood sample. Here, we characterize the genomes and life cycle kinetics of our STM phage collection. We hypothesize that genetically distinct phages give rise to unique lytic life cycles that can enhance bacterial killing when combined into a phage cocktail compared to the individual phages alone. We identified three genetically distinct clusters of phages, and a representative from each group was screened for potential therapeutic use and investigated for infection kinetics. The results demonstrated that the three-phage cocktail significantly suppressed bacterial growth compared to individual phages when observed for 48 hours. We also assessed the lytic impacts of our three-phage cocktail against a collection of 46 STM strains to determine if a multi-phage cocktail can expand the host range of individual phages. Our phages remained strain-specific and infect >50% of tested strains. The multi-phage cocktail maintains bacterial growth suppression and prevents the emergence of phage-resistant strains throughout our 40-hour assay. These findings suggest specialized phage cocktails may be an effective avenue of treatment for recalcitrant STM infections resistant to current antibiotics. IMPORTANCEPhage therapy could provide a vital strategy in the fight against antimicrobial resistance (AMR) bacterial infections; however, significant knowledge gaps remain. This study investigates phage cocktail development for the opportunistic pathogen Stenotrophomonas maltophilia (STM). Our findings contribute novel phages, their lytic characteristics, and limitations when exposed to an array of clinically relevant STM strains. Eighteen bacteriophages were isolated from wastewater influent from Escondido, California, and subjected to genomic analysis. We investigated genetically distinct phages to establish their infection kinetics and developed them into a phage cocktail. Our findings suggest that a genetically distinct STM phage cocktail provides an effective strategy for bacterial suppression of host strain B28B and five other clinically relevant STM strains. Phage therapy against STM remains poorly understood, as only 39 phages have been previously isolated. Future research into the underlying mechanism of how phage cocktails overwhelm the host bacteria will provide essential information that could aid in optimizing phage applications and impact alternative treatment options.

microbiology↗

bioRxiv2024

βA3/A1-crystallin is an epigenetic regulator of histone deacetylase 3 (HDAC3) in the retinal pigmented epithelial (RPE) cells

Introductory paragraphThe retinal pigmented epithelial (RPE) cells maintain retinal homeostasis, and alterations in their function contribute to non-exudative age-related macular degeneration (AMD)1,2. Here, we explore the intricate relationship between RPE cells, epigenetic modifications, and the development of AMD. Importantly, the study reveals a substantial decrease in histone deacetylase 3 (HDAC3) activity and elevated histone acetylation in the RPE of human AMD donor eyes. To investigate epigenetic mechanisms in AMD development, we used a mouse model with RPE-specific Cryba1 knockout3-5, revealing that the loss of {beta}A3/A1-crystallin selectively reduces HDAC3 activity, resulting in increased histone acetylation. {beta}A3/A1-crystallin activates HDAC3 by facilitating its interaction with the casein kinase II (CK2) and phosphorylating HDAC3, as well as by regulating intracellular InsP6 (phytic acid) levels, required for activating HDAC3. These findings highlight a novel function of {beta}A3/A1-crystallin as an epigenetic regulator of HDAC3 in the RPE cells and provide insights into potential therapeutic strategies in non-exudative AMD.

cell biology↗